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charset="UTF-8" Since you're running in debug mode, you should get a namd config file produced in your working directory. What happens when you try running namd with that config file? Best, Peter On Fri, Jan 1, 2021 at 12:23 AM Khoualdi Asma Feriel < asma.feriel.khoualdi@umontreal.ca> wrote: > I used the following script to calculate the electrostatic energy but the > output file gives me only the column header without any values for frames > or energy or anything, I'd appreciate input. > > set nfiles 144 > set str > /lustre04/scratch/asma97/charmm-gui-8960705840/namd/step5_charmm2namd.psf > > > set TITLE_FIRST step > set TITLE_SECOND _production.dcd > > mol new $str type psf waitfor all > > for {set j 7} {$j <= $nfiles} {incr j} { > > mol addfile > /lustre04/scratch/asma97/charmm-gui-8960705840/namd/$TITLE_FIRST$j$TITLE_SECOND > type dcd waitfor all > } > > set RESIDUE [atomselect top "resid 96 and protein"] > set LIGAND [atomselect top "resid 174 and not water and not protein"] > > package require namdenergy 1.4 > > namdenergy -elec -sel $RESIDUE $LIGAND -keepforce -timemult 2 -updatesel > -debug -cutoff 12 -switch 10 -pme -tempname "namd" -ofile "namdEnergy.txt" > -exe /home/asma97/.licenses/namd-multicore -timemult 2 -par > toppar/par_all36m_prot.prm -par toppar/par_all36_na.prm -par > toppar/par_all36_carb.prm -par toppar/par_all36_lipid.prm -par > toppar/par_all36_cgenff.prm -par toppar/par_interface.prm -par > toppar/toppar_all36_nano_lig.str -par toppar/toppar_all36_nanolig_patch.str > -par toppar/toppar_all36_synthetic_polymer.str -par > toppar/toppar_all36_synthetic_polymer_patch.str -par > toppar/toppar_all36_polymer_solvent.str -par toppar/toppar_water_ions.str > -par toppar/toppar_dum_noble_gases.str -par toppar/toppar_ions_won.str -par > toppar/toppar_all36_prot_arg0.str -par > toppar/toppar_all36_prot_c36m_d_aminoacids.str -par > toppar/toppar_all36_prot_fluoro_alkanes.str -par > toppar/toppar_all36_prot_heme.str -par > toppar/toppar_all36_prot_na_combined.str -par > toppar/toppar_all36_prot_retinol.str -par > toppar/toppar_all36_prot_modify_res.str -par > toppar/toppar_all36_na_nad_ppi.str -par > toppar/toppar_all36_na_rna_modified.str -par > toppar/toppar_all36_lipid_bacterial.str -par > toppar/toppar_all36_lipid_cardiolipin.str -par > toppar/toppar_all36_lipid_cholesterol.str -par > toppar/toppar_all36_lipid_dag.str -par > toppar/toppar_all36_lipid_inositol.str -par > toppar/toppar_all36_lipid_lps.str -par > toppar/toppar_all36_lipid_miscellaneous.str -par > toppar/toppar_all36_lipid_model.str -par toppar/toppar_all36_lipid_prot.str > -par toppar/toppar_all36_lipid_sphingo.str -par > toppar/toppar_all36_lipid_yeast.str -par toppar/toppar_all36_lipid_hmmm.str > -par toppar/toppar_all36_lipid_detergent.str -par > toppar/toppar_all36_lipid_ether.str -par > toppar/toppar_all36_carb_glycolipid.str -par > toppar/toppar_all36_carb_glycopeptide.str -par > toppar/toppar_all36_carb_imlab.str -par toppar/toppar_all36_label_spin.str > -par toppar/toppar_all36_label_fluorophore.str -par > toppar/toppar_all36_lipid_cationpi_wyf.str > > --000000000000d9637905b7d0c9ae Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Since you're running in debug mode, you should ge= t a namd config file produced in your working directory. What happens when = you try running namd with that config file?
Best,
P= eter

On Fri, Jan 1, 2021 at 12:23 AM Khoualdi Asma Feriel <asma.feriel.khoualdi@umo= ntreal.ca> wrote:
I used the following script to calculate the electrostatic energy but the o= utput file gives me only the column header without any values for frames or= energy or anything, I'd appreciate input.

set nfiles 144
set str /lustre04/scratch/asma97/charmm-gui-8960705840/namd/step5_char= mm2namd.psf


set TITLE_FIRST step
set TITLE_SECOND _production.dcd

mol new $str type psf waitfor all

for {set j 7} {$j <=3D $nfiles} {incr j} {

mol addfile /lustre04/scratch/asma97/charmm-gui-8960705840/namd/$TITLE= _FIRST$j$TITLE_SECOND type dcd waitfor all
}=C2=A0

set RESIDUE [atomselect top "resid 96 and protein"]
set LIGAND [atomselect top "resid 174 and not water and not prote= in"]

package require namdenergy 1.4

namdenergy -elec -sel $RESIDUE $LIGAND -keepforce -timemult 2 -updates= el -debug -cutoff 12 -switch 10 =C2=A0-pme -tempname "namd" -ofil= e "namdEnergy.txt" -exe /home/asma97/.licenses/namd-multicore -ti= memult 2 -par toppar/par_all36m_prot.prm -par toppar/par_all36_na.prm -par toppar/par_all36_carb.prm -par toppar/par_all36_lipid.prm -par toppar= /par_all36_cgenff.prm -par toppar/par_interface.prm -par toppar/toppar_all3= 6_nano_lig.str -par toppar/toppar_all36_nanolig_patch.str -par toppar/toppa= r_all36_synthetic_polymer.str -par toppar/toppar_all36_synthetic_polymer_patch.str -par toppar/toppar_all36_p= olymer_solvent.str -par toppar/toppar_water_ions.str -par toppar/toppar_dum= _noble_gases.str -par toppar/toppar_ions_won.str -par toppar/toppar_all36_p= rot_arg0.str -par toppar/toppar_all36_prot_c36m_d_aminoacids.str -par toppar/toppar_all36_prot_fluoro_alkanes.str -par toppar/toppar_all36_= prot_heme.str -par toppar/toppar_all36_prot_na_combined.str -par toppar/top= par_all36_prot_retinol.str -par toppar/toppar_all36_prot_modify_res.str -pa= r toppar/toppar_all36_na_nad_ppi.str -par toppar/toppar_all36_na_rna_modified.str -par toppar/toppar_all36_lipi= d_bacterial.str -par toppar/toppar_all36_lipid_cardiolipin.str -par toppar/= toppar_all36_lipid_cholesterol.str -par toppar/toppar_all36_lipid_dag.str -= par toppar/toppar_all36_lipid_inositol.str -par toppar/toppar_all36_lipid_lps.str -par toppar/toppar_all36_lipid_misc= ellaneous.str -par toppar/toppar_all36_lipid_model.str -par toppar/toppar_a= ll36_lipid_prot.str -par toppar/toppar_all36_lipid_sphingo.str -par toppar/= toppar_all36_lipid_yeast.str -par toppar/toppar_all36_lipid_hmmm.str -par toppar/toppar_all36_lipid_detergen= t.str -par toppar/toppar_all36_lipid_ether.str -par toppar/toppar_all36_car= b_glycolipid.str -par toppar/toppar_all36_carb_glycopeptide.str -par toppar= /toppar_all36_carb_imlab.str -par toppar/toppar_all36_label_spin.str -par toppar/toppar_all36_label_fluoroph= ore.str -par toppar/toppar_all36_lipid_cationpi_wyf.str

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boundary="000000000000c25cb205b81605a6" X-CLX-Response: 1TFkXHBoeEQpMehcZGx0RCllEF29+eBplaFx+UFh8EQpYWBdnbGEcbnpeTm8 BaBEKeE4XY1Nja3sTWH4aX14RCnlMF29EbX1+clxDaWEfEQpDSBcHHh8bEQpDWRcHHR0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwZcRsGGxgfdwYbHh4GGxoaQh0GGgYTHQYYGhpxGxoaEBp3BhoGG gYaBhoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XQm1Zc2dfZ2R1TG5/ YE5zUxNjGRtCYR5ZTXlgeG95YlMRClhcFx8EGgQYGBoFGxoEGxoaBB4SBBsTEBseGh8aEQpeWRd yYWUeGxEKTVwXGxMfEQpMWhdoaU1NaxEKTEYXb2tra2trEQpCTxdgZGsfZ0QYcGYYWhEKQ1oXGB oTBBIfBBgYGAQeExEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E 1h+Gl9eEQpCRRdte0weRRNhRUZTXREKQk4XY1Nja3sTWH4aX14RCkJMF2dsYRxuel5ObwFoEQpC bBdvY2VtYWdGRWNgUhEKQkAXZHJyXHxrX18cX2wRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBc ZEQp5QxdkZFplX0EeeUJcbBEKWUsXExgdHBEKcGgXawFNbgVrExxSR0UQGRoRCnBoF2QTeF4YAU 16WkJ/EBkaEQpwaBdvGHNuZxNQRh9sQhAZGhEKcGgXbhlbRBlOQG4aXhMQGRoRCnBoF2RJaU1NH 2JfaxJPEBkaEQpwfRdoeXlEQ1tSQ0NwbxAZGhEKcH0XZEkbXRIYUk9gchkQGRoRCnB/F2VYchgd SRheRml8EBsaGREKcF8XZRwYGmNOfBleHHkQGRoRCnBfF2ZfEnhDZlt6awVaEBkaEQpwbBdkWRN JG09tfhgBEhAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 malwarescore=0 priorityscore=317 impostorscore=0 phishscore=0 spamscore=0 bulkscore=0 suspectscore=0 adultscore=0 mlxlogscore=572 clxscore=604 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101040110 domainage_hfrom=9276 X-Spam-Score: 0 X-Spam-OrigSender: haohua0116@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, hua hao --000000000000c25cb205b81605a6 Content-Type: text/plain; charset="UTF-8" Hi NAMD developers and users, I am learning Tutorial_QMMM_String_eABF recently, which was introduced to be an advanced tutorial for QMMM in NAMD page ( http://www.ks.uiuc.edu/Research/qmmm/). When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessary files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only present in the first replica (i..e 0), but not in other replicas (i.e. 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above calculations, and these packages were both complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts and Linux-x86_64-verbs, the error was still present. Normally, these files should appear in each replica. Could you help me with this issue? Thank you very much. *Hua Hao* --000000000000c25cb205b81605a6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi NAMD developers and users,

<= /div>
I am learning Tutorial_QMMM_String_eABF re= cently, which was introduced to be an advanced tutorial for QMMM in NAMD pa= ge (htt= p://www.ks.uiuc.edu/Research/qmmm/).
=
<= br>
When running the eABF job by "mpirun -n 28 namd2 +replica= s 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it is strange th= at some necessary files with the suffix .grad, .count, .pmf, .zcount, and .= zgrad were only present in the first=C2=A0replica (i..e 0), but not in othe= r=C2=A0replicas (i.e. 1-13).=C2=A0NAMD-2.14 and=C2=A0NAMD-Gib-2020-12-07=C2= =A0were used to perform the above calculations, and these packages were bot= h complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-co= mpiled Linux-x86_64-netlrts and=C2=A0Linux-x86_64-verbs, the error was stil= l present.

Normally, these files should appear in each=C2=A0re= plica.

Could you help me with this issue? Thank you very m= uch.

<= div dir=3D"ltr">
Hua Hao
<= br>
=
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boundary="_000_DM6PR08MB53383140B0D1C217CABD07E3E5AE0DM6PR08MB5338namp_" MIME-Version: 1.0 X-OriginatorOrg: ndsu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: DM6PR08MB5338.namprd08.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: c154d421-d9b8-426f-b195-08d8b3895f2f X-MS-Exchange-CrossTenant-originalarrivaltime: 08 Jan 2021 03:56:26.0638 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: ec37a091-b9a6-47e5-98d0-903d4a419203 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: BHS5xzwTuFCgGyHnqZtpgJyj/Sw11UK37nlQ11a7o1qi9JTWP8NPILZG74Q8F/YVIBIOtiE+oBf0mbUWD/OPwdRTMkvlco3FsYNNW7D8VNs= X-MS-Exchange-Transport-CrossTenantHeadersStamped: DM6PR08MB5420 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwcEQpMehcaEQpZRBd6YgFHWx5PfGh4AREKWFgXel5uT0BaGUtTT0I RCnhOF2sdXRlIckJoZnAcEQp5TBdhYBp4E31ZchxrbBEKQ0gXBx4aHBEKQ1kXBxsSEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ccRgSEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF0NkWH1Eb1lSWR1OaX9jfl4bZFB9XBl6WGlib0F+cxtsEQpYXBcfBBoEGBgaBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JmclNiEQpNXBcYHhkRCkxaF2xpTU1rEQpMRhdvb2tra2t rEQpCTxdmcH9uYktyf2NdbxEKQ1oXHhoEGxodBB0cBBsbHREKQl4XGxEKRFgXGREKRF4XGBEKRE kXHhEKQlwXGxEKXk4XGxEKQksXax1dGUhyQmhmcBwRCkJJF2sdXRlIckJoZnAcEQpCRRdmBRIBS EF8XVBDUBEKQk4Xax1dGUhyQmhmcBwRCkJMF3pebk9AWhlLU09CEQpCbBdtX2lzXmwaH2twcBEK QkAXbWAFBR5rfXobXFIRCk1eFxsRClpYFxkRCnlDF2NrHmgeW2tdaXJfEQpZSxcdHRIbEQpwaBd mZm5dHVlaXWZaXBAZGhEKcGgXbUdmHk1Sc25aGWwQHRwRCnBoF2cdcGJ5WUdNfFh7EBkaEQpwaB dtWh16f34SX3wZHhAZGhEKcGgXY2FzTXBnaRp7U0IQGRoRCnBsF2cTZ2MZQ1NOcGNnEBkaEQptf hcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 suspectscore=0 phishscore=0 adultscore=0 malwarescore=0 clxscore=166 spamscore=0 priorityscore=0 lowpriorityscore=0 mlxlogscore=486 impostorscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101080019 domainage_hfrom=7781 X-Spam-Score: 0 X-Spam-OrigSender: hmnasrullah.faisal@ndsu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Faisal, H M Nasrullah" --_000_DM6PR08MB53383140B0D1C217CABD07E3E5AE0DM6PR08MB5338namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I am trying to minimize a clay model with TIP4 water. But every time my sim= ulation is getting crashed. In the log file I am getting this error message LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan [0] Stack Traceback: [4] Stack Traceback: [4:0] [0xf89027] [4:1] [0xb031c6] [0:0] [0xf89027] [0:1] [0xb031c6] [0:2] [0x10853ce] [0:3] [0x11a8f67] [0:4] [0x1320ba5] [0:5] [0x101d769] [0:6] TclInvokeStringCommand+0x88 [0x1371e88] [0:7] [0x1374aa7] [0:8] [0x1375ec2] [0:9] [0x13766e6] [0:10] [0x13d8891] [0:11] [0x13d8a4e] [0:12] [0x1019da0] [0:13] [0x50fc71] [0:14] __libc_start_main+0xf5 [0x2aaaab930545] [0:15] _ZNSt8ios_base4InitD1Ev+0x49 [0x40e4e9] At the same time, In another generated file I am getting another error mess= age: ------------- Processor 0 Exiting: Caught Signal ------------ Signal: segmentation violation Suggestion: Try running with '++debug', or linking with '-memory paranoid' = (memory paranoid requires '+netpoll' at runtime). ------------- Processor 4 Exiting: Caught Signal ------------ Signal: segmentation violation Suggestion: Try running with '++debug', or linking with '-memory paranoid' = (memory paranoid requires '+netpoll' at runtime). Fatal error on PE 0> segmentation violation I have gone through the structure. There is no possibility of nuclear crash= es as the same model is working TIP3 water. I have also checked the coordin= ates of TIP4 water very carefully. I am really stuck here. Could anybody gi= ve me some insight? Thanks in advance. Faisal --_000_DM6PR08MB53383140B0D1C217CABD07E3E5AE0DM6PR08MB5338namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
[0] Stack Traceback:
[4] Stack Traceback:
  [4:0]   [0xf89027]
  [4:1]   [0xb031c6]
  [0:0]   [0xf89027]
  [0:1]   [0xb031c6]
  [0:2]   [0x10853ce]
  [0:3]   [0x11a8f67]
  [0:4]   [0x1320ba5]
  [0:5]   [0x101d769]
  [0:6] TclInvokeStringCommand+0x88  [0= x1371e88]
  [0:7]   [0x1374aa7]
  [0:8]   [0x1375ec2]
  [0:9]   [0x13766e6]
  [0:10]   [0x13d8891]
  [0:11]   [0x13d8a4e]
  [0:12]   [0x1019da0]
  [0:13]   [0x50fc71]
  [0:14] __libc_start_main+0xf5  [0x2aa= aab930545]
  [0:15] _ZNSt8ios_base4InitD1Ev+0x49  = [0x40e4e9]

At the same time, In another generated file I = am getting another error message:
------------- Processor 0 Exiting: Caught Signal = ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linkin= g with '-memory paranoid' (memory paranoid requires '+netpoll' at runtime).=
------------- Processor 4 Exiting: Caught Signal = ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linkin= g with '-memory paranoid' (memory paranoid requires '+netpoll' at runtime).=
Fatal error on PE 0> segmentation violation

I have = gone through the structure. There is no possibility of nuclear crashes as t= he same model is working TIP3 water. I have also checked the coordinates of= TIP4 water very carefully. I am really stuck here. Could anybody give me some insight?
Thanks in advance.

Faisal

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charset="UTF-8" Hi everyone, I'm trying to simulate a circular DNA molecule. To do this, I apply the patch seen below but when I run the simulation I get the following error message: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR ON5 P (ATOMS 2304 2271) ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR ON5 P (ATOMS 2304 2271) This error does not happen for regular DNA, so I think I'm doing something wrong with the patch. I've been trying different things but nothing seems to work. Any help would be appreciated! Thanks, Sebastian Code to apply the patch (the dsDNA was built with nab and has 70 base-pairss) resetpsf mol load pdb DNA.pdb set newfile DNA_psfgen set TOPOFILE ./top_all36_na.inp pdbalias residue DT THY pdbalias residue DG GUA pdbalias residue DC CYT pdbalias residue DA ADE proc psfalias {} { # Define common aliases # Here's for nucleics pdbalias residue G GUA pdbalias residue C CYT pdbalias residue A ADE pdbalias residue T THY foreach bp { GUA CYT ADE THY URA } { pdbalias atom $bp "O5\*" O5' pdbalias atom $bp "C5\*" C5' pdbalias atom $bp "O4\*" O4' pdbalias atom $bp "C4\*" C4' pdbalias atom $bp "C3\*" C3' pdbalias atom $bp "O3\*" O3' pdbalias atom $bp "C2\*" C2' pdbalias atom $bp "O2\*" O2' pdbalias atom $bp "C1\*" C1' } } package require psfgen topology $TOPOFILE psfalias set sel [atomselect top "chain A"] set listA [lsort -unique [$sel get {resid resname}] ] foreach selatom $sel { $selatom set segid ADNA } $sel writepdb ADNA.pdb set sel [atomselect top "chain B"] set listB [lsort -unique [$sel get {resid resname}] ] foreach selatom $sel { $selatom set segid BDNA } $sel writepdb BDNA.pdb # splitting the input pdb set segidList {ADNA BDNA} set patchList [list $listA $listB] segment ADNA { first 5TER last 3TER pdb ADNA.pdb } segment BDNA { first 5TER last 3TER pdb BDNA.pdb } puts "Begin to patch to make DEOXYribose" # patch to make DEOXYribose # purine use patch DEO2 # pyrimidine use patch DEO1 foreach segid $segidList tmpList $patchList { puts "segid: $segid tmpList:$tmpList" foreach record $tmpList { foreach {resid resname} $record { break } if {$resname == "THY" || $resname == "CYT" } { patch DEO1 ${segid}:$resid puts "patch DEO1 ${segid}:$resid" } if {$resname == "ADE" || $resname == "GUA" } { puts "patch DEO2 ${segid}:$resid" patch DEO2 ${segid}:$resid } } coordpdb ${segid}.pdb } puts "End of DEOXYribose " guesscoord patch CY35 ADNA:70 patch CY35 BDNA:70 patch LKNA ADNA:1 ADNA:70 patch LKNA BDNA:1 BDNA:70 regenerate angles dihedrals writepsf $newfile.psf writepdb $newfile.pdb --000000000000c889bd05b8aa23e4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi everyone,=C2=A0

I'm t= rying to simulate a circular DNA molecule. To do this, I apply the patch se= en below but when I run the simulation I get the following error message:

FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR ON5= P (ATOMS 2304 2271)
------------- Processor 0 Exiting: Called CmiAbort = ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR ON5= P (ATOMS 2304 2271)

This error does not happen for regul= ar DNA, so I think I'm doing something wrong with the patch. I've b= een trying different things but nothing seems to work. Any help would be ap= preciated!

Thanks,

Sebast= ian

Code to apply the patch (the dsDNA was built w= ith nab and has 70 base-pairss)

resetpsf
mol load pdb DNA.p= db
set newfile DNA_psfgen
set TOPOFILE ./top_all36_na.inp
pdbalias= residue DT THY
pdbalias residue DG GUA
pdbalias residue DC CYT
pd= balias residue DA ADE
proc psfalias {} {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 = # Define common aliases
=C2=A0 =C2=A0 =C2=A0 =C2=A0 # Here's for nuc= leics
=C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias residue G GUA
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 pdbalias residue C CYT
=C2=A0 =C2=A0 =C2=A0 =C2=A0 pdb= alias residue A ADE
=C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias residue T THY=C2=A0 =C2=A0 =C2=A0 =C2=A0 foreach bp { GUA CYT ADE THY URA } {
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias atom $bp &quo= t;O5\*" O5'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 pdbalias atom $bp "C5\*" C5'
=C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias atom $bp "O4\*" O4= 9;
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias atom= $bp "C4\*" C4'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 pdbalias atom $bp "C3\*" C3'
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias atom $bp "O3\*"= ; O3'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbali= as atom $bp "C2\*" C2'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 pdbalias atom $bp "O2\*" O2'
=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pdbalias atom $bp "C1= \*" C1'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0}<= br>package require psfgen
topology $TOPOFILE
psfalias
set sel [ato= mselect top "chain A"]
set listA [lsort -unique [$sel get {res= id resname}] ]
foreach selatom $sel {
$selatom set segid ADNA
}$sel writepdb ADNA.pdb
set sel [atomselect top "chain B"]
= set listB [lsort -unique [$sel get {resid resname}] ]
foreach selatom $s= el {
$selatom set segid BDNA
}
$sel writepdb BDNA.pdb
# splitti= ng the input pdb
set segidList {ADNA BDNA}
set patchList [list $listA= $listB]
segment ADNA {
=C2=A0 =C2=A0 =C2=A0first 5TER
=C2=A0 =C2= =A0 =C2=A0last 3TER
=C2=A0 =C2=A0 =C2=A0pdb ADNA.pdb
}
segment BDN= A {
=C2=A0 =C2=A0 =C2=A0first 5TER
=C2=A0 =C2=A0 =C2=A0last 3TER
= =C2=A0 =C2=A0 =C2=A0pdb BDNA.pdb
}

puts "Begin to patch to m= ake DEOXYribose"
=C2=A0 # patch to make DEOXYribose
=C2=A0 # pur= ine use patch DEO2
=C2=A0 # pyrimidine use patch DEO1

foreach seg= id $segidList tmpList $patchList {
puts "segid: $segid tmpList:$tmp= List"
=C2=A0 =C2=A0 =C2=A0foreach record $tmpList {
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 foreach {resid resname} $record { break }
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 if {$resname =3D=3D "THY" || $resname =3D=3D &q= uot;CYT" } {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 patch DEO1 $= {segid}:$resid
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 puts "patc= h DEO1 ${segid}:$resid"
=C2=A0 =C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 if {$resname =3D=3D "ADE" || $resname =3D=3D &q= uot;GUA" } {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 puts "p= atch DEO2 ${segid}:$resid"
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 patch DEO2 ${segid}:$resid
=C2=A0 =C2=A0 =C2=A0 =C2=A0 }
=C2=A0 = =C2=A0 =C2=A0}
=C2=A0 =C2=A0 =C2=A0coordpdb ${segid}.pdb
}

put= s "End of DEOXYribose "
guesscoord
patch CY35 ADNA:70
pa= tch CY35 BDNA:70
patch LKNA ADNA:1 ADNA:70
patch LKNA BDNA:1 BDNA:70<= br>regenerate angles dihedrals
writepsf $newfile.psf
writepdb $newfil= e.pdb
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charset="UTF-8" Hello: I compute the total charge for the QM part in QM/MM (QM is specified as residue sidechains), but the total charge is 2.5 not integer. Is it OK to run QM/MM? Thanks, Best, *Chunli* --0000000000002af9c905b8e0019a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello:

I compute the total charge for t= he QM part in QM/MM (QM is specified as residue sidechains), but the total = charge is 2.5 not integer.
Is it OK to run QM/MM?

<= /div>
Thanks,

Bes= t,


Chunli


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zimbra.polytechnique.fr ([127.0.0.1]) by localhost (zimbra.polytechnique.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id aI4n4BcMWvCx for ; Fri, 15 Jan 2021 18:51:39 +0100 (CET) Received: from [192.168.1.104] (webmail-69.polytechnique.fr [129.104.69.39]) by zimbra.polytechnique.fr (Postfix) with ESMTPSA id D20D2621151 for ; Fri, 15 Jan 2021 18:51:38 +0100 (CET) From: Paula Mihaljevic-Juric Content-Type: multipart/alternative; boundary="Apple-Mail=_FBD58A54-6DE3-4D06-8FA6-0FF6F096EC42" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.80.23.2.2\)) Subject: namd-l: FATAL ERROR: patch has 127043 atoms, maximum allowed is 65535 Message-Id: <68872CE6-960A-48F6-8556-AD8C038EC308@polytechnique.edu> Date: Fri, 15 Jan 2021 18:51:37 +0100 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3608.80.23.2.2) X-AntiVirus: Checked by MX [20200131] X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBdtTxpPfH1lbXtnWhEKWFgXY2tHeAVFeBpoZW0 RCnhOF2gYZ1hETn0ZZWtEEQp5TBd6RwVPAWUBTnxSaBEKQ0gXBxkYGREKQ1kXBxsaGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseGXEfGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdlGFBjTU9Ab3tSR0YZXUQcYnN/U2YfQFNnUhJ4YlkfYBEKWFwXHwQaBBgYGAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JkGVhjEQpNXBcbExkRCkxaF2xpTU1NEQpMRhdpaxEKQk8 XblAfc0xoemZnQ1ARCkNaFxsYEwQbGh4EGRoEGx4RCkJeFxsRCkJFF20cSH1EcHpiU35TEQpCTh doGGdYRE59GWVrRBEKQkwXY2tHeAVFeBpoZW0RCkJsF2EffmFaY0xzbUVnEQpCQBdkSxp8eHhLU 3NuQBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxsRCnlDF25ieX8fe2MeYWJiEQpwaBdgeQUF a0kYTB5PZRAeEhEKcGgXZRNpemhNSWhGW30QGRoRCnBoF2FFH395XENHf0tNEBkaEQpwaBdjeEh kAVBcHl9nZRAZGhEKcGgXZx5mE0JAfUtGRkEQGRoRCnBsF29TE1MZfBx/WH8fEBkaEQptfhcbEQ pYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 priorityscore=0 adultscore=0 mlxlogscore=380 clxscore=163 mlxscore=0 lowpriorityscore=0 malwarescore=0 bulkscore=0 suspectscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101150108 X-Spam-Score: 0 X-Spam-OrigSender: paula.mihaljevic-juric@polytechnique.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Paula Mihaljevic-Juric --Apple-Mail=_FBD58A54-6DE3-4D06-8FA6-0FF6F096EC42 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi, I obtained an error regarding too small patch as my system is around 1.3 = million atoms with the box. I tried adding "twoAwayX yes, twoAwayY yes and twoAwayZ yes" in the = input file as it was advised on the forum, but I still obtain the same = error. I am running on 8 nodes (total of 224 CPUs). I would appreciate someone=E2=80=99s help with this! Best Paula OUTPUT FILE: Info: PATCH GRID IS 36 (PERIODIC) BY 38 (PERIODIC) BY 35 (PERIODIC) Info: PATCH GRID IS 2-AWAY BY 2-AWAY BY 2-AWAY Info: REMOVING COM VELOCITY -0.00689324 0.000639769 -0.00426937 Info: LARGEST PATCH (23958) HAS 127043 ATOMS Info: TORUS A SIZE 9 USING 0 1 2 3 4 5 6 7 8 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 9 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 1.75417 s, 1619.45 MB of memory in use Info: PME using 160 and 168 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 3 5 6 7 9 10 11 13 14 ... Info: PME TRANS LOCATIONS: 1 2 4 5 6 8 9 10 12 13 ... Info: PME USING 160 GRID NODES AND 168 TRANS NODES Info: Startup phase 7 took 0.0144551 s, 1619.45 MB of memory in use Info: Startup phase 8 took 0.000203848 s, 1619.45 MB of memory in use Info: Startup phase 9 took 95.2695 s, 1619.45 MB of memory in use Info: Startup phase 10 took 0.00026989 s, 1619.45 MB of memory in use Info: Startup phase 11 took 1.02239 s, 1599.13 MB of memory in use LDB: Central LB being created... Info: Startup phase 12 took 0.0644171 s, 1599.13 MB of memory in use Info: CREATING 3304855 COMPUTE OBJECTS Info: Startup phase 13 took 0.584059 s, 1826.06 MB of memory in use Info: Startup phase 14 took 0.000277042 s, 1826.06 MB of memory in use Info: Startup phase 15 took 0.000103951 s, 1826.06 MB of memory in use Info: Finished startup at 114.515 s, 1826.06 MB of memory in use TCL: Minimizing for 1000 steps Info: useSync: 0 useProxySync: 0 ERROR: Constraint failure in RATTLE algorithm for atom 1! FATAL ERROR: patch has 127043 atoms, maximum allowed is 65535= --Apple-Mail=_FBD58A54-6DE3-4D06-8FA6-0FF6F096EC42 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Hi,

I obtained an error regarding too small patch as my system is = around 1.3 million atoms with the box.

I tried adding "twoAwayX yes, twoAwayY = yes and twoAwayZ yes" in the input file as it was advised on the forum, = but I still obtain the same error.

I am running on 8 nodes (total of 224 = CPUs).

I would appreciate someone=E2=80=99s help with = this!

Best
Paula

OUTPUT FILE:

Info: PATCH GRID IS 36 (PERIODIC) BY 38 (PERIODIC) BY 35 = (PERIODIC)
Info: PATCH GRID IS 2-AWAY BY 2-AWAY BY = 2-AWAY
Info: REMOVING COM VELOCITY -0.00689324 = 0.000639769 -0.00426937
Info: LARGEST PATCH (23958) HAS = 127043 ATOMS
Info: TORUS A SIZE 9 USING 0 1 2 3 4 5 6 = 7 8
Info: TORUS B SIZE 1 USING = 0
Info: TORUS C SIZE 1 USING = 0
Info: TORUS MINIMAL MESH SIZE IS 9 BY 1 = BY 1
Info: Placed 100% of base nodes on same = physical node as patch
Info: = Startup phase 6 took 1.75417 s, 1619.45 MB of memory in = use
Info: PME using 160 and 168 processors = for FFT and reciprocal sum.
Info: = PME GRID LOCATIONS: 1 3 5 6 7 9 10 11 13 14 ...
Info: PME TRANS LOCATIONS: 1 2 4 5 6 8 9 10 12 13 = ..
Info: PME USING 160 GRID NODES AND 168 = TRANS NODES
Info: Startup phase 7 took 0.0144551 s, = 1619.45 MB of memory in use
Info: = Startup phase 8 took 0.000203848 s, 1619.45 MB of memory in = use
Info: Startup phase 9 took 95.2695 s, = 1619.45 MB of memory in use
Info: = Startup phase 10 took 0.00026989 s, 1619.45 MB of memory in = use
Info: Startup phase 11 took 1.02239 s, = 1599.13 MB of memory in use
LDB: = Central LB being created...
Info: = Startup phase 12 took 0.0644171 s, 1599.13 MB of memory in = use
Info: CREATING 3304855 COMPUTE = OBJECTS
Info: Startup phase 13 took 0.584059 s, = 1826.06 MB of memory in use
Info: = Startup phase 14 took 0.000277042 s, 1826.06 MB of memory in = use
Info: Startup phase 15 took 0.000103951 = s, 1826.06 MB of memory in use
Info: = Finished startup at 114.515 s, 1826.06 MB of memory in = use

TCL: = Minimizing for 1000 steps
Info: = useSync: 0 useProxySync: 0
ERROR: = Constraint failure in RATTLE algorithm for atom 1!
FATAL ERROR: patch has 127043 atoms, maximum allowed is = 65535
= --Apple-Mail=_FBD58A54-6DE3-4D06-8FA6-0FF6F096EC42-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 15 13:46:03 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10FJk3bo025671; Fri, 15 Jan 2021 13:46:03 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10FJk2JW025670; Fri, 15 Jan 2021 13:46:02 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10FJk2gA025666; Fri, 15 Jan 2021 13:46:02 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10FJk2BB025665; Fri, 15 Jan 2021 13:46:02 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10FJjr9i025654 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Hi, I am trying to run free energy calculations on a transmembrane helical dimer. I have been trying to closely follow the protein ligand tutorial to do these calculations ( http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf). I have a question about judging convergence of the PMFs. Taking the bound conformation calculation as an example, using the RMSD colvar, could one look at the protein's rmsd plateauing as a sign that the PMFs are also converging. Or should I be looking for my PMF values to also be plateauing? In a similar vein, around how many steps should convergence be happening around. Thank you for the help, Ethan Croitoru --000000000000a25cd005b8f59eea Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I am trying to run free energy calc= ulations on a transmembrane helical dimer. I have been trying to closely fo= llow the protein ligand=C2=A0tutorial to do these calculations (http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-li= gand.pdf). I have a question about judging convergence of the PMFs. Tak= ing the bound conformation calculation as an example, using the RMSD colvar= , could one look at the protein's rmsd plateauing as a sign that the PM= Fs are also converging. Or should I be looking for my PMF values to also be= plateauing? In a similar vein, around how many steps should convergence be= happening around.

Thank you for the help,
Ethan Croitoru
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charset=utf-8 Content-Transfer-Encoding: 8bit Hi Ethan, What I like to do is analyze different snapshots of my simulation. If the first half of the trajectory and the last half of the trajectory yield the same PMF (within some tolerance) when analyzed independently, I judge the PMF to be converged. Sometimes, the first few nanoseconds aren't representative of the rest, and so it can also be useful to analyze the PMFs from 5-10 nanosecond chunks of trajectory. -Josh On 1/15/21 2:45 PM, Ethan Croitoru wrote: > Hi, > > I am trying to run free energy calculations on a transmembrane helical > dimer. I have been trying to closely follow the protein > ligand tutorial to do these calculations > (http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf > ). > I have a question about judging convergence of the PMFs. Taking the > bound conformation calculation as an example, using the RMSD colvar, > could one look at the protein's rmsd plateauing as a sign that the > PMFs are also converging. Or should I be looking for my PMF values to > also be plateauing? In a similar vein, around how many steps should > convergence be happening around. > > Thank you for the help, > Ethan Croitoru --------------C9F034357506DE957F87D874 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Hi Ethan,

What I like to do is analyze different snapshots of my simulation. If the first half of the trajectory and the last half of the trajectory yield the same PMF (within some tolerance) when analyzed independently, I judge the PMF to be converged. Sometimes, the first few nanoseconds aren't representative of the rest, and so it can also be useful to analyze the PMFs from 5-10 nanosecond chunks of trajectory.

-Josh

On 1/15/21 2:45 PM, Ethan Croitoru wrote:
Hi,

I am trying to run free energy calculations on a transmembrane helical dimer. I have been trying to closely follow the protein ligand tutorial to do these calculations (http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf). I have a question about judging convergence of the PMFs. Taking the bound conformation calculation as an example, using the RMSD colvar, could one look at the protein's rmsd plateauing as a sign that the PMFs are also converging. Or should I be looking for my PMF values to also be plateauing? In a similar vein, around how many steps should convergence be happening around.

Thank you for the help,
Ethan Croitoru

--------------C9F034357506DE957F87D874-- From owner-namd-l@halifax.ks.uiuc.edu Sun Jan 17 11:21:18 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10HHLI8Y022872; Sun, 17 Jan 2021 11:21:18 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10HHLI1H022871; Sun, 17 Jan 2021 11:21:18 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10HHLHDS022867; Sun, 17 Jan 2021 11:21:17 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10HHLHTX022865; Sun, 17 Jan 2021 11:21:17 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10HHKwGL022843 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sun, 17 Jan 2021 11:21:04 -0600 (CST) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 10HHIovj016890 for ; Sun, 17 Jan 2021 17:20:58 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=nikolaev@spbau.ru Received: from abuse.spbau.ru (mail.spbau.ru [91.151.191.254]) by mx0a-00007101.pphosted.com with ESMTP id 363s0w7b8m-1 for ; Sun, 17 Jan 2021 17:20:57 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by abuse.spbau.ru (Postfix) with ESMTP id 0720256C33 for ; Sun, 17 Jan 2021 20:20:56 +0300 (MSK) X-Virus-Scanned: Debian amavisd-new at abuse.spbau.ru Received: from abuse.spbau.ru ([127.0.0.1]) by localhost (abuse.spbau.ru [127.0.0.1]) (amavisd-new, port 10024) with LMTP id x17kbAqpGVGF for ; Sun, 17 Jan 2021 20:20:54 +0300 (MSK) Received: from mail.spbau.ru (localhost.localdomain [127.0.0.1]) by abuse.spbau.ru (Postfix) with ESMTP id 6426756673 for ; Sun, 17 Jan 2021 20:20:54 +0300 (MSK) Received: from 217.66.157.49 (SquirrelMail authenticated user nikolaev) by mail.spbau.ru with HTTP; Sun, 17 Jan 2021 20:20:54 +0300 Message-ID: <933af968722a2926dce384a67c1e2a8e.squirrel@mail.spbau.ru> Date: Sun, 17 Jan 2021 20:20:54 +0300 Subject: namd-l: NAMD QMMM Scheme From: nikolaev@spbau.ru To: namd-l@ks.uiuc.edu User-Agent: SquirrelMail/1.4.23 [SVN] MIME-Version: 1.0 Content-Type: text/plain;charset=UTF-8 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-CLX-Response: 1TFkXGRwaEQpMehcaEQpZRBd6HF9sYhp9cxtlbhEKWFgXZl9scG9+GmJyEnA RCnhOF2QabFh7GQFdX1luEQp5TBduYgFMbxhIfnNlXxEKQ0gXBx0aEQpDWRcHHxEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGx8fcRIGGRJ3BhwTBhoGGgYbEgYbGxJxGx4QGncGGgYaBhoGGgYaBhpxG hAadwYaEQpZXhdoY3kRCklGF19DX0l1QkVZXk9OEQpDThdsZmRzSBscHmEcWFtMBxMTcBJrXEdf Z30fRkkaSHJTTBEKWFwXHwQaBBgYGAUbGgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JlQkt8EQpNXBc ZHBEKTFoXaGlNb00RCkJPF2J9bUlhbGZNBXoFEQpDWhcTGwQbHxsEGxMbBBgfHhEKQl4XGxEKQk UXZl9scG9+GmJyEnARCkJOF2QabFh7GQFdX1luEQpCTBdmX2xwb34aYnIScBEKQmwXZl9scG9+G mJyEnARCkJAF2BYUh9tTWN/fmFvEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKeUMXb3prXWEbQXkZ eHIRCnBoF29FZnNOfF0BT3pLEBkaEQpwaBdkfmRFe31sXWJ8ARAZGhEKcEMXbm1Oe15HHnpSBU8 QGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 mlxlogscore=477 clxscore=360 mlxscore=0 malwarescore=0 priorityscore=0 phishscore=0 suspectscore=0 bulkscore=0 spamscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101170109 X-Spam-Score: 0 X-Spam-OrigSender: nikolaev@spbau.ru X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, nikolaev@spbau.ru Dear all, I have a quick and silly question - does NAMD use an additive or a subtractive scheme in QM/MM? 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Sun, 17 Jan 2021 21:23:33 +0000 Received: from BY5PR19MB3474.namprd19.prod.outlook.com ([fe80::616b:3e46:2483:193b]) by BY5PR19MB3474.namprd19.prod.outlook.com ([fe80::616b:3e46:2483:193b%7]) with mapi id 15.20.3763.014; Sun, 17 Jan 2021 21:23:32 +0000 From: Rafael Bernardi To: "namd-l@ks.uiuc.edu" , "nikolaev@spbau.ru" Subject: Re: namd-l: NAMD QMMM Scheme Thread-Topic: namd-l: NAMD QMMM Scheme Thread-Index: AQHW7PzUJLLOvYpYYk6nS9hdDEGcoKor72SA Date: Sun, 17 Jan 2021 21:23:32 +0000 Message-ID: <6601FBB7-6CB1-4310-84A7-EC4052EC2F6A@auburn.edu> References: <933af968722a2926dce384a67c1e2a8e.squirrel@mail.spbau.ru> In-Reply-To: <933af968722a2926dce384a67c1e2a8e.squirrel@mail.spbau.ru> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=auburn.edu; x-originating-ip: [2600:1700:4317:40:bc7a:54fa:163c:f24a] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 2ed14cad-41c7-44a3-463f-08d8bb2e24a0 x-ms-traffictypediagnostic: BY3PR19MB4977: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:3631; 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charset="utf-8" Content-ID: MIME-Version: 1.0 X-OriginatorOrg: auburn.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BY5PR19MB3474.namprd19.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 2ed14cad-41c7-44a3-463f-08d8bb2e24a0 X-MS-Exchange-CrossTenant-originalarrivaltime: 17 Jan 2021 21:23:32.7590 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: ccb6deed-bd29-4b38-8979-d72780f62d3b X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: IuyReb6LE05cSjWQrxKNba9TXN94fe3BlLawg+639rYSt8//s4JXVO7Aq/i+1TBczGwRBLR8tiaKH2EAT2fxUw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BY3PR19MB4977 X-CLX-Response: 1TFkXGx0cEQpMehcaEQpZRBdsYxtBXE4FGnAdfREKWFgXekdaR2x9GhhhEkA RCnhOF2JwUGlYUhNZZVobEQp5TBdjHx5uaGRPGh5oSxEKQ0gXBxIcEQpDWRcHGR4RCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHxxxGR8QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XHxxFaH0ZeUhYTV0afBMbTU1nYBNIcxJiGUtyWF5laW0RClhcFx8EGgQYGBgFGxoE GxsaBB8aBBseGxAbHhofGhEKXlkXcmVBE1ARCk1cFx8RCkxaF3hpTU1NEQpFWRdvaxEKTF8XegU FBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF21yaV5uT0wTUh8cEQpDWhceGgQbGh0EEx4EEx4RCk JeFxsRCkReFx4RCkJFF2MYenIZRG1HWEVaEQpCThdicFBpWFITWWVaGxEKQkwXekdaR2x9GhhhE kARCkJsF2YBbR8fZRtLcGRrEQpCQBdsY35cc0hJc0x6bhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsR ClpYFxkRCnlDF254U0FBXk5leH0TEQpZSxcbGxMZEhEKcGcXb31iSXkbfF1dYx4QGRoRCnBoF29 FZnNOfF0BT3pLEB4SEQpwaBdkfmRFe31sXWJ8ARAeEhEKcGgXZBtcE0ZmEx1uGWIQGRoRCnBoF2 BsBVABZlpia29PEBkaEQpwaBdmf1oFAWUbGXlfWRAZGhEKcH0XZkl+R0NSHVhuSV8QGRoRCnBnF 21HYWtNYxlMU2luEBkaEQpwfxdlWHIYHUkYXkZpfBAbGxMRCnBfF2VYaBlBUmZ9HR9CEBkaEQpw bBdiUmdyZ0lHHFxAYRAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 spamscore=0 mlxscore=0 clxscore=176 adultscore=0 lowpriorityscore=0 mlxlogscore=880 bulkscore=0 malwarescore=0 priorityscore=0 phishscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101170135 domainage_hfrom=11938 X-Spam-Score: 0 X-Spam-OrigSender: rcbernardi@auburn.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by halifax.ks.uiuc.edu id 10HLNbkM005343 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Rafael Bernardi additive ……………………………………………………………………... Rafael C. Bernardi Biophysics Cluster - Department of Physics at Auburn University NIH Center for Macromolecular Modeling & Bioinformatics rcbernardi@auburn.edu rcbernardi@ks.uiuc.edu www.ks.uiuc.edu/~rcbernardi +1 (334) 844-4393 On 1/17/21, 12:16 PM, "owner-namd-l@ks.uiuc.edu on behalf of nikolaev@spbau.ru" wrote: Dear all, I have a quick and silly question - does NAMD use an additive or a subtractive scheme in QM/MM? Best, Dmitrii From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 18 12:17:06 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10IIH6vn001322; Mon, 18 Jan 2021 12:17:06 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10IIH6jj001321; Mon, 18 Jan 2021 12:17:06 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10IIH5Z0001317; Mon, 18 Jan 2021 12:17:05 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10IIH5BA001315; Mon, 18 Jan 2021 12:17:05 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10IIGpsI001305 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Mon, 18 Jan 2021 18:16:44 +0000 Received: from BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM (2a01:111:e400:7ebe::42) by PU1APC01FT021.mail.protection.outlook.com (2a01:111:e400:7ebe::221) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.3763.12 via Frontend Transport; Mon, 18 Jan 2021 18:16:44 +0000 Received: from BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM ([fe80::8c8f:4b20:6edd:b0d1]) by BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM ([fe80::8c8f:4b20:6edd:b0d1%6]) with mapi id 15.20.3763.014; Mon, 18 Jan 2021 18:16:42 +0000 From: Raman Preet Singh To: NAMD list Subject: namd-l: Maximum and minimum box size Thread-Topic: Maximum and minimum box size Thread-Index: AQHW7cSsVNRwnfSxsE6BWGnrzoA60g== Date: Mon, 18 Jan 2021 18:16:42 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-incomingtopheadermarker: OriginalChecksum:4C4DC9D618073A6E23FBDC0255AC56648FBBEB621F5D1A180E86F9C0FA9C323C;UpperCasedChecksum:FB40E0E086F494FC105E835DB2F4992BCBB18E51D1F171E174C13A220C60E94F;SizeAsReceived:6602;Count:41 x-tmn: [vrYJ/EgAOaz+IyjfrJE97u1+3796/Rp4] x-ms-publictraffictype: Email x-incomingheadercount: 41 x-eopattributedmessage: 0 x-ms-office365-filtering-correlation-id: 8e35fb8d-429a-4d9f-3fe2-08d8bbdd352e x-ms-traffictypediagnostic: PU1APC01HT120: x-microsoft-antispam: BCL:0; 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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear All, I am interested in performing a simulation where one of the box dimensions = is expected to reach 50 nm. I have seen publications with 20+ nm water box = sides but not sure if 50 nm or higher dimensions are supported in NAMD. I w= ill be using MARTINI CG models. If 50 nm is supported, do I need to make an= y changes in the NAMD conf file? A related question is: what is the minimum box size supported? A 1 nm dista= nce from the sides of the solute is the ideal situation. However, if it is = just a solvent box, what is the minimum supported size (for AA and CG model= s)? Thank you in advance for your time and inputs. Regards, Raman --_000_BMXPR01MB352612A3D5F0491969EDBA0EB3A40BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Dear All,

I am interested in performing a simulation where one of the box dimensions = is expected to reach 50 nm. I have seen publications with 20+ nm water box = sides but not sure if 50 nm or higher dimensions are supported in NAMD. I w= ill be using MARTINI CG models. If 50 nm is supported, do I need to make any changes in the NAMD conf file= ?

A related question is: what is the minimum box size supported? A 1 nm dista= nce from the sides of the solute is the ideal situation. However, if it is = just a solvent box, what is the minimum supported size (for AA and CG model= s)?

Thank you in advance for your time and inputs.

Regards,
Raman


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Mon, 18 Jan 2021 18:21:24 +0000 Received: from BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM (2a01:111:e400:7ebe::42) by PU1APC01FT021.mail.protection.outlook.com (2a01:111:e400:7ebe::221) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.3763.12 via Frontend Transport; Mon, 18 Jan 2021 18:21:23 +0000 Received: from BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM ([fe80::8c8f:4b20:6edd:b0d1]) by BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM ([fe80::8c8f:4b20:6edd:b0d1%6]) with mapi id 15.20.3763.014; Mon, 18 Jan 2021 18:21:23 +0000 From: Raman Preet Singh To: NAMD list Subject: namd-l: Infrared spectrum prediction Thread-Topic: Infrared spectrum prediction Thread-Index: AQHW7cYTYT4Dz/wOrEWROuny16TDIg== Date: Mon, 18 Jan 2021 18:21:23 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-incomingtopheadermarker: OriginalChecksum:FD10E59659B121FE24A4FBD064A378A40FD39ADA025DB206D2CA26FB09E9EF44;UpperCasedChecksum:1744921904F913FAF8E784A25E1AFE5E50B8E924C49E742D7DCC42C397E149EF;SizeAsReceived:6602;Count:41 x-tmn: [2bFKe23zWnpQHdlScdUt+cbZsV6a1oeV] x-ms-publictraffictype: Email x-incomingheadercount: 41 x-eopattributedmessage: 0 x-ms-office365-filtering-correlation-id: 90a699db-dd59-42da-cd78-08d8bbdddcc8 x-ms-traffictypediagnostic: PU1APC01HT034: x-microsoft-antispam: BCL:0; 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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear All, I have come across some papers where MD has been used to predict IR spectr= um of proteins. Is it possible to predict IR spectrum of small organic mole= cules from NAMD simulations? Can changes in IR spectra due to interactions = between two molecules (H-bonding, pi-pi interactions, etc ) be also predict= ed? Any papers, tutorials, scripts, etc. would be highly appreciated. Thanks in advance. Regards, Raman --_000_BMXPR01MB352685B6CC0C75222A638E04B3A40BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Dear All,

I have come across some papers where MD has been  used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


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boundary="000000000000045ee705b9b8528c" --000000000000045ee705b9b8528c Content-Type: text/plain; charset="UTF-8" Dear NAMD Developers and Users, I have a protein(solvated and neutralized with 0.15mM NaCl concentration) simulation system under classical MD scenario with charmm36 ff parameters implemented in VMD/NAMD. I have prepared my system with both GROMACS and NAMD* (*preferred because I would like to run Accelerated MD later on). The system consists of 148943 atoms all together, I have tried to test the speed and scaling of NAMD using 1,2,4,8,16 and 32 nodes and found a linear scaling. I get ~50ns/day of yield with NAMD on 32 nodes (768 processing cores), while if I run the similar system with gromacs on 20 nodes (480 processing cores) and I get ~270ns/day. Would it be possible for someone in the group to look at my issue, as ~150000 atoms simulation system should not require this much of resources to run this short simulation. I think I am wasting my HPC resources and I am in need of dire intervention from experts. Please find Attached the configuration and run script. I would greatly appreciate your expert intervention and help, so that I can make the best use of the HPC resources. Thanking you Best regards Raghav --000000000000045ee705b9b8528c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD Developers and Users,
I have a = protein(solvated and neutralized with 0.15mM NaCl concentration) simulation= system under classical MD scenario with charmm36 ff parameters implemented= in VMD/NAMD.=C2=A0
I have prepared my system with both GROMACS and N= AMD* (*preferred because I would like to run Accelerated MD later on). The = system consists of 148943 atoms all together, I have tried to test the spee= d and scaling of NAMD using 1,2,4,8,16 and 32 nodes and found a linear scal= ing.=C2=A0I get ~50ns/day of yield with NAMD on 32 nodes (768 proce= ssing cores), while if I run the similar system with gromacs on 20 nodes (4= 80 processing cores) and I get ~270ns/day.

Would it be possible for so= meone in the group to look at my issue, as ~150000 atoms simulation system = should not require this much of resources to run this short simulation. I t= hink I am wasting my HPC resources and I am in need of dire intervention fr= om experts.

Please find Attached the configuration and run script. I w= ould greatly appreciate your expert intervention and help, so that I can ma= ke the best=C2=A0use of the HPC resources.

Thanking you

Best rega= rds
Raghav
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Mon, 25 Jan 2021 05:27:42 -0800 (PST) MIME-Version: 1.0 From: "Dr. Eddie" Date: Mon, 25 Jan 2021 07:27:32 -0600 Message-ID: Subject: namd-l: Supervised MD using NAMD To: "namd-l@ks.uiuc.edu" Content-Type: multipart/alternative; boundary="000000000000aab43c05b9b9807a" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0cEQpMehcZGhgRCllEF3pfQXkSS0tBQh9QEQpYWBdgHV1gS2lyR14 ZeREKeE4XY1Nja3sTWH4aX14RCnlMF2xtQ0dwUmNGG19sEQpDSBcHGxIeEQpDWRcHEhkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxxxGR8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWENhegdZZX5Qa2RMZR0SaF1PcGl8Q0JiGVJ7HGR8YGgRClhcFx8EGgQYGBgF GxoEGxsaBB8aBBseHxAbHhofGhEKXlkXcnhtXFgRCk1cFxgZEhEKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGx0TEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2tAcBtne05hGHh+EQpCT hdjU2NrexNYfhpfXhEKQkwXYB1dYEtpckdeGXkRCkJsF2JjQR1hUEVtEhITEQpCQBdlYmlBZHtu ZHxpSBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2x4fhhGeGZhf1AbEQpZSxcTGBM dEQpwaBdhZ35NY3heWlgeRxAZGhEKcGgXYWh6Ul1eE1NnU3MQGRoRCnBoF2YSSGxYW2dYcEV6EB kaEQpwaBdnY3BNYAFYeHlkcxAZGhEKcGgXYlNPR11Ccn5rXnIQGRoRCnBsF2xtWB1nXkJ/YWJaE BkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=302 spamscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 suspectscore=0 phishscore=0 clxscore=176 bulkscore=0 mlxscore=0 malwarescore=0 mlxlogscore=576 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101250076 domainage_hfrom=9297 X-Spam-Score: 0 X-Spam-OrigSender: eackad@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Eddie" --000000000000aab43c05b9b9807a Content-Type: text/plain; charset="UTF-8" Hello all, I'd like to perform a supervised MD (SuMD) where basically I evaluate the distance of a ligand from its target every so often and reload a previous trajectory to continue if the new distance is larger or continue if the distance is smaller. I can kinda see how I can do this with a python script that writes the slurm/namd config file, but it would need mdtraj (or something similar) in order for me to be able to evaluate the distance I'm interested in. I don't know if that is common on Bridges and other XSEDE systems. The python script would need to sit in the queue with a dependency on the actual MD calculation each time. Is there a better way? Can the tcl config file handle full tcl commands (atomselect, distance etc) and conditionaly load other restore points? Much appreciated! Eddie --000000000000aab43c05b9b9807a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello all,
I'd like to perform a supervised MD (Su= MD) where basically I evaluate the distance of a ligand from its target eve= ry so often and reload a previous trajectory to continue if the new distanc= e is larger or continue if the distance is smaller. I can kinda see how I c= an do this with a python script that writes the slurm/namd config file, but= it would need mdtraj (or something similar) in order for me to be able to = evaluate the distance I'm interested in. I don't know if that is co= mmon on Bridges and other XSEDE systems. The python script would need to si= t in the queue with a dependency on the actual MD calculation each time. Is= there a better way? Can the tcl config file handle full tcl commands (atom= select, distance etc) and conditionaly load other restore points?
Much appreciated!
Eddie


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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=d+Nq8h/Oh8q5SD88CXPqPNEElMBxEYZhQDIPfkNP4r8=; b=HO8AlSBhUQ0GWZpT8tMutNCXBIalJAHOWRO3xXvKAsbXpZ3sKL/iBfAYDvbDyFw7sa eVlKE2uDrsB8BtXWn9KXINnvywyRIRKnyYVhK3UuQ+3unbv8rBx3NNjPMVqUNEuVKZNL Gr649DvhHrMbtf96qYh3dVWw8ZeZQwY8yKnbPXlE7vV3I0hZYN/yakYAoj9KRQSmp912 Qarx9iMVB0Me6CS4kOVDqet3drniNNBSDprfBGcnEysKr0sdWFnO9B7OiflL3hwHb7LJ XtOVfI0qxFXFJyGcKtawz2MI5z6H7XyxXpnIMEWhl+4h8NPvyhEkAXi8FNgituLgTTZ7 9zqQ== X-Gm-Message-State: AOAM531R8P8vVRzCpvPzQ7yUeVGPqN3KmI/fSnGP8yng+TS9/sto5qZp qGAboLrUzj4ySrD/OC8XpttmdeGV9d+ehPKc8h5RJGCKzos= X-Google-Smtp-Source: ABdhPJzHj3VMWwReDebrCwuUjyl126WhG4X3YrgzmAi+0a/WHl10BAAMiquZkQ9G7dPL+pthqQ5eR+qzEA963IfWWxA= X-Received: by 2002:a2e:9d8e:: with SMTP id c14mr213653ljj.477.1611582004399; Mon, 25 Jan 2021 05:40:04 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: Seke Keretsu Date: Mon, 25 Jan 2021 22:39:55 +0900 Message-ID: Subject: Re: namd-l: Supervised MD using NAMD To: namd-l@ks.uiuc.edu, "Dr. Eddie" Content-Type: multipart/alternative; boundary="000000000000e6101605b9b9ac65" X-CLX-Response: 1TFkXGx4cEQpMehcZGxwRCllEF2BbUFpIT2NFQBlvEQpYWBdpHx0aWk1PTVl dYBEKeE4XY1Nja3sTWH4aX14RCnlMF2dHWgFaQB9AE0kbEQpDSBcHGBwdEQpDWRcHGxoaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxgccRsdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2RGRHpZWB8Za1pDaVt4XmNHeG1BZF9CW3VvHBpkUnJpEQpYXBcfBBoEGBgY BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXcnhtHXkRCk1cFxseHhEKTFoXeGlNa2sRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrfFlQWBlpXhhmWhEKQ1oXGBoTBBIfBBgaEg QbHRsRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZ1lmSXhCc3JyTW4RCkJOF2NTY2t7E1h+Gl9eEQpCTBdpHx0aWk1PTVldYBEKQmwX Z11efmBhQkBpaRMRCkJAF29ERmZkGWxPEhtJEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXZ10aSEUcHWNyYwERCllLFxMYEx0RCnBoF2Fnfk1jeF5aWB5HEBoRCnBoF2djcE1gAVh4eW RzEBoRCnBoF2BAQkliR35QYVJhEBkaEQpwaBdjR05LZmlvUBhdbhAZGhEKcGgXZ2FSbW5pfRIFW W8QGRoRCnBsF29FaGRmQV1nRmVDEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 bulkscore=0 clxscore=146 lowpriorityscore=0 spamscore=0 mlxscore=0 malwarescore=0 adultscore=0 priorityscore=316 impostorscore=0 mlxlogscore=660 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101250078 domainage_hfrom=9297 X-Spam-Score: 0 X-Spam-OrigSender: sekekeretsu@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Seke Keretsu --000000000000e6101605b9b9ac65 Content-Type: text/plain; charset="UTF-8" Hi Dr Eddie, I was setting up my system for SUMD when this mail arrived. This can be implemented within the namd configuration file. If you like I can share the script with you. (Let me know which email) Best Seke On Mon, Jan 25, 2021 at 10:29 PM Dr. Eddie wrote: > Hello all, > I'd like to perform a supervised MD (SuMD) where basically I evaluate the > distance of a ligand from its target every so often and reload a previous > trajectory to continue if the new distance is larger or continue if the > distance is smaller. I can kinda see how I can do this with a python script > that writes the slurm/namd config file, but it would need mdtraj (or > something similar) in order for me to be able to evaluate the distance I'm > interested in. I don't know if that is common on Bridges and other XSEDE > systems. The python script would need to sit in the queue with a dependency > on the actual MD calculation each time. Is there a better way? Can the tcl > config file handle full tcl commands (atomselect, distance etc) and > conditionaly load other restore points? > Much appreciated! > Eddie > > > --000000000000e6101605b9b9ac65 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Dr Eddie,

I was setting up my system= for SUMD when this mail arrived.=C2=A0
This can be implemented w= ithin the namd configuration file. If you like I can share the script with = you. (Let me know which email)

Best Seke



On Mon, Jan 25, 2021 at 10:29 PM Dr. Eddie <eackad@gmail.com> wrote:
=
Hello al= l,
I'd like to perform a supervised MD (SuMD) where basically I eva= luate the distance of a ligand from its target every so often and reload a = previous trajectory to continue if the new distance is larger or continue i= f the distance is smaller. I can kinda see how I can do this with a python = script that writes the slurm/namd config file, but it would need mdtraj (or= something similar) in order for me to be able to evaluate the distance I&#= 39;m interested in. I don't know if that is common on Bridges and other= XSEDE systems. The python script would need to sit in the queue with a dep= endency on the actual MD calculation each time. Is there a better way? Can = the tcl config file handle full tcl commands (atomselect, distance etc) and= conditionaly load other restore points?
Much ap= preciated!
Eddie

=

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[73.167.60.93]) by smtp.gmail.com with ESMTPSA id c81sm3590121qkb.88.2021.01.25.13.50.04 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 25 Jan 2021 13:50:05 -0800 (PST) From: Victor Zhao Content-Type: multipart/alternative; boundary="Apple-Mail=_EF300D1F-2201-4094-ACD5-77D6C5B942C5" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.17\)) Subject: namd-l: Protein RMSF in replica exchange simulations Message-Id: <313BAFD0-73DE-416A-85D3-7E0F56AB13B9@g.harvard.edu> Date: Mon, 25 Jan 2021 16:50:03 -0500 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3445.104.17) X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIaEQpMehcaEQpZRBdkG11eGVp9YGd4UhEKWFgXbhNTWBxiaBt/f1A RCnhOF3prH3tpRxxLUlB7EQp5TBdpTl9pU2BAXmFbRBEKQ0gXBxgSHBEKQ1kXBxsdEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGnEZExAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdCdW15RhhTQxlBRU5IGmAeRBxIYBJFaWNpTkhhQFlhWBEKWFwXHwQaBBgYGAUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3J4ZW1YEQpNXBcYHRsRCkxaF2hpTU1rEQpCTxdrQVNMHhJ ab08SbBEKQ1oXGBoTBBIfBBscGgQbEhsRCkJeFxsRCkJFF2YZRFxZE0t4f015EQpCThd6ax97aU ccS1JQexEKQkwXbhNTWBxiaBt/f1ARCkJsF2tmc11uaBxDaUN4EQpCQBdkUhsBZlBwQ39TSREKQ lgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF3p5WmgBaU5iXWdeEQpwZxdjGGhkfmlHRnB+ QRAZGhEKcGgXbRhea28eGVkaZhMQGRoRCnBoF29mcF9uWW5vfUliEBkaEQpwaBdgHG5mTHBvRnI BThAZGhEKcGgXYWgbBV5yHR1dZ20QGRoRCnBoF25kAUxYfmRvYBtEEBkaEQpwbBdhWWNwQhseQ3 9cRRAeEhEKcEMXbBoSWhpHb2ZcWE0QGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 bulkscore=0 mlxlogscore=999 mlxscore=0 suspectscore=0 priorityscore=0 lowpriorityscore=0 phishscore=0 clxscore=180 spamscore=0 malwarescore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101250110 X-Spam-Score: 0 X-Spam-OrigSender: yzhao01@g.harvard.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Victor Zhao --Apple-Mail=_EF300D1F-2201-4094-ACD5-77D6C5B942C5 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear all, I have been running replica exchange simulations (REST2). So far, I have = focused on observables calculated on a per-frame basis and averaged to = obtain ensemble values. But I am wondering, is it useful to calculate = RMSF in a replica exchange simulation? Presumably you would do it over = the replica index of interest (i.e. replica 0). But the trajectory at = each replica setting includes exchanges between replicas. And yet I=E2=80=99= ve read papers where RMSF is still calculated in replica exchange = simulations. Often, RMSF calculations presented in papers don=E2=80=99t appear to = make a larger point beyond that different parts of the protein differ in = flexibility, so I think RMSF calculations in a replica exchange = simulation could serve the same purpose. But when it comes to the issue = of comparing RMSF between different replica exchange simulations, = wouldn=E2=80=99t different exchange acceptance rates prevent comparison = between simulations? That is, suppose one simulation has a 0 <-> 1 = exchange rate of 0.2 whereas another has an exchange rate of 0.25. In = this case, the average time between exchanges would be different, which = could affect RMSF. I am wondering what the experts on this list think. Best regards, Victor Zhao PhD Candidate, Chemistry Shakhnovich Lab, Harvard University yzhao01@g.harvard.edu --Apple-Mail=_EF300D1F-2201-4094-ACD5-77D6C5B942C5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Dear all,

I have been running replica exchange simulations (REST2). So = far, I have focused on observables calculated on a per-frame basis and = averaged to obtain ensemble values. But I am wondering, is it useful to = calculate RMSF in a replica exchange simulation? Presumably you would do = it over the replica index of interest (i.e. replica 0). But the = trajectory at each replica setting includes exchanges between replicas. = And yet I=E2=80=99ve read papers where RMSF is still calculated in = replica exchange simulations.

Often, RMSF calculations presented in = papers don=E2=80=99t appear to make a larger point beyond that different = parts of the protein differ in flexibility, so I think RMSF calculations = in a replica exchange simulation could serve the same purpose. But when = it comes to the issue of comparing RMSF between different replica = exchange simulations, wouldn=E2=80=99t different exchange acceptance = rates prevent comparison between simulations? That is, suppose one = simulation has a 0 <-> 1 exchange rate of 0.2 whereas another has = an exchange rate of 0.25. In this case, the average time between = exchanges would be different, which could affect RMSF. I am wondering = what the experts on this list think.

Best regards,

Victor Zhao
PhD Candidate, = Chemistry
Shakhnovich Lab, Harvard University

= --Apple-Mail=_EF300D1F-2201-4094-ACD5-77D6C5B942C5-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 25 16:22:51 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10PMMpXZ004134; Mon, 25 Jan 2021 16:22:51 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10PMMpLL004133; Mon, 25 Jan 2021 16:22:51 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10PMMo8b004129; Mon, 25 Jan 2021 16:22:50 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10PMMojZ004128; Mon, 25 Jan 2021 16:22:50 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10PMMfNf004118 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 25 Jan 2021 16:22:42 -0600 (CST) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 10PMAVLP024999 for ; Mon, 25 Jan 2021 22:22:41 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=brian.radak@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qt1-f172.google.com (mail-qt1-f172.google.com [209.85.160.172]) by mx0b-00007101.pphosted.com with ESMTP id 368amrhkr1-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 25 Jan 2021 22:22:41 +0000 Received: by mail-qt1-f172.google.com with SMTP id e15so10907612qte.9 for ; Mon, 25 Jan 2021 14:22:41 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:references:from:message-id:date:user-agent:mime-version :in-reply-to:content-language; bh=qFfm8G1C2d0UiGCjcKjt+buaKkmDFCeFH77GKirWNfM=; b=CXeGocDdEtI0s/SDFGoRWnBJAVaUtYLfWHgsIAAc9M2iZBAh4yEapfqbcEhWq5pyXP UO6XDVYf1KL2Ks6MbQRFXPnKw83Re+Wnhx1mvSsPEHe5YTZ5o0an3c/rM9Q8SsvmiF8b zif2UxomZVOrdRT0weCCJAUVCGnTXvu6/W+SqgvvJiQNSDkyLmlAf1lq8snw+sl0VKXH GQCc2KatnxCmNo3cNGHoQfW+nESx5227dhJ0DDLAfUm8nZDqowgW7uyMsMEVZlCss1Yy SmgipFokN4LCPGI4/A6gexePf7e2Ycyo3eRCBCuNBMyHnAQdchR11IhKFp9XaW1EUMXp SvGg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language; bh=qFfm8G1C2d0UiGCjcKjt+buaKkmDFCeFH77GKirWNfM=; b=IOpNm3ghKfd8uqkZVYEx2slAgI6yTbXOUIN9upCNf5iDXM71VtU680dIgkwJ9Z1ZyL o/PBn8mhsFqe4cPSD++5ctRGN2GPg25Xg+6qh0xpJysQHSU5pOLZaC5YlK9Ib9Cod5tV IWoHRlM6uh1f8LIZv4SRhmnGKWKLP7iZgHV4Eubla5NhYCQ978cGFfLa3FoRRhmT9f5c ErDVbn4IWkh+vV5zHHoJUrooco1qr8tQO4MNwenA2c5bW38Bu8oky75zW5sAJ89pcWPD 4LSGeu8xBGeb1Hiq25h/NalzKCK5xmvTuRLpnqDu7kl8ZRPW4MvKKLk4aVTWFaBEH+KV YGvw== X-Gm-Message-State: AOAM531g9NdMqso7DN/lPfdlCDdakdZz9eXCVVNgBoNSebA49QlD/EWA 2eUaW3BQ2p4Vl+R2QT3jznE= X-Google-Smtp-Source: ABdhPJwHnjWbt6FuBAGu1mvSr0bynU+XbADrLxAr4aQi0lsBezZs8O0qGtGSyUgXAB/3EdzMUjNWTA== X-Received: by 2002:aed:2be7:: with SMTP id e94mr2679297qtd.110.1611613360949; Mon, 25 Jan 2021 14:22:40 -0800 (PST) Received: from ?IPv6:2601:184:497f:c640:8980:767:2e1a:d0c6? ([2601:184:497f:c640:8980:767:2e1a:d0c6]) by smtp.gmail.com with ESMTPSA id e5sm12207148qtp.86.2021.01.25.14.22.39 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Mon, 25 Jan 2021 14:22:40 -0800 (PST) Subject: Re: namd-l: Protein RMSF in replica exchange simulations To: namd-l@ks.uiuc.edu, Victor Zhao References: <313BAFD0-73DE-416A-85D3-7E0F56AB13B9@g.harvard.edu> From: Brian Radak Message-ID: <6115821a-af6e-bd4c-3759-bdde86e531c3@gmail.com> Date: Mon, 25 Jan 2021 17:22:39 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 MIME-Version: 1.0 In-Reply-To: <313BAFD0-73DE-416A-85D3-7E0F56AB13B9@g.harvard.edu> Content-Type: multipart/alternative; boundary="------------22AF6FE68E899CABD6D49E3D" Content-Language: en-US X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwZEQpMehcZHxoRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGRoTEQpDWRcHGx8bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ZcRgcEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx1AZWJnG01SYG96HnJnUkNZckRLZXptfkhiXm0ZRnhGEQpYXBcfBBoEGBgY BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3J4ZUZnEQpNXBcYHRsRCkxaF3xpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29va2tsa2sRCkJPF2tBU0weElpvTxJsEQpDWhcYGhMEEh8EGx waBBsdGBEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E 1h+Gl9eEQpCRRdrExphTl9eWBgdZREKQk4XY1Nja3sTWH4aX14RCkJMF2lJSBpLfmlGG3hzEQpC bBdhHhl4Wm5sZ2NfYhEKQkAXZntkHl5/e3xJa1MRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBc YEQp5QxduHRtiGmZsfWkBaREKWUsXExgTHREKcGcXYxhoZH5pR0ZwfkEQHBoRCnBoF2F+Y05SY1 ptQUBwEBkaEQpwaBdtcx1CQklmS0ZkRxAZGhEKcGgXZUIfeGJ7XFhfHwUQGRoRCnBoF2N5U1xGY 2dGX35DEBkaEQpwaBdlbkgSZBlecExcGBAZGhEKcGcXaUtoTWVofEVYTWIQGRoRCnBsF24dZnsS Sxp4ElxtEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=350 spamscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 suspectscore=0 phishscore=0 clxscore=163 bulkscore=0 mlxscore=0 malwarescore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101250111 domainage_hfrom=9297 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------22AF6FE68E899CABD6D49E3D Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Victor, How you calculate any observable (including RMSF) with replica exchange depends on the implementation. I'm pretty sure (although I might be wrong) that all of the REMD scripts distributed with NAMD track replicas (i.e. the state parameter, here the REST2 "temperature", changes over the course of the trajectory). In this case, the RMSF should be the same over all trajectories within statistical uncertainty. This also means that:  1. The trajectory statistics can be pooled under the assumption that they are independent  2. Any differences across trajectories are entirely sampling artifacts. I would also contend that the RMSF computed this way is a completely unphysical quantity that only gives you an impression of sampling efficiency. It does not even describe real population thermodynamics. For that you would have to apply a WHAM-like scheme. I don't know if any scripts for that purpose are readily available. HTH, BKR On 1/25/21 4:50 PM, Victor Zhao wrote: > Dear all, > > I have been running replica exchange simulations (REST2). So far, I > have focused on observables calculated on a per-frame basis and > averaged to obtain ensemble values. But I am wondering, is it useful > to calculate RMSF in a replica exchange simulation? Presumably you > would do it over the replica index of interest (i.e. replica 0). But > the trajectory at each replica setting includes exchanges between > replicas. And yet I’ve read papers where RMSF is still calculated in > replica exchange simulations. > > Often, RMSF calculations presented in papers don’t appear to make a > larger point beyond that different parts of the protein differ in > flexibility, so I think RMSF calculations in a replica exchange > simulation could serve the same purpose. But when it comes to the > issue of comparing RMSF between different replica exchange > simulations, wouldn’t different exchange acceptance rates prevent > comparison between simulations? That is, suppose one simulation has a > 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate of > 0.25. In this case, the average time between exchanges would be > different, which could affect RMSF. I am wondering what the experts on > this list think. > > Best regards, > > Victor Zhao > PhD Candidate, Chemistry > Shakhnovich Lab, Harvard University > yzhao01@g.harvard.edu > --------------22AF6FE68E899CABD6D49E3D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Victor,

How you calculate any observable (including RMSF) with replica exchange depends on the implementation. I'm pretty sure (although I might be wrong) that all of the REMD scripts distributed with NAMD track replicas (i.e. the state parameter, here the REST2 "temperature", changes over the course of the trajectory).

In this case, the RMSF should be the same over all trajectories within statistical uncertainty. This also means that:

 1. The trajectory statistics can be pooled under the assumption that they are independent

 2. Any differences across trajectories are entirely sampling artifacts.

I would also contend that the RMSF computed this way is a completely unphysical quantity that only gives you an impression of sampling efficiency. It does not even describe real population thermodynamics. For that you would have to apply a WHAM-like scheme. I don't know if any scripts for that purpose are readily available.

HTH,

BKR


On 1/25/21 4:50 PM, Victor Zhao wrote:
Dear all,

I have been running replica exchange simulations (REST2). So far, I have focused on observables calculated on a per-frame basis and averaged to obtain ensemble values. But I am wondering, is it useful to calculate RMSF in a replica exchange simulation? Presumably you would do it over the replica index of interest (i.e. replica 0). But the trajectory at each replica setting includes exchanges between replicas. And yet I’ve read papers where RMSF is still calculated in replica exchange simulations.

Often, RMSF calculations presented in papers don’t appear to make a larger point beyond that different parts of the protein differ in flexibility, so I think RMSF calculations in a replica exchange simulation could serve the same purpose. But when it comes to the issue of comparing RMSF between different replica exchange simulations, wouldn’t different exchange acceptance rates prevent comparison between simulations? That is, suppose one simulation has a 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate of 0.25. In this case, the average time between exchanges would be different, which could affect RMSF. I am wondering what the experts on this list think.

Best regards,

Victor Zhao
PhD Candidate, Chemistry
Shakhnovich Lab, Harvard University

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[73.167.60.93]) by smtp.gmail.com with ESMTPSA id l22sm3686257qtl.96.2021.01.25.14.26.25 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 25 Jan 2021 14:26:25 -0800 (PST) From: Victor Zhao Message-Id: <4FAEA9AF-A15B-4025-A382-B45F2991C73B@g.harvard.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_4AD79900-DA70-407D-9170-58A7D7EA287C" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.17\)) Subject: Re: namd-l: Protein RMSF in replica exchange simulations Date: Mon, 25 Jan 2021 17:26:23 -0500 In-Reply-To: <6115821a-af6e-bd4c-3759-bdde86e531c3@gmail.com> Cc: namd-l@ks.uiuc.edu To: Brian Radak References: <313BAFD0-73DE-416A-85D3-7E0F56AB13B9@g.harvard.edu> <6115821a-af6e-bd4c-3759-bdde86e531c3@gmail.com> X-Mailer: Apple Mail (2.3445.104.17) X-CLX-Response: 1TFkXGxIYEQpMehccGhEKWUQXZBtdXhlafWBneFIRClhYF24TU1gcYmgbf39 QEQp4Thd6ax97aUccS1JQexEKeUwXaU5faVNgQF5hW0QRCkNIFwceHRoRCkNZFwcbHxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBhxHhsQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04XRBpDdU8YHGJQZ21DZmhFcB5/UB9wfGdBb28HGGVHZksRClhcFx8EGgQYGBgF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcnhlRV4RCk1cFxkfGhEKTFoXfGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEwQfHh EKQl4XGxEKREkXGxEKQkUXZhlEXFkTS3h/TXkRCkJOF3prH3tpRxxLUlB7EQpCTBduE1NYHGJoG 39/UBEKQmwXa2ZzXW5oHENpQ3gRCkJAF2Z7ZB5ef3t8SWtTEQpCWBdnc2VzQG5hYUxdYhEKWlgX GBEKeUMXbh0bYhpmbH1pAWkRCnBnF2MYaGR+aUdGcH5BEBkaEQpwaBdlQh94YntcWF8fBRAZGhE KcGgXYERwR3lvYUluYmUQGRoRCnBoF2xHQmVbHXtuRBl/EBkaEQpwaBdlZUATZ0BYeB5+YRAZGh EKcGgXek1nHGlyeEtNbwEQGRoRCnBnF2lLaE1laHxFWE1iEBkaEQpwbBdhWWNwQhseQ39cRRAeE hEKcEMXbBoSWhpHb2ZcWE0QGRoRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 mlxlogscore=999 malwarescore=0 priorityscore=60 bulkscore=0 suspectscore=0 clxscore=182 spamscore=0 mlxscore=0 lowpriorityscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101250111 X-Spam-Score: 0 X-Spam-OrigSender: yzhao01@g.harvard.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Victor Zhao --Apple-Mail=_4AD79900-DA70-407D-9170-58A7D7EA287C Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Brian, It is possible to rewrite the trajectories so that you have trajectories = by replica rung. The sortreplicas script included with NAMD does that. I = am asking about RMSF computed over a single rung, which would be made up = of many individual trajectories as they passed through that rung. Best regards, Victor > On Jan 25, 2021, at 5:22 PM, Brian Radak = wrote: >=20 > Hi Victor, >=20 > How you calculate any observable (including RMSF) with replica = exchange depends on the implementation. I'm pretty sure (although I = might be wrong) that all of the REMD scripts distributed with NAMD track = replicas (i.e. the state parameter, here the REST2 "temperature", = changes over the course of the trajectory).=20 >=20 > In this case, the RMSF should be the same over all trajectories within = statistical uncertainty. This also means that: >=20 > 1. The trajectory statistics can be pooled under the assumption that = they are independent >=20 > 2. Any differences across trajectories are entirely sampling = artifacts. >=20 > I would also contend that the RMSF computed this way is a completely = unphysical quantity that only gives you an impression of sampling = efficiency. It does not even describe real population thermodynamics. = For that you would have to apply a WHAM-like scheme. I don't know if any = scripts for that purpose are readily available. >=20 > HTH, >=20 > BKR >=20 >=20 >=20 > On 1/25/21 4:50 PM, Victor Zhao wrote: >> Dear all, >>=20 >> I have been running replica exchange simulations (REST2). So far, I = have focused on observables calculated on a per-frame basis and averaged = to obtain ensemble values. But I am wondering, is it useful to calculate = RMSF in a replica exchange simulation? Presumably you would do it over = the replica index of interest (i.e. replica 0). But the trajectory at = each replica setting includes exchanges between replicas. And yet I=E2=80=99= ve read papers where RMSF is still calculated in replica exchange = simulations. >>=20 >> Often, RMSF calculations presented in papers don=E2=80=99t appear to = make a larger point beyond that different parts of the protein differ in = flexibility, so I think RMSF calculations in a replica exchange = simulation could serve the same purpose. But when it comes to the issue = of comparing RMSF between different replica exchange simulations, = wouldn=E2=80=99t different exchange acceptance rates prevent comparison = between simulations? That is, suppose one simulation has a 0 <-> 1 = exchange rate of 0.2 whereas another has an exchange rate of 0.25. In = this case, the average time between exchanges would be different, which = could affect RMSF. I am wondering what the experts on this list think. >>=20 >> Best regards, >>=20 >> Victor Zhao >> PhD Candidate, Chemistry >> Shakhnovich Lab, Harvard University >> yzhao01@g.harvard.edu --Apple-Mail=_4AD79900-DA70-407D-9170-58A7D7EA287C Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear = Brian,

It is = possible to rewrite the trajectories so that you have trajectories by = replica rung. The sortreplicas script included with NAMD does that. I am = asking about RMSF computed over a single rung, which would be made up of = many individual trajectories as they passed through that rung.

Best regards,
Victor

On Jan 25, 2021, at 5:22 PM, Brian Radak <brian.radak@gmail.com> wrote:

=20 =20

Hi Victor,

How you calculate any observable (including RMSF) = with replica exchange depends on the implementation. I'm pretty sure (although I might be wrong) that all of the REMD scripts distributed with NAMD track replicas (i.e. the state parameter, here the REST2 "temperature", changes over the course of the trajectory).

In this case, the RMSF should be the same over all = trajectories within statistical uncertainty. This also means that:

 1. The trajectory statistics can be pooled under the = assumption that they are independent

 2. Any differences across trajectories are = entirely sampling artifacts.

I would also contend that the RMSF = computed this way is a completely unphysical quantity that only gives you an impression of sampling efficiency. It does not even describe real population thermodynamics. For that you would have to apply a WHAM-like scheme. I don't know if any scripts for that purpose are readily available.

HTH,

BKR
=


On 1/25/21 4:50 PM, Victor Zhao = wrote:
Dear all,

I have been running replica exchange simulations (REST2). So far, I have focused on observables calculated on a per-frame basis and averaged to obtain ensemble values. But I am wondering, is it useful to calculate RMSF in a replica exchange simulation? Presumably you would do it over the replica index of interest (i.e. replica 0). But the trajectory at each replica setting includes exchanges between replicas. And yet I=E2=80=99ve = read papers where RMSF is still calculated in replica exchange simulations.

Often, RMSF calculations presented in papers = don=E2=80=99t appear to make a larger point beyond that different parts of the protein differ in flexibility, so I think RMSF calculations in a replica exchange simulation could serve the same purpose. But when it comes to the issue of comparing RMSF between different replica exchange simulations, wouldn=E2=80=99t different = exchange acceptance rates prevent comparison between simulations? That is, suppose one simulation has a 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate of 0.25. In this case, the average time between exchanges would be different, which could affect RMSF. I am wondering what the experts on this list think.

Best regards,

Victor Zhao
PhD Candidate, Chemistry
Shakhnovich Lab, Harvard University


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boundary="00000000000000b97805b9cb662c" X-CLX-Response: 1TFkXGx8SEQpMehcYExkRCllEF29BQ2B7QH9sE1BPEQpYWBdvT1BvWU9dGG5 TbxEKeE4XY1Nja3sTWH4aX14RCnlMF2JbTkkcUn9dHB1hEQpDSBcHGRMSEQpDWRcHGx8cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxkScRgZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0NkT0NFWVB4YhNgWUdTfnpfTXJCf0x5W1BjWmFQbXpkEQpYXBcfBBoEGBgY BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3J4cE1FEQpNXBcbEhMRCkxaF2xpa01NEQpMRhdva2t ra2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh8EGxwcBB4fEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hOT1JYHX9uXEASEQpCThdjU2Nre xNYfhpfXhEKQkwXb09Qb1lPXRhuU28RCkJsF2tlWk8ecEJpQH9DEQpCQBdmQk9oU0gdYgFSQREK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2YbQnxLQUJdSVJsEQpZSxcTGBMSEQpwaBd maW5SZERmcgVGGhAZGhEKcGgXYUYeQWgdcGJdZx8QGRoRCnBoF2ZgaEhFXExNG0l6EBkaEQpwaB dnfX5MG1xce11rGxAZGhEKcGgXYhJwckBdQR9JXVsQGRoRCnBsF2MeXm5+AWhTe115EBkaEQpwT BdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 mlxlogscore=663 malwarescore=0 priorityscore=293 bulkscore=0 suspectscore=0 clxscore=158 spamscore=0 mlxscore=0 lowpriorityscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101260056 domainage_hfrom=9298 X-Spam-Score: 0 X-Spam-OrigSender: abhi117acharya@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Abhishek Acharya --00000000000000b97805b9cb662c Content-Type: text/plain; charset="UTF-8" Hi all, I am using NAMD 2.13 and Intel MPI 19.0.5. One of my simulations have stopped with the following error: colvars: shared ABF: Sharing gradient and samples among replicas at step 10546000 colvars: shared ABF: Sharing gradient and samples among replicas at step 10546000 colvars: shared ABF: Sharing gradient and samples among replicas at step 10546000 colvars: shared ABF: Sharing gradient and samples among replicas at step 10547000 colvars: shared ABF: Sharing gradient and samples among replicas at step 10547000 colvars: shared ABF: Sharing gradient and samples among replicas at step 10547000 bcn1855.437302namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437304namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437298namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437306namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437310namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437251namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437309namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437297namd2: Reading from remote process' memory failed. Disabling CMA support bcn1855.437307namd2: Reading from remote process' memory failed. Disabling CMA support The run directory has a lot of files printed with the following backtrace: namd2:298454 terminated with signal 11 at PC=d2122f SP=7fffffff7f40. Backtrace: namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x193f)[0xd2122f] namd2(_ZN10ComputePme6doWorkEv+0x163f)[0xa88faf] namd2(_ZN19CkIndex_WorkDistrib29_call_enqueuePme_LocalWorkMsgEPvS0_+0xe)[0xdf321e] namd2(CkDeliverMessageFree+0x22)[0x112f9f2] namd2(_Z15_processHandlerPvP11CkCoreState+0x7b6)[0x1128846] namd2(CsdScheduleForever+0x7d)[0x1245b6d] namd2(CsdScheduler+0x1e)[0x1245aee] namd2(_ZN7BackEnd4initEiPPc+0x3b9)[0x758ff9] namd2(main+0xac)[0x74dccc] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaaabfa1555] namd2[0x6a2529] Has anyone faced this issue before? I am able to continue the simulations though. Sincerely, Abhi --00000000000000b97805b9cb662c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,

I am using NAMD 2.13 and I= ntel MPI 19.0.5.

One of my simulations have stopped with the following error:

colva= rs: =C2=A0 shared ABF: Sharing gradient and samples among replicas at step = 10546000
colvars: =C2=A0 shared ABF: Sharing gradient and samples among = replicas at step 10546000
colvars: =C2=A0 shared ABF: Sharing gradient a= nd samples among replicas at step 10546000
colvars: =C2=A0 shared ABF: S= haring gradient and samples among replicas at step 10547000
colvars: =C2= =A0 shared ABF: Sharing gradient and samples among replicas at step 1054700= 0
colvars: =C2=A0 shared ABF: Sharing gradient and samples among replica= s at step 10547000
bcn1855.437302namd2: Reading from remote process'= memory failed. Disabling CMA support
bcn1855.437304namd2: Reading from = remote process' memory failed. Disabling CMA support
bcn1855.437298n= amd2: Reading from remote process' memory failed. Disabling CMA support=
bcn1855.437306namd2: Reading from remote process' memory failed. Di= sabling CMA support
bcn1855.437310namd2: Reading from remote process'= ; memory failed. Disabling CMA support
bcn1855.437251namd2: Reading from= remote process' memory failed. Disabling CMA support
bcn1855.437309= namd2: Reading from remote process' memory failed. Disabling CMA suppor= t
bcn1855.437297namd2: Reading from remote process' memory failed. D= isabling CMA support
bcn1855.437307namd2: Reading from remote process= 9; memory failed. Disabling CMA support
The run directory has a lot of files pr= inted with the following backtrace:
namd2:298454 terminated with signal 11 = at PC=3Dd2122f SP=3D7fffffff7f40.=C2=A0 Backtrace:
namd2(_ZN12PmeRealSpa= ce12fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x193f)[0xd2122f]
namd2(= _ZN10ComputePme6doWorkEv+0x163f)[0xa88faf]
namd2(_ZN19CkIndex_WorkDistri= b29_call_enqueuePme_LocalWorkMsgEPvS0_+0xe)[0xdf321e]
namd2(CkDeliverMes= sageFree+0x22)[0x112f9f2]
namd2(_Z15_processHandlerPvP11CkCoreState+0x7b= 6)[0x1128846]
namd2(CsdScheduleForever+0x7d)[0x1245b6d]
namd2(CsdSche= duler+0x1e)[0x1245aee]
namd2(_ZN7BackEnd4initEiPPc+0x3b9)[0x758ff9]
n= amd2(main+0xac)[0x74dccc]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aa= aabfa1555]
namd2[0x6a2529]

Has anyone faced this issue before? I am ab= le to continue the simulations though.
Sincerely,
Abhi
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([2601:184:497f:c640:9f78:5af5:31b3:e6b9]) by smtp.gmail.com with ESMTPSA id z30sm13698769qtd.21.2021.01.26.10.01.45 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Tue, 26 Jan 2021 10:01:45 -0800 (PST) Subject: Re: namd-l: Protein RMSF in replica exchange simulations To: Victor Zhao Cc: namd-l@ks.uiuc.edu References: <313BAFD0-73DE-416A-85D3-7E0F56AB13B9@g.harvard.edu> <6115821a-af6e-bd4c-3759-bdde86e531c3@gmail.com> <4FAEA9AF-A15B-4025-A382-B45F2991C73B@g.harvard.edu> From: Brian Radak Message-ID: Date: Tue, 26 Jan 2021 13:01:44 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 MIME-Version: 1.0 In-Reply-To: <4FAEA9AF-A15B-4025-A382-B45F2991C73B@g.harvard.edu> Content-Type: multipart/alternative; boundary="------------E21AF2F0FC7D0E43D46FE980" Content-Language: en-US X-CLX-Response: 1TFkXGx0cEQpMehcZGBoRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGRkeEQpDWRcHGxkaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxlBHXphfEAeRGlmGG5BeVhJT09OckxjWUB7Xh1aWFluEQpYXBcfBBoEGBgY BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXcnhMGEQRCk1cFxgbHhEKTFoXfGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb29ra2xraxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGx MEHxkRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaxMaYU5fXlgYHWURCkJOF2NTY2t7E1h+Gl9eEQpCTBdpSUgaS35pRht4cxEKQmwX YR4ZeFpubGdjX2IRCkJAF2Z7ZB5ef3t8SWtTEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXbh0bYhpmbH1pAWkRCllLFxMYExIRCnBnF2MYaGR+aUdGcH5BEBkaEQpwaBdlUhhzTEdAU0 4fZhAZGhEKcGgXZUIfeGJ7XFhfHwUQGRoRCnBoF2BEcEd5b2FJbmJlEBkaEQpwaBdvUhhsGRJmG H4SXhAZGhEKcGgXbwF8HUJ9XWxQG1wQGRoRCnBnF2lMX19ZRUB8HG1rEBkaEQpwZxdpS2hNZWh8 RVhNYhAZGhEKcGwXbh1mexJLGngSXG0QGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 bulkscore=0 clxscore=176 lowpriorityscore=0 spamscore=0 mlxscore=0 malwarescore=0 adultscore=0 priorityscore=320 impostorscore=0 mlxlogscore=999 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101260093 domainage_hfrom=9298 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------E21AF2F0FC7D0E43D46FE980 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit In this case you can compute RMSF in the sorted trajectories and there is no issue other than the usual sampling problems. A WHAM scheme may reduce error but requires quite a bit more work. On 1/25/21 5:26 PM, Victor Zhao wrote: > Dear Brian, > > It is possible to rewrite the trajectories so that you have > trajectories by replica rung. The sortreplicas script included with > NAMD does that. I am asking about RMSF computed over a single rung, > which would be made up of many individual trajectories as they passed > through that rung. > > Best regards, > Victor > >> On Jan 25, 2021, at 5:22 PM, Brian Radak > > wrote: >> >> Hi Victor, >> >> How you calculate any observable (including RMSF) with replica >> exchange depends on the implementation. I'm pretty sure (although I >> might be wrong) that all of the REMD scripts distributed with NAMD >> track replicas (i.e. the state parameter, here the REST2 >> "temperature", changes over the course of the trajectory). >> >> In this case, the RMSF should be the same over all trajectories >> within statistical uncertainty. This also means that: >> >>  1. The trajectory statistics can be pooled under the assumption that >> they are independent >> >>  2. Any differences across trajectories are entirely sampling artifacts. >> >> I would also contend that the RMSF computed this way is a completely >> unphysical quantity that only gives you an impression of sampling >> efficiency. It does not even describe real population thermodynamics. >> For that you would have to apply a WHAM-like scheme. I don't know if >> any scripts for that purpose are readily available. >> >> HTH, >> >> BKR >> >> >> On 1/25/21 4:50 PM, Victor Zhao wrote: >>> Dear all, >>> >>> I have been running replica exchange simulations (REST2). So far, I >>> have focused on observables calculated on a per-frame basis and >>> averaged to obtain ensemble values. But I am wondering, is it useful >>> to calculate RMSF in a replica exchange simulation? Presumably you >>> would do it over the replica index of interest (i.e. replica 0). But >>> the trajectory at each replica setting includes exchanges between >>> replicas. And yet I’ve read papers where RMSF is still calculated in >>> replica exchange simulations. >>> >>> Often, RMSF calculations presented in papers don’t appear to make a >>> larger point beyond that different parts of the protein differ in >>> flexibility, so I think RMSF calculations in a replica exchange >>> simulation could serve the same purpose. But when it comes to the >>> issue of comparing RMSF between different replica exchange >>> simulations, wouldn’t different exchange acceptance rates prevent >>> comparison between simulations? That is, suppose one simulation has >>> a 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate >>> of 0.25. In this case, the average time between exchanges would be >>> different, which could affect RMSF. I am wondering what the experts >>> on this list think. >>> >>> Best regards, >>> >>> Victor Zhao >>> PhD Candidate, Chemistry >>> Shakhnovich Lab, Harvard University >>> yzhao01@g.harvard.edu >>> > --------------E21AF2F0FC7D0E43D46FE980 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

In this case you can compute RMSF in the sorted trajectories and there is no issue other than the usual sampling problems. A WHAM scheme may reduce error but requires quite a bit more work.

On 1/25/21 5:26 PM, Victor Zhao wrote:
Dear Brian,

It is possible to rewrite the trajectories so that you have trajectories by replica rung. The sortreplicas script included with NAMD does that. I am asking about RMSF computed over a single rung, which would be made up of many individual trajectories as they passed through that rung.

Best regards,
Victor

On Jan 25, 2021, at 5:22 PM, Brian Radak <brian.radak@gmail.com> wrote:

Hi Victor,

How you calculate any observable (including RMSF) with replica exchange depends on the implementation. I'm pretty sure (although I might be wrong) that all of the REMD scripts distributed with NAMD track replicas (i.e. the state parameter, here the REST2 "temperature", changes over the course of the trajectory).

In this case, the RMSF should be the same over all trajectories within statistical uncertainty. This also means that:

 1. The trajectory statistics can be pooled under the assumption that they are independent

 2. Any differences across trajectories are entirely sampling artifacts.

I would also contend that the RMSF computed this way is a completely unphysical quantity that only gives you an impression of sampling efficiency. It does not even describe real population thermodynamics. For that you would have to apply a WHAM-like scheme. I don't know if any scripts for that purpose are readily available.

HTH,

BKR


On 1/25/21 4:50 PM, Victor Zhao wrote:
Dear all,

I have been running replica exchange simulations (REST2). So far, I have focused on observables calculated on a per-frame basis and averaged to obtain ensemble values. But I am wondering, is it useful to calculate RMSF in a replica exchange simulation? Presumably you would do it over the replica index of interest (i.e. replica 0). But the trajectory at each replica setting includes exchanges between replicas. And yet I’ve read papers where RMSF is still calculated in replica exchange simulations.

Often, RMSF calculations presented in papers don’t appear to make a larger point beyond that different parts of the protein differ in flexibility, so I think RMSF calculations in a replica exchange simulation could serve the same purpose. But when it comes to the issue of comparing RMSF between different replica exchange simulations, wouldn’t different exchange acceptance rates prevent comparison between simulations? That is, suppose one simulation has a 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate of 0.25. In this case, the average time between exchanges would be different, which could affect RMSF. I am wondering what the experts on this list think.

Best regards,

Victor Zhao
PhD Candidate, Chemistry
Shakhnovich Lab, Harvard University


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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Jerome, thanks Stefano Il giorno mar 29 dic 2020 alle ore 17:00 J=C3=A9r=C3=B4me H=C3=A9nin ha scritto: > Hi Stefano, > > Yes, you can also specify a PDB file with any number of atoms to provide > coordinates. What matters is that exactly the right number of atoms are > flagged on the O or B column. > > https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-namd/= colvars-refman-namd.html*sec:colvars_pdb_format__;Iw!!DZ3fjg!v3UZvjyBp2WFSe= p_TKM9QCpbsLuKRN54w-VYHdj0Ts5iS0GswB5SJifx9LalNIm0QQ$=20 > > Jerome > > ----- On 18 D=C3=A9c 20, at 18:22, Stefano Guglielmo stefano.guglielmo@un= ito.it > wrote: > > > Hello Giacomo, > > thanks for your reply. > > Would it work if I include the pdb files of the whole protein (without > > solvent and so on) and then specify atoms with atomNumbers for > calculating > > the path? and eventually can I specify fittingAtoms the same way, i.e. > > using atomNumbers referring to the refPositionsFileN files? > > > > Thanks > > > > Il giorno ven 18 dic 2020 alle ore 17:36 Giacomo Fiorin < > > giacomo.fiorin@gmail.com> ha scritto: > > > >> Hello Stefano, yes. The simplest would be to just include in each file > >> only coordinates for the atoms that were selected, in the same order as > the > >> selection. For precision, XYZ files are recommended: > >> > >> > https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd= /colvars-refman-namd.html*sec:colvars_xyz_format__;Iw!!DZ3fjg!v3UZvjyBp2WFS= ep_TKM9QCpbsLuKRN54w-VYHdj0Ts5iS0GswB5SJifx9Lbb7BOvcQ$=20 > >> > >> > >> > >> On Fri, Dec 18, 2020 at 9:50 AM Stefano Guglielmo < > >> stefano.guglielmo@unito.it> wrote: > >> > >>> Dear all, > >>> is it possible to use as refPositionsFileN N files containing only a > part > >>> of the system, let's say the protein without water and ions? > >>> > >>> Thanks > >>> Stefano > >>> > >>> -- > >>> Stefano GUGLIELMO PhD > >>> Associate Professor of Medicinal Chemistry > >>> Department of Drug Science and Technology > >>> Via P. Giuria 9 > >>> 10125 Turin, ITALY > >>> ph. +39 (0)11 6707178 > >>> > >>> > > > > -- > > Stefano GUGLIELMO PhD > > Associate Professor of Medicinal Chemistry > > Department of Drug Science and Technology > > Via P. Giuria 9 > > 10125 Turin, ITALY > > ph. +39 (0)11 6707178 > --=20 Stefano GUGLIELMO PhD Associate Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178 --000000000000ff74d005b9f16e52 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Jerome,
thanks

= Stefano

Il giorno mar 29 dic 2020 alle ore 17:00 J=C3=A9r=C3=B4me = H=C3=A9nin <jerome.henin@ibpc.fr= > ha scritto:
Hi Stefano,

Yes, you can also specify a PDB file with any number of atoms to provide co= ordinates. What matters is that exactly the right number of atoms are flagg= ed on the O or B column.
http://colvars.github.io/colvars-refman-namd/colv= ars-refman-namd.html#sec:colvars_pdb_format

Jerome

----- On 18 D=C3=A9c 20, at 18:22, Stefano Guglielmo stefano.guglielmo@unito.it wr= ote:

> Hello Giacomo,
> thanks for your reply.
> Would it work if I include the pdb files of the whole protein (without=
> solvent and so on) and then specify atoms with atomNumbers for calcula= ting
> the path? and eventually can I specify fittingAtoms the same way, i.e.=
> using atomNumbers referring to the refPositionsFileN files?
>
> Thanks
>
> Il giorno ven 18 dic 2020 alle ore 17:36 Giacomo Fiorin <
> giacomo.= fiorin@gmail.com> ha scritto:
>
>> Hello Stefano, yes.=C2=A0 The simplest would be to just include in= each file
>> only coordinates for the atoms that were selected, in the same ord= er as the
>> selection.=C2=A0 For precision, XYZ files are recommended:
>>
>> https://colvars.github.io/colvars-refma= n-namd/colvars-refman-namd.html#sec:colvars_xyz_format
>>
>>
>>
>> On Fri, Dec 18, 2020 at 9:50 AM Stefano Guglielmo <
>> st= efano.guglielmo@unito.it> wrote:
>>
>>> Dear all,
>>> is it possible to use as refPositionsFileN N files containing = only a part
>>> of the system, let's say the protein without water and ion= s?
>>>
>>> Thanks
>>> Stefano
>>>
>>> --
>>> Stefano GUGLIELMO PhD
>>> Associate Professor of Medicinal Chemistry
>>> Department of Drug Science and Technology
>>> Via P. Giuria 9
>>> 10125 Turin, ITALY
>>> ph. +39 (0)11 6707178
>>>
>>>
>
> --
> Stefano GUGLIELMO PhD
> Associate Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178


--
=
Stefano GUGLIELMO PhD
Associate Professor of Medicinal Chemis= try
Department of Drug Science and Technology
Via P. Giur= ia 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
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charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi, If you read the release note, it clearly states -- Multi-Copy Algorithm Support -- Multi-copy algorithms (such as replica exchange) require at least one process per replica, plus a Charm++ build based on "LRTS" (low-level run-time system). Multi-copy-capable builds include netlrts, verbs, ucx, and mpi. V. On Thu, Jan 28, 2021, 6:42 AM =E8=BE=9B=E5=BF=97=E5=AE=8F wrote: > Dear NAMD, > > My computer setup 2 CPU, 28 cores per CPU, 56 cores in all, it works very > well for multithreading calculation by Amber, > > mpirun -np 50 sander.MPI -O -i=E3=80=82=E3=80=82=E3=80=82=E3=80=82=E3=80= =82=E3=80=82 > > > However, an error occurred when I carried out a umbrella sample example b= y > Namd2 according to the tutorial, Namd is a compiled 2020 version and can > works in a single thread, does it only works when compile a namd from a > source code? > > I will be much appreciate if there is any suggesstion. > > mpirun -np 16 +auto-provision namd2 +replicas 16 job0.conf +stdout > output/%d/job0.%d.log > The error information is as follows: > > Charm++> No provisioning arguments specified. Running with a single PE. > > Use +auto-provision to fully subscribe resources or +p1 to > silence this message. > > Charm++: standalone mode (not using charmrun) > > Charm++> Running in Multicore mode: 1 threads (PEs) > > ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------ > > Reason: +partitions other than 1 is not allowed for multicore build > > > [0] Stack Traceback: > > [0:0] namd2 0x17ce9e7 > > [0:1] namd2 0x53d375 > > [0:2] namd2 0x52e7c2 > > [0:3] libc.so.6 0x2b4a719cf555 __libc_start_main > > [0:4] namd2 0x4145f5 > > -------------------------------------------------------------------------= - > > Primary job terminated normally, but 1 process returned > > a non-zero exit code. Per user-direction, the job has been aborted. > > -------------------------------------------------------------------------= - > > ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------ > > Reason: +partitions other than 1 is not allowed for multicore build > > > Charm++> No provisioning arguments specified. Running with a single PE. > > Use +auto-provision to fully subscribe resources or +p1 to > silence this message. > > Charm++: standalone mode (not using charmrun) > > Charm++> Running in Multicore mode: 1 threads (PEs) > > [0] Stack Traceback: > > [0:0] namd2 0x17ce9e7 > > [0:1] namd2 0x53d375 > > [0:2] namd2 0x52e7c2 > > [0:3] libc.so.6 0x2b2104bab555 __libc_start_main > > [0:4] namd2 0x4145f5 > > -------------------------------------------------------------------------= - > mpirun noticed that process rank 0 with PID 0 on node bogon exited on > signal 11 (Segmentation fault). > > > Zhihong Xin, > Nanjing Agricultural University > > --000000000000d88f0705b9f87bca Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi,

If you rea= d the release note, it clearly states

-- Multi-Copy Algorithm Support --

Multi-copy algorithms (such as replica exchange) require at least one
process per replica, plus a Charm++ build based on "LRTS" (low-le=
vel
run-time system). Multi-copy-capable builds include netlrts, verbs, ucx,
and mpi. 

V.

On Thu, Jan 28,= 2021, 6:42 AM =E8=BE=9B=E5=BF=97=E5=AE=8F <xzhfood@njau.edu.cn> wrote:

Dear NAMD,

My computer setup 2 CPU, 28 cores per CPU= , 56 cores in all, it works very well for multithreading calculation by Amb= er,   

mpirun -np 50 sander.MPI -O -i=E3=80=82=E3=80=82=E3= =80=82=E3=80=82=E3=80=82=E3=80=82


However, an error occurr= ed when I carried out a umbrella sample example by Namd2 according to the t= utorial, Namd  is a compiled 2020 version and can works in a single th= read, does it only works when compile a namd from a source code?

I wi= ll be much appreciate if there is any suggesstion.

mpirun -np 16 +aut= o-provision namd2 +replicas 16 job0.conf +stdout output/%d/job0.%d.log

<= div>The error information is as follows:

Charm++&g= t; No provisioning arguments specified. Running with a single PE.

&= nbsp;        Use +auto-provision to fully subscribe res= ources or +p1 to silence this message.

Charm++: standalone mode (not = using charmrun)

Charm++> Running in Multicore mode: 1 threads (PEs= )

------- Partition 0 Processor 0 Exiting: Called CmiAbort ------

=

Reason: +partitions other than 1 is not allowed for multicore build

<= p>

[0] Stack Traceback:

  [0:0] namd2 0x17ce9e7 <= /p>

  [0:1] namd2 0x53d375 

  [0:2] namd2 0x52e7c2&n= bsp;

  [0:3] libc.so.6 0x2b4a719cf555 __libc_start_main

&n= bsp; [0:4] namd2 0x4145f5 

-------------------------------------= -------------------------------------

Primary job  terminated no= rmally, but 1 process returned

a non-zero exit code. Per user-directi= on, the job has been aborted.

---------------------------------------= -----------------------------------

------- Partition 0 Processor 0 E= xiting: Called CmiAbort ------

Reason: +partitions other than 1 is no= t allowed for multicore build


Charm++> No provisioning = arguments specified. Running with a single PE.

      &= nbsp;  Use +auto-provision to fully subscribe resources or +p1 to sile= nce this message.

Charm++: standalone mode (not using charmrun)

Charm++> Running in Multicore mode: 1 threads (PEs)

[0] Stack Tra= ceback:

  [0:0] namd2 0x17ce9e7 

  [0:1] namd2 0= x53d375 

  [0:2] namd2 0x52e7c2 

  [0:3] li= bc.so.6 0x2b2104bab555 __libc_start_main

  [0:4] namd2 0x4145f5&= nbsp;

---------------------------------------------------------------= -----------

mpirun noticed that process rank 0 with PID 0 on node b= ogon exited on signal 11 (Segmentation fault).

Zhihong Xin,
Nanjing Agricultural University

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Thu, 28 Jan 2021 20:14:26 +0000 From: "Athreya, Nagendra Bala Murali" To: "namd-l@ks.uiuc.edu" Subject: namd-l: Implementing decaying potential (non-linear potential) Thread-Topic: Implementing decaying potential (non-linear potential) Thread-Index: AQHW9bIRdbFYHbLmDkm2dT09qBPnTQ== Date: Thu, 28 Jan 2021 20:14:26 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=illinois.edu; x-originating-ip: [66.253.183.210] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 4cd9723e-d162-45f7-d27a-08d8c3c94f93 x-ms-traffictypediagnostic: CH2PR11MB4197: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:10000; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: d1PB+085ii/8u5aRNpHP1M0b00dxcXsNUZplRBZwrLG7j9HVxim5gY//1blZYXNu4al1KbL2imzfFN/QRDdgpnz0EkD7KXYQBzgYOnc+vFo5KtqYutFLh2LSBG8HlZgJ2Z5s405dKWM9to0OijdNE2iOssk9aOhnD8cJqbd2JEm0d7R9yqN4dcK4NGz5kMFJkWvwcpQr5w8xgaZnwRiyBvs3pJjb7c9sgyW1L4LBAJgMGHIUOvDqiGPY3N5BIBFbtx2ERrqlRjxaFYGLseROK819QkXKpIjfWWZ/Lwsu/CKvhrWvupVqPrl6U3ohIhqYdrKYVWfykVeUiwIBiG8jInqGGqIVXFiil1zFKa5KmLYPmK5d8+KCq0am4nJIyawFCe4V+8uvXwPItfsGeXURxKzaSRtUw9yF19PGKF+N8DfUN7/WE+X2YJ9VjoAfAfl0tyMEXs4LzsZhrQQ90G4J+hysaA1SPEl4A7PYdUC2xlPEnfWxYoyqv9y6anWiFTVzko87eD/myZe7qBcOaAlkGg== x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:CH2PR11MB4293.namprd11.prod.outlook.com;PTR:;CAT:NONE;SFS:(376002)(39860400002)(366004)(136003)(396003)(346002)(86362001)(66946007)(33656002)(186003)(8676002)(75432002)(26005)(316002)(55016002)(786003)(76116006)(8936002)(9686003)(64756008)(66476007)(7696005)(66556008)(71200400001)(5660300002)(19627405001)(6506007)(52536014)(478600001)(6916009)(4744005)(2906002)(66446008);DIR:OUT;SFP:1101; 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boundary="_000_CH2PR11MB429390168C8F9D7AED62BCB5A7BA9CH2PR11MB4293namp_" MIME-Version: 1.0 X-OriginatorOrg: illinois.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR11MB4293.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 4cd9723e-d162-45f7-d27a-08d8c3c94f93 X-MS-Exchange-CrossTenant-originalarrivaltime: 28 Jan 2021 20:14:26.2916 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 44467e6f-462c-4ea2-823f-7800de5434e3 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: oN74qS+yoZzwXI5MyOMlsiHtPTOTan2cSqfXD+nQ0zW6tmOjCz66quS6n5OF0m/yHRSp50jm782gijC0vPyQ2A== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR11MB4197 X-CLX-Response: 1TFkXHhkSEQpMehcbHhIRCllEF2l8ExJ4RWABaRtwEQpYWBdjXBp7Y1lIfE1 lHxEKeE4XbxwZfxxfaEZcYRIRCnlMF2xbR25+E15ielgeEQpDSBcHGxoaEQpDWRcHHBkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwdcRgGHBx3BhgaGgYaBhoGGBsGGBoacRsaGxAadwYaBgcfGgYaB hoGGgYacRoQGncGGhEKWV4XaG55EQpJRhdfQ19JdUJFWV5PThEKQ04XU14caUAcaUYaHE4adW5z GUxQSVtHa0xGfX0dQRxBREQRClhcFx8EGgQYGBgFGxoEGxsaBB8aBBseHxAbHhofGhEKXlkXcnl mAQURCk1cFx4YEQpMWhdsaU1NaxEKTEYXb2tra2traxEKQk8XbXJpXm5PTBNSHxwRCkNaFxsaHg QeHQQfHwQbGhsRCkJeFxsRCkReFxgRCkJFF29EUFpIE1lpHR1ZEQpCThdvHBl/HF9oRlxhEhEKQ kwXY1wae2NZSHxNZR8RCkJsF2lic2ZFflthfQFyEQpCQBd6WlNtelJffgVHfhEKQlgXZ3Nlc0Bu YWFMXWIRCk1eFxsRClpYFxgRCnlDF20FYmdBQlhvXlNdEQpZSxcSHRIbEQpwaBd6WEtSZlNPek0 dGRAZGhEKcGgXZn4YZ1t4BURcBXoQGRoRCnBoF2ZAQmZwHn59Hl9yEBkaEQpwaBdteV98YEBpe0 8YUBAdHBEKcGgXekITYHxZen4bW34QGRoRCnBsF3psARhwRF9saBtAEBkaEQptfhcbEQpYTRdLE SA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 mlxscore=0 priorityscore=148 malwarescore=0 suspectscore=0 clxscore=438 phishscore=0 lowpriorityscore=0 mlxlogscore=869 spamscore=0 bulkscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101280098 domainage_hfrom=8781 X-Spam-Score: 0 X-Spam-OrigSender: nathreya@illinois.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Athreya, Nagendra Bala Murali" --_000_CH2PR11MB429390168C8F9D7AED62BCB5A7BA9CH2PR11MB4293namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I am trying to simulate a system where screening of potential can be observ= ed in the system. Briefly, I would like to see a decaying potential applied= along z-direction in a system containing some salt solution. The voltage i= s applied from +Z to -Z-axis. When I implement eField in the NAMD script, i= t applies a constant uniform electric field along z-direction. However, the= re is no exponential decay in the potential as one would observe in experim= ental setup. How would one go about imposing a decaying potential in the system? I would appreciate any help I can get (papers, links, etc..). Thank you, Nagendra --_000_CH2PR11MB429390168C8F9D7AED62BCB5A7BA9CH2PR11MB4293namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
 would appreciate a= ny help I can get (papers, links, etc..).

Thank you,
Nagendra
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boundary="0000000000002880d005b9fba207" X-CLX-Response: 1TFkXGxwfEQpMehcZGhkRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGBwaEQpDWRcHGxgcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4fcRgdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF011GWdvTGVCE39cWkxYZRp8fUYbX3JpH1lSXkdib0l4EQpYXBcfBBoEGBgY BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3J5Z2xEEQpNXBcbGRgRCkxaF3hpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGx0ZEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9YeGARCkJs F2FfelMZQ0Qaeht+EQpCQBdvaWJ6fE0afWATEhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxg RCnlDF2ZNUG9SeXBDW39HEQpZSxcTGRoaEQpwaBdkE1p6RhtgXFNBfBAZGhEKcGgXaFJbeWweWn tpH30QGRoRCnBoF2ZpBU1wHn9+WGcdEBkaEQpwaBd6XVNncAFjb1gYRhAZGhEKcGgXZh1DHkFTU ExgH0kQHBIRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0X SxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 lowpriorityscore=0 spamscore=0 impostorscore=0 clxscore=165 mlxscore=0 suspectscore=0 bulkscore=0 priorityscore=303 malwarescore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101280098 domainage_hfrom=9300 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --0000000000002880d005b9fba207 Content-Type: text/plain; charset="UTF-8" Hi Nagendra, GridForces has the ability among others to apply a voltage that depends on the position in space. You'll need to create an OpenDX file for your potential for your decaying voltage. One way that I used for this was a Python script that uses the gridData module packaged with MDAnalysis. There are certainly other solutions. Giacomo On Thu, Jan 28, 2021 at 3:16 PM Athreya, Nagendra Bala Murali < nathreya@illinois.edu> wrote: > Hi, > > I am trying to simulate a system where screening of potential can be > observed in the system. Briefly, I would like to see a decaying potential > applied along z-direction in a system containing some salt solution. The > voltage is applied from +Z to -Z-axis. When I implement eField in the NAMD > script, it applies a constant uniform electric field along z-direction. > However, there is no exponential decay in the potential as one would > observe in experimental setup. > > How would one go about imposing a decaying potential in the system? > > I would appreciate any help I can get (papers, links, etc..). > > Thank you, > Nagendra > --0000000000002880d005b9fba207 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Nagendra, GridForces has the ability among others = to apply a voltage that depends on the position in space.

You'll need to create an OpenDX file for your potential for you= r decaying voltage.=C2=A0 One way that I used for this was a Python script = that uses the gridData module packaged with MDAnalysis.=C2=A0 There are cer= tainly other solutions.

Giacomo
On Thu, J= an 28, 2021 at 3:16 PM Athreya, Nagendra Bala Murali <nathreya@illinois.edu> wrote:
Hi,
=
= I am trying to simulate a system where screening of potential can be observ= ed in the system. Briefly, I would like to see a decaying potential applied= along z-direction in a system containing some salt solution. The voltage is applied from +Z to -Z-axis. When I impl= ement eField in the NAMD script, it applies a constant uniform electric fie= ld along z-direction. However, there is no exponential decay in the potenti= al as one would observe in experimental setup.=C2=A0
=
= How would one go about imposing a decaying potential in the system?=C2=A0
=
= I=C2=A0would appreciate any help I can g= et (papers, links, etc..).
=
= Thank you,
Nagendra
--0000000000002880d005b9fba207-- From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 28 18:08:55 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T08tQk014526; Thu, 28 Jan 2021 18:08:55 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10T08t7r014525; Thu, 28 Jan 2021 18:08:55 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T08s4g014521; Thu, 28 Jan 2021 18:08:54 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10T08sAx014520; Thu, 28 Jan 2021 18:08:54 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T08i8R014510 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 28 Jan 2021 18:08:44 -0600 (CST) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 10T08DxL000915 for ; Fri, 29 Jan 2021 00:08:43 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qv1-f47.google.com (mail-qv1-f47.google.com [209.85.219.47]) by mx0b-00007101.pphosted.com with ESMTP id 36c27kbmxs-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 29 Jan 2021 00:08:43 +0000 Received: by mail-qv1-f47.google.com with SMTP id l11so3743596qvt.1 for ; Thu, 28 Jan 2021 16:08:43 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=Yeq4pbtbhwFu2gd55MxGB5zzRB7XwZB2olrqjKAWCj0=; b=tfioKIS8YGHBo94fOzdhCfqVnBxcwwPOPcSWWbYkHGesmgG/4YM+G2kA1OK14Ff5H1 jPITF9x5jdIl1yyc212SrWClHSkVHnWK3dN31pisGYA024r3rf9nwuYm+L5R5g4r8o3u 0zO/vgQ0CTWS0a1UxWsZ7jk2rVcuwBaATlrTOc5+PXn/LpMOi4odw41Q0+1FoJe02ZUL odQ92zIkYuejs5EJf+LITjEi/p9t1DjcfwBDYYSFPY4cCEn+EIXis9Gv8q5IogZXw1j7 M6M3COLHi4/tQ/74QJ050r4tN5epRC4J0IZaX2NJPupoG+53XjR9iGZfNSgG8N+HCRib yctg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=Yeq4pbtbhwFu2gd55MxGB5zzRB7XwZB2olrqjKAWCj0=; b=X++4fxHuWhNwNWgI5gKrqJ50MsFq6v/hbBEkgwXwybXgHD3/GEIFSDzhvBo0AxTveY niAlkaSl16fFfbyifcJa1aVBF+SsyQLCWUzLwJmdR2NquAlOxzhe8QqM2sxjqcGMoDzT t6yE3xtS/6R/pfQ6N5fGGZ+y1kGTxUm216AGHMYkwumtY6geXNDX+67SO7tKcNI4NFhD m4Xe8DlZQ/YD2R8aPIj30ytgXIKOQkV+ysfOlLWuXVxrhh8B8zPFTmZ1/c4oG3ZuYh9s X1rfLinEkwCsqG6JiBhiQxkv6Hz7YH2xhno2ZlysEgnhTJOE7eNoAUSubQnGQPQyejDi sJvw== X-Gm-Message-State: AOAM530dSzhwQUonX2gZotwFh4db2TX/hiHi0I4TP4S5zdxosisQ3Hkt 46qAd6tNW2NK3bWuFAP7Hgre7rdbJJUr0WXQ X-Google-Smtp-Source: ABdhPJyiHIJQAyEhtCPBpe1TzEZNOEFxPFBZxhxNzqxnTYirlCIaHwliFknHGwwBldPDKCZ50Hn47A== X-Received: by 2002:a0c:aedc:: with SMTP id n28mr1744433qvd.21.1611878922758; Thu, 28 Jan 2021 16:08:42 -0800 (PST) Received: from [192.168.1.33] ([181.64.230.100]) by smtp.gmail.com with ESMTPSA id z20sm4044957qki.93.2021.01.28.16.08.41 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 28 Jan 2021 16:08:42 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 28 Jan 2021 19:08:39 -0500 Subject: namd-l: Improve performance From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: <8D96FCAC-F48F-4141-810A-57B5A749D7CB@gmail.com> Thread-Topic: Improve performance Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3694705721_742275367" X-CLX-Response: 1TFkXGxwTEQpMehcYGhwRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGR8eEQpDWRcHExIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhNxGRoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XTE16RV51f2lAe1NYQ29fW3JcbkJOHkRFZWNwBxloHn8RClhcFx8EGgQYGBkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcnl6S0cRCk1cFxgTGBEKTFoXbGlNTWsRCkxGF29ra2t raxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGxMEHh0RCkJeFxsRCkReFxgRCkJcFxsRCl 5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF 2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXY2lZb3pPHXJHT38RCkJAF2dER25AT0ET SVxpEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUMXehwFaWdcR05AZ30RCllLFxMZGhs RCnBoF2JIXB1hTx9HUHgTEBkaEQpwaBdiXUZtRn9neX9MSBAZGhEKcGgXY2B8TEBlREh9cx4QGR oRCnBoF2lucAVGQxxaZlxhEBsfHBEKcGgXbHN9TG9/WUhfcHsQGx8SEQpwbBd6R0BrGFl5fx4bS BAZGhEKcEMXbX5He2ZyZ3pneVkQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 priorityscore=206 lowpriorityscore=0 impostorscore=0 malwarescore=0 mlxscore=0 mlxlogscore=433 spamscore=0 suspectscore=0 bulkscore=0 phishscore=0 clxscore=169 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101280116 domainage_hfrom=9301 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3694705721_742275367 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear namd users, How can i improve namd2.14 performance on GPU? I`m using namd2.14 for run membrane protein simulation, but namd only use nor more the 50% of GPU, as can I make to improve this performance. For other hand, if during equilibration of protein-membrane is necessary keep water out membrane? Thanks, Best, Geo. --B_3694705721_742275367 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dea= r namd users,

 

How can i improve namd2.14 performance on GPU?

 

I`m using na= md2.14 for run membrane protein simulation, but namd only use nor more the 5= 0% of GPU, as can I make to improve this performance.

=

 

For other hand, if durin= g equilibration of protein-membrane is necessary keep water out membrane?

&= nbsp;

Than= ks,

=  

Best,

 

Geo.

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Subject: Re: namd-l: Improve performance Thread-Topic: namd-l: Improve performance Thread-Index: AQHW9dgYtqUn2qSQPkK4lQOcwDld3Q== Date: Fri, 29 Jan 2021 00:45:52 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/16.44.20121301 authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=msu.edu; x-originating-ip: [68.62.59.7] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 1cac91e7-b758-4e52-3881-08d8c3ef3b1c x-ms-traffictypediagnostic: CY4PR12MB1926: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:9508; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:CY4PR12MB1351.namprd12.prod.outlook.com;PTR:;CAT:NONE;SFS:(4636009)(39860400002)(136003)(366004)(376002)(396003)(346002)(66556008)(4744005)(66946007)(64756008)(66446008)(478600001)(76116006)(26005)(6486002)(66476007)(8676002)(966005)(186003)(86362001)(786003)(91956017)(316002)(110136005)(6506007)(5660300002)(8936002)(2616005)(33656002)(53546011)(71200400001)(36756003)(2906002)(83380400001)(6512007)(75432002)(166002)(45980500001);DIR:OUT;SFP:1101; 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boundary="_000_BA325438A2404B40A43C8048C9CFA1B1msuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 1cac91e7-b758-4e52-3881-08d8c3ef3b1c X-MS-Exchange-CrossTenant-originalarrivaltime: 29 Jan 2021 00:45:52.7731 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: jGQB5sKrLUHqcC+pF38S/IaPzJxDafeiICoAh0BnAJyclNfMYNau7MXC0lANT63o8nHgR2yBVt71vDPSiE1P6A== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR12MB1926 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIZEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxgdHBEKQ1kXBxseHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGXEeGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdESWlZQ1h1fkNLfFx+HAdpXEwdaR1CTk0ZQktDRR97TREKWFwXHwQaBBgYGQUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3J5ehNOEQpNXBcTGBEKTFoXeGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2tra2traxEKQk8Xel5zQRJPG2kcRnMRCkNaFx4aBBsaHQQYGRwEHR oRCkJeFxsRCkReFxkRCkJFF2hta2B5EktAWh59EQpCThdob0xmAXJmZEtdEhEKQkwXb2FYExpLX RtDQWURCkJsF2F5HB8SXHtPWmlCEQpCQBdmYmQbQmtaXE15QBEKQlgXZ3Nlc0BuYWFMXWIRCk1e FxsRClpYFxkRCnlDF2hCRHJMYUEFGRhiEQpZSxcbGBkYGBEKcGcXbUdha01jGUxTaW4QGRoRCnB oF2VwbVlMS1kSfQVvEBkaEQpwaBdlY2tZW2tybnNZXhAZGhEKcGgXY24bS0cTH3tNaH4QGRoRCn BoF2xtGm9PfmZAS0Z6EBkaEQpwaBdrX1hDbWF4RGBcExAZGhEKcH0XZlB7GRwTZmJNTFIQGRoRC nBnF2lDblABWXNHAR5TEBkaEQpwfxdsBXpDGkBHWxMYYxAdGREKcF8Xb15NHGwFT0BQW10QGRoR CnBsF2d4GkBiGEkafnlNEBkaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 clxscore=183 mlxlogscore=777 impostorscore=0 malwarescore=0 bulkscore=0 lowpriorityscore=0 phishscore=0 adultscore=0 priorityscore=0 spamscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101290001 domainage_hfrom=12322 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_BA325438A2404B40A43C8048C9CFA1B1msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable For the best NAMD performance on a GPU, use NAMD 3. This blog from NVIDIA h= as been my goto for explaining the differences to folks that haven=E2=80=99= t used NAMD 3 yet. https://urldefense.com/v3/__https://developer.nvidia.com= /blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!= vErMA_5hejJ5-oln1IxckaY1cpcxTvRb3IU8etFNVACiJupnxLudR08VJT6z6BnRcw$=20 -Josh From: on behalf of "Ropon-Palacios G." Reply-To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." Date: Thursday, January 28, 2021 at 7:18 PM To: "namd-l@ks.uiuc.edu" Subject: namd-l: Improve performance Dear namd users, How can i improve namd2.14 performance on GPU? I`m using namd2.14 for run membrane protein simulation, but namd only use n= or more the 50% of GPU, as can I make to improve this performance. For other hand, if during equilibration of protein-membrane is necessary ke= ep water out membrane? Thanks, Best, Geo. --_000_BA325438A2404B40A43C8048C9CFA1B1msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: Content-Transfer-Encoding: Quoted-printable

For the best NAMD p= erformance on a GPU, use NAMD 3. This blog from NVIDIA has been my goto for= explaining the differences to folks that haven=E2=80=99t used NAMD 3 yet. https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-= v3-and-a100-gpu/

 

-Josh

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of "= ;Ropon-Palacios G." <biodano.geo@gmail.com>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>,= "Ropon-Palacios G." <biodano.geo@gmail.com>
Date: Thursday, January 28, 2021 at 7:18 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: Improve performance

 

Dear na= md users,

 <= /span>

How can i improve n= amd2.14 performance on GPU?

 <= /o:p>

I`m using namd2.14 = for run membrane protein simulation, but namd only use nor more the 50% of = GPU, as can I make to improve this performance.

 <= /o:p>

For other hand, if = during equilibration of protein-membrane is necessary keep water out membra= ne?

 <= /o:p>

Thanks,

 <= /o:p>

Best, <= /o:p>

 <= /o:p>

Geo.

--_000_BA325438A2404B40A43C8048C9CFA1B1msuedu_-- From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 28 19:02:41 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T12flO019545; Thu, 28 Jan 2021 19:02:41 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10T12fle019544; Thu, 28 Jan 2021 19:02:41 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T12eUi019540; Thu, 28 Jan 2021 19:02:40 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10T12e7B019539; Thu, 28 Jan 2021 19:02:40 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T12XW0019530 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000000d1e2105b9ff8ff0" X-CLX-Response: 1TFkXGxwcEQpMehcZGxgRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHh8eEQpDWRcHEhIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhxxHx0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XQlNTS3x8HB5ubG1teW17GFxGZmF6chMdX1tyQGRNYkIRClhcFx8EGgQYGBkF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyeXtkbhEKTVwXHBoRCkxaF3hpa01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx 0ZEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9YeGARCkJsF2Ff elMZQ0Qaeht+EQpCQBdlTlhhHX1wcmJPQhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnl DF2NfZ0hsSEhBZXtyEQpZSxcTGRobEQpwaBdoXmhueWxsZht+ehAZGhEKcGgXbUESUl5sbAFhbB 4QGRoRCnBoF25rZ01DSRJCc0YdEBkaEQpwaBdpRh4aQkd6fkkfRhAZGhEKcGgXZXtyS0hFa2MYa XIQGRoRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 mlxlogscore=999 suspectscore=0 adultscore=0 lowpriorityscore=0 spamscore=0 phishscore=0 mlxscore=0 clxscore=166 impostorscore=0 priorityscore=312 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101290002 domainage_hfrom=9301 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --0000000000000d1e2105b9ff8ff0 Content-Type: text/plain; charset="UTF-8" Hi Raghav, without knowing the details of how NAMD and GROMACS were built on your cluster, advice can only be quite generic. There are a lot of factors that may affect how each code goes. Two general pieces of advice: 1) Review each line of input in the NAMD and GROMACS scripts, and make sure you are using the same parameters in each (cutoffs, pairlist frequencies, etc), and that GROMACS is built with double precision (unless you're running both codes on GPU nodes). You need to compare apples with apples. Speaking from experience (I built and benchmarked both codes for my colleagues on our internal cluster) I found GROMACS to be faster at lower node counts, and NAMD overtaking it at higher node counts before scaling out. This with equivalent inputs, though. 2) Pick the code and build configuration that work best for the given set of features and the problem that you are dealing with. It is common to use multiple codes on the same project, when each has unique advantages or features. And there are also other codes that can handle well a system your size with CHARMM force field on different hardware including single-GPUs. Giacomo On Mon, Jan 25, 2021 at 7:05 AM raghav singh wrote: > Dear NAMD Developers and Users, > I have a protein(solvated and neutralized with 0.15mM NaCl concentration) > simulation system under classical MD scenario with charmm36 ff parameters > implemented in VMD/NAMD. > I have prepared my system with both GROMACS and NAMD* (*preferred because > I would like to run Accelerated MD later on). The system consists of 148943 > atoms all together, I have tried to test the speed and scaling of NAMD > using 1,2,4,8,16 and 32 nodes and found a linear scaling. I get ~50ns/day > of yield with NAMD on 32 nodes (768 processing cores), while if I run the > similar system with gromacs on 20 nodes (480 processing cores) and I get > ~270ns/day. > > Would it be possible for someone in the group to look at my issue, as > ~150000 atoms simulation system should not require this much of resources > to run this short simulation. I think I am wasting my HPC resources and I > am in need of dire intervention from experts. > > Please find Attached the configuration and run script. I would greatly > appreciate your expert intervention and help, so that I can make the > best use of the HPC resources. > > Thanking you > > Best regards > Raghav > --0000000000000d1e2105b9ff8ff0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Raghav, without knowing the detai= ls of how NAMD and GROMACS were built on your cluster, advice can only be q= uite generic.=C2=A0 There are a lot of factors that may affect how each cod= e goes.

Two general pieces of advice:
1) Review each line of input in the NAMD and GROMACS scripts, = and make sure you are using the same parameters in each (cutoffs, pairlist = frequencies, etc), and that GROMACS is built with double precision (unless = you're running both codes on GPU nodes).=C2=A0 You need to compare appl= es with apples.=C2=A0
Speaking from experience (I built and benchm= arked both codes for my colleagues on our internal cluster) I found GROMACS= to be faster at lower node counts, and NAMD overtaking it at higher node c= ounts before scaling out.=C2=A0 This with equivalent inputs, though.

2) Pick the code and build configuration that = work best for the given set of features and the problem that you are dealin= g with.=C2=A0 It is common to use multiple
codes on the same= project, when each has unique advantages or features.=C2=A0 And there are = also other codes that can handle well a system your size with CHARMM force = field on different hardware including single-GPUs.

=
Giacomo

--0000000000000d1e2105b9ff8ff0-- From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 28 19:21:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T1Lqk3021946; Thu, 28 Jan 2021 19:21:52 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10T1Lpsv021945; Thu, 28 Jan 2021 19:21:51 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T1LpJk021941; Thu, 28 Jan 2021 19:21:51 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 10T1Lp7J021940; Thu, 28 Jan 2021 19:21:51 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 10T1LcuD021929 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 28 Jan 2021 19:21:38 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 10T1EDSq026058 for ; Fri, 29 Jan 2021 01:21:38 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qk1-f177.google.com (mail-qk1-f177.google.com [209.85.222.177]) by mx0a-00007101.pphosted.com with ESMTP id 36c278c4fh-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 29 Jan 2021 01:21:37 +0000 Received: by mail-qk1-f177.google.com with SMTP id k193so7360640qke.6 for ; Thu, 28 Jan 2021 17:21:37 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic:references :in-reply-to:mime-version; bh=boUGCZq7Gv/CMgI9F2S6ELKR1f2PrNjPoEcPKNaSRII=; b=NcEodS9/JKpr7efaaZDi3QkplUht5MT3Iql6ZKkYOaEj6IN/mhxNybourZQjU/eyCH 5KiMa0fIer+8P7vjqvI8wAqoeXTJTg0R93nnp4YUmDYXTe3xMMf0ggCCHMeXvZVzj+Lo cFIVA1LaBcRluSAv3W70QdFzqzL8g62Qlk4bdgGAnFeRPFE09hEK76Sey7O8GHB7kDQ0 JaO4dm1nFLtr0sSTo1W56a8FoUp8spS1i6KrXoet2gDabkCqIQSQ0tMN00gNcBegJG2D ekHpPy8Z0reS5bJgE6CM6x8pBlBZfW0bupvxkI9T0G/mkWij/kKeIXLM6dVtOBeW2RSq 2LRg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:references:in-reply-to:mime-version; bh=boUGCZq7Gv/CMgI9F2S6ELKR1f2PrNjPoEcPKNaSRII=; b=N/Y9kIvjbWCaUHyRoXZROcMyS5472SwmPZ8rTZZCigmNqQAyxEQqWvNiQnQXPPYaMh gUBV+uckwB8RmwW9APUVuM0git5x1earI7DYu5NAYNo+yp6gh3B1+bp3yPJ+sZocZBnC vTeXSraOGALbV0qR78w4AhVjMlLabKxlPUEbZUq6dDDpuzQkQ0UTNdRmQwH6xN31RBug eedCpldyOs5BixVlf6yNPe0tY0bfZmvkHSXl3BuQwboGU/0DMa2bq7Bs2qhUXKyYibEz NgLXFEmTFk0m1wzsZIX3uk2ZhT08b0t+pVbwBCUlImsa2JH4iqIadPS2KVVe3Ops1GMx AMdA== X-Gm-Message-State: AOAM532H5St/ggHdEAqJy1O+wz/jnxxLVEAaoXH7KWcWbYJxxRwUkFy6 Y4n9TYHAS/eT+h4I8h+Nmxw= X-Google-Smtp-Source: ABdhPJzIBD7N3zhaZCO9Pq7Un3DL7hLoMjw2TsfgNM85jMiGEZf9DN/a4rEtCJzG/dEPmR2qS+0OxQ== X-Received: by 2002:a37:4d12:: with SMTP id a18mr2139035qkb.371.1611883296548; Thu, 28 Jan 2021 17:21:36 -0800 (PST) Received: from [192.168.1.33] ([2001:1388:3cc3:678e:e4a4:cf03:2337:f09e]) by smtp.gmail.com with ESMTPSA id e1sm4832829qkd.135.2021.01.28.17.21.34 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 28 Jan 2021 17:21:36 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 28 Jan 2021 20:21:33 -0500 Subject: Re: namd-l: Improve performance From: "Ropon-Palacios G." To: "Vermaas, Josh" , "namd-l@ks.uiuc.edu" Message-ID: <5A97C027-E9C6-4763-9FA7-CD9E4F843B7C@gmail.com> Thread-Topic: namd-l: Improve performance References: In-Reply-To: Content-type: multipart/alternative; boundary="B_3694710095_1694492374" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwcEQpMehcZGxkRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHhMfEQpDWRcHGx4SEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ccRgSEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1BDS0VuZmVue04Tf3xzbR5MZxllWx51cx1wHUBYWkRoEQpYXBcfBBoEGBgZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXcnl7TxIRCk1cFx8dGhEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGA QbHR0RCkJeFxsRCkReFxkRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwX Y2lZb3pPHXJHT38RCkJAF2ZiZBtCa1pcTXlAEQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXaEJ EckxhQQUZGGIRCllLFxMZGhsRCnBnF2lDblABWXNHAR5TEBwaEQpwaBdlUGlQXkMSfEhNbxAZGh EKcGgXaUh5SxtIaHhSaWQQGRoRCnBoF29SWnBPUkVaElJjEBkaEQpwaBdrHmJoU09MX1gZchAZG hEKcGgXbG0ab09+ZkBLRnoQHBoRCnB9F2ZQexkcE2ZiTUxSEBkaEQpwZxdtR2FrTWMZTFNpbhAc GhEKcH8XbAV6QxpAR1sTGGMQEhsRCnBfF29eTRxsBU9AUFtdEBkaEQpwbBd6R0BrGFl5fx4bSBA bEhEKbX4XGhEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 clxscore=166 mlxlogscore=757 impostorscore=0 malwarescore=0 bulkscore=0 lowpriorityscore=0 phishscore=0 adultscore=0 priorityscore=313 spamscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101290003 domainage_hfrom=9301 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3694710095_1694492374 Content-type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Josh,=20 =20 Namd3 have implement umbrella sampling, colvar, and smd protocols ?=20 =20 Geo.=20 =20 From: "Vermaas, Josh" Date: Thursday, January 28, 2021 at 7:45 PM To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." Subject: Re: namd-l: Improve performance =20 For the best NAMD performance on a GPU, use NAMD 3. This blog from NVIDIA h= as been my goto for explaining the differences to folks that haven=E2=80=99= t used NAMD 3 yet. https://urldefense.com/v3/__https://developer.nvidia.com= /blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!= tjYMkz_rYz0-mcygjKo9GeKdRm_0FZD8S4mIIgeJcpPHpSrKAvJF-wFdVk0GayNq_w$=20 =20 -Josh =20 From: on behalf of "Ropon-Palacios G." Reply-To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." Date: Thursday, January 28, 2021 at 7:18 PM To: "namd-l@ks.uiuc.edu" Subject: namd-l: Improve performance =20 Dear namd users,=20 =20 How can i improve namd2.14 performance on GPU? =20 I`m using namd2.14 for run membrane protein simulation, but namd only use n= or more the 50% of GPU, as can I make to improve this performance.=20 =20 For other hand, if during equilibration of protein-membrane is necessary ke= ep water out membrane?=20 =20 Thanks,=20 =20 Best,=20 =20 Geo.=20 --B_3694710095_1694492374 Content-type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

D= ear Josh,

 

Namd3 have implement umbrella sampling, colvar, and smd p= rotocols ?

 

Geo.

 

From: "Vermaas, Josh" <vermaasj@msu.edu>
Date: Thursday, January 28, 2021 at 7:45 PM
To: "namd-l@ks.uiuc.e= du" <namd-l@ks.uiuc.edu>, "Ropon-Palacios G." <biod= ano.geo@gmail.com>
Subject: Re: namd-l: Improve performance

 

For the best NAMD performance on a GPU, use NAMD 3. T= his blog from NVIDIA has been my goto for explaining the differences to fol= ks that haven=E2=80=99t used NAMD 3 yet. https://developer.nvidia.com/blog/delivering-up-= to-9x-throughput-with-namd-v3-and-a100-gpu/

 

-Josh

 <= o:p>

= From: <owner-namd-l@ks.uiuc.edu&g= t; on behalf of "Ropon-Palacios G." <biodano.geo@gmail.com>=
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu&= gt;, "Ropon-Palacios G." <biodano.geo@gmail.com>
Date= : Thursday, January 28, 2021 at 7:18 PM
To: "namd-l@ks.u= iuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: Improve= performance

 

Dear namd users,

=  

How can i improve namd2.14 performance on GPU?

=

 

I`m using namd= 2.14 for run membrane protein simulation, but namd only use nor more the 50= % of GPU, as can I make to improve this performance.

=

 

For other hand= , if during equilibration of protein-membrane is necessary keep water out m= embrane?

 

Thanks,

 

= Best,

 

Geo.

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namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000fabdc705ba1874c9" X-CLX-Response: 1TFkXGxgaEQpMehcZHx4RCllEF2BbUFpIT2NFQBlvEQpYWBdpHx0aWk1PTVl dYBEKeE4XY1Nja3sTWH4aX14RCnlMF2dHWgFaQB9AE0kbEQpDSBcHHhsSEQpDWRcHExgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGhpxExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdGYB9TTURsU31TRh5CE0FTem5AYW1BT398aFNhTUxcQxEKWFwXHwQaBBgYGQUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdyeVt+ExEKTVwXGx4fEQpMWhdoaU1raxEKTEYXb2tra2t rEQpCTxdrfFlQWBlpXhhmWhEKQ1oXGBoTBBIfBBgaEgQbEhgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZ1lmSXhCc3JyTW4RCkJOF2NTY2t7E 1h+Gl9eEQpCTBdpHx0aWk1PTVldYBEKQmwXZ11efmBhQkBpaRMRCkJAF2tnY28aXUUaG0h5EQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXYh5GYl5abG59W28RCllLFxMZGhgRCnBoF2x +fkRoSExTR2RcEBkaEQpwaBdkZEwbcnBCAV9HXBAZGhEKcGgXYEFBExpIHUZQYnMQGRoRCnBoF2 J8ewF7GnAbTF5jEBkaEQpwaBdgeAVjfUceGhpPXBAZGhEKcGwXb0VoZGZBXWdGZUMQGRoRCm1+F xsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 malwarescore=0 bulkscore=0 phishscore=0 impostorscore=0 priorityscore=354 adultscore=0 clxscore=120 mlxscore=0 suspectscore=0 spamscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101300034 domainage_hfrom=9302 X-Spam-Score: 0 X-Spam-OrigSender: sekekeretsu@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Seke Keretsu --000000000000fabdc705ba1874c9 Content-Type: text/plain; charset="UTF-8" Dear Expert, I came across the following error during the equilibration of my protein ligand system which has a CL atom (in ligand). I prepared the system using CHARMMGUI ERROR: Atom 4737 velocity is -11982.1 12908.1 -3406.91 (limit is 12000, atom 983 of 1008 on patch 17 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 17 pe 1). Here, the atom no. 4737 corresponds to the lone pair connected to CL atom in the system. I have checked the mailing list which suggested to perform the simulation gradually from low temperature for atoms moving fast. However, I could not find a solution for dealing with lone pairs. I keep getting the same error regardless of the temperature. Is there a command I need to give in the configuration file? Please give me some advice or link to a solution. The configuration file used during equilibration is given below. XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX structure ionized.psf coordinates ionized.pdb set temp 50; set outputname equilibration03; #source step5_charmm2namd.str set inputname equilibration; outputname $outputname; binCoordinates equilibration.restart.coor; binVelocities equilibration.restart.vel; extendedSystem equilibration.restart.xsc; firsttimestep 50000; restartfreq 1000; # 1000 steps = every 2ps dcdfreq 5000; dcdUnitCell yes; # the file will contain unit cell info in the style of # charmm dcd files. if yes, the dcd files will contain # unit cell information in the style of charmm DCD files. xstFreq 5000; # XSTFreq: control how often the extended systen configuration # will be appended to the XST file outputEnergies 125; # 125 steps = every 0.25ps # The number of timesteps between each energy output of NAMD outputTiming 1000; # The number of timesteps between each timing output shows # time per step and time to completion # Force-Field Parameters paraTypeCharmm on; # We're using charmm type parameter file(s) # multiple definitions may be used but only one file per definition parameters jz4/jz4.prm parameters toppar/par_all36_carb.prm parameters toppar/par_all36_cgenff.prm parameters toppar/par_all36_lipid.prm parameters toppar/par_all36m_prot.prm parameters toppar/par_all36_na.prm parameters toppar/par_interface.prm parameters toppar_water_ions.str # These are specified by CHARMM exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4" # 1-2: all atoms pairs that are bonded are going to be ignored # 1-3: 3 consecutively bonded are excluded # scaled1-4: include all the 1-3, and modified 1-4 interactions # electrostatic scaled by 1-4scaling factor 1.0 # vdW special 1-4 parameters in charmm parameter file. 1-4scaling 1.0 switching on vdwForceSwitching yes; # New option for force-based switching of vdW # if both switching and vdwForceSwitching are on CHARMM force # switching is used for vdW forces. # You have some freedom choosing the cutoff cutoff 12.0; # may use smaller, maybe 10., with PME switchdist 10.0; # cutoff - 2. # switchdist - where you start to switch # cutoff - where you stop accounting for nonbond interactions. # correspondence in charmm: # (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist) pairlistdist 16.0; # stores the all the pairs with in the distance it should be larger # than cutoff( + 2.) stepspercycle 20; # 20 redo pairlists every ten steps pairlistsPerCycle 2; # 2 is the default # cycle represents the number of steps between atom reassignments # this means every 20/2=10 steps the pairlist will be updated # Integrator Parameters timestep 1.0; # fs/step rigidBonds all; # Bound constraint all bonds involving H are fixed in length nonbondedFreq 1; # nonbonded forces every step fullElectFrequency 1; # PME every step # Constant Temperature Control ONLY DURING EQUILB reassignFreq 500; # reassignFreq: use this to reassign velocity every 500 steps reassignTemp $temp; cellBasisVector1 69.61299896240234 0 0 cellBasisVector2 0 76.30400085449219 0 cellBasisVector3 0 0 74.61400032043457 cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496 wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too #wrapNearest $wrapnearst; # use for non-rectangular cells (wrap to the nearest image) # PME (for full-system periodic electrostatics) PME yes; PMEInterpOrder 6; # interpolation order (spline order 6 in charmm) PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size # Pressure and volume control useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE) useFlexibleCell yes; # yes for anisotropic system like membrane useConstantRatio yes; # keeps the ratio of the unit cell in the x-y plane constant A=B langevin on langevinDamping 1.0 langevinTemp $temp langevinHydrogen off constraints on consexp 2 consref prot_posres.ref conskfile prot_posres.ref conskcol B constraintScaling 5.0 minimize 5000 run 125000 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Thank you. 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priorityscore=60 suspectscore=0 phishscore=0 mlxlogscore=999 clxscore=188 mlxscore=0 bulkscore=0 spamscore=0 adultscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2101300095 X-Spam-Score: 0 X-Spam-OrigSender: andrewpang@gatech.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Pang, Yui Tik" --_000_BN7PR07MB4468FF5373CD26911910686BAFB89BN7PR07MB4468namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Seke, I suspect NAMD did not recognize the LP correctly. If you look into your ps= f file, do you find a line like =85 !NUMLP NUMLPH ? What does that line and= the following line says? Best, Andrew From: Seke Keretsu Sent: Saturday, January 30, 2021 1:54 AM To: namd-l@ks.uiuc.edu Subject: namd-l: Dealing with lone pairs (LP) during simulation Dear Expert, I came across the following error during the equilibration of my protein li= gand system which has a CL atom (in ligand). I prepared the system using CH= ARMMGUI ERROR: Atom 4737 velocity is -11982.1 12908.1 -3406.91 (limit is 12000, ato= m 983 of 1008 on patch 17 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 17 pe 1). Here, the atom no. 4737 corresponds to the lone pair connected to CL atom = in the system. I have checked the mailing list which suggested to perform the simulation g= radually from low temperature for atoms moving fast. However, I could not f= ind a solution for dealing with lone pairs. I keep getting the same error = regardless of the temperature. Is there a command I need to give in the configuration file? Please give me some advice or link to a solution. The configuration file used during equilibration is given below. XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX= XX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX= XX structure ionized.psf coordinates ionized.pdb set temp 50; set outputname equilibration03; #source step5_charmm2namd.str set inputname equilibration; outputname $outputname; binCoordinates equilibration.restart.coor; binVelocities equilibration.restart.vel; extendedSystem equilibration.restart.xsc; firsttimestep 50000; restartfreq 1000; # 1000 steps =3D every 2ps dcdfreq 5000; dcdUnitCell yes; # the file will contain unit ce= ll info in the style of # charmm dcd files. if yes, the= dcd files will contain # unit cell information in the = style of charmm DCD files. xstFreq 5000; # XSTFreq: control how often th= e extended systen configuration # will be appended to the XST f= ile outputEnergies 125; # 125 steps =3D every 0.25ps # The number of timesteps betwe= en each energy output of NAMD outputTiming 1000; # The number of timesteps betwe= en each timing output shows # time per step and time to com= pletion # Force-Field Parameters paraTypeCharmm on; # We're using charmm type param= eter file(s) # multiple definitions may be u= sed but only one file per definition parameters jz4/jz4.prm parameters toppar/par_all36_carb.prm parameters toppar/par_all36_cgenff.prm parameters toppar/par_all36_lipid.prm parameters toppar/par_all36m_prot.prm parameters toppar/par_all36_na.prm parameters toppar/par_interface.prm parameters toppar_water_ions.str # These are specified by CHARMM exclude scaled1-4 # non-bonded exclusion policy t= o use "none,1-2,1-3,1-4,or scaled1-4" # 1-2: all atoms pairs that are= bonded are going to be ignored # 1-3: 3 consecutively bonded a= re excluded # scaled1-4: include all the 1-= 3, and modified 1-4 interactions # electrostatic scaled by 1-4sc= aling factor 1.0 # vdW special 1-4 parameters in= charmm parameter file. 1-4scaling 1.0 switching on vdwForceSwitching yes; # New option for force-based sw= itching of vdW # if both switching and vdwForc= eSwitching are on CHARMM force # switching is used for vdW for= ces. # You have some freedom choosing the cutoff cutoff 12.0; # may use smaller, maybe 10., w= ith PME switchdist 10.0; # cutoff - 2. # switchdist - where you start = to switch # cutoff - where you stop accou= nting for nonbond interactions. # correspondence in charmm: # (cutnb,ctofnb,ctonnb =3D pair= listdist,cutoff,switchdist) pairlistdist 16.0; # stores the all the pairs with= in the distance it should be larger # than cutoff( + 2.) stepspercycle 20; # 20 redo pairlists every ten s= teps pairlistsPerCycle 2; # 2 is the default # cycle represents the number o= f steps between atom reassignments # this means every 20/2=3D10 st= eps the pairlist will be updated # Integrator Parameters timestep 1.0; # fs/step rigidBonds all; # Bound constraint all bonds in= volving H are fixed in length nonbondedFreq 1; # nonbonded forces every step fullElectFrequency 1; # PME every step # Constant Temperature Control ONLY DURING EQUILB reassignFreq 500; # reassignFreq: use this to re= assign velocity every 500 steps reassignTemp $temp; cellBasisVector1 69.61299896240234 0 0 cellBasisVector2 0 76.30400085449219 0 cellBasisVector3 0 0 74.61400032043457 cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496 wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too #wrapNearest $wrapnearst; # use for non-rectangular cell= s (wrap to the nearest image) # PME (for full-system periodic electrostatics) PME yes; PMEInterpOrder 6; # interpolation order (spline o= rder 6 in charmm) PMEGridSpacing 1.0; # maximum PME grid space / used= to calculate grid size # Pressure and volume control useGroupPressure yes; # use a hydrogen-group based ps= eudo-molecular viral to calcualte pressure and # has less fluctuation, is need= ed for rigid bonds (rigidBonds/SHAKE) useFlexibleCell yes; # yes for anisotropic system li= ke membrane useConstantRatio yes; # keeps the ratio of the unit c= ell in the x-y plane constant A=3DB langevin on langevinDamping 1.0 langevinTemp $temp langevinHydrogen off constraints on consexp 2 consref prot_posres.ref conskfile prot_posres.ref conskcol B constraintScaling 5.0 minimize 5000 run 125000 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Thank you. Best, Seke --_000_BN7PR07MB4468FF5373CD26911910686BAFB89BN7PR07MB4468namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Hi Seke,

 

I suspect NAMD did not recognize the LP correctly. I= f you look into your psf file, do you find a line like =85 !NUMLP NUMLPH ? = What does that line and the following line says?

 

Best,

Andrew

 

From: Seke Keretsu
Sent: Saturday, January 30, 2021 1:54 AM
To: namd-l@ks.uiuc.edu
Subject: namd-l: Dealing with lone pairs (LP) during simulation

 

Dear Expert,

 

I came across the following error during the equilib= ration of my protein ligand system which has a CL atom (in ligand). I prepa= red the system using CHARMMGUI

 

ERROR: Atom 4737 velocity is -11982.1 12908.1 -3406.= 91 (limit is 12000, atom 983 of 1008 on patch 17 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 17 pe 1).

 

Here, the atom no. 4737 corresponds to  the lon= e pair connected to CL atom in the system.

 

I have checked the mailing list which suggested to p= erform the simulation gradually from low temperature for atoms moving fast.= However, I could not find a solution for dealing with lone pairs. I keep g= etting the same error  regardless of the temperature.

 

Is there a command I need to give in the configurati= on file?

Please give me some advice or link to a solution.

 

The configuration file used during equilibration is = given below.

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX= XXXXXXXXXXXXXXXXXXXXXXXXX

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX= XXXXXXXXXXXXXXXXXXXXXXXXX

structure          ionized.= psf
coordinates        ionized.pdb

set temp                50;
set outputname          equilibration03;

#source                  step5= _charmm2namd.str
set inputname           equilibration;
outputname              $outputname;
binCoordinates          equilibration.restart.coor= ;
binVelocities           equilibration.restart.vel;=
extendedSystem          equilibration.restart.xsc;=

firsttimestep           50000;
restartfreq             1000;     &= nbsp;         # 1000 steps =3D every 2ps
dcdfreq                 5000;
dcdUnitCell             yes;     &n= bsp;          # the file will contain unit cell in= fo in the style of
                     = ;                     &nb= sp; # charmm dcd files. if yes, the dcd files will contain
                     = ;                     &nb= sp; # unit cell information in the style of charmm DCD files.
xstFreq                 5000;  = ;             # XSTFreq: control how often th= e extended systen configuration
                     = ;                     &nb= sp; # will be appended to the XST file
outputEnergies          125;       =          # 125 steps =3D every 0.25ps
                     = ;                     &nb= sp; # The number of timesteps between each energy output of NAMD
outputTiming            1000;     &= nbsp;         # The number of timesteps between each ti= ming output shows
                     = ;                     &nb= sp; # time per step and time to completion

# Force-Field Parameters
paraTypeCharmm          on;       &= nbsp;         # We're using charmm type parameter file(= s)
                     = ;                     &nb= sp; # multiple definitions may be used but only one file per definition
parameters jz4/jz4.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_interface.prm
parameters toppar_water_ions.str
# These are specified by CHARMM
exclude                 scaled1-4 &= nbsp;         # non-bonded exclusion policy to use &quo= t;none,1-2,1-3,1-4,or scaled1-4"
                     = ;                     &nb= sp; # 1-2: all atoms pairs that are bonded are going to be ignored
                     = ;                     &nb= sp; # 1-3: 3 consecutively bonded are excluded
                     = ;                     &nb= sp; # scaled1-4: include all the 1-3, and modified 1-4 interactions
                     = ;                     &nb= sp; # electrostatic scaled by 1-4scaling factor 1.0
                     = ;                     &nb= sp; # vdW special 1-4 parameters in charmm parameter file.
1-4scaling              1.0
switching               on
vdwForceSwitching       yes;         &nb= sp;      # New option for force-based switching of vdW
                     = ;                     &nb= sp; # if both switching and vdwForceSwitching are on CHARMM force
                     = ;                     &nb= sp; # switching is used for vdW forces.

# You have some freedom choosing the cutoff
cutoff                  12.0; =               # may use smaller, maybe 1= 0., with PME
switchdist              10.0;   &nb= sp;           # cutoff - 2.
                     = ;                     &nb= sp; # switchdist - where you start to switch
                     = ;                     &nb= sp; # cutoff - where you stop accounting for nonbond interactions.
                     = ;                     &nb= sp; # correspondence in charmm:
                     = ;                     &nb= sp; # (cutnb,ctofnb,ctonnb =3D pairlistdist,cutoff,switchdist)
pairlistdist            16.0;     &= nbsp;         # stores the all the pairs with in the di= stance it should be larger
                     = ;                     &nb= sp; # than cutoff( + 2.)
stepspercycle           20;       &= nbsp;         # 20 redo pairlists every ten steps
pairlistsPerCycle       2;          = ;        # 2 is the default
                     = ;                     &nb= sp; # cycle represents the number of steps between atom reassignments
                     = ;                     &nb= sp; # this means every 20/2=3D10 steps the pairlist will be updated

# Integrator Parameters
timestep                1.0;  =              # fs/step
rigidBonds              all;   &nbs= p;            # Bound constraint all bonds in= volving H are fixed in length
nonbondedFreq           1;       &n= bsp;          # nonbonded forces every step
fullElectFrequency      1;          = ;        # PME every step

# Constant Temperature Control ONLY DURING EQUILB
reassignFreq            500;     &n= bsp;          # reassignFreq:  use this to re= assign velocity every 500 steps
reassignTemp            $temp;

cellBasisVector1 69.61299896240234 0 0
cellBasisVector2 0 76.30400085449219 0
cellBasisVector3 0 0 74.61400032043457
cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496

wrapWater               on;    = ;             # wrap water to central cell wrapAll                 on;   =               # wrap other molecules too=
#wrapNearest             $wrapnearst;   =      # use for non-rectangular cells (wrap to the nearest im= age)

# PME (for full-system periodic electrostatics)
PME                     y= es;
PMEInterpOrder          6;       &n= bsp;          # interpolation order (spline order = 6 in charmm)
PMEGridSpacing          1.0;       =          # maximum PME grid space / used to calcul= ate grid size

# Pressure and volume control
useGroupPressure        yes;        = ;        # use a hydrogen-group based pseudo-molecular = viral to calcualte pressure and
                     = ;                     &nb= sp; # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE) useFlexibleCell         yes;        = ;        # yes for anisotropic system like membrane
useConstantRatio        yes;        = ;        # keeps the ratio of the unit cell in the x-y = plane constant A=3DB

langevin                on
langevinDamping         1.0
langevinTemp            $temp
langevinHydrogen        off

constraints             on
consexp                 2
consref                 prot_posres= .ref
conskfile               prot_posres.ref<= br> conskcol                B
constraintScaling       5.0
minimize        5000
run                     1= 25000

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX<= /o:p>

 

Thank you.

 

Best, Seke

 

 

 

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boundary="00000000000021612e05ba426789" X-CLX-Response: 1TFkXGR4dEQpMehcZGxoRCllEF3pDExJ9b1hYeklbEQpYWBdoExIBemR6aEt GAREKeE4XY1Nja3sTWH4aX14RCnlMF2sTaFhZaXBME11SEQpDSBcHExgRCkNZFwcfHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXHRlxGQYeEncGEh4GGxoaQhwGGgYbGQYdEnEfEBp3BhoGGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XbEV4aF9wW0UfZwcdXX8YZhlP RnkbW095eV0YGAdoR30RClhcFx8EGgQYGBkFGxoEGxsaBB8aBBseGBAbHhofGhEKXlkXcn59eR4 RCk1cFxgcEQpMWhdoaU1raxEKTEYXb2tra2trEQpCTxd6TENJc2l5AVtAexEKQ1oXGBoTBBIfBB gbGgQfGxEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eE QpCRRdsSWRhGG5zTlpNeBEKQk4XY1Nja3sTWH4aX14RCkJMF2gTEgF6ZHpoS0YBEQpCbBduaWZL BXlScFABfhEKQkAXaGh+eW1PeGdLGEQRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5Qxd gRF1dTRpmElpLYBEKWUsXExkaHhEKcGgXbVt+TkcTBWgdRR8QGRoRCnBoF2RAf1heehIFGFNuEB kaEQpwaBdiH0kfQBsbeXwZZxAZGhEKcGgXbHlTHkxEH1tEQ2YQGRoRCnBoF2RyGnBbYBNQR2xnE BkaEQpwfRdiBWF+W2NaTBhtZxAZGhEKcH8XaRIbQWEabB1lGWYQGxoeEQpwXxdpWH9db35iQktE WxAZGhEKcGwXbBxlcERwHRhyRUYQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=1 lowpriorityscore=0 adultscore=0 mlxlogscore=196 bulkscore=0 mlxscore=1 impostorscore=0 suspectscore=0 malwarescore=0 clxscore=347 spamscore=1 phishscore=0 priorityscore=310 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102010044 domainage_hfrom=9304 X-Spam-Score: 1 X-Spam-OrigSender: luba.simhaev0703@gmail.com X-Spam-Bar: * Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Luba Simhaev --00000000000021612e05ba426789 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear NAMD users, I'm trying to perform alchemical FEP simulation to a system consisting of a membrane protein, which is an ion exchanger. Prior to FEP, the system was equilibrated for 250 ns. Although while I'm turning to FEP calculations, they are halted due to "Constraint failure in RATTLE algorithm" error. I know that this error indicates an unstable system,but as I mentioned the system was equilibrated, and by visual inspection seems to be stable. Could you please suggest how to solve this problem? I would appreciate your help. Thanks, Luba --=20 Dr. Ischakov Simhaev Luba, Ph.D. Computational assisted drug-design unit *Blavatnik Center for Drug Discovery* Cohen-Porter Family United Kingdom Building (Britannia), 1st floor Tel Aviv University, Ramat Aviv Tel Aviv, Israel, 6997801 Tel:+972-3-640-9842, 9654 Web-site: https://urldefense.com/v3/__http://www.bcdd.tau.ac.il/__;!!DZ3fjg= !rSJRpZrOF58ja1Um-I6ulgX7wAExY62gjgNXLXMZtFaoiB6Nzq4r5QS_Ye1N098C1w$=20 --00000000000021612e05ba426789 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear NAMD users,
I'm trying to perform alchemical = FEP simulation to a system consisting of a membrane protein, which is an io= n exchanger. Prior to FEP, the system was equilibrated for 250 ns. Although= while I'm turning to FEP calculations, they are halted due to "Co= nstraint failure in RATTLE algorithm" error.
I know that thi= s error indicates an unstable system,but as I mentioned the system was equi= librated, and by visual inspection seems to be stable.=C2=A0
Coul= d you please suggest how to solve this problem?=C2=A0=C2=A0

<= /div>
I would appreciate your help.
Thanks,
Luba

--
Dr. Ischakov Simhaev Luba, Ph.D= .

Computational assisted drug-design unit
Blavat= nik Center for Drug Discovery
Co= hen-Porter Family United Kingdom Building
(Britannia), 1st=C2=A0floor
Tel Aviv University, Ramat Av= iv
Tel Aviv, Israel, 6997801
Tel:+972-3-640-9842, 9654
Web-site= :=C2=A0http://www.bcdd.tau.ac.il/
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charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear All I'm trying to output the MDFF results to Phenix, for finer tuning. However,= I kept having format issues. Any insight would be appreciated. Thank you! Here are what I did, output single frame from dcd convert HSE/HSD to HIS convert CD ILE to CD1 ILE convert O1P to OP1, O2P to OP2 (it has nucleic acids) convert THY to DT ... write out PDB without "H" (did I miss any pdb alias? thanks!) Thanks, Ming Disclaimer The information contained in this communication from the sender is confiden= tial. It is intended solely for use by the recipient and others authorized = to receive it. If you are not the recipient, you are hereby notified that a= ny disclosure, copying, distribution or taking action in relation of the co= ntents of this information is strictly prohibited and may be unlawful. --_000_BL0PR18MB21302F8B2B39DBF951AE6A8FB7B69BL0PR18MB2130namp_ Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <= /head>
Dear All

I'm trying to output the MDFF results to Phenix, for finer tuning. However,= I kept having format issues. Any insight would be appreciated. Thank you!&= nbsp;

Here are what I did,

output single frame from dcd
convert HSE/HSD to HIS
convert CD ILE to CD1 ILE
convert O1P to OP1, O2P to OP2
(it has nucleic acids) convert THY to DT ...
write out PDB without "H"

(did I miss any pdb alias? thanks!) 

Thanks,
Ming


<= b>Disclaimer

The information contained in this communication from the sender i= s confidential. It is intended solely for use by the recipient and others a= uthorized to receive it. If you are not the recipient, you are hereby notif= ied that any disclosure, copying, distribution or taking action in relation= of the contents of this information is strictly prohibited and may be unla= wful.

--_000_BL0PR18MB21302F8B2B39DBF951AE6A8FB7B69BL0PR18MB2130namp_-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 1 12:03:14 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 111I3EBd010558; Mon, 1 Feb 2021 12:03:14 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 111I3E18010557; Mon, 1 Feb 2021 12:03:14 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 111I3D9x010553; Mon, 1 Feb 2021 12:03:13 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 111I3D1E010552; Mon, 1 Feb 2021 12:03:13 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 111I32jT010543 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 1 Feb 2021 12:03:02 -0600 (CST) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 111Hx4qx024658 for ; Mon, 1 Feb 2021 18:03:01 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qk1-f171.google.com (mail-qk1-f171.google.com [209.85.222.171]) by mx0b-00007101.pphosted.com with ESMTP id 36cx9rmamv-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 01 Feb 2021 18:03:01 +0000 Received: by mail-qk1-f171.google.com with SMTP id r77so17122580qka.12 for ; Mon, 01 Feb 2021 10:03:01 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=duk+LApVKLB3CQYXyEEjGdBoZHMOCyhQLBp6B8FoL0A=; b=p6pWJ1Y8FrxmUaJgrE38UMNXZsvro1eR2i74yF3/l6VyAoLhfpAtpIGBsJUtkjctmh +rln57MIt9DcLuxUFzbr3dpVd2+II6q4zQgzSOOCtLeQk19tbCadyogS+y9Z5sU+upuZ 30HkPp8y2PlkNaz9jZ6A6nuUFToMIN5amt3uufkNrjuOs/TJHz83z/2iw/VKCHbgfGwe DvbzCQSRWFDcquJbkAYJbL8KpuZNbnxLmTXcu68GFuaZ5f/gIPq8hJxxWuwHgHSBz39C VJnDu8swI/23W6w0dMMelodjHlQwrdMdYGD8GVjQ/6ED8/gvobykWx4CriOeh5y0IrZj OTpg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=duk+LApVKLB3CQYXyEEjGdBoZHMOCyhQLBp6B8FoL0A=; b=FEULcX0XdoQLWD9MUf/5Gogl+zOCAq9f+z/wvGyOfjDZ9S7gOmlMs4l+mv7NdZNvDJ ZeJWrEVun45XytGco1DEB61+DKNNu06dMxyHQx5HCh3zpbJCmKXOcHhtqG5JZoglI/GJ K4Rs0ruH7zRzvn8Uk2VRD1uOg/PxmN39tFYmOrQ03qPA4sUo6ViULA4W0Tahr+X0MplO ymQmUO1BK2tzuZiNLe7LTzM0mfrQzPiUssLHe2VO/1jTYMXYpOx9NWVHKVpyRQo56PJU mKZ/Tt3ZETFeMue3Je+ztQIVPLDEB5wCDbD1NRHxu6BoT+HP9Lei+sBY1K/So2s627S3 91UQ== X-Gm-Message-State: AOAM530RHZvR9koZ+fRjyIr9k1pBml1Nn1QEXcjp2utM2BWgEBQfw1Kp ACFxYR/WD4NuI3INQr1ZEDj5wcZbYNX0sg== X-Google-Smtp-Source: ABdhPJxb2aJrIji7wAbFoDimp14IpsCFro7Q2KatyHdX9l+lzf1zlkApUqsy0bdrhceHizM8E8umhg== X-Received: by 2002:a37:a1d4:: with SMTP id k203mr16993755qke.401.1612202580649; Mon, 01 Feb 2021 10:03:00 -0800 (PST) Received: from [192.168.1.33] ([190.42.120.144]) by smtp.gmail.com with ESMTPSA id s15sm13868103qtn.35.2021.02.01.10.02.58 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 01 Feb 2021 10:02:59 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Mon, 01 Feb 2021 13:02:56 -0500 Subject: namd-l: Convert mmCIF to PDB From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: Thread-Topic: Convert mmCIF to PDB Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3695029379_1844018558" X-CLX-Response: 1TFkXGx0bEQpMehcZGBkRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGBIdEQpDWRcHHR4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxtxGRsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XbEtrSBliSBJic1NHSVJcTFJMeEhwaF1IE29ceW9bQmERClhcFx8EGgQYGBkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcn5PSF0RCk1cFxgfGxEKTFoXbGlNTWsRCkxGF29ra2t raxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx0bEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hPHWFFcFlwBU0aEQpCT hdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2NpWW96Tx1yR09/EQpCQBdiSXIdGUdI YUB4RxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2kdZUJFGmxfSFhDEQpZSxcTGRo eEQpwaBdgS1tNfm98QlxFQRAZGhEKcGgXa0NLGUFLaEsYX0IQGRoRCnBoF2sYSAVcUkQTc2ZbEB kaEQpwaBdpbnAFRkMcWmZcYRAbGB4RCnBoF2hOGUBmX017SE8dEBkaEQpwbBd6R0BrGFl5fx4bS BAZGhEKcEMXYGgeYVgeQRNdXXgQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=368 malwarescore=0 bulkscore=0 phishscore=0 impostorscore=0 priorityscore=323 adultscore=0 clxscore=171 mlxscore=0 suspectscore=0 spamscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102010093 domainage_hfrom=9304 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3695029379_1844018558 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear namd user, Anybody have a script for convert mmCIF to PDB as charm-gui PDBreader protocol? I like process bulk data, and use charmm-gui not is good pathway. Best, Geo. --B_3695029379_1844018558 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dea= r namd user,

 

Anybody have a script for convert mmCIF to PDB as charm-g= ui PDBreader protocol?

 

I like process bulk data, and use charmm-gui not is good= pathway.

 

Best,

 

Geo.

 

--B_3695029379_1844018558-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 1 12:04:43 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 111I4gwT011208; Mon, 1 Feb 2021 12:04:42 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 111I4gKh011205; Mon, 1 Feb 2021 12:04:42 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 111I4fT6011191; Mon, 1 Feb 2021 12:04:41 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 111I4f1U011189; Mon, 1 Feb 2021 12:04:41 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 111I4Vn0011129 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 1 Feb 2021 12:04:32 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 111HwxQg010185 for ; Mon, 1 Feb 2021 18:04:31 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qt1-f182.google.com (mail-qt1-f182.google.com [209.85.160.182]) by mx0a-00007101.pphosted.com with ESMTP id 36cvhyd08d-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 01 Feb 2021 18:04:30 +0000 Received: by mail-qt1-f182.google.com with SMTP id e15so12895197qte.9 for ; Mon, 01 Feb 2021 10:04:30 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic:references :in-reply-to:mime-version; bh=+ziqP2/NddQBHjy1WwiWEJVkO5jQFyzW+3b7EbdgtHA=; b=jDYl/L2A3qDhxZQU4OgADWmdPLlE0YKSFiXOn+1tAlGVVLY2OfVVTifvjmjeaveQ0e xE8+KiPcOX12kMuqMbTdUle0OkoI66jxMFrUYC7uyW0lwdHM2RIQPLA9QVdK9ohfeCAL 04ftZbol4rsmDcNn5eyFY8h6a0KtWPplUsPl8RkmphtBgI44G6Beuy9ULOvvG3FpboRD 9J3Xg4suAF4+B0WIQF5VB9OnX2KBLfy76uCemJ5NwARwky/9C5ykdmo4MypmqKkmIOUN Vj7iyqqE/vh+im62xdlYtTpLUwLXcW0YXbnJLGP39aSszJ4XV/lOhHKzIMSmb7hVpLIt DEDw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:references:in-reply-to:mime-version; bh=+ziqP2/NddQBHjy1WwiWEJVkO5jQFyzW+3b7EbdgtHA=; b=QCMm6R64LIzJajnG7RwhLP0OmSxPa/+p66lE1tFzPEkrdqBmOATRY2EU6b+bQkw6ap FB6q3tK/kX/5jvE+fAms9i1eErLwydSZ2yZuZbzPK7pbCjtQdMWe0DuiQb1EgcR13QTj XNfhUrZjtHeZcdaWygixG+OFZWzIhOl2NcrZMCcYtlVCwypB9cWPD57M+D6Qx1Adg2xc 9kCX8EhVT+L5/F9Y40dSIdZjI6fJOdU4ZmyF4ns1GAd0uXtqBEu1w3EgeTsfn/AqQkHs rhQ3XTXtBC2woIZ6pmZzCW0WHoCibyWqMFPW+5utJ7XWs092yLwkdcYv3RjZDU7lX0c0 Sgxg== X-Gm-Message-State: AOAM533igrTgGYavE3X8SxhlI74OcWNm8bCyyRFYrf0qpHXz9YYEj2gg iwIppP/oBJvDHsR2a5dc8lQBmbOWxwkogA== X-Google-Smtp-Source: ABdhPJwBfqvhK5IdJB0cJQUrWVAW/PxLxRxe6ycLKgOcyKZnwCR1GhhoBn3Vucdll5kBt3+YWTKiKA== X-Received: by 2002:ac8:3571:: with SMTP id z46mr16774880qtb.83.1612202669674; Mon, 01 Feb 2021 10:04:29 -0800 (PST) Received: from [192.168.1.33] ([190.42.120.144]) by smtp.gmail.com with ESMTPSA id s15sm13868103qtn.35.2021.02.01.10.04.28 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 01 Feb 2021 10:04:29 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Mon, 01 Feb 2021 13:04:27 -0500 Subject: Re: namd-l: output results to phenix From: "Ropon-Palacios G." To: , Ming Sun Message-ID: <04A69F26-03E2-45C4-BB89-71AA0AB453B5@gmail.com> Thread-Topic: namd-l: output results to phenix References: In-Reply-To: Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3695029468_1975990930" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0cEQpMehcZHx4RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHh8SEQpDWRcHGx8cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxpZeXNgbhpmQEwfT1NTE3B6cBtDbhJyGUESfGUHfX5iEQpYXBcfBBoEGBgZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXcn5PTmERCk1cFxgbExEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbEhgRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwX Y2lZb3pPHXJHT38RCkJAF2BsZ2kSRBloZHlMEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGRE KeUMXZRoeU0waeFJ4THoRCllLFxMZGh4RCnBnF21HYWtNYxlMU2luEBkaEQpwaBdlQ1hfbH1hRh ppUBAZGhEKcGgXYEBsaVxeaEFSXHoQGxsfEQpwaBduZ2VeZVBTHn4fGBAZGhEKcGgXaWJ9RQV4Q V9zY0QQGRoRCnBoF2R9cG4cbUdbXWZwEBkaEQpwZxdpQ25QAVlzRwEeUxAZGhEKcGwXekdAaxhZ eX8eG0gQGRoRCnBDF2BoHmFYHkETXV14EBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 spamscore=0 mlxscore=0 priorityscore=354 impostorscore=0 lowpriorityscore=0 phishscore=0 mlxlogscore=611 bulkscore=0 clxscore=176 adultscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102010093 domainage_hfrom=9304 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3695029468_1975990930 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit You can use PDBalias sytaxis for this. From: on behalf of Ming Sun Reply-To: , Ming Sun Date: Monday, February 1, 2021 at 12:29 PM To: "namd-l@ks.uiuc.edu" Subject: namd-l: output results to phenix Dear All I'm trying to output the MDFF results to Phenix, for finer tuning. However, I kept having format issues. Any insight would be appreciated. Thank you! Here are what I did, output single frame from dcd convert HSE/HSD to HIS convert CD ILE to CD1 ILE convert O1P to OP1, O2P to OP2 (it has nucleic acids) convert THY to DT ... write out PDB without "H" (did I miss any pdb alias? thanks!) Thanks, Ming Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. --B_3695029468_1975990930 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

You can use PDBalias sytaxis for this.

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of= Ming Sun <msun@beamtx.com>
Reply-To: <namd-l@ks.uiuc.edu= >, Ming Sun <msun@beamtx.com>
Date: Monday, February 1, 2= 021 at 12:29 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.u= iuc.edu>
Subject: namd-l: output results to phenix

 

Dear All

 <= /span>

I'm trying to output the MDFF results to Phe= nix, for finer tuning. However, I kept having format issues. Any insight wou= ld be appreciated. Thank you! 

 

Here are what I did,

 

<= div>

output single frame from dcd

=

convert HSE/HSD to HIS

convert CD ILE to CD1 ILE

conver= t O1P to OP1, O2P to OP2

(it has = nucleic acids) convert THY to DT ...

write out PDB without "H"

 

(did I miss any pdb= alias? thanks!) 

 = ;

Thanks,

<= div>

Ming

 

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boundary="_000_SN6PR01MB5309AB09327318194E277CD2B0B69SN6PR01MB5309prod_" MIME-Version: 1.0 X-OriginatorOrg: ku.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SN6PR01MB5309.prod.exchangelabs.com X-MS-Exchange-CrossTenant-Network-Message-Id: b3927dc2-fb61-47db-edb4-08d8c6ea95e8 X-MS-Exchange-CrossTenant-originalarrivaltime: 01 Feb 2021 19:50:11.2092 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 3c176536-afe6-43f5-b966-36feabbe3c1a X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 9xdJgk5oLH/DoLbAjay9URK8nz+VykCeCkSUd0TFJsG3tCUjJGKhkFcEL6l6EQQCt5kLkgELgpsnMQ5MWYY2lQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SN6PR01MB3855 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0ZEQpMehcbGh4RCllEF25NTHBGe0dAH017EQpYWBdjZh1/QW5gUx9 NUBEKeE4XYlx+QkteW2d8bl8RCnlMF24aQmdafl94XkVnEQpDSBcHGRkTEQpDWRcHHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGXEZGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdPUEFdf1x+RR5faWFIGH8aRElFRnBHGHVwXFofXlsefBEKWFwXHwQaBBgYGQUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3J+TWt6EQpNXBceGhEKTFoXeGlNTWsRCkVZF2kRCkxfF3o FBQUFBQUFBQVEEQpMRhdvb2tra2trEQpCTxd6XnNBEk8baRxGcxEKQ1oXHhoEGxodBBgZHAQbGB wRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2JcfkJLXltnfG5fEQpCSRdiXH5CS15bZ3xuX xEKQkUXaxJ4SVB6HVkTBWsRCkJOF2JcfkJLXltnfG5fEQpCTBdjZh1/QW5gUx9NUBEKQmwXb2hz GFNLeVhMWFgRCkJAF2Z7WxtwfxxsGW9kEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUM XY0lAS2JseltEcGcRCllLFxISGhwRCnBoF3phHAFPfxgTSFBQEBkaEQpwaBdsUnhzAW1cEwFJYR AZGhEKcGgXYBNGc154ax1BZhMQGRoRCnBoF2NtXVtZZVgdc2V4EBkaEQpwaBdpWFltfhJoEl5fQ BAZGhEKcGwXaUdLfEETSAVEXmMQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=104 suspectscore=0 clxscore=173 mlxlogscore=748 spamscore=0 adultscore=0 bulkscore=0 phishscore=0 lowpriorityscore=0 malwarescore=0 impostorscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102010105 domainage_hfrom=8806 X-Spam-Score: 0 X-Spam-OrigSender: stevesei@ku.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Seibold, Steve Allan" --_000_SN6PR01MB5309AB09327318194E277CD2B0B69SN6PR01MB5309prod_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello I have down loaded the binary cuda version of NAMD, NAMD_2.14_x86_64-multic= ore-CUDA onto my Ubuntu (16.04) machine. Using the "nvidia-smi", I found my= GPU card Quadro P5000, NIVIDIA-SMI 415.27, Driver Version: 415.27 and the = CUDA vesion 10.0. When I attempt to run namd2 get the following: "CUDA driver version is insu= fficient for CUDA runtime version"...I'm a novice at this, but, is this a b= arrier that cannot be overcome? Thanks, Steve --_000_SN6PR01MB5309AB09327318194E277CD2B0B69SN6PR01MB5309prod_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello

I have down loaded the binary cuda version of NAMD, = NAMD_2.14_x86_64-multicore-CUDA onto my Ubuntu (16.04) machine. Using the &= #8220;nvidia-smi”, I found my GPU card Quadro P5000, NIVIDIA-SMI 415.= 27, Driver Version: 415.27 and the CUDA vesion 10.0.

 

When I attempt to run namd2 get the following: ̶= 0;CUDA driver version is insufficient for CUDA runtime version”…= ;I’m a novice at this, but, is this a barrier that cannot be overcome= ?  

 

Thanks, Steve

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15.20.3805.026; Mon, 1 Feb 2021 20:12:51 +0000 From: "Vermaas, Josh" To: "namd-l@ks.uiuc.edu" , "Seibold, Steve Allan" Subject: Re: namd-l: NAMD CUDA Thread-Topic: namd-l: NAMD CUDA Thread-Index: AQHW+NadLZwvZnytIUKo2xcEByNaRQ== Date: Mon, 1 Feb 2021 20:12:51 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/16.44.20121301 authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=msu.edu; x-originating-ip: [68.62.59.7] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 07170505-19c4-4b76-40dd-08d8c6edc097 x-ms-traffictypediagnostic: MW2PR12MB2409: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:9508; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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([2601:184:497f:c640:a1c4:55af:b283:d830]) by smtp.gmail.com with ESMTPSA id k12sm15407750qkj.72.2021.02.01.13.11.44 for (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Mon, 01 Feb 2021 13:11:44 -0800 (PST) Subject: Re: namd-l: NAMD CUDA To: namd-l@ks.uiuc.edu References: From: Brian Radak Message-ID: <86c51357-4d1d-8fd1-ea57-750864b386e9@gmail.com> Date: Mon, 1 Feb 2021 16:11:43 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------AB0D6807AA47D2FDD10D8F60" Content-Language: en-US X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIYEQpMehcZGhIRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGRMSEQpDWRcHHh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBhxHhsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XZUdbck9mUnp5RBIdUERPXE9PX11vfXN6aEhMbF5GZVgRClhcFx8EGgQYGBkF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXcn5CZ14RCk1cFxgbHhEKTFoXeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb29ra2xraxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHB oEGxIbEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RC kJFF2sTGmFOX15YGB1lEQpCThdjU2NrexNYfhpfXhEKQkwXaUlIGkt+aUYbeHMRCkJsF2EeGXha bmxnY19iEQpCQBdvbUVoGHpaG35zRxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnlDF2B 7YB9tAXxrb2djEQpZSxcTGRoeEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXZFBaHmJTcAVyH0QQGR oRCnBoF2d/E3AYeF5aWlISEBMfEQpwaBdocFoaa2xGT2FiZBAbGh0RCnBoF2VtUH8FBX54XW1pE BsYGBEKcGgXYHpDfFh4WlNdQ38QGRoRCnBnF2VZE31aWwVfZWkFEBkaEQpwZxdpQ25QAVlzRwEe UxAZGhEKcGcXY39gQ0ZFRWFfTVoQGRoRCnBsF24dZnsSSxp4ElxtEBkaEQptfhcbEQpYTRdLESA = X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=963 priorityscore=308 adultscore=0 suspectscore=0 mlxscore=0 clxscore=182 spamscore=0 malwarescore=0 phishscore=0 impostorscore=0 bulkscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102010116 domainage_hfrom=9304 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------AB0D6807AA47D2FDD10D8F60 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit A warning on compiling with Cuda versions older than 10.1/10.2 - these occasionally do not work with newer gcc compilers (I've had this issue with 9.1 for sure). It might be harder to get an old deprecated compiler than to get a new version of Cuda, so I'd recommend the first route suggested by Josh. HTH, BKR On 2/1/21 3:12 PM, Vermaas, Josh wrote: > > Hi Steve, > > There are two ways around this: > > 1. Update CUDA/your driver to correspond to be greater than or equal > to the CUDA/driver version NAMD was compiled against. CUDA 10.0 is > from a few years ago, and the driver may just be too old. > 2. Compile NAMD yourself with your existing CUDA installation. NAMD > requires CUDA 9.1 according to the release notes, so you are good > there. > > -Josh > > *From: * on behalf of "Seibold, Steve Allan" > > *Reply-To: *"namd-l@ks.uiuc.edu" , "Seibold, Steve > Allan" > *Date: *Monday, February 1, 2021 at 2:58 PM > *To: *"namd-l@ks.uiuc.edu" > *Subject: *namd-l: NAMD CUDA > > Hello > > I have down loaded the binary cuda version of NAMD, > NAMD_2.14_x86_64-multicore-CUDA onto my Ubuntu (16.04) machine. Using > the “nvidia-smiâ€, I found my GPU card Quadro P5000, NIVIDIA-SMI > 415.27, Driver Version: 415.27 and the CUDA vesion 10.0. > > When I attempt to run namd2 get the following: “CUDA driver version is > insufficient for CUDA runtime versionâ€â€¦I’m a novice at this, but, is > this a barrier that cannot be overcome? > > Thanks, Steve > --------------AB0D6807AA47D2FDD10D8F60 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

A warning on compiling with Cuda versions older than 10.1/10.2 - these occasionally do not work with newer gcc compilers (I've had this issue with 9.1 for sure). It might be harder to get an old deprecated compiler than to get a new version of Cuda, so I'd recommend the first route suggested by Josh.

HTH,

BKR

On 2/1/21 3:12 PM, Vermaas, Josh wrote:

Hi Steve,

 

There are two ways around this:

 

  1. Update CUDA/your driver to correspond to be greater than or equal to the CUDA/driver version NAMD was compiled against. CUDA 10.0 is from a few years ago, and the driver may just be too old.
  2. Compile NAMD yourself with your existing CUDA installation. NAMD requires CUDA 9.1 according to the release notes, so you are good there.

-Josh

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of "Seibold, Steve Allan" <stevesei@ku.edu>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, "Seibold, Steve Allan" <stevesei@ku.edu>
Date: Monday, February 1, 2021 at 2:58 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: NAMD CUDA

 

Hello

I have down loaded the binary cuda version of NAMD, NAMD_2.14_x86_64-multicore-CUDA onto my Ubuntu (16.04) machine. Using the “nvidia-smiâ€, I found my GPU card Quadro P5000, NIVIDIA-SMI 415.27, Driver Version: 415.27 and the CUDA vesion 10.0.

 

When I attempt to run namd2 get the following: “CUDA driver version is insufficient for CUDA runtime versionâ€â€¦I’m a novice at this, but, is this a barrier that cannot be overcome?  

 

Thanks, Steve

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Mon, 1 Feb 2021 21:32:51 +0000 Received: from MN2PR02MB6383.namprd02.prod.outlook.com ([fe80::41b4:ccfc:89a0:612c]) by MN2PR02MB6383.namprd02.prod.outlook.com ([fe80::41b4:ccfc:89a0:612c%6]) with mapi id 15.20.3805.028; Mon, 1 Feb 2021 21:32:51 +0000 From: "Prince, Chandler" To: "namd-l@ks.uiuc.edu" , "Seibold, Steve Allan" Subject: namd-l: Re: NAMD CUDA Thread-Topic: NAMD CUDA Thread-Index: Adb403K06P1lsUy2SgOsF27N3ryyWQADdDdg Date: Mon, 1 Feb 2021 21:32:51 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=wustl.edu; x-originating-ip: [2600:1700:a110:4c50:bcf1:fa5a:3442:f864] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: d38ae1ac-bffd-4475-43a7-08d8c6f8edb0 x-ms-traffictypediagnostic: MN2PR02MB6448: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:8882; 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boundary="_000_MN2PR02MB638395B3BCA8D724B7C596AE9AB69MN2PR02MB6383namp_" X-OriginatorOrg: wustl.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: MN2PR02MB6383.namprd02.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: d38ae1ac-bffd-4475-43a7-08d8c6f8edb0 X-MS-Exchange-CrossTenant-originalarrivaltime: 01 Feb 2021 21:32:51.3776 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 4ccca3b5-71cd-4e6d-974b-4d9beb96c6d6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: Av0hCck7JdqEG2ZgcQmKq+/D4aJUMSNTWP6IjwsOAuakydOMOVyjxo97Ar3g/jlUgV26xCI7fceUdcmXIFGUSA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: MN2PR02MB6448 X-CLX-Shades: MLX X-CLX-Response: 1TFkXHxgTEQpMehcbGx8RCllEF2USHx0bSBhye3N7EQpYWBdibWxJW2ROWH8 bUxEKeE4XaEJHbGlpS25QREURCnlMF2JIGURGeFJnRWEeEQpDSBcHHhocEQpDWRcHHhgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxITcR4GHh53BhgaGgYbGhpCHwYaBh8cBhIfcRwQGncGGgYaBhoGG gYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThd8WFxrQ0JjfkhcXUhcGXNa fUwHXhNYY3xjRmJ/fllNGREKWFwXHwQaBBgYGQUbGgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3J+Qk1 CEQpNXBcbGxkRCkxaF2hpTWtrEQpMRhdvb2trbGtrEQpCTxd6Hn9mb0IfU3JrfREKQ1oXGxoeBB 4dBB8TBBsdHhEKQl4XGxEKRF4XGREKQlwXGxEKXk4XGxEKQksXaEJHbGlpS25QREURCkJJF2hCR 2xpaUtuUERFEQpCRRdtQFt9WwUdWWtfHREKQk4XaEJHbGlpS25QREURCkJMF2JtbElbZE5YfxtT EQpCbBdiQmYaaWNhQAFeRBEKQkAXbhJSeVpOEx1AS2IRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQp aWBceEQp5QxdjSUBLYmx6W0RwZxEKWUsXGxgbGxoRCnBnF21HYWtNYxlMU2luEBkaEQpwaBdsQk tdUERTQUJfGhAZGhEKcGgXehhCW2RMRFgaQXAQGRoRCnBoF2sfUGleZ04aTEB7EBkaEQpwaBdnR 1hOHG54e0gBSxAZGhEKcGgXYkR6aHxgTR16XFkQGxoYEQpwfRdrfkdlHnh+QBtSRxAZGhEKcGcX aUNuUAFZc0cBHlMQGRoRCnB/F2wFekMaQEdbExhjEB0eEQpwXxdjaEscc2JSZ3AZehAZGhEKcGw XZV54WhJoaU5pE0MQGRoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=115 suspectscore=0 clxscore=529 mlxlogscore=999 spamscore=0 adultscore=0 bulkscore=0 phishscore=0 lowpriorityscore=0 malwarescore=0 impostorscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102010117 domainage_hfrom=12110 X-Spam-Score: 0 X-Spam-OrigSender: david.prince@wustl.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Prince, Chandler" --_000_MN2PR02MB638395B3BCA8D724B7C596AE9AB69MN2PR02MB6383namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable On the NVIDIA site, they have a handy table for CUDA Compatibility. The tro= uble is knowing what version of CUDA NAMD was compiled with. If someone tel= ls me or you how to determine that, knowing what Driver is needed becomes e= asy. https://urldefense.com/v3/__https://docs.nvidia.com/deploy/cuda-compatibili= ty/index.html__;!!DZ3fjg!pSWhg-vZZtlXZJJSqAxxcvIjJrs0HWSNsDQoi2ji74SVHykHrF= OZMi4mvozSB70tiQ$=20 See Table 1. CUDA Toolkit and Compatible Driver Versions CUDA 10.0 (10.0.130) >=3D 410.48 ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of Seib= old, Steve Allan Sent: Monday, February 1, 2021 1:50 PM To: namd-l@ks.uiuc.edu Subject: namd-l: NAMD CUDA Hello I have down loaded the binary cuda version of NAMD, NAMD_2.14_x86_64-multic= ore-CUDA onto my Ubuntu (16.04) machine. Using the =93nvidia-smi=94, I foun= d my GPU card Quadro P5000, NIVIDIA-SMI 415.27, Driver Version: 415.27 and = the CUDA vesion 10.0. When I attempt to run namd2 get the following: =93CUDA driver version is in= sufficient for CUDA runtime version=94=85I=92m a novice at this, but, is th= is a barrier that cannot be overcome? Thanks, Steve --_000_MN2PR02MB638395B3BCA8D724B7C596AE9AB69MN2PR02MB6383namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable
On the NVIDIA site, they have a handy table for CUDA Compatibility. The tro= uble is knowing what version of CUDA NAMD was compiled with. If someone tel= ls me or you how to determine that, knowing what Driver is needed becomes e= asy.


See Table 1. CUDA Toolkit and Compatible Driver= Versions

CUDA 10.0 (1= 0.0.130) >=3D 410.= 48

From: owner-namd-l@ks.uiuc.= edu <owner-namd-l@ks.uiuc.edu> on behalf of Seibold, Steve Allan <= stevesei@ku.edu>
Sent: Monday, February 1, 2021 1:50 PM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>
Subject: namd-l: NAMD CUDA
 

Hello

I have down loaded the binary cuda version of NAMD= , NAMD_2.14_x86_64-multicore-CUDA onto my Ubuntu (16.04) machine. Using the= =93nvidia-smi=94, I found my GPU card Quadro P5000, NIVIDIA-SMI 415.27, Dr= iver Version: 415.27 and the CUDA vesion 10.0.

 

When I attempt to run namd2 get the following: =93= CUDA driver version is insufficient for CUDA runtime version=94=85I=92m a n= ovice at this, but, is this a barrier that cannot be overcome?  

 

Thanks, Steve

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charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable For 2.14, the last paragraph of [1] indicates the binary was built against = CUDA 10.1. If so, the compatibility matrix below indicates you'll need driv= er 418.39 for the current release of 10.1. The driver search at [2] indicat= es a P5000 can support up through driver 460.39. [1] http://www.ks.uiuc.edu/Research/namd/2.14/features.html [2] https://urldefense.com/v3/__https://www.nvidia.com/Download/Find.aspx?l= ang=3Den-us&QNF=3D1__;!!DZ3fjg!s-0deLC7V9kmcG2aue_yJSo4jAN9KWDFPxRhHyr37DuF= rhKn0ZKgHh2uMl60WXkagw$=20 From: owner-namd-l@ks.uiuc.edu on behalf of Prin= ce, Chandler Date: Monday, February 1, 2021 at 3:40 PM To: namd-l@ks.uiuc.edu , Seibold, Steve Allan Subject: namd-l: Re: NAMD CUDA External Email Warning This email originated from outside the university. Please use caution when = opening attachments, clicking links, or responding to requests. ________________________________ On the NVIDIA site, they have a handy table for CUDA Compatibility. The tro= uble is knowing what version of CUDA NAMD was compiled with. If someone tel= ls me or you how to determine that, knowing what Driver is needed becomes e= asy. https://urldefense.com/v3/__https://docs.nvidia.com/deploy/cuda-compatibili= ty/index.html__;!!DZ3fjg!s-0deLC7V9kmcG2aue_yJSo4jAN9KWDFPxRhHyr37DuFrhKn0Z= KgHh2uMl6SUJUcWA$ See Table 1. CUDA Toolkit and Compatible Driver Versions CUDA 10.0 (10.0.130) >=3D 410.48 ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of Seib= old, Steve Allan Sent: Monday, February 1, 2021 1:50 PM To: namd-l@ks.uiuc.edu Subject: namd-l: NAMD CUDA Hello I have down loaded the binary cuda version of NAMD, NAMD_2.14_x86_64-multic= ore-CUDA onto my Ubuntu (16.04) machine. Using the =93nvidia-smi=94, I foun= d my GPU card Quadro P5000, NIVIDIA-SMI 415.27, Driver Version: 415.27 and = the CUDA vesion 10.0. When I attempt to run namd2 get the following: =93CUDA driver version is in= sufficient for CUDA runtime version=94=85I=92m a novice at this, but, is th= is a barrier that cannot be overcome? Thanks, Steve --_000_BN7PR07MB424176EF1B991E4CF1A817D6A2B69BN7PR07MB4241namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable

For 2.14, the last paragraph of [1] indicates the bi= nary was built against CUDA 10.1. If so, the compatibility matrix below ind= icates you'll need driver 418.39 for the current release of 10.1. The drive= r search at [2] indicates a P5000 can support up through driver 460.39.

 

[1] http://www.ks.uiuc.edu/Research/namd/2.14/features.html

[2] https://www.nvidia.com/Download/Find.aspx?lang=3Den-us&QNF=3D1=

 

From: owner-namd-l@ks.uiu= c.edu <owner-namd-l@ks.uiuc.edu> on behalf of Prince, Chandler <da= vid.prince@wustl.edu>
Date: Monday, February 1, 2021 at 3:40 PM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>, Seibold, Steve Al= lan <stevesei@ku.edu>
Subject: namd-l: Re: NAMD CUDA

External Email Warning=

This email originated from ou= tside the university. Please use caution when opening attachments, clicking= links, or responding to requests.


On the = NVIDIA site, they have a handy table for CUDA Compatibility. The trouble is= knowing what version of CUDA NAMD was compiled with. If someone tells me o= r you how to determine that, knowing what Driver is needed becomes easy.

&n= bsp;

&n= bsp;

See Table 1. CUDA Toolkit and Compatible Driver Versions

&n= bsp;

CUDA 10.0 (10.0.130)

>=3D 410.48


From: owner-namd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.e= du> on behalf of Seibold, Steve Allan <stevesei@ku.edu>
Sent: Monday, February 1, 2021 1:50 PM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>
Subject: namd-l: NAMD CUDA

 

Hello

I have down loaded the binary cuda version of NAMD,= NAMD_2.14_x86_64-multicore-CUDA onto my Ubuntu (16.04) machine. Using the = =93nvidia-smi=94, I found my GPU card Quadro P5000, NIVIDIA-SMI 415.27, Dri= ver Version: 415.27 and the CUDA vesion 10.0.

 

When I attempt to run namd2 get the following: =93C= UDA driver version is insufficient for CUDA runtime version=94=85I=92m a no= vice at this, but, is this a barrier that cannot be overcome?  

 

Thanks, Steve

--_000_BN7PR07MB424176EF1B991E4CF1A817D6A2B69BN7PR07MB4241namp_-- From owner-namd-l@halifax.ks.uiuc.edu Tue Feb 2 18:32:13 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130WDEr028167; Tue, 2 Feb 2021 18:32:13 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130WDQL028166; Tue, 2 Feb 2021 18:32:13 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130WC6I028162; Tue, 2 Feb 2021 18:32:12 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130WCfD028161; Tue, 2 Feb 2021 18:32:12 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130VuR0028149 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 2 Feb 2021 18:31:57 -0600 (CST) From: David Hardy Message-Id: <153684DA-B2E4-4FCD-9A9B-90AEEE00D2E2@ks.uiuc.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_FC33AE2D-EE37-43C5-A9F6-07D66C430339" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Improve performance Date: Tue, 2 Feb 2021 18:31:51 -0600 In-Reply-To: <5A97C027-E9C6-4763-9FA7-CD9E4F843B7C@gmail.com> Cc: "Vermaas, Josh" To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." References: <5A97C027-E9C6-4763-9FA7-CD9E4F843B7C@gmail.com> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_FC33AE2D-EE37-43C5-A9F6-07D66C430339 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Geo, Unfortunately, most of the enhanced sampling methods in NAMD, including = the ones you mention, do not yet work for the GPU-resident integrator. = We are still working on porting features to the GPU. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Jan 28, 2021, at 7:21 PM, Ropon-Palacios G. = wrote: >=20 > Dear Josh,=20 > =20 > Namd3 have implement umbrella sampling, colvar, and smd protocols ?=20 > =20 > Geo.=20 > =20 > From: "Vermaas, Josh" > Date: Thursday, January 28, 2021 at 7:45 PM > To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." = > Subject: Re: namd-l: Improve performance > =20 > For the best NAMD performance on a GPU, use NAMD 3. This blog from = NVIDIA has been my goto for explaining the differences to folks that = haven=E2=80=99t used NAMD 3 yet. = https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd= -v3-and-a100-gpu/ = > =20 > -Josh > =20 > From: on behalf of "Ropon-Palacios G." = > Reply-To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios = G." > Date: Thursday, January 28, 2021 at 7:18 PM > To: "namd-l@ks.uiuc.edu" > Subject: namd-l: Improve performance > =20 > Dear namd users,=20 > =20 > How can i improve namd2.14 performance on GPU? > =20 > I`m using namd2.14 for run membrane protein simulation, but namd only = use nor more the 50% of GPU, as can I make to improve this performance.=20= > =20 > For other hand, if during equilibration of protein-membrane is = necessary keep water out membrane?=20 > =20 > Thanks,=20 > =20 > Best,=20 > =20 > Geo.=20 --Apple-Mail=_FC33AE2D-EE37-43C5-A9F6-07D66C430339 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear = Geo,

Unfortunately, = most of the enhanced sampling methods in NAMD, including the ones you = mention, do not yet work for the GPU-resident integrator. We are still = working on porting features to the GPU.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Jan 28, 2021, at 7:21 PM, Ropon-Palacios G. <biodano.geo@gmail.com> wrote:

Dear Josh, 
 
Namd3 have = implement umbrella sampling, colvar, and smd protocols ? 
 
Geo. 
 
From: "Vermaas, Josh" <vermaasj@msu.edu>
Date: 
Thursday, January 28, = 2021 at 7:45 PM
To: "namd-l@ks.uiuc.edu" = <namd-l@ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo@gmail.com>
Subject: Re: namd-l: Improve = performance
 
For the best NAMD performance on a GPU, use NAMD 3. This blog = from NVIDIA has been my goto for explaining the differences to folks = that haven=E2=80=99t used NAMD 3 yet. https://developer.nvidia.com/blog/delivering-up-to-9x-throughpu= t-with-namd-v3-and-a100-gpu/
 
-Josh
 
From: <owner-namd-l@ks.uiuc.edu> on behalf of "Ropon-Palacios = G." <biodano.geo@gmail.com>
Reply-To: "namd-l@ks.uiuc.edu" = <namd-l@ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo@gmail.com>
Date: Thursday, January 28, = 2021 at 7:18 PM
To: "namd-l@ks.uiuc.edu" = <namd-l@ks.uiuc.edu>
Subject: namd-l: Improve = performance
 
Dear namd users, 
 
How can i improve namd2.14 = performance on GPU?
 
I`m using = namd2.14 for run membrane protein simulation, but namd only use nor more = the 50% of GPU, as can I make to improve this performance. 
 
For other hand, if during = equilibration of protein-membrane is necessary keep water out = membrane? 
 
Thanks, 
 
Best, 
 
Geo. 

= --Apple-Mail=_FC33AE2D-EE37-43C5-A9F6-07D66C430339-- From owner-namd-l@halifax.ks.uiuc.edu Tue Feb 2 18:35:26 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130ZPSI028902; Tue, 2 Feb 2021 18:35:25 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130ZPNW028901; Tue, 2 Feb 2021 18:35:25 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130ZOCq028897; Tue, 2 Feb 2021 18:35:24 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130ZOdH028896; Tue, 2 Feb 2021 18:35:24 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130ZGsr028884 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 2 Feb 2021 18:35:17 -0600 (CST) Content-Type: multipart/alternative; boundary="Apple-Mail=_3CAAEE08-3561-466F-BAA4-6FF41D039F6F" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Re:Re: namd-l: Namd can not be launched for umbrella sample From: David Hardy X-Priority: 3 In-Reply-To: Date: Tue, 2 Feb 2021 18:35:14 -0600 Cc: Victor Kwan Message-Id: References: To: namd-l@ks.uiuc.edu, =?utf-8?B?6L6b5b+X5a6P?= X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_3CAAEE08-3561-466F-BAA4-6FF41D039F6F Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Zhihong, =46rom your output, it looks like you are running the multicore version. = The multicore version supports only single-copy simulation. For running = replicas, I would recommend you use the netlrts build of NAMD. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Jan 28, 2021, at 8:42 PM, =E8=BE=9B=E5=BF=97=E5=AE=8F = wrote: >=20 > Thank you for your suggestion, I try the following command, however, = it fail again >=20 > charmrun namd2 ++local +p16 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log > or=20 > charmrun namd2 ++local +p32 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log >=20 > Running command: namd2 +p16 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log >=20 > Charm++: standalone mode (not using charmrun) > Charm++> Running in Multicore mode: 16 threads (PEs) > ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------ > Reason: +partitions other than 1 is not allowed for multicore build >=20 > [0] Stack Traceback: > [0:0] namd2 0x17ce9e7=20 > [0:1] namd2 0x53d375=20 > [0:2] namd2 0x52e7c2=20 > [0:3] libc.so.6 0x2aff0e324555 __libc_start_main > [0:4] namd2 0x4145f5=20 > Segmentation fault (core dumped) >=20 > Zhihong XIn >=20 > =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9AVictor Kwan > =E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A2021-01-29 00:35:45 > =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9ANAMD Listserve = ,"=E8=BE=9B=E5=BF=97=E5=AE=8F" > =E4=B8=BB=E9=A2=98=EF=BC=9ARe: namd-l: Namd can not be launched for = umbrella sample > Hi, >=20 > If you read the release note, it clearly states >=20 > -- Multi-Copy Algorithm Support -- >=20 > Multi-copy algorithms (such as replica exchange) require at least one > process per replica, plus a Charm++ build based on "LRTS" (low-level > run-time system). Multi-copy-capable builds include netlrts, verbs, = ucx, > and mpi.=20 >=20 > V. >=20 > On Thu, Jan 28, 2021, 6:42 AM =E8=BE=9B=E5=BF=97=E5=AE=8F = > wrote: > Dear NAMD, >=20 > My computer setup 2 CPU, 28 cores per CPU, 56 cores in all, it works = very well for multithreading calculation by Amber, =20 >=20 > mpirun -np 50 sander.MPI -O -i=E3=80=82=E3=80=82=E3=80=82=E3=80=82=E3=80= =82=E3=80=82 >=20 >=20 >=20 > However, an error occurred when I carried out a umbrella sample = example by Namd2 according to the tutorial, Namd is a compiled 2020 = version and can works in a single thread, does it only works when = compile a namd from a source code? >=20 > I will be much appreciate if there is any suggesstion. >=20 > mpirun -np 16 +auto-provision namd2 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log >=20 > The error information is as follows: >=20 > Charm++> No provisioning arguments specified. Running with a single = PE. > Use +auto-provision to fully subscribe resources or +p1 to = silence this message. >=20 > Charm++: standalone mode (not using charmrun) >=20 > Charm++> Running in Multicore mode: 1 threads (PEs) >=20 > ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------ >=20 > Reason: +partitions other than 1 is not allowed for multicore build >=20 >=20 >=20 > [0] Stack Traceback: >=20 > [0:0] namd2 0x17ce9e7=20 >=20 > [0:1] namd2 0x53d375=20 >=20 > [0:2] namd2 0x52e7c2=20 >=20 > [0:3] libc.so.6 0x2b4a719cf555 __libc_start_main >=20 > [0:4] namd2 0x4145f5=20 >=20 > = --------------------------------------------------------------------------= >=20 > Primary job terminated normally, but 1 process returned >=20 > a non-zero exit code. Per user-direction, the job has been aborted. >=20 > = --------------------------------------------------------------------------= >=20 > ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------ >=20 > Reason: +partitions other than 1 is not allowed for multicore build >=20 >=20 >=20 > Charm++> No provisioning arguments specified. Running with a single = PE. >=20 > Use +auto-provision to fully subscribe resources or +p1 to = silence this message. >=20 > Charm++: standalone mode (not using charmrun) >=20 > Charm++> Running in Multicore mode: 1 threads (PEs) >=20 > [0] Stack Traceback: >=20 > [0:0] namd2 0x17ce9e7=20 >=20 > [0:1] namd2 0x53d375=20 >=20 > [0:2] namd2 0x52e7c2=20 >=20 > [0:3] libc.so.6 0x2b2104bab555 __libc_start_main >=20 > [0:4] namd2 0x4145f5=20 >=20 > = --------------------------------------------------------------------------= >=20 > mpirun noticed that process rank 0 with PID 0 on node bogon exited on = signal 11 (Segmentation fault). >=20 >=20 > Zhihong Xin, > Nanjing Agricultural University >=20 >=20 --Apple-Mail=_3CAAEE08-3561-466F-BAA4-6FF41D039F6F Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear = Zhihong,

=46rom your = output, it looks like you are running the multicore version. The = multicore version supports only single-copy simulation. For running = replicas, I would recommend you use the netlrts build of NAMD.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Jan 28, 2021, at 8:42 PM, =E8=BE=9B=E5=BF=97=E5=AE=8F = <xzhfood@njau.edu.cn> wrote:

Thank you for your suggestion, I try the following command, = however, it fail again

charmrun namd2 ++local +p16 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log
or 
charmrun namd2 ++local +p32 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log

Running command: namd2 +p16 +replicas 16 job0.conf +stdout = output/%d/job0.%d.log

Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 16 threads = (PEs)
------- Partition 0 Processor 0 Exiting: = Called CmiAbort ------
Reason: +partitions other = than 1 is not allowed for multicore build

[0] Stack Traceback:
  [0:0] namd2 0x17ce9e7 
  = [0:1] namd2 0x53d375 
  [0:2] namd2 = 0x52e7c2 
  [0:3] libc.so.6 = 0x2aff0e324555 __libc_start_main
  [0:4] namd2 = 0x4145f5 
Segmentation fault (core = dumped)

Zhihong XIn

=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9AVictor Kwan <vkwan8@uwo.ca>
=E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A2021-01-29 = 00:35:45
=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9ANAMD = Listserve <namd-l@ks.uiuc.edu>,"=E8=BE=9B=E5=BF=97=E5=AE=8F" = <xzhfood@njau.edu.cn>
=E4=B8=BB=E9=A2=98=EF= =BC=9ARe: namd-l: Namd can not be launched for umbrella sample
Hi,

If you read the release = note, it clearly states

-- =
Multi-Copy Algorithm Support --

Multi-copy algorithms (such as replica exchange) require at least one
process per replica, plus a Charm++ build based on "LRTS" (low-level
run-time system). Multi-copy-capable builds include netlrts, verbs, ucx,
and mpi. 

V.

On Thu, Jan = 28, 2021, 6:42 AM =E8=BE=9B=E5=BF=97=E5=AE=8F <xzhfood@njau.edu.cn>= wrote:

Dear NAMD,

My computer setup 2 CPU, 28 cores per CPU, 56 cores in all, = it works very well for multithreading calculation by Amber,  =  

mpirun -np 50 sander.MPI -O = -i=E3=80=82=E3=80=82=E3=80=82=E3=80=82=E3=80=82=E3=80=82


However, an error occurred = when I carried out a umbrella sample example by Namd2 according to the = tutorial, Namd  is a compiled 2020 version and can works in a = single thread, does it only works when compile a namd from a source = code?

I will be much appreciate if there is any = suggesstion.

mpirun -np 16 +auto-provision namd2 = +replicas 16 job0.conf +stdout output/%d/job0.%d.log

The error information is as follows:

Charm++> No provisioning arguments = specified. Running with a single PE.

    =      Use +auto-provision to fully subscribe resources or = +p1 to silence this message.

Charm++: standalone mode = (not using charmrun)

Charm++> Running in Multicore = mode: 1 threads (PEs)

------- Partition 0 Processor 0 = Exiting: Called CmiAbort ------

Reason: +partitions = other than 1 is not allowed for multicore build


[0] Stack Traceback:

  = [0:0] namd2 0x17ce9e7 

  [0:1] namd2 = 0x53d375 

  [0:2] namd2 0x52e7c2 

  [0:3] libc.so.6 0x2b4a719cf555 __libc_start_main

  [0:4] namd2 0x4145f5 

---------------------------------------------------------------= -----------

Primary job  terminated normally, but = 1 process returned

a non-zero exit code. Per = user-direction, the job has been aborted.

---------------------------------------------------------------= -----------

------- Partition 0 Processor 0 Exiting: = Called CmiAbort ------

Reason: +partitions other than 1 = is not allowed for multicore build


Charm++> No provisioning arguments specified. Running with = a single PE.

         Use = +auto-provision to fully subscribe resources or +p1 to silence this = message.

Charm++: standalone mode (not using = charmrun)

Charm++> Running in Multicore mode: 1 = threads (PEs)

[0] Stack Traceback:

  [0:0] namd2 0x17ce9e7 

  = [0:1] namd2 0x53d375 

  [0:2] namd2 = 0x52e7c2 

  [0:3] libc.so.6 0x2b2104bab555 = __libc_start_main

  [0:4] namd2 = 0x4145f5 

---------------------------------------------------------------= -----------

mpirun noticed that process rank 0 with = PID 0 on node bogon exited on signal 11 (Segmentation fault).


Zhihong Xin,
Nanjing Agricultural = University



= --Apple-Mail=_3CAAEE08-3561-466F-BAA4-6FF41D039F6F-- From owner-namd-l@halifax.ks.uiuc.edu Tue Feb 2 18:44:08 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130i8JD002474; Tue, 2 Feb 2021 18:44:08 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130i7a3002473; Tue, 2 Feb 2021 18:44:07 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130i7B4002469; Tue, 2 Feb 2021 18:44:07 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130i7C4002468; Tue, 2 Feb 2021 18:44:07 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130i2Tq002458 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 2 Feb 2021 18:44:03 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_B484F21A-F6ED-4692-9B51-65EE40193614" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Problem with FEP simulations Date: Tue, 2 Feb 2021 18:43:57 -0600 References: To: NAMD list , Luba Simhaev In-Reply-To: Message-Id: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_B484F21A-F6ED-4692-9B51-65EE40193614 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Luba, As you point out, this does indicate some kind of instability. It is = possible that you introduced the problem with your FEP parameter = settings. It would help if you provide more details on how you are running NAMD = and how the error manifests. Even better if you could provide the files = that are producing this error. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Feb 1, 2021, at 2:48 AM, Luba Simhaev = wrote: >=20 > Dear NAMD users, > I'm trying to perform alchemical FEP simulation to a system consisting = of a membrane protein, which is an ion exchanger. Prior to FEP, the = system was equilibrated for 250 ns. Although while I'm turning to FEP = calculations, they are halted due to "Constraint failure in RATTLE = algorithm" error. > I know that this error indicates an unstable system,but as I mentioned = the system was equilibrated, and by visual inspection seems to be = stable.=20 > Could you please suggest how to solve this problem? =20 >=20 > I would appreciate your help. > Thanks, > Luba >=20 > --=20 > Dr. Ischakov Simhaev Luba, Ph.D. >=20 > Computational assisted drug-design unit > Blavatnik Center for Drug Discovery > Cohen-Porter Family United Kingdom Building > (Britannia), 1st floor > Tel Aviv University, Ramat Aviv > Tel Aviv, Israel, 6997801 > Tel:+972-3-640-9842, 9654 > Web-site: http://www.bcdd.tau.ac.il/ = --Apple-Mail=_B484F21A-F6ED-4692-9B51-65EE40193614 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = Luba,

As you point = out, this does indicate some kind of instability. It is possible that = you introduced the problem with your FEP parameter settings.

It would help if you = provide more details on how you are running NAMD and how the error = manifests. Even better if you could provide the files that are producing = this error.

Best= regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Feb 1, 2021, at 2:48 AM, Luba Simhaev <luba.simhaev0703@gmail.com> wrote:

Dear NAMD users,
I'm trying to perform = alchemical FEP simulation to a system consisting of a membrane protein, = which is an ion exchanger. Prior to FEP, the system was equilibrated for = 250 ns. Although while I'm turning to FEP calculations, they are halted = due to "Constraint failure in RATTLE algorithm" error.
I know that this error indicates an unstable system,but as I = mentioned the system was equilibrated, and by visual inspection seems to = be stable. 
Could you please suggest how to = solve this problem?  

I would appreciate your help.
Thanks,
Luba

--
Dr. Ischakov Simhaev Luba, Ph.D.

Computational assisted drug-design = unit
Blavatnik = Center for Drug Discovery
Cohen-Porter Family United = Kingdom Building
(Britannia), 1st floor
Tel Aviv = University, Ramat Aviv
Tel Aviv, = Israel, 6997801
Tel:+972-3-640-9842, = 9654
Web-site: http://www.bcdd.tau.ac.il/
<= /div>

= --Apple-Mail=_B484F21A-F6ED-4692-9B51-65EE40193614-- From owner-namd-l@halifax.ks.uiuc.edu Tue Feb 2 18:51:50 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130po1q004663; Tue, 2 Feb 2021 18:51:50 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130poqo004662; Tue, 2 Feb 2021 18:51:50 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130pnGA004658; Tue, 2 Feb 2021 18:51:49 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1130pnno004657; Tue, 2 Feb 2021 18:51:49 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1130pkWT004647 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 2 Feb 2021 18:51:47 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_C149571C-625B-437F-9470-51161869329A" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: NAMD CUDA Date: Tue, 2 Feb 2021 18:51:41 -0600 References: <86c51357-4d1d-8fd1-ea57-750864b386e9@gmail.com> To: NAMD list , Brian Radak In-Reply-To: <86c51357-4d1d-8fd1-ea57-750864b386e9@gmail.com> Message-Id: <942D990E-21C6-47C0-98CE-4FFFABC1E891@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_C149571C-625B-437F-9470-51161869329A Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Steve, The 2.14 Linux builds of NAMD were compiled against CUDA 10.1, which = requires driver version >=3D 418.39. Best regards, Dave > On Feb 1, 2021, at 3:11 PM, Brian Radak wrote: >=20 > A warning on compiling with Cuda versions older than 10.1/10.2 - these = occasionally do not work with newer gcc compilers (I've had this issue = with 9.1 for sure). It might be harder to get an old deprecated compiler = than to get a new version of Cuda, so I'd recommend the first route = suggested by Josh. >=20 > HTH, >=20 > BKR >=20 > On 2/1/21 3:12 PM, Vermaas, Josh wrote: >> Hi Steve, >> =20 >> There are two ways around this: >> =20 >> Update CUDA/your driver to correspond to be greater than or equal to = the CUDA/driver version NAMD was compiled against. CUDA 10.0 is from a = few years ago, and the driver may just be too old. >> Compile NAMD yourself with your existing CUDA installation. NAMD = requires CUDA 9.1 according to the release notes, so you are good there. >> -Josh >> =20 >> From: on = behalf of "Seibold, Steve Allan" = >> Reply-To: "namd-l@ks.uiuc.edu" = , "Seibold, Steve = Allan" >> Date: Monday, February 1, 2021 at 2:58 PM >> To: "namd-l@ks.uiuc.edu" = >> Subject: namd-l: NAMD CUDA=20 >> =20 >> Hello >> I have down loaded the binary cuda version of NAMD, = NAMD_2.14_x86_64-multicore-CUDA onto my Ubuntu (16.04) machine. Using = the =E2=80=9Cnvidia-smi=E2=80=9D, I found my GPU card Quadro P5000, = NIVIDIA-SMI 415.27, Driver Version: 415.27 and the CUDA vesion 10.0.=20 >> =20 >> When I attempt to run namd2 get the following: =E2=80=9CCUDA driver = version is insufficient for CUDA runtime version=E2=80=9D=E2=80=A6I=E2=80=99= m a novice at this, but, is this a barrier that cannot be overcome?=20 >> =20 >> Thanks, Steve --Apple-Mail=_C149571C-625B-437F-9470-51161869329A Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Steve,

The 2.14 = Linux builds of NAMD were compiled against CUDA 10.1, which requires = driver version >=3D 418.39.

Best regards,
Dave

On Feb 1, 2021, at 3:11 PM, = Brian Radak <brian.radak@gmail.com> wrote:

A = warning on compiling with Cuda versions older than 10.1/10.2 - these = occasionally do not work with newer gcc compilers (I've had this issue = with 9.1 for sure). It might be harder to get an old deprecated compiler = than to get a new version of Cuda, so I'd recommend the first route = suggested by Josh.

HTH,

BKR

On 2/1/21 3:12 PM, Vermaas, Josh wrote:
Hi Steve,
 
There are two ways around = this:
 
  1. Update CUDA/your driver to correspond = to be greater than or equal to the CUDA/driver version NAMD was compiled = against. CUDA 10.0 is from a few years ago, and the driver may just be = too old.
  2. Compile NAMD yourself with your existing CUDA installation. = NAMD requires CUDA 9.1 according to the release notes, so you are good = there.
-Josh
 
From: <owner-namd-l@ks.uiuc.edu><= /a> on behalf of = "Seibold, Steve Allan"<stevesei@ku.edu>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, = "Seibold, Steve Allan"<stevesei@ku.edu>
Date: Monday, February 1, = 2021 at 2:58 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: NAMD CUDA 
 
Hello
I have down loaded the = binary cuda version of NAMD, NAMD_2.14_x86_64-multicore-CUDA onto my = Ubuntu (16.04) machine. Using the =E2=80=9Cnvidia-smi=E2=80=9D, I found = my GPU card Quadro P5000, NIVIDIA-SMI 415.27, Driver Version: 415.27 and = the CUDA vesion 10.0. 
 
When I attempt to run = namd2 get the following: =E2=80=9CCUDA driver version is insufficient = for CUDA runtime version=E2=80=9D=E2=80=A6I=E2=80=99m a novice at this, = but, is this a barrier that cannot be overcome?  
 
Thanks, = Steve

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boundary="000000000000884b4705ba6ab18c" X-CLX-Response: 1TFkXGx0eEQpMehcZGxgRCllEF2BbUFpIT2NFQBlvEQpYWBdpHx0aWk1PTVl dYBEKeE4XY1Nja3sTWH4aX14RCnlMF2dHWgFaQB9AE0kbEQpDSBcHHhsYEQpDWRcHEhwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHx5xGR4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XXR58TWVgY0thfF9YQU99eEt7ehleYhlrZm1HS0lnb2kRClhcFx8EGgQYGBkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcn9rQ1IRCk1cFxkeExEKTFoXbGlNTWsRCkxGF29ra2t raxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGxIYEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2dZZkl4QnNyck1uEQpCThdjU2Nre xNYfhpfXhEKQkwXaR8dGlpNT01ZXWARCkJsF2ddXn5gYUJAaWkTEQpCQBdvHBhiQx9naXwYfxEK QlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2IeRmJeWmxufVtvEQpZSxcTGRocEQpwaBdiZEwFZ0B HS2kZRBAZGhEKcGgXel8ZUm5+RxNda14QGRoRCnBoF2RCQEJNelhBH2JDEBkaEQpwaBdnaUFrfF N6GhJjZxAZGhEKcGgXbmRiGGhiZXx5fR4QGRoRCnBsF29FaGRmQV1nRmVDEBkaEQptfhcaEQpYT RdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 mlxlogscore=865 bulkscore=0 mlxscore=0 impostorscore=0 suspectscore=0 malwarescore=0 clxscore=174 spamscore=0 phishscore=0 priorityscore=312 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102030054 domainage_hfrom=9306 X-Spam-Score: 0 X-Spam-OrigSender: sekekeretsu@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Seke Keretsu --000000000000884b4705ba6ab18c Content-Type: text/plain; charset="UTF-8" Dear Experts, I am posting this again as follow up to my previous post. Since then, I followed and tried all the advice but the error was not resolved. I am using NAMD2.14 for a protein ligand complex in which there is a lone pair on the chlorobenzene of the ligand. The psf files were built in Charmm-Gui and solvated and ionized with VMD 1.9.4. As suggested, I have added 'lonepairs on' to the configuration file. In the psf file (ionized.psf), I added the lines for the one lone pair as advised (by Pang, Yui Tik): 1 3 !NUMLP NUMLPH 2 1 F 1.64000 0.00000 0.00000 4737 4710 4697 Here in the second line, I have tried 1.64 and -1.64 for distance between lonepair and host. For polarized water it was negative, why? In the third line, 4737 4710 4697 are the atomic ID of lonepair, host and atom connected to host. I still get the error as shown below regardless of the temperature I use. *ERROR MESSAGE:* ENERGY: 50020 287.8329 875.2009 2562.5041 35.3830 -139424.9435 155009.5692 0.0000 0.0000 0.0000 19345.5467 0.0000 19345.5467 19345.5467 0.0000 123095.5120 107654.6219 396330.9410 123095.5120 107654.6219 TCL: Running for 500000 steps ERROR: Margin is too small for 1 atom during timestep 50026. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 (limit is 12000, atom 395 of 507 on patch 37 pe 0) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 37 pe 0). FATAL ERROR: Exiting prematurely; see error messages above. As suggested (by Laurent Chaloin), I have also checked the content of "par_all36_cgenff.prm." Since I am using NAMD for simulation I assume the lines should not be comment-out. LPH CLGR1 0.00 0.0000 ! aromatic halogen to lone pair LPH BRGR1 0.00 0.0000 ! aromatic halogen to lone pair LPH IGR1 0.00 0.0000 ! aromatic halogen to lone pair However I could not find the following lines in my .prm file. I tried running a few times by appending the lines to my par_all36_cgenff.prm file. Did not change the outcome. Please advise if I missed something here. Also, Is there an alternative to this, such as building a system without a lone pair without badly compromising my simulation protocol ? Thank you. Seke CONFIGURATION FILE: ############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # Ubiquitin in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ionized.psf coordinates ionized.pdb set temperature 100 set outputname equilibration02 firsttimestep 50000 bincoordinates equilibration.restart.coor #binvelocities equilibration.restart.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters jz4/jz4.prm parameters toppar/par_all36_carb.prm parameters toppar/par_all36_cgenff.prm parameters toppar/par_all36_lipid.prm parameters toppar/par_all36m_prot.prm parameters toppar/par_all36_na.prm parameters toppar/par_interface.prm parameters toppar_water_ions.str temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14.0 # Integrator Parameters timestep 1.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 1/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions cellBasisVector1 69.61299896240234 0 0 cellBasisVector2 0 76.30400085449219 0 cellBasisVector3 0 0 74.61400032043457 cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #manual grid definition #PMEGridSizeX 45 #PMEGridSizeY 45 #PMEGridSizeZ 48 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100.0 langevinPistonDecay 50.0 langevinPistonTemp $temperature constraints on consexp 2 consref prot_posres.ref conskfile prot_posres.ref conskcol B constraintScaling 10.0 # Output outputName $outputname restartfreq 500 ;# 500steps = every 1ps dcdfreq 250 xstFreq 250 outputEnergies 100 outputPressure 100 lonepairs on ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 20 #system was minimized already #reinitvels $temperature run 500000 ;# 50ps --000000000000884b4705ba6ab18c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Experts,

I am posting t= his again as follow up to my previous post. Since then, I followed and trie= d all the advice but the error was not resolved.

I am using NAMD2.14 for a protein ligand complex in which there is a lon= e pair on the chlorobenzene of the ligand. The psf files were built in Char= mm-Gui and solvated and ionized with VMD 1.9.4.

As suggested, I have added=C2=A0 'lonepairs on' to the configurat= ion file.

In the psf file (ionized.psf), I added t= he lines for the one lone pair as advised (by= =C2=A0Pang, Yui Tik):

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A01 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3 !NUMLP NUMLPH
=C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A02 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 F 1.64000= =C2=A0 =C2=A0 =C2=A00.00000 =C2=A0 =C2=A0 =C2=A00.00000 =C2=A0
=C2=A0 = =C2=A0 =C2=A0 4737 =C2=A0 =C2=A0 =C2=A04710 =C2=A0 =C2=A0 =C2=A0 4697
=

Here in the second line, I have tried 1.64 and -1.64 fo= r distance between lonepair and host. For polarized water it was negative, = why?
In the third line, 4737 =C2=A0 =C2=A0 =C2=A04710 =C2=A0 =C2= =A0 =C2=A0 4697 are the atomic ID of lonepair, host and atom connected to h= ost.

I still get the error as shown below regardle= ss of the temperature I use.

ERROR MESSAGE:=

ENERGY: =C2=A0 50020 =C2=A0 =C2=A0 =C2=A0 287.8329= =C2=A0 =C2=A0 =C2=A0 875.2009 =C2=A0 =C2=A0 =C2=A02562.5041 =C2=A0 =C2=A0 = =C2=A0 =C2=A035.3830 =C2=A0 =C2=A0 =C2=A0 =C2=A0-139424.9435 =C2=A0 =C2=A01= 55009.5692 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0= .0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 19345.5467 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 19345.5467 =C2= =A0 =C2=A0 19345.5467 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 123095.5120 =C2=A0 =C2=A0107654.6219 =C2=A0 =C2=A0396330.9410 = =C2=A0 =C2=A0123095.5120 =C2=A0 =C2=A0107654.6219

TCL: Running for 5= 00000 steps
ERROR: Margin is too small for 1 atom during timestep 50026.=
ERROR: Incorrect nonbonded forces and energies may be calculated!
ER= ROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 (limit is 12000, atom= 395 of 507 on patch 37 pe 0)
ERROR: Atoms moving too fast; simulation h= as become unstable (1 atoms on patch 37 pe 0).
FATAL ERROR: Exiting= prematurely; see error messages above.


=
As suggested (by=C2=A0Laurent Chaloin), I have also checked the content of "par_all36_cgenff.prm."= ; Since I am using NAMD for simulation I assume the lines should not be com= ment-out.
LPH =C2=A0 =C2=A0CLGR1 =C2=A0 =C2=A0 0.00 =C2=A0 = =C2=A0 0.0000 ! aromatic halogen to lone pair
LPH =C2=A0 =C2=A0BRGR1 =C2= =A0 =C2=A0 0.00 =C2=A0 =C2=A0 0.0000 ! aromatic halogen to lone pair
LPH= =C2=A0 =C2=A0IGR1 =C2=A0 =C2=A0 =C2=A00.00 =C2=A0 =C2=A0 0.0000 ! aromatic= halogen to lone pair
However I could not find the following line= s in my .prm file. I tried running a few times by appending the lines to my= par_all36_cgenff.prm file. Did not change the outcome.

Please advise if I missed something here. Also, Is there an alternati= ve to this, such as building a system without a lone pair without badly com= promising my simulation protocol ?

Thank you.
<= /div>
Seke


CONFIGURATION FILE:<= br>

##############################################= ###############
## JOB DESCRIPTION =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ##
#####################################= ########################

# Minimization and Equilibration of
# Ub= iquitin in a Water Box


#########################################= ####################
## ADJUSTABLE PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 ##
################################################= #############

structure =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0ionized.ps= f
coordinates =C2=A0 =C2=A0 =C2=A0 =C2=A0ionized.pdb

set temperat= ure =C2=A0 =C2=A0100
set outputname =C2=A0 =C2=A0 equilibration02
firsttimestep =C2=A0 =C2=A0 =C2=A050000
bincoordinates =C2=A0 =C2=A0 = =C2=A0 =C2=A0equilibration.restart.coor
#binvelocities =C2=A0 =C2=A0 =C2= =A0 =C2=A0 equilibration.restart.vel

###############################= ##############################
## SIMULATION PARAMETERS =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ##
#####################################= ########################

# Input
paraTypeCharmm =C2=A0 =C2=A0on
parameters jz4/jz4.= prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_= cgenff.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/pa= r_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppa= r/par_interface.prm
parameters toppar_water_ions.str
temperatu= re =C2=A0 =C2=A0 =C2=A0 =C2=A0 $temperature


# Force-Field Parame= ters
exclude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scaled1-4
1-4s= caling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
cutoff =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A012.0
switching =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 on
switchdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A010.0
pairlistd= ist =C2=A0 =C2=A0 =C2=A0 =C2=A014.0


# Integrator Parameters
t= imestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0 =C2=A0;# 2fs/step
r= igidBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0all =C2=A0;# needed for 2fs ste= ps
nonbondedFreq =C2=A0 =C2=A0 =C2=A0 1
fullElectFrequency =C2=A02 = =C2=A0
stepspercycle =C2=A0 =C2=A0 =C2=A0 10


# Constant Tempe= rature Control
langevin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on =C2= =A0 =C2=A0;# do langevin dynamics
langevinDamping =C2=A0 =C2=A0 1 =C2=A0= =C2=A0 ;# damping coefficient (gamma) of 1/ps
langevinTemp =C2=A0 =C2= =A0 =C2=A0 =C2=A0$temperature
langevinHydrogen =C2=A0 =C2=A0off =C2=A0 = =C2=A0;# don't couple langevin bath to hydrogens


# Periodic = Boundary Conditions
cellBasisVector1 69.61299896240234 0 0
cellBasisVector2 0 76.30400= 085449219 0
cellBasisVector3 0 0 74.61400032043457
cellOrigin 12.2572= 86071777344 7.4436726570129395 -19.06593894958496




wrapAll =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on


# PME (for full-system periodic= electrostatics)
PME =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 yes
PMEGridSpacing =C2=A0 =C2=A0 =C2=A01.0

#manual = grid definition
#PMEGridSizeX =C2=A0 =C2=A0 =C2=A0 =C2=A045
#PMEGridS= izeY =C2=A0 =C2=A0 =C2=A0 =C2=A045
#PMEGridSizeZ =C2=A0 =C2=A0 =C2=A0 = =C2=A048


# Constant Pressure Control (variable volume)
useGro= upPressure =C2=A0 =C2=A0 =C2=A0yes ;# needed for rigidBonds
useFlexibleC= ell =C2=A0 =C2=A0 =C2=A0 no
useConstantArea =C2=A0 =C2=A0 =C2=A0 no
<= br>langevinPiston =C2=A0 =C2=A0 =C2=A0 =C2=A0on
langevinPistonTarget =C2= =A01.01325 ;# =C2=A0in bar -> 1 atm
langevinPistonPeriod =C2=A0100.0<= br>langevinPistonDecay =C2=A0 50.0
langevinPistonTemp =C2=A0 =C2=A0$temp= erature
=C2=A0
=
constraints =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on
consexp =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 2
consref =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 prot_posres.ref
conskfi= le =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 prot_posres.ref
cons= kcol =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0B
con= straintScaling =C2=A0 =C2=A0 =C2=A0 10.0

# Output
outputName =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$outputname

restartfreq =C2=A0 =C2=A0= =C2=A0 =C2=A0 500 =C2=A0 =C2=A0 ;# 500steps =3D every 1ps
dcdfreq =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 250
xstFreq =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 250
outputEnergies =C2=A0 =C2=A0 =C2=A0100
outpu= tPressure =C2=A0 =C2=A0 =C2=A0100

lonepairs on

##############= ###############################################
## EXTRA PARAMETERS =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0##
#######= ######################################################


#########= ####################################################
## EXECUTION SCRIPT= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0##
###= ##########################################################

# Minimiz= ation
minimize =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020 #system was m= inimized already
#reinitvels =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperat= ure

run 500000 ;# 50ps
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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Seke, Would you share your psf and pdb files, as well as the NAMD output log file= so that we can better assess what the problem might be? Best, Andrew From: Seke Keretsu Sent: Wednesday, February 3, 2021 4:05 AM To: namd-l@ks.uiuc.edu Subject: namd-l: Dealing with lone pairs Dear Experts, I am posting this again as follow up to my previous post. Since then, I fol= lowed and tried all the advice but the error was not resolved. I am using NAMD2.14 for a protein ligand complex in which there is a lone p= air on the chlorobenzene of the ligand. The psf files were built in Charmm-= Gui and solvated and ionized with VMD 1.9.4. As suggested, I have added 'lonepairs on' to the configuration file. In the psf file (ionized.psf), I added the lines for the one lone pair as a= dvised (by Pang, Yui Tik): 1 3 !NUMLP NUMLPH 2 1 F 1.64000 0.00000 0.00000 4737 4710 4697 Here in the second line, I have tried 1.64 and -1.64 for distance between l= onepair and host. For polarized water it was negative, why? In the third line, 4737 4710 4697 are the atomic ID of lonepair,= host and atom connected to host. I still get the error as shown below regardless of the temperature I use. ERROR MESSAGE: ENERGY: 50020 287.8329 875.2009 2562.5041 35.3830= -139424.9435 155009.5692 0.0000 0.0000 0= .0000 19345.5467 0.0000 19345.5467 19345.5467 = 0.0000 123095.5120 107654.6219 396330.9410 123095.5120= 107654.6219 TCL: Running for 500000 steps ERROR: Margin is too small for 1 atom during timestep 50026. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 (limit is 12000, at= om 395 of 507 on patch 37 pe 0) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 37 pe 0). FATAL ERROR: Exiting prematurely; see error messages above. As suggested (by Laurent Chaloin), I have also checked the content of "par_= all36_cgenff.prm." Since I am using NAMD for simulation I assume the lines = should not be comment-out. LPH CLGR1 0.00 0.0000 ! aromatic halogen to lone pair LPH BRGR1 0.00 0.0000 ! aromatic halogen to lone pair LPH IGR1 0.00 0.0000 ! aromatic halogen to lone pair However I could not find the following lines in my .prm file. I tried runni= ng a few times by appending the lines to my par_all36_cgenff.prm file. Did = not change the outcome. Please advise if I missed something here. Also, Is there an alternative to = this, such as building a system without a lone pair without badly compromis= ing my simulation protocol ? Thank you. Seke CONFIGURATION FILE: ############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # Ubiquitin in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ionized.psf coordinates ionized.pdb set temperature 100 set outputname equilibration02 firsttimestep 50000 bincoordinates equilibration.restart.coor #binvelocities equilibration.restart.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters jz4/jz4.prm parameters toppar/par_all36_carb.prm parameters toppar/par_all36_cgenff.prm parameters toppar/par_all36_lipid.prm parameters toppar/par_all36m_prot.prm parameters toppar/par_all36_na.prm parameters toppar/par_interface.prm parameters toppar_water_ions.str temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14.0 # Integrator Parameters timestep 1.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 1/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions cellBasisVector1 69.61299896240234 0 0 cellBasisVector2 0 76.30400085449219 0 cellBasisVector3 0 0 74.61400032043457 cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #manual grid definition #PMEGridSizeX 45 #PMEGridSizeY 45 #PMEGridSizeZ 48 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100.0 langevinPistonDecay 50.0 langevinPistonTemp $temperature constraints on consexp 2 consref prot_posres.ref conskfile prot_posres.ref conskcol B constraintScaling 10.0 # Output outputName $outputname restartfreq 500 ;# 500steps =3D every 1ps dcdfreq 250 xstFreq 250 outputEnergies 100 outputPressure 100 lonepairs on ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 20 #system was minimized already #reinitvels $temperature run 500000 ;# 50ps --_000_BN7PR07MB4468D21B68993365AB16E770AFB49BN7PR07MB4468namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Seke,

 

Would you share your psf and pdb files, as well as t= he NAMD output log file so that we can better assess what the problem might= be?

 

Best,

Andrew

 

From: Seke Keretsu
Sent: Wednesday, February 3, 2021 4:05 AM
To: namd-l@ks.uiuc.edu
Subject: namd-l: Dealing with lone pairs

 

Dear Experts,

 

I am posting this again as follow up to my previous = post. Since then, I followed and tried all the advice but the error was not= resolved.

 

I am using NAMD2.14 for a protein ligand complex in = which there is a lone pair on the chlorobenzene of the ligand. The psf file= s were built in Charmm-Gui and solvated and ionized with VMD 1.9.4.

 

As suggested, I have added  'lonepairs on' to t= he configuration file.

 

In the psf file (ionized.psf), I added the lines for= the one lone pair as advised (by Pang, Yui Tik):


         1         3 !NUMLP NU= MLPH
         2         1   &n= bsp;   F 1.64000      0.00000      0.000= 00  
      4737      4710       469= 7

 

Here in the second line, I have tried 1.64 and -1.64= for distance between lonepair and host. For polarized water it was negativ= e, why?

In the third line, 4737      4710 &nb= sp;     4697 are the atomic ID of lonepair, host and atom connect= ed to host.

 

I still get the error as shown below regardless of t= he temperature I use.

 

ERROR MESSAGE:

 

ENERGY:   50020       287.8329 &= nbsp;     875.2009      2562.5041     &n= bsp;  35.3830        -139424.9435    155= 009.5692         0.0000         0.0= 000         0.0000          19= 345.5467         0.0000     19345.5467  =   19345.5467         0.0000         123095.5120    107654.6219   &n= bsp;396330.9410    123095.5120    107654.6219

TCL: Running for 500000 steps
ERROR: Margin is too small for 1 atom during timestep 50026.
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 (limit is 12000, at= om 395 of 507 on patch 37 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 37 pe 0).

FATAL ERROR: Exiting prematurely; see error messages= above.

 

 

As suggested (by Laurent Chaloin), I have also = checked the content of "par_all36_cgenff.prm." Since I am using N= AMD for simulation I assume the lines should not be comment-out.=

LPH    CLGR1     0.00   &nb= sp; 0.0000 ! aromatic halogen to lone pair
LPH    BRGR1     0.00     0.0000 ! aromatic h= alogen to lone pair
LPH    IGR1      0.00     0.0000 ! aroma= tic halogen to lone pair

However I could not find the following lines in my .= prm file. I tried running a few times by appending the lines to my par_all3= 6_cgenff.prm file. Did not change the outcome.

 

Please advise if I missed something here. Also, Is t= here an alternative to this, such as building a system without a lone pair = without badly compromising my simulation protocol ?

 

Thank you.

Seke

 

 

CONFIGURATION FILE:

 

####################################################= #########
## JOB DESCRIPTION                 =                      = ;   ##
#############################################################

# Minimization and Equilibration of
# Ubiquitin in a Water Box


#############################################################
## ADJUSTABLE PARAMETERS               &= nbsp;                   ##
#############################################################

structure          ionized.psf
coordinates        ionized.pdb

set temperature    100
set outputname     equilibration02

firsttimestep      50000
bincoordinates        equilibration.restart.coor
#binvelocities         equilibration.restart.vel

#############################################################
## SIMULATION PARAMETERS               &= nbsp;                   ##
#############################################################

# Input
paraTypeCharmm    on
parameters jz4/jz4.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_interface.prm
parameters toppar_water_ions.str
temperature         $temperature


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.0
switching           on
switchdist          10.0
pairlistdist        14.0


# Integrator Parameters
timestep            1.0  ;# 2fs/step
rigidBonds          all  ;# needed for 2fs st= eps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       10


# Constant Temperature Control
langevin            on    ;# do lan= gevin dynamics
langevinDamping     1     ;# damping coefficient (gamma= ) of 1/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bat= h to hydrogens


# Periodic Boundary Conditions

cellBasisVector1 69.61299896240234 0 0
cellBasisVector2 0 76.30400085449219 0
cellBasisVector3 0 0 74.61400032043457
cellOrigin 12.257286071777344 7.4436726570129395 -= 19.06593894958496




wrapAll             on


# PME (for full-system periodic electrostatics)
PME             &nbs= p;   yes
PMEGridSpacing      1.0

#manual grid definition
#PMEGridSizeX        45
#PMEGridSizeY        45
#PMEGridSizeZ        48


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.0
langevinPistonDecay   50.0
langevinPistonTemp    $temperature<= br>  

constraints           &nb= sp; on
consexp             =     2
consref             =     prot_posres.ref
conskfile            = ;   prot_posres.ref
conskcol            =    B
constraintScaling       10.0

# Output
outputName          $outputname

restartfreq         500     ;# 500steps =3D e= very 1ps
dcdfreq             250
xstFreq             250
outputEnergies      100
outputPressure      100

lonepairs on

#############################################################
## EXTRA PARAMETERS                =                     &nbs= p;  ##
#############################################################


#############################################################
## EXECUTION SCRIPT                =                     &nbs= p;  ##
#############################################################

# Minimization
minimize            20 #system was minimized = already
#reinitvels          $temperature

run 500000 ;# 50ps

 

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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi All, I have a quick question on NAMD3. I have 3 GPUs in my workstation. Is it advisable to run 3 jobs simultaneous= ly on different GPUs using NAMD3? Or should one job be run at a time? Should the +devices argument be used to define which job runs on which GPU? Any specific things to look at (if multiple jobs are run simultaneously) ex= cept those mentioned on the NAMD3 download page (CUDASOAintegrate and margi= n)? Thanks in advance. RPS --_000_BMXPR01MB3526CAC035D8C995198AEA73B3B49BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hi All,

I have a quick question on NA= MD3.

I have 3 GPUs in my workstati= on. Is it advisable to run 3 jobs simultan= eously on different GPUs using NAMD3? Or should one job be run at a time?

Should the +devices argument be used to define which job runs on which = GPU?

Any specific things to look at (if multiple jobs are run simultaneously= ) except those mentioned on the NAMD3 download page (CUDASOAintegrate and m= argin)?

Thanks in advance.

RPS




--_000_BMXPR01MB3526CAC035D8C995198AEA73B3B49BMXPR01MB3526INDP_-- From owner-namd-l@halifax.ks.uiuc.edu Wed Feb 3 14:31:39 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 113KVdne003259; Wed, 3 Feb 2021 14:31:39 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 113KVdQX003258; Wed, 3 Feb 2021 14:31:39 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 113KVcMJ003253; Wed, 3 Feb 2021 14:31:39 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 113KVcu7003252; Wed, 3 Feb 2021 14:31:38 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 113KVZj9003243 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Wed, 3 Feb 2021 14:31:35 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_C98293A6-6545-42CC-82DE-D110F4B89541" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Dealing with lone pairs Date: Wed, 3 Feb 2021 14:31:29 -0600 References: To: namd-l@ks.uiuc.edu, Seke Keretsu In-Reply-To: Message-Id: <5A65A14F-CEBD-4C72-8D92-31DA18419124@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_C98293A6-6545-42CC-82DE-D110F4B89541 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Seke, Please at least post the log file (redirected output from NAMD run). Even better if you could post all of the simulation files so that we can = reproduce your error. The error message seems to indicate that NAMD is not actually treating = the particle as a lone pair, but we can=E2=80=99t tell without seeing = the actual output. Thanks, Dave > On Feb 3, 2021, at 2:51 AM, Seke Keretsu = wrote: >=20 > Dear Experts, >=20 > I am posting this again as follow up to my previous post. Since then, = I followed and tried all the advice but the error was not resolved. >=20 > I am using NAMD2.14 for a protein ligand complex in which there is a = lone pair on the chlorobenzene of the ligand. The psf files were built = in Charmm-Gui and solvated and ionized with VMD 1.9.4. >=20 > As suggested, I have added 'lonepairs on' to the configuration file. >=20 > In the psf file (ionized.psf), I added the lines for the one lone pair = as advised (by Pang, Yui Tik): >=20 > 1 3 !NUMLP NUMLPH > 2 1 F 1.64000 0.00000 0.00000 =20 > 4737 4710 4697 >=20 > Here in the second line, I have tried 1.64 and -1.64 for distance = between lonepair and host. For polarized water it was negative, why? > In the third line, 4737 4710 4697 are the atomic ID of = lonepair, host and atom connected to host. >=20 > I still get the error as shown below regardless of the temperature I = use. >=20 > ERROR MESSAGE: >=20 > ENERGY: 50020 287.8329 875.2009 2562.5041 = 35.3830 -139424.9435 155009.5692 0.0000 0.0000 = 0.0000 19345.5467 0.0000 19345.5467 = 19345.5467 0.0000 123095.5120 107654.6219 = 396330.9410 123095.5120 107654.6219 >=20 > TCL: Running for 500000 steps > ERROR: Margin is too small for 1 atom during timestep 50026. > ERROR: Incorrect nonbonded forces and energies may be calculated! > ERROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 (limit is = 12000, atom 395 of 507 on patch 37 pe 0) > ERROR: Atoms moving too fast; simulation has become unstable (1 atoms = on patch 37 pe 0). > FATAL ERROR: Exiting prematurely; see error messages above. >=20 >=20 > As suggested (by Laurent Chaloin), I have also checked the content of = "par_all36_cgenff.prm." Since I am using NAMD for simulation I assume = the lines should not be comment-out. > LPH CLGR1 0.00 0.0000 ! aromatic halogen to lone pair > LPH BRGR1 0.00 0.0000 ! aromatic halogen to lone pair > LPH IGR1 0.00 0.0000 ! aromatic halogen to lone pair > However I could not find the following lines in my .prm file. I tried = running a few times by appending the lines to my par_all36_cgenff.prm = file. Did not change the outcome. >=20 > Please advise if I missed something here. Also, Is there an = alternative to this, such as building a system without a lone pair = without badly compromising my simulation protocol ? >=20 > Thank you. > Seke >=20 >=20 > CONFIGURATION FILE: >=20 > ############################################################# > ## JOB DESCRIPTION ## > ############################################################# >=20 > # Minimization and Equilibration of > # Ubiquitin in a Water Box >=20 >=20 > ############################################################# > ## ADJUSTABLE PARAMETERS ## > ############################################################# >=20 > structure ionized.psf > coordinates ionized.pdb >=20 > set temperature 100 > set outputname equilibration02 >=20 > firsttimestep 50000 > bincoordinates equilibration.restart.coor > #binvelocities equilibration.restart.vel >=20 > ############################################################# > ## SIMULATION PARAMETERS ## > ############################################################# >=20 > # Input > paraTypeCharmm on > parameters jz4/jz4.prm > parameters toppar/par_all36_carb.prm > parameters toppar/par_all36_cgenff.prm > parameters toppar/par_all36_lipid.prm > parameters toppar/par_all36m_prot.prm > parameters toppar/par_all36_na.prm > parameters toppar/par_interface.prm > parameters toppar_water_ions.str > temperature $temperature >=20 >=20 > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12.0 > switching on > switchdist 10.0 > pairlistdist 14.0 >=20 >=20 > # Integrator Parameters > timestep 1.0 ;# 2fs/step > rigidBonds all ;# needed for 2fs steps > nonbondedFreq 1 > fullElectFrequency 2 =20 > stepspercycle 10 >=20 >=20 > # Constant Temperature Control > langevin on ;# do langevin dynamics > langevinDamping 1 ;# damping coefficient (gamma) of 1/ps > langevinTemp $temperature > langevinHydrogen off ;# don't couple langevin bath to hydrogens >=20 >=20 > # Periodic Boundary Conditions >=20 > cellBasisVector1 69.61299896240234 0 0 > cellBasisVector2 0 76.30400085449219 0 > cellBasisVector3 0 0 74.61400032043457 > cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496 >=20 >=20 >=20 >=20 > wrapAll on >=20 >=20 > # PME (for full-system periodic electrostatics) > PME yes > PMEGridSpacing 1.0 >=20 > #manual grid definition > #PMEGridSizeX 45 > #PMEGridSizeY 45 > #PMEGridSizeZ 48 >=20 >=20 > # Constant Pressure Control (variable volume) > useGroupPressure yes ;# needed for rigidBonds > useFlexibleCell no > useConstantArea no >=20 > langevinPiston on > langevinPistonTarget 1.01325 ;# in bar -> 1 atm > langevinPistonPeriod 100.0 > langevinPistonDecay 50.0 > langevinPistonTemp $temperature > =20 >=20 > constraints on > consexp 2 > consref prot_posres.ref > conskfile prot_posres.ref > conskcol B > constraintScaling 10.0 >=20 > # Output > outputName $outputname >=20 > restartfreq 500 ;# 500steps =3D every 1ps > dcdfreq 250 > xstFreq 250 > outputEnergies 100 > outputPressure 100 >=20 > lonepairs on >=20 > ############################################################# > ## EXTRA PARAMETERS ## > ############################################################# >=20 >=20 > ############################################################# > ## EXECUTION SCRIPT ## > ############################################################# >=20 > # Minimization > minimize 20 #system was minimized already > #reinitvels $temperature >=20 > run 500000 ;# 50ps --Apple-Mail=_C98293A6-6545-42CC-82DE-D110F4B89541 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Seke,

Please at = least post the log file (redirected output from NAMD run).

Even better if you could = post all of the simulation files so that we can reproduce your = error.

The = error message seems to indicate that NAMD is not actually treating the = particle as a lone pair, but we can=E2=80=99t tell without seeing the = actual output.

Thanks,
Dave

On Feb = 3, 2021, at 2:51 AM, Seke Keretsu <sekekeretsu@gmail.com> wrote:

Dear Experts,

I am posting this again as follow up to = my previous post. Since then, I followed and tried all the advice but = the error was not resolved.

I am using NAMD2.14 for a protein = ligand complex in which there is a lone pair on the chlorobenzene of the = ligand. The psf files were built in Charmm-Gui and solvated and ionized = with VMD 1.9.4.

As suggested, I have added  = 'lonepairs on' to the configuration file.

In the psf file (ionized.psf), I added = the lines for the one lone pair as advised (by Pang, Yui Tik):

         1       =   3 !NUMLP NUMLPH
         2 =         1       F 1.64000   =    0.00000      0.00000  
      4737      4710   =     4697

Here in the second line, I have tried 1.64 and -1.64 for = distance between lonepair and host. For polarized water it was negative, = why?
In the third line, 4737     =  4710       4697 are the atomic ID of lonepair, host = and atom connected to host.

I still get the error as shown below regardless of the = temperature I use.

ERROR MESSAGE:

ENERGY:   50020     =   287.8329       875.2009     =  2562.5041        35.3830       =  -139424.9435    155009.5692         = 0.0000         0.0000         = 0.0000          19345.5467       =   0.0000     19345.5467     19345.5467   =       0.0000         123095.5120 =    107654.6219    396330.9410   =  123095.5120    107654.6219

TCL: Running for 500000 steps
ERROR: Margin is = too small for 1 atom during timestep 50026.
ERROR: = Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 = (limit is 12000, atom 395 of 507 on patch 37 pe 0)
ERROR: = Atoms moving too fast; simulation has become unstable (1 atoms on patch = 37 pe 0).
FATAL ERROR: Exiting = prematurely; see error messages above.


As = suggested (by Laurent = Chaloin), I have also checked the content of = "par_all36_cgenff.prm." Since I am using NAMD for simulation I assume = the lines should not be comment-out.
LPH    CLGR1     0.00     = 0.0000 ! aromatic halogen to lone pair
LPH   =  BRGR1     0.00     0.0000 ! aromatic halogen = to lone pair
LPH    IGR1     =  0.00     0.0000 ! aromatic halogen to lone = pair
However I could not find the following lines = in my .prm file. I tried running a few times by appending the lines to = my par_all36_cgenff.prm file. Did not change the outcome.

Please advise if I = missed something here. Also, Is there an alternative to this, such as = building a system without a lone pair without badly compromising my = simulation protocol ?

Thank you.
Seke


CONFIGURATION FILE:

############################################################### JOB DESCRIPTION           =                     =           ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box


############################################################### ADJUSTABLE PARAMETERS           =                     =     ##
#############################################################
structure         =  ionized.psf
coordinates       =  ionized.pdb

set temperature   =  100
set outputname     equilibration02

firsttimestep      50000
bincoordinates       =  equilibration.restart.coor
#binvelocities   =       equilibration.restart.vel

############################################################### SIMULATION PARAMETERS           =                     =     ##
#############################################################
# Input
paraTypeCharmm   =  on
parameters jz4/jz4.prm
parameters = toppar/par_all36_carb.prm
parameters = toppar/par_all36_cgenff.prm
parameters = toppar/par_all36_lipid.prm
parameters = toppar/par_all36m_prot.prm
parameters = toppar/par_all36_na.prm
parameters = toppar/par_interface.prm
parameters = toppar_water_ions.str
temperature     =     $temperature


# = Force-Field Parameters
exclude         =     scaled1-4
1-4scaling       =    1.0
cutoff           =    12.0
switching         =   on
switchdist         =  10.0
pairlistdist        14.0


# Integrator Parameters
timestep            1.0 =  ;# 2fs/step
rigidBonds         =  all  ;# needed for 2fs steps
nonbondedFreq =       1
fullElectFrequency  2 =  
stepspercycle       10


# Constant Temperature = Control
langevin           =  on    ;# do langevin dynamics
langevinDamping     1     ;# damping = coefficient (gamma) of 1/ps
langevinTemp     =    $temperature
langevinHydrogen   =  off    ;# don't couple langevin bath to hydrogens


# Periodic Boundary = Conditions

cellBasisVector1 69.61299896240234 0 0
cellBasisVector2 0 76.30400085449219 0
cellBasisVector3 0 0 74.61400032043457
cellOrigin= 12.257286071777344 7.4436726570129395 -19.06593894958496




wrapAll             = on

# PME (for full-system periodic = electrostatics)
PME           =       yes
PMEGridSpacing   =    1.0

#manual grid definition
#PMEGridSizeX        45
#PMEGridSizeY        45
#PMEGridSizeZ        48


# Constant Pressure Control (variable = volume)
useGroupPressure      yes ;# needed = for rigidBonds
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 = atm
langevinPistonPeriod  100.0
langevinPistonDecay   50.0
langevinPistonTemp    $temperature
 

constraints           =   on
consexp           =       2
consref         =         prot_posres.ref
conskfile =               prot_posres.ref
conskcol               =  B
constraintScaling       = 10.0

# Output
outputName =          $outputname

restartfreq         500     ;# = 500steps =3D every 1ps
dcdfreq         =     250
xstFreq         =     250
outputEnergies     =  100
outputPressure      100

lonepairs on

############################################################### EXTRA PARAMETERS           =                     =          ##
#############################################################

############################################################### EXECUTION SCRIPT           =                     =          ##
#############################################################
# Minimization
minimize   =          20 #system was minimized already
#reinitvels          $temperature

run 500000 ;# 50ps

= --Apple-Mail=_C98293A6-6545-42CC-82DE-D110F4B89541-- From owner-namd-l@halifax.ks.uiuc.edu Wed Feb 3 14:38:08 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 113Kc8am004320; Wed, 3 Feb 2021 14:38:08 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 113Kc8Dm004315; Wed, 3 Feb 2021 14:38:08 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 113Kc8NX004310; Wed, 3 Feb 2021 14:38:08 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 113Kc8go004309; Wed, 3 Feb 2021 14:38:08 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 113Kc3Ej004229 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Wed, 3 Feb 2021 14:38:04 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_012A0F9C-4DAF-478C-A349-9FCF90B46ECC" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: NAMD3 Multiple Instances Date: Wed, 3 Feb 2021 14:37:58 -0600 References: To: NAMD list , Raman Preet Singh In-Reply-To: Message-Id: <2A3BFC56-3848-4B8F-9F02-6DE6FFBFADE8@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_012A0F9C-4DAF-478C-A349-9FCF90B46ECC Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi RPS, Yes, it is certainly possible to run three instances of NAMD 3 (with = CUDASOAintegrate on) at the same time. When running with = CUDASOAintegrate, you do not need much CPU core support. Ultimately, how = much CPU core support depends on the size of your system, but for system = sizes of a few thousand atoms, you shouldn=E2=80=99t need more than one = core per GPU, and probably not more than four CPU cores for systems as = large as one million atoms. You will need to set +devices so that the = simultaneous jobs do not try to use all of the GPUs or the same GPU. Best regards, Dave > On Feb 3, 2021, at 11:50 AM, Raman Preet Singh = wrote: >=20 > Hi All, >=20 > I have a quick question on NAMD3. >=20 > I have 3 GPUs in my workstation. Is it advisable to run 3 jobs = simultaneously on different GPUs using NAMD3? Or should one job be run = at a time? >=20 > Should the +devices argument be used to define which job runs on which = GPU? >=20 > Any specific things to look at (if multiple jobs are run = simultaneously) except those mentioned on the NAMD3 download page = (CUDASOAintegrate and margin)? >=20 > Thanks in advance. >=20 > RPS >=20 >=20 >=20 >=20 --Apple-Mail=_012A0F9C-4DAF-478C-A349-9FCF90B46ECC Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = RPS,

Yes, it is = certainly possible to run three instances of NAMD 3 (with = CUDASOAintegrate on) at the same time. When running with = CUDASOAintegrate, you do not need much CPU core support. Ultimately, how = much CPU core support depends on the size of your system, but for system = sizes of a few thousand atoms, you shouldn=E2=80=99t need more than one = core per GPU, and probably not more than four CPU cores for systems as = large as one million atoms. You will need to set +devices so that the = simultaneous jobs do not try to use all of the GPUs or the same = GPU.

Best = regards,
Dave

On Feb = 3, 2021, at 11:50 AM, Raman Preet Singh <ramanpreetsingh@hotmail.com> wrote:

Hi All,

I have a quick = question on NAMD3.

I have 3 GPUs = in my workstation. Is it advisable to run 3 jobs simultaneously on different GPUs = using NAMD3? Or should one job be run at a time?

Should the +devices argument be = used to define which job runs on which GPU?

Any specific things to look at (if = multiple jobs are run simultaneously) except those mentioned on the = NAMD3 download page (CUDASOAintegrate and margin)?

Thanks in advance.

RPS





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Thu, 4 Feb 2021 08:23:30 +0000 Date: Thu, 4 Feb 2021 08:21:28 +0000 (UTC) From: Vidhya Sankar To: "namd-l@ks.uiuc.edu" Message-ID: <1545223321.1959398.1612426888420@mail.yahoo.com> Subject: namd-l: Mail about error in namd MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1959397_1670791599.1612426888419" References: <1545223321.1959398.1612426888420.ref@mail.yahoo.com> X-Mailer: WebService/1.1.17648 YMailNorrin Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.104 Safari/537.36 X-CLX-Response: 1TFkXGx4bEQpMehcZHh4RCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHHxkRCkNZFwcbGBoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsecRsGGBJ3BhsdHwYaBhoGGAYacRoQGncGGgYHHxoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF3UdU04HX3seHU9bfRIYfkMHR0dP QEx1WHJQXU1YWUkYEQpYXBcfBBoEGBgZBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3J/fGVCEQp NXBcfEQpMWhdsaU1raxEKTEYXb2trb2trEQpCTxdiSR96XFgfW3kbHhEKQ1oXGxocBBsaBBgeGw QbGhMRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0Vsb URDZhEKQkUXehltQ1tFX2hpfWURCkJOF3pEHB1vRWxtRENmEQpCTBdmYWITYW1ia0lcQhEKQmwX ax0fcBlsaUVveFwRCkJAF2x5XmJhElxQGxNvEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxg RCnlDF2UdSGgSS08BTh9PEQpZSxcTHxseEQpwaBdmaUNEZx4aGW1aWhAHGRoRCnBoF2Z/f2RAeG RySxMbEAcZGhEKcGgXZGlDa3tIGE1LGlkQBxkaEQpwbBdkb05cRn5TaHxZWhAHGRoRCm1+FwcbE QpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 priorityscore=344 malwarescore=0 lowpriorityscore=0 suspectscore=0 bulkscore=0 clxscore=141 mlxscore=0 phishscore=0 mlxlogscore=551 spamscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102040050 domainage_hfrom=9514 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_1959397_1670791599.1612426888419 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd user I have prepared the system well (PDB)=C2=A0 also I=C2=A0 Min= imized and equilibrated=C2=A0 well But=C2=A0 During Dynamics=C2=A0 it shows= Low CUDA global exclusion count and end in error I used=C2=A0 =C2=A030 ams= trong for cut-off=C2=A0Does Any body help me to solve the error=C2=A0 With RegardsSVIDHYA SANKAR=C2=A0=C2=A0 ------=_Part_1959397_1670791599.1612426888419 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Dear Namd user I have prepared the system well (PDB)  also I  Minimized and equilibrated  well But  During Dynamics  it shows Low CUDA global exclusion count and end in error I used   30 amstrong for cut-off 
Does Any body help me to solve the error 

With Regards
SVIDHYA SANKAR  
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A" Date: Fri, 5 Feb 2021 14:56:01 +0330 Message-ID: Subject: namd-l: the centers value in colvar.in file for binding free energy (BFEE) To: NAMD Content-Type: multipart/alternative; boundary="0000000000000edcfa05ba9517af" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwbEQpMehcYExkRCllEF2xoH2xzXEYbehoYEQpYWBdvWU9DRXNFZUt SXREKeE4XY1Nja3sTWH4aX14RCnlMF2Ede2NlWE1OekBhEQpDSBcHGBIZEQpDWRcHExkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhtxHxsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XHn1PeV5PXk5tS2IbQEBhfAcaHUUYeBJjaUwZExgZWkMRClhcFx8EGgQYGBkF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXcn9ZBR0RCk1cFx4cGxEKTFoXaGlNTU0RCkxGF29ra2t raxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGxMEHhwRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZx0fSRhOWURgW1IRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdvWU9DRXNFZUtSXREKQmwXbF9OYB9hbWABARgRCkJAF2t8Qn9CcF9haFBGEQpC WBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXZmASeGhCU2RbYkIRCllLFxMZGhIRCnBoF2FbR0N9Uhs dGUQbEBkaEQpwaBdiRF5sfhtuaXlmThAZGhEKcGgXY1lOaRhzcxISBR8QGRoRCnBoF2QZTmVZYE BuG3tsEBkaEQpwaBdpfBpkU1JrT2loQxAZGhEKcH0XZRtLZWJ6ZmJHAUUQGRoRCnB/F2dgGEVkb 3Mcc0cbEBkaEQpwXxdlG0tlYnpmYkcBRRAZGhEKcGwXax18ZRJ9GVNEcE4QGRoRCm1+FxoRClhN F0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 lowpriorityscore=0 phishscore=0 priorityscore=293 mlxscore=0 bulkscore=0 impostorscore=0 suspectscore=0 spamscore=0 mlxlogscore=571 clxscore=161 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102050075 domainage_hfrom=9308 X-Spam-Score: 0 X-Spam-OrigSender: matabay2010@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "M. A" --0000000000000edcfa05ba9517af Content-Type: text/plain; charset="UTF-8" Dear all, I simulated protein and ligand with NAMD successfully. Now I want to calculate the binding free energy of this interaction with the BFEE plugin of VMD. I have a problem when I run configure files of 001_RMSD_bound, 006_polar_phi, 007_r and 008_RMSD_unbound folders of computations. From the kind of the error I guess it is related to the centers value that was 0.0 while the other steps executed correctly and the centers value was 0.0 for all steps by default of the VMD. I don't know how I can define centers value in harmonic parameters because I konow that I should change the center value from 0.0. Could you please help me to solve this problem? for example: the error in 006_polar_phi step was: *** Error in `/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2': invalid fastbin entry (free): 0x00002ad7a8258330 *** ======= Backtrace: ========= /lib64/libc.so.6[0x31c047413e] /lib64/libc.so.6[0x31c0479b7e] /lib64/libc.so.6[0x31c047a31f] /home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x129aaa9] /home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x5fd53e] /home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x10d1173] /home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x1295780] /home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x127a884] /home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x12774a8] /lib64/libpthread.so.0[0x31c10071f3] /lib64/libc.so.6(clone+0x6d)[0x31c04ea9dd] ======= Memory map: ======== 00400000-0d438000 r-xp 00000000 00:16 1723597063 0d637000-0d643000 r-xp 0d037000 00:16 1723597063 0d643000-0d6ab000 rwxp 0d043000 00:16 1723597063 0d6ab000-0d731000 rwxp 00000000 00:00 0 0e6d2000-18a10000 rwxp 00000000 00:00 0 [heap] 200000000-200200000 ---p 00000000 00:00 0 200200000-200400000 rwxs 00000000 00:05 383465 /dev/nvidiactl 200400000-202400000 rwxs 00000000 00:05 383465 /dev/nvidiactl 202400000-205400000 rwxs 00000000 00:05 383465 /dev/nvidiactl 205400000-206000000 ---p 00000000 00:00 0 206000000-206200000 rwxs 00000000 00:05 383465 /dev/nvidiactl 206200000-206400000 rwxs 00000000 00:05 383465 /dev/nvidiactl 206400000-206600000 rwxs 206400000 00:05 383471 /dev/nvidia-uvm 206600000-206800000 rwxs 00000000 00:05 383465 /dev/nvidiactl 206800000-206a00000 ---p 00000000 00:00 0 206a00000-206c00000 rwxs 00000000 00:05 383465 /dev/nvidiactl 206c00000-300200000 ---p 00000000 00:00 0 31c0000000-31c0021000 r-xp 00000000 08:01 788872 /lib64/ld-2.18.so 31c0220000-31c0221000 r-xp 00020000 08:01 788872 /lib64/ld-2.18.so 31c0221000-31c0222000 rwxp 00021000 08:01 788872 /lib64/ld-2.18.so 31c0222000-31c0223000 rwxp 00000000 00:00 0 31 Bests -- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology --0000000000000edcfa05ba9517af Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear all,

I simulated protei= n and ligand with NAMD successfully. Now I want to calculate the binding fr= ee energy of this interaction with the BFEE plugin of VMD. I have a problem= when I run configure files of 001_RMSD_bound, 006_polar_phi, 007_r and 008= _RMSD_unbound folders of computations. From the kind of the error I guess i= t is related to the centers value that was 0.0 while the other steps execut= ed correctly and the centers value was 0.0 for all steps by default of the = VMD.
I don't know how I can define centers value in harm= onic parameters because I konow that I should change the center value from = 0.0. Could you please help me to solve this problem?
for example:= the error in 006_polar_phi step was:
*** Error in `/NAMD_Git-201= 9-11-26_Linux-x86_64-multicore-CUDA/namd2': invalid fastbin entry (free= ): 0x00002ad7a8258330 ***
=3D=3D=3D=3D=3D=3D=3D Backtrace: =3D=3D=3D=3D= =3D=3D=3D=3D=3D
/lib64/libc.so.6[0x31c047413e]
/lib64/libc.so.6[0x31c= 0479b7e]
/lib64/libc.so.6[0x31c047a31f]
/home/atabay.che.sharif/NAMD_= Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x129aaa9]
/home/atabay= .che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x5fd53e]=
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA= /namd2[0x10d1173]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_= 64-multicore-CUDA/namd2[0x1295780]
/home/atabay.che.sharif/NAMD_Git-2019= -11-26_Linux-x86_64-multicore-CUDA/namd2[0x127a884]
/home/atabay.che.sha= rif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x12774a8]
/li= b64/libpthread.so.0[0x31c10071f3]
/lib64/libc.so.6(clone+0x6d)[0x31c04ea= 9dd]
=3D=3D=3D=3D=3D=3D=3D Memory map: =3D=3D=3D=3D=3D=3D=3D=3D
00400= 000-0d438000 r-xp 00000000 00:16 1723597063 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
0d637000-0d643000 r= -xp 0d037000 00:16 1723597063 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0
0d643000-0d6ab000 rwxp 0d043000 00:16 17235970= 63 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0
0d6ab000-0d731000 rwxp 00000000 00:00 0
0e6d2000-18a10= 000 rwxp 00000000 00:00 0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[heap]=
200000000-200200000 ---p 00000000 00:00 0
200200000-200400000 rwxs = 00000000 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
200400000-20240000= 0 rwxs 00000000 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
202400000-2= 05400000 rwxs 00000000 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
2054= 00000-206000000 ---p 00000000 00:00 0
206000000-206200000 rwxs 00000000= 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
206200000-206400000 rwxs = 00000000 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
206400000-20660000= 0 rwxs 206400000 00:05 383471 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0/dev/nvidia-uvm
206600000-2= 06800000 rwxs 00000000 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
2068= 00000-206a00000 ---p 00000000 00:00 0
206a00000-206c00000 rwxs 00000000= 00:05 383465 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /dev/nvidiactl
206c00000-300200000 ---p = 00000000 00:00 0
31c0000000-31c0021000 r-xp 00000000 08:01 788872 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 /lib64/ld-2.18.so
31c0220000-31c0221000 r-xp 00020000 08:01 788872 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 /lib64/ld= -2.18.so
31c0221000-31c0222000 rwxp 00021000 08:01 788872 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 /= lib64/ld-2.18= .so
31c0222000-31c0223000 rwxp 00000000 00:00 0
31
Bests

--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology

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boundary="000000000000839ad505bb050fa9" X-CLX-Response: 1TFkXGxwaEQpMehcYEhoRCllEF25jfE1gTBlkb19hEQpYWBdiRUVda01CeUx JXxEKeE4XY1Nja3sTWH4aX14RCnlMF29nGH9QHB4fE2kcEQpDSBcHGBoYEQpDWRcHGx4aEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4acRgeEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF35Ia30dS01Nf3p7ZkZFcklSfXgdZWRTS15EaEdOWmF8EQpYXBcfBBoEGBge BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXcn1DS2ARCk1cFxsaGREKTFoXaWxpTU1NEQpMRhdva2t ra2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh8EGxwcBB8ZEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF3pwYBJGaGx8H05JEQpCThdjU2Nre xNYfhpfXhEKQkwXYkVFXWtNQnlMSV8RCkJsF2hTT1sba2xSUkhZEQpCQBdpS2Jyb2RbGVlSaBEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2ttU0lTcxxeRFkdEQpZSxcTGRseEQpwaBd gbGASQGJHUhpHUxAaEQpwaBdoYkhJUEhSS3wcXhAaEQpwaBd6QgFSWGZ5SVxZbxAaEQpwaBdofG 9ueVhgU0MeYhAaEQpwaBdgWERSHWl+UGJIHhAaEQpwbBdkWWJsGkJFSWB8HRAZGhEKbX4XGxEKW E0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 spamscore=0 clxscore=160 phishscore=0 priorityscore=280 bulkscore=0 malwarescore=0 suspectscore=0 mlxscore=0 mlxlogscore=791 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102110004 domainage_hfrom=9314 X-Spam-Score: 0 X-Spam-OrigSender: moradkhantig@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Tiglath Moradkhan --000000000000839ad505bb050fa9 Content-Type: text/plain; charset="UTF-8" To the NAMD community I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein system via a simple minimization and equilibration simulation. I've written the required NAMD config file using the NAMD tutorials but when I try running it I get the following error message: FATAL ERROR: tried before startup to read config file parameter that was not set while executing "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm" (file "CSApoA1.conf" line 30) I don't understand what the issue is. I've checked online to resolve the issue and found that the .prm extension are for the parameter files so there shouldn't be a problem with providing the correct parameter files. Therefore I'm confused why I'm getting this error message because I got these files from the provided plugin tcl folder. I would be very glad for your help. Thanks Tiglath Moradkhan --000000000000839ad505bb050fa9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
To the NAMD community

I'm a new a N= AMD user and I'm trying to equilibrate a lipoprotein system via a simpl= e minimization and equilibration simulation. I've written the required = NAMD config file using the NAMD tutorials but when I try running it I get t= he following error message:=C2=A0

FATAL ERROR: tri= ed before startup to read config file parameter that was not set
=C2=A0 = =C2=A0 while executing
"C:/Users/tig_m/Documents/ThesisProjectMDSim= ulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm&= quot;
=C2=A0 =C2=A0 (file "CSApoA1.conf" line 30)

I don't understand what the issue is. I've checked= online to resolve the issue and found that the .prm extension are for the = parameter files so there shouldn't be a problem with providing the corr= ect parameter files. Therefore I'm confused why I'm getting this er= ror message because I got these files from the provided plugin tcl folder.= =C2=A0

I would be very glad for your help.


Thanks

Tiglath Mo= radkhan
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Wed, 10 Feb 2021 20:06:34 -0800 (PST) Content-Type: text/plain; charset=utf-8 From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: Problem with running NAMD config file Date: Wed, 10 Feb 2021 23:06:31 -0500 Message-Id: <32B11EAC-D582-43D1-81C5-FC48CE5D45E3@gmail.com> References: In-Reply-To: To: namd-l@ks.uiuc.edu, Tiglath Moradkhan X-Mailer: iPhone Mail (18B92) X-CLX-Response: 1TFkXGxMaEQpMehcZGxIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGBsdEQpDWRcHHx8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHRpxHhMQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XH3Jzc214fXxDc0BadUVoWk1sQ2xoTmRDXB1zUhkcQ1IRClhcFx8EGgQYGB4F GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyfUZiRBEKTVwXGx8SEQpMWhd8aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBB sdGBEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmS21YRhhPY0VDQBEKQk4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdv T2RBWkJQbWZrWREKQkAXem9heV9FSHAeE2kRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdhHV9ORHBjQRweHBEKWUsXExkbHhEKcGgXY2Z9QEQbaE18fF8QGRoRCnBoF25DUEd/c2JfGm Z+EBkaEQpwaBdtTGtlHWMcaxwFHhAZGhEKcGgXYGxgEkBiR1IaR1MQGRoRCnBoF2hiSElQSFJLf BxeEBkaEQpwbBdnaENrcxJ5GE1iXBAZGhEKcEMXaUZHWWZ/QEkaeBkQGRoRCm1+FxsRClhNF0sR IA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 spamscore=0 clxscore=190 phishscore=0 priorityscore=318 bulkscore=0 malwarescore=0 suspectscore=0 mlxscore=0 mlxlogscore=999 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102110028 domainage_hfrom=9314 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 11B46cew014088 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= You can attach config file. Enviado desde mi iPhone > El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan escribió: > >  > To the NAMD community > > I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein system via a simple minimization and equilibration simulation. I've written the required NAMD config file using the NAMD tutorials but when I try running it I get the following error message: > > FATAL ERROR: tried before startup to read config file parameter that was not set > while executing > "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm" > (file "CSApoA1.conf" line 30) > > I don't understand what the issue is. I've checked online to resolve the issue and found that the .prm extension are for the parameter files so there shouldn't be a problem with providing the correct parameter files. Therefore I'm confused why I'm getting this error message because I got these files from the provided plugin tcl folder. > > I would be very glad for your help. > > > Thanks > > Tiglath Moradkhan From owner-namd-l@halifax.ks.uiuc.edu Thu Feb 11 11:28:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BHSjdP001197; Thu, 11 Feb 2021 11:28:45 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11BHSj0R001196; Thu, 11 Feb 2021 11:28:45 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BHSifp001190; Thu, 11 Feb 2021 11:28:44 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11BHSiw0001189; Thu, 11 Feb 2021 11:28:44 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BHSWw1001180 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000264c3605bb12d9b2" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx4SEQpMehcZGxoRCllEF25jfE1gTBlkb19hEQpYWBdiRUVda01CeUx JXxEKeE4XY1Nja3sTWH4aX14RCnlMF29nGH9QHB4fE2kcEQpDSBcHGBIbEQpDWRcHHh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGBJxGxIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYXJPfW57UlpCSWddQ3wZB0tndUFzG0t/GUhuaHBEcnkRClhcFx8EGgQYGB4F GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyfV0ZSxEKTVwXGB0cEQpMWhd4aU1raxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF21tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBB sdHhEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRd6cGASRmhsfB9OSREKQk4XY1Nja3sTWH4aX14RCkJMF2JFRV1rTUJ5TElfEQpCbBdo U09bG2tsUlJIWREKQkAXem9heV9FSHAeE2kRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdhHV9ORHBjQRweHBEKWUsXExkbHhEKcGgXbhxeG1twTlxgBUkQGRoRCnBoF2BsYBJAYkdSGk dTEBgYEQpwaBdkAWRcWXgZU2dLGBAZGhEKcGgXYHxnXVx6Z0F/HWAQGRoRCnBoF2hiSElQSFJLf BxeEBkaEQpwaxd6ZBpdTGlyAWtcSRAZGhEKcEsXaGlJQh5bAVJrbW0QGRoRCnBrF2IcR01ySUtH ZE9gEBkaEQpwbBdkWWJsGkJFSWB8HRAbGBEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 suspectscore=0 spamscore=0 malwarescore=0 priorityscore=310 adultscore=0 bulkscore=0 lowpriorityscore=0 impostorscore=0 mlxscore=0 phishscore=0 clxscore=148 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102110144 domainage_hfrom=9314 X-Spam-Score: 0 X-Spam-OrigSender: moradkhantig@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Tiglath Moradkhan --000000000000264c3605bb12d9b2 Content-Type: multipart/alternative; boundary="000000000000264c3405bb12d9b0" --000000000000264c3405bb12d9b0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Yes. Here it is. On Wed, Feb 10, 2021 at 8:06 PM "ROP=C3=93N-PALACIOS G." wrote: > You can attach config file. > > Enviado desde mi iPhone > > > El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan < > moradkhantig@gmail.com> escribi=C3=B3: > > > > =EF=BB=BF > > To the NAMD community > > > > I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein syste= m > via a simple minimization and equilibration simulation. I've written the > required NAMD config file using the NAMD tutorials but when I try running > it I get the following error message: > > > > FATAL ERROR: tried before startup to read config file parameter that wa= s > not set > > while executing > > > "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/Californ= iaSeaLionApoA1/LipidBound/par_all36_lipid.prm" > > (file "CSApoA1.conf" line 30) > > > > I don't understand what the issue is. I've checked online to resolve th= e > issue and found that the .prm extension are for the parameter files so > there shouldn't be a problem with providing the correct parameter files. > Therefore I'm confused why I'm getting this error message because I got > these files from the provided plugin tcl folder. > > > > I would be very glad for your help. > > > > > > Thanks > > > > Tiglath Moradkhan > --000000000000264c3405bb12d9b0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Yes. Here it is.

On Wed, Feb 10, 2021 at 8:06 PM "ROP= =C3=93N-PALACIOS G." <biod= ano.geo@gmail.com> wrote:
You can attach config file.

Enviado desde mi iPhone

> El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan <moradkhantig@gmail.com= > escribi=C3=B3:
>
> =EF=BB=BF
> To the NAMD community
>
> I'm a new a NAMD user and I'm trying to equilibrate a lipoprot= ein system via a simple minimization and equilibration simulation. I've= written the required NAMD config file using the NAMD tutorials but when I = try running it I get the following error message:
>
> FATAL ERROR: tried before startup to read config file parameter that w= as not set
>=C2=A0 =C2=A0 =C2=A0while executing
> "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/= CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm"
>=C2=A0 =C2=A0 =C2=A0(file "CSApoA1.conf" line 30)
>
> I don't understand what the issue is. I've checked online to r= esolve the issue and found that the .prm extension are for the parameter fi= les so there shouldn't be a problem with providing the correct paramete= r files. Therefore I'm confused why I'm getting this error message = because I got these files from the provided plugin tcl folder.
>
> I would be very glad for your help.
>
>
> Thanks
>
> Tiglath Moradkhan
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X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_f77375c5da42f69a6633baaef0bb55a6msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Ahh! Multiple parameter files all need to be prefixed with "parameters" so = the parser doesn't break. Try: parameters C:/Users/tig_m/Documents/ThesisProjectMDSimulations/Py= ModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_prot.prm parameters C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels= /CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm #you'll probably also need to add water parameters somewhere? -Josh On 2/11/21 12:28 PM, Tiglath Moradkhan wrote: Yes. Here it is. On Wed, Feb 10, 2021 at 8:06 PM "ROP=C3=93N-PALACIOS G." > wrote: You can attach config file. Enviado desde mi iPhone > El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan > escribi=C3=B3: > > =EF=BB=BF > To the NAMD community > > I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein system = via a simple minimization and equilibration simulation. I've written the re= quired NAMD config file using the NAMD tutorials but when I try running it = I get the following error message: > > FATAL ERROR: tried before startup to read config file parameter that was = not set > while executing > "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/Californ= iaSeaLionApoA1/LipidBound/par_all36_lipid.prm" > (file "CSApoA1.conf" line 30) > > I don't understand what the issue is. I've checked online to resolve the = issue and found that the .prm extension are for the parameter files so ther= e shouldn't be a problem with providing the correct parameter files. Theref= ore I'm confused why I'm getting this error message because I got these fil= es from the provided plugin tcl folder. > > I would be very glad for your help. > > > Thanks > > Tiglath Moradkhan -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!tBZ46npBhXgpE62liIHjaXck1Gcy0oqPJL625oCsHWGf4CoscwdQ5qI= 3PgBkDSA2WQ$=20 --_000_f77375c5da42f69a6633baaef0bb55a6msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <10E71BBF4C21B84DA0856EA4DF7E113B@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Ahh! Multiple parameter files all need to be prefixed with "parameters= " so the parser doesn't break. Try:

parameters           C:/U= sers/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLi= onApoA1/LipidBound/par_all36_prot.prm

parameters  C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModM= odels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm
#you'll probably also need to add water parameters somewhere?

-Josh

On 2/11/21 12:28 PM, Tiglath Moradkhan wrote= :
Yes. Here it is.

On Wed, Feb 10, 2021 at 8:06 PM "= ;ROP=C3=93N-PALACIOS G." <biodano.geo@gmail.com> wrote:
You can attach config file.

Enviado desde mi iPhone

> El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan <m= oradkhantig@gmail.com> escribi=C3=B3:
>
> =EF=BB=BF
> To the NAMD community
>
> I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein syst= em via a simple minimization and equilibration simulation. I've written the= required NAMD config file using the NAMD tutorials but when I try running = it I get the following error message:
>
> FATAL ERROR: tried before startup to read config file parameter that w= as not set
>     while executing
> "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/= CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm"
>     (file "CSApoA1.conf" line 30)
>
> I don't understand what the issue is. I've checked online to resolve t= he issue and found that the .prm extension are for the parameter files so t= here shouldn't be a problem with providing the correct parameter files. The= refore I'm confused why I'm getting this error message because I got these files from the provided plugin tcl = folder.
>
> I would be very glad for your help.
>
>
> Thanks
>
> Tiglath Moradkhan

--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
--_000_f77375c5da42f69a6633baaef0bb55a6msuedu_-- From owner-namd-l@halifax.ks.uiuc.edu Thu Feb 11 14:19:54 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BKJsiX009281; Thu, 11 Feb 2021 14:19:54 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11BKJrcc009280; Thu, 11 Feb 2021 14:19:53 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BKJrwI009276; Thu, 11 Feb 2021 14:19:53 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11BKJrsO009275; Thu, 11 Feb 2021 14:19:53 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BKJi57009265 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 11 Feb 2021 14:19:45 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 11BKIrR4024593 for ; Thu, 11 Feb 2021 20:19:44 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qk1-f172.google.com (mail-qk1-f172.google.com [209.85.222.172]) by mx0a-00007101.pphosted.com with ESMTP id 36m6rebuvw-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 11 Feb 2021 20:19:44 +0000 Received: by mail-qk1-f172.google.com with SMTP id b14so6615019qkk.0 for ; Thu, 11 Feb 2021 12:19:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:cc:message-id:thread-topic :references:in-reply-to:mime-version; bh=JcbfreoomDTMyLWpPakbxTpvNYJGTl32/d522IVWluM=; b=YcRK1y+tLDz3et4b+BaQ1/uRA4vjpCKgGhmPpkN4verM88aQVDoRCgTJk24zp6Pz/Q lw0hpkt44A9YN4stm1KMNmt1FUTlwzcafHMx8hzLAiUkf51wkAVk0gMAWSR4h/x3Tjma N0cVQkcDkUZgOJw45TWp6eDBuY0RUhNG/rZZ57QylGEbg+9a7ex4pntZV2kDSsCJcK5l yBvIro+zzW6P12VWU3dGoWZc9ABsVuruQT7zmHnbdCiVQnQ8y3XfurZnSxTvTkFTzugr UBti3HnDqoO1WaWmVBprZkJxGlSCtlSfxdlbtYTgIzANyr+hw6KrRhvnu5VGHgbVdcUw uPUQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:cc:message-id :thread-topic:references:in-reply-to:mime-version; bh=JcbfreoomDTMyLWpPakbxTpvNYJGTl32/d522IVWluM=; b=ACQiTW1oBvc3weA3XR03eNjiud+44MPaLg7rtGoN5iHUoOJcIh1kK3/X1fukDqQ8ps EEblsP2mJSv1LjY4EGrV4mI12qXZ5MSYU5DqbBoi1kJfKSRCnu7OMF0QA67WyunEJzoM 9K5f4xjVSdTVZ+texF9gO0Xu/NqUaEBrrGI4K9GAZJfLO+KTp/ywetc/ERoP6Vvttt79 KNivEShN30I31TpqmBrJK9X/lNjuqixmRHVB3VgFqEi/F7M2iKQ2e2wlQoOU47FKgkrM zeSAh5DQmnADxV2ktkH5noMpEyVbzMq94AQQWFuKcRBP2pM7rMA7EJPeDqCYWWzCACrI NLuA== X-Gm-Message-State: AOAM531Xy7toAxv0fM62LJnpk9atDTR94CdDnxUOiZlgO+gWZpdI7rWV SGBczdDtN6ILZ3bPcrQNMQ0= X-Google-Smtp-Source: ABdhPJwNl2whJVfP36ZdFWveaiqf4lmCHkGb4WyFalfAbCPiULDHL6t59M4yQIUih00rfEmIYxAipQ== X-Received: by 2002:a37:9003:: with SMTP id s3mr10122596qkd.117.1613074783170; Thu, 11 Feb 2021 12:19:43 -0800 (PST) Received: from [192.168.1.38] ([181.64.64.152]) by smtp.gmail.com with ESMTPSA id r25sm2655935qtt.89.2021.02.11.12.19.40 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 11 Feb 2021 12:19:42 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 11 Feb 2021 15:19:37 -0500 Subject: Re: namd-l: Problem with running NAMD config file From: "Ropon-Palacios G." To: Tiglath Moradkhan CC: Message-ID: <53852F79-E1F0-4772-B2D4-45EC969AD71D@gmail.com> Thread-Topic: namd-l: Problem with running NAMD config file References: <32B11EAC-D582-43D1-81C5-FC48CE5D45E3@gmail.com> In-Reply-To: Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3695901581_2066150501" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcZHxsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGxIaEQpDWRcHHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfG3EZGxAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdydXpaEkx9bGRmS159QWhyehxdT19kRXNgRUdcHE0cWhEKWFwXHwQaBBgYHgUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3J9UHIdEQpNXBcZHR0RCkxaF3hpTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx 0YEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2Np WW96Tx1yR09/EQpCQBd6b2F5X0VIcB4TaREKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2EdX05 EcGNBHB4cEQpZSxcTGRseEQpwZxdpQ25QAVlzRwEeUxAZGhEKcGgXbVh6QF4dbGJORE8QHhIRCn BoF2EYXRNpHBNyfhpGEBkaEQpwaBdoa11CTn9bcExoXxAZGhEKcGgXY3pkf09QRnB7Hn4QHhIRC nBoF2dvH0NCGXpDW35TEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEMXYEJre2ZybntBQxoQGRoR Cm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 bulkscore=0 clxscore=171 lowpriorityscore=0 malwarescore=0 mlxlogscore=999 impostorscore=0 mlxscore=0 priorityscore=351 suspectscore=0 spamscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102110159 domainage_hfrom=9314 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3695901581_2066150501 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable =20 Nu need add =E2=80=9Cparameters synxtaxis for your second parm file=E2=80=9D=20 From: Tiglath Moradkhan Date: Thursday, February 11, 2021 at 12:28 PM To: "ROP=C3=93N-PALACIOS G." Cc: Subject: Re: namd-l: Problem with running NAMD config file =20 Yes. Here it is. =20 On Wed, Feb 10, 2021 at 8:06 PM "ROP=C3=93N-PALACIOS G." wrote: You can attach config file.=20 Enviado desde mi iPhone > El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan escribi=C3=B3: >=20 > =EF=BB=BF > To the NAMD community >=20 > I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein system = via a simple minimization and equilibration simulation. I've written the req= uired NAMD config file using the NAMD tutorials but when I try running it I = get the following error message:=20 >=20 > FATAL ERROR: tried before startup to read config file parameter that was = not set > while executing > "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/Californ= iaSeaLionApoA1/LipidBound/par_all36_lipid.prm" > (file "CSApoA1.conf" line 30) >=20 > I don't understand what the issue is. I've checked online to resolve the = issue and found that the .prm extension are for the parameter files so there= shouldn't be a problem with providing the correct parameter files. Therefor= e I'm confused why I'm getting this error message because I got these files = from the provided plugin tcl folder.=20 >=20 > I would be very glad for your help. >=20 >=20 > Thanks >=20 > Tiglath Moradkhan --B_3695901581_2066150501 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

 

Nu need ad= d =E2=80=9Cparameters synxtaxis for your second parm file=E2=80=9D

=

From: Tiglath Moradkhan <morad= khantig@gmail.com>
Date: Thursday, February 11, 2021 at 12:28 P= M
To: "ROP=C3=93N-PALACIOS G." <biodano.geo@gmail.com>=
Cc: <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: Pro= blem with running NAMD config file

 

Yes. Here it is= .

 

On Wed, Feb 10, 2021 at 8:06 PM "ROP=C3=93N-PALACIOS G."= ; <biodano.geo@gmail.com> w= rote:

<= p class=3DMsoNormal>You can attach config file.

Enviado desde mi iPhon= e

> El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan <moradkhantig@gmail.com<= /a>> escribi=C3=B3:
>
> =EF=BB=BF
> To the NAMD community
>= ;
> I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein= system via a simple minimization and equilibration simulation. I've written= the required NAMD config file using the NAMD tutorials but when I try runni= ng it I get the following error message:
>
> FATAL ERROR: trie= d before startup to read config file parameter that was not set
> = ;    while executing
> "C:/Users/tig_m/Documents/Thesis= ProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36= _lipid.prm"
>     (file "CSApoA1.conf" l= ine 30)
>
> I don't understand what the issue is. I've checked = online to resolve the issue and found that the .prm extension are for the pa= rameter files so there shouldn't be a problem with providing the correct par= ameter files. Therefore I'm confused why I'm getting this error message beca= use I got these files from the provided plugin tcl folder.
>
>= I would be very glad for your help.
>
>
> Thanks
>= ;
> Tiglath Moradkhan

<= /html> --B_3695901581_2066150501-- From owner-namd-l@halifax.ks.uiuc.edu Thu Feb 11 15:46:59 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BLkxx4012984; Thu, 11 Feb 2021 15:46:59 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11BLkxWJ012983; Thu, 11 Feb 2021 15:46:59 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BLkwwA012979; Thu, 11 Feb 2021 15:46:58 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11BLkwkb012977; Thu, 11 Feb 2021 15:46:58 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11BLkjQg012968 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000aa064905bb1674a2" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwSEQpMehcYHR4RCllEF25jfE1gTBlkb19hEQpYWBdiRUVda01CeUx JXxEKeE4XY1Nja3sTWH4aX14RCnlMF29nGH9QHB4fE2kcEQpDSBcHGBgcEQpDWRcHHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseEnEYExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThccX25ueExMQV5la0J8Znt/XXMdSGkTflhnTRJuWRlyRREKWFwXHwQaBBgYHgUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3J9GlpNEQpNXBcbEx4RCkxaF39pTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHBwEGx 0ZEQpCXhcbEQpEXhcYEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja 3sTWH4aX14RCkJFF3pwYBJGaGx8H05JEQpCThdjU2NrexNYfhpfXhEKQkwXYkVFXWtNQnlMSV8R CkJsF2hTT1sba2xSUkhZEQpCQBd6b2F5X0VIcB4TaREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClp YFxgRCnlDF2EdX05EcGNBHB4cEQpZSxcTGRseEQpwZxdpQ25QAVlzRwEeUxAaEQpwaBdmRmVZSV oBUkxEYBAaEQpwaBdoYkhJUEhSS3wcXhAaEQpwaBdkb3xpWU1Ff11YfRAaEQpwaBdkQWYacGV/G 2dBHBAaEQpwaBdtHEQBGW8bTR9meRAaEQpwbBdkWWJsGkJFSWB8HRAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 suspectscore=0 spamscore=0 malwarescore=0 priorityscore=274 adultscore=0 bulkscore=0 lowpriorityscore=0 impostorscore=0 mlxscore=0 phishscore=0 clxscore=168 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102110168 domainage_hfrom=9314 X-Spam-Score: 0 X-Spam-OrigSender: moradkhantig@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Tiglath Moradkhan --000000000000aa064905bb1674a2 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Josh OK. Thanks. That makes sense. Is there a parameter file in the tcl plugin for water? Thanks Tiglath On Thu, Feb 11, 2021 at 12:19 PM Ropon-Palacios G. wrote: > > > Nu need add =E2=80=9Cparameters synxtaxis for your second parm file=E2=80= =9D > > *From: *Tiglath Moradkhan > *Date: *Thursday, February 11, 2021 at 12:28 PM > *To: *"ROP=C3=93N-PALACIOS G." > *Cc: * > *Subject: *Re: namd-l: Problem with running NAMD config file > > > > Yes. Here it is. > > > > On Wed, Feb 10, 2021 at 8:06 PM "ROP=C3=93N-PALACIOS G." > wrote: > > You can attach config file. > > Enviado desde mi iPhone > > > El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan < > moradkhantig@gmail.com> escribi=C3=B3: > > > > =EF=BB=BF > > To the NAMD community > > > > I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein syste= m > via a simple minimization and equilibration simulation. I've written the > required NAMD config file using the NAMD tutorials but when I try running > it I get the following error message: > > > > FATAL ERROR: tried before startup to read config file parameter that wa= s > not set > > while executing > > > "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/Californ= iaSeaLionApoA1/LipidBound/par_all36_lipid.prm" > > (file "CSApoA1.conf" line 30) > > > > I don't understand what the issue is. I've checked online to resolve th= e > issue and found that the .prm extension are for the parameter files so > there shouldn't be a problem with providing the correct parameter files. > Therefore I'm confused why I'm getting this error message because I got > these files from the provided plugin tcl folder. > > > > I would be very glad for your help. > > > > > > Thanks > > > > Tiglath Moradkhan > > --000000000000aa064905bb1674a2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Josh

OK. Thanks. That makes sense. I= s there a parameter file in the tcl plugin for water?=C2=A0

<= /div>

Thanks

Tiglath

=C2=A0

Nu need add =E2=80=9Cparameters synxtaxis f= or your second parm file=E2=80=9D

From: Tiglath Moradkhan <moradkhantig@gmail.com>
Date: Thursday, Feb= ruary 11, 2021 at 12:28 PM
To: "ROP=C3=93N-PALACIOS G."= <biodano.geo= @gmail.com>
Cc: <namd-l@ks.uiuc.edu>
Subject: Re: namd-l:= Problem with running NAMD config file

<= p class=3D"MsoNormal">=C2=A0

Yes. Here it is.

= =C2=A0

On Wed, Feb 10, 2021 at 8= :06 PM "ROP=C3=93N-PALACIOS G." <biodano.geo@gmail.com> wrote:

You can attach= config file.

Enviado desde mi iPhone

> El 10 feb. 2021, = a la(s) 8:04 p. m., Tiglath Moradkhan <moradkhantig@gmail.com> escribi=C3=B3:>
> =EF=BB=BF
> To the NAMD community
>
> I&#= 39;m a new a NAMD user and I'm trying to equilibrate a lipoprotein syst= em via a simple minimization and equilibration simulation. I've written= the required NAMD config file using the NAMD tutorials but when I try runn= ing it I get the following error message:
>
> FATAL ERROR: tr= ied before startup to read config file parameter that was not set
>= =C2=A0 =C2=A0 =C2=A0while executing
> "C:/Users/tig_m/Documents/= ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/pa= r_all36_lipid.prm"
>=C2=A0 =C2=A0 =C2=A0(file "CSApoA1.conf= " line 30)
>
> I don't understand what the issue is. = I've checked online to resolve the issue and found that the .prm extens= ion are for the parameter files so there shouldn't be a problem with pr= oviding the correct parameter files. Therefore I'm confused why I'm= getting this error message because I got these files from the provided plu= gin tcl folder.
>
> I would be very glad for your help.
&g= t;
>
> Thanks
>
> Tiglath Moradkhan

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charset="us-ascii" Content-Transfer-Encoding: Quoted-printable Dear All, I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it. Thanks in advance. RPS Get Outlook for Android ________________________________ From: Raman Preet Singh Sent: Monday, January 18, 2021 11:51:23 PM To: NAMD list Subject: Infrared spectrum prediction Dear All, I have come across some papers where MD has been used to predict IR spectr= um of proteins. Is it possible to predict IR spectrum of small organic mole= cules from NAMD simulations? Can changes in IR spectra due to interactions = between two molecules (H-bonding, pi-pi interactions, etc ) be also predict= ed? Any papers, tutorials, scripts, etc. would be highly appreciated. Thanks in advance. Regards, Raman --_000_BMXPR01MB3526DCD754FC43A35A3E9D14B38B9BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: Quoted-printable
Dear All,

I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it.

Thanks in advance.

RPS


From: Raman Preet Singh
Sent: Monday, January 18, 2021 11:51:23 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Infrared spectrum prediction
 
Dear All,

I have come across some papers where MD has been  used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


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Fri, 12 Feb 2021 10:35:31 +0000 Received: from BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM (10.152.252.58) by PU1APC01FT023.mail.protection.outlook.com (10.152.253.4) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.3846.25 via Frontend Transport; Fri, 12 Feb 2021 10:35:31 +0000 Received: from BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM ([fe80::2828:baff:dcc1:f64d]) by BMXPR01MB3526.INDPRD01.PROD.OUTLOOK.COM ([fe80::2828:baff:dcc1:f64d%7]) with mapi id 15.20.3846.029; Fri, 12 Feb 2021 10:35:31 +0000 From: Raman Preet Singh To: NAMD list Subject: namd-l: Re: Maximum and minimum box size Thread-Topic: Maximum and minimum box size Thread-Index: AQHW7cSsVNRwnfSxsE6BWGnrzoA60qpUeb4b Date: Fri, 12 Feb 2021 10:35:31 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-incomingtopheadermarker: OriginalChecksum:DEEDB31D50F7B1EFBCABA8BB6BF5DD0EDA595819E17B29D0233C588285BEB614;UpperCasedChecksum:D96E813B28D43CC986686797E12DA4BA073876E43DF220C9CA3EFF1D424A1E6D;SizeAsReceived:6843;Count:44 x-ms-exchange-messagesentrepresentingtype: 1 x-tmn: [OOAmGWU9iR/3iGqdDUakCE1MakLdiMqr] x-ms-publictraffictype: Email x-incomingheadercount: 44 x-eopattributedmessage: 0 x-ms-office365-filtering-correlation-id: e881f235-ed37-4d66-f46b-08d8cf41ec2c x-ms-traffictypediagnostic: PU1APC01HT180: x-microsoft-antispam: BCL:0; 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charset="us-ascii" Content-Transfer-Encoding: Quoted-printable Dear NAMD Community, Reposting the question in case someone might help me. Regards, RPS Get Outlook for Android ________________________________ From: Raman Preet Singh Sent: Monday, January 18, 2021 11:46:42 PM To: NAMD list Subject: Maximum and minimum box size Dear All, I am interested in performing a simulation where one of the box dimensions = is expected to reach 50 nm. I have seen publications with 20+ nm water box = sides but not sure if 50 nm or higher dimensions are supported in NAMD. I w= ill be using MARTINI CG models. If 50 nm is supported, do I need to make an= y changes in the NAMD conf file? A related question is: what is the minimum box size supported? A 1 nm dista= nce from the sides of the solute is the ideal situation. However, if it is = just a solvent box, what is the minimum supported size (for AA and CG model= s)? Thank you in advance for your time and inputs. Regards, Raman --_000_BMXPR01MB35267360483817849054F4D1B38B9BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: Quoted-printable
Dear NAMD Community,

Reposting the question in case someone might help me.

Regards,
RPS


From: Raman Preet Singh
Sent: Monday, January 18, 2021 11:46:42 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Maximum and minimum box size
 
Dear All,

I am interested in performing a simulation where one of the box dimensions = is expected to reach 50 nm. I have seen publications with 20+ nm water box = sides but not sure if 50 nm or higher dimensions are supported in NAMD. I w= ill be using MARTINI CG models. If 50 nm is supported, do I need to make any changes in the NAMD conf file= ?

A related question is: what is the minimum box size supported? A 1 nm dista= nce from the sides of the solute is the ideal situation. However, if it is = just a solvent box, what is the minimum supported size (for AA and CG model= s)?

Thank you in advance for your time and inputs.

Regards,
Raman


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boundary="0000000000001d20f905bb218680" X-CLX-Response: 1TFkXGBITEQpMehcaEQpZRBdrR35TUmRfYmhEQhEKWFgXbH9ub3B8TlN5XB0 RCnhOF25+Q3J4RwVJAR5nEQp5TBdsSRpwR0ZGQhNaRxEKQ0gXBxgSGhEKQ1kXGxgYEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbHXEbBhkZdwYbEhkGGxoaQh0GGgYbGhoGGnEaEBp3BhoGBx8aBhoGB xwaBhoGGnEaEBp3BhoRClleF2hueREKSUYXX0NfSXVCRVleT04RCkNOF0IYY2J9TXhZe0lLQ0lZ W39SbB9wbV5HT11dXU1AQWdjEQpYXBcfBBoEGBgeBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3J ya3t4EQpNXBcYGR8RCkxaF3xpTWtrEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF2xraxEKQk 8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHBoEGx0ZEQpCXhcbEQpEXhcYEQpCRRdnWBlORUJwc 2RAZhEKQk4Xbn5DcnhHBUkBHmcRCkJMF2x/bm9wfE5TeVwdEQpCbBdua3xJfmIcEn55GhEKQkAX ekN/HkMYf0Z/eFwRCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGREKeUMXZlJgYF0aZ0Vscmw RCnBnF2lDblABWXNHAR5TEBkaEQpwaBdpWWJQAR1EXh5LbRAHGRoRCnBoF2NlT219fGFpYUFmEA cZGhEKcGgXZEV+ZHpeW1preWMQBxkaEQpwaBduR25tSUEaZRl5YhAHGRoRCnBoF25YE1BDbxhMW GQTEAcZGhEKcH0Xa2wZaFheQ0AYBWIQBxkaEQpwfxdhZm9bGmdkQkgdWxAbGx8RCnBfF2NiElBI Y3gffEJ9EBIfEQpwbBdjRGAfbFx5H1BJRxAHGRoRCm1+FwcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 bulkscore=0 impostorscore=0 mlxlogscore=881 malwarescore=0 suspectscore=0 lowpriorityscore=0 clxscore=289 adultscore=0 priorityscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102120085 X-Spam-Score: 0 X-Spam-OrigSender: moura@ufscar.br X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Andre Farias de Moura --0000000000001d20f905bb218680 Content-Type: text/plain; charset="UTF-8" Dear Raman, Although most people to date have relied on normal mode analysis to predict IR features, MD simulations can be used as well, with the advantage of sampling multiple energy minima (as compared to the single minimum in energy minimization protocols). It does not matter whether you have a large protein or small molecule in vacuum, procedures will be pretty much the same (maybe you might want to look at the TRAVIS program, which can handle MD simulations to extract IR). Please mind that you will still need normal mode analysis to assign the IR bands, since MD-based spectra yield only the convoluted bands. Regards Andre On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh < ramanpreetsingh@hotmail.com> wrote: > Dear All, > > I posted this earlier but received no directions. Reposting the same in > case someone who might help me missed it. > > Thanks in advance. > > RPS > > Get Outlook for Android > > > ------------------------------ > *From:* Raman Preet Singh > *Sent:* Monday, January 18, 2021 11:51:23 PM > *To:* NAMD list > *Subject:* Infrared spectrum prediction > > Dear All, > > I have come across some papers where MD has been used to predict IR > spectrum of proteins. Is it possible to predict IR spectrum of small > organic molecules from NAMD simulations? Can changes in IR spectra due to > interactions between two molecules (H-bonding, pi-pi interactions, etc ) be > also predicted? Any papers, tutorials, scripts, etc. would be highly > appreciated. > > Thanks in advance. > > Regards, > Raman > > > --0000000000001d20f905bb218680 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Raman,

Although most pe= ople to date have relied on normal mode analysis to predict IR features, MD= simulations can be used as well, with the advantage of sampling multiple e= nergy minima (as compared to the single minimum in energy minimization prot= ocols). It does not matter whether you have a large protein or small molecu= le in vacuum, procedures will be pretty much the same (maybe you might want= to look at the TRAVIS program, which can handle MD simulations to extract = IR).

Please mind that you will still need normal m= ode analysis to assign the IR bands, since MD-based spectra yield only the = convoluted bands.

Regards

Andre

On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh <ramanpreetsingh@hotmail.com&g= t; wrote:
Dear All,=

I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it.

Thanks in advance.

RPS


From= : Raman Preet Singh
Sent: Monday, January 18, 2021 11:51:23 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Infrared spectrum prediction
=C2=A0
Dear All,

I have come across some papers where MD has been=C2=A0 used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


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charset="us-ascii" Content-Transfer-Encoding: Quoted-printable Thanks Andre for the info. This was indeed very useful. Regards, Raman Get Outlook for Android ________________________________ From: Andre Farias de Moura Sent: Friday, February 12, 2021 4:29:00 PM To: namd-l@ks.uiuc.edu ; Raman Preet Singh Subject: Re: namd-l: Re: Infrared spectrum prediction Dear Raman, Although most people to date have relied on normal mode analysis to predict= IR features, MD simulations can be used as well, with the advantage of sam= pling multiple energy minima (as compared to the single minimum in energy m= inimization protocols). It does not matter whether you have a large protein= or small molecule in vacuum, procedures will be pretty much the same (mayb= e you might want to look at the TRAVIS program, which can handle MD simulat= ions to extract IR). Please mind that you will still need normal mode analysis to assign the IR = bands, since MD-based spectra yield only the convoluted bands. Regards Andre On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh > wrote: Dear All, I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it. Thanks in advance. RPS Get Outlook for Android ________________________________ From: Raman Preet Singh Sent: Monday, January 18, 2021 11:51:23 PM To: NAMD list > Subject: Infrared spectrum prediction Dear All, I have come across some papers where MD has been used to predict IR spectr= um of proteins. Is it possible to predict IR spectrum of small organic mole= cules from NAMD simulations? Can changes in IR spectra due to interactions = between two molecules (H-bonding, pi-pi interactions, etc ) be also predict= ed? Any papers, tutorials, scripts, etc. would be highly appreciated. Thanks in advance. Regards, Raman --_000_BMXPR01MB3526713F01510FB7F5C1AE16B38B9BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: Quoted-printable
Thanks Andre for the info. This was indeed very useful.

Regards,
Raman


From: Andre Farias de Moura= <moura@ufscar.br>
Sent: Friday, February 12, 2021 4:29:00 PM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>; Raman Preet Singh= <ramanpreetsingh@hotmail.com>
Subject: Re: namd-l: Re: Infrared spectrum prediction
 
Dear Raman,

Although most people to date have relied on normal mode analysis to pr= edict IR features, MD simulations can be used as well, with the advantage o= f sampling multiple energy minima (as compared to the single minimum in ene= rgy minimization protocols). It does not matter whether you have a large protein or small molecule in vacu= um, procedures will be pretty much the same (maybe you might want to look a= t the TRAVIS program, which can handle MD simulations to extract IR).

Please mind that you will still need normal mode analysis to assign th= e IR bands, since MD-based spectra yield only the convoluted bands.

Regards

Andre

On Fri, Feb 12, 2021 at 7:41 AM Ram= an Preet Singh <ramanpree= tsingh@hotmail.com> wrote:
Dear All,

I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it.

Thanks in advance.

RPS


Fr= om: Raman Preet Singh
Sent: Monday, January 18, 2021 11:51:23 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Infrared spectrum prediction
 
Dear All,

I have come across some papers where MD has been  used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


--_000_BMXPR01MB3526713F01510FB7F5C1AE16B38B9BMXPR01MB3526INDP_-- From owner-namd-l@halifax.ks.uiuc.edu Fri Feb 12 07:08:41 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11CD8fg6012006; Fri, 12 Feb 2021 07:08:41 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11CD8eEG012005; Fri, 12 Feb 2021 07:08:40 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11CD8ecb012001; Fri, 12 Feb 2021 07:08:40 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11CD8e7s012000; Fri, 12 Feb 2021 07:08:40 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11CD8UF7011990 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 12 Feb 2021 07:08:30 -0600 (CST) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 11CClhT9022971 for ; Fri, 12 Feb 2021 13:08:30 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 36m4p7cpbg-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 12 Feb 2021 13:08:29 +0000 Received: from [IPv6:2a02:810c:300:6724:a439:25ac:9bdc:ba55] ([IPv6:2a02:810c:300:6724:a439:25ac:9bdc:ba55]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 11CD8LpE192948 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 12 Feb 2021 14:08:26 +0100 To: "namd-l@ks.uiuc.edu" From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Subject: namd-l: Question about merging MW-eABF Message-ID: <6c7ada15-50e6-daad-7827-5a23da856f53@physik.uni-kl.de> Date: Fri, 12 Feb 2021 14:08:21 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="------------6DBCCB77F5DA2AC2E7162D57" Content-Language: de-DE X-Spam-Status: No, hits=2.002, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,URIBL_BLOCKED=0.001,URI_DOTEDU=1.999 X-Spam-Score: ** (2.002) X-Spam-Flag: NO X-CLX-Response: 1TFkXGxIaEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxkbGhEKQ1kXBxgaGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGnEZExAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdbfkIHXx5lRxxlWHl4fh1rb0tQY2tJGHhJUlIYE3JDeREKWFwXHwQaBBgYHgUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdycmlgWhEKTVwXGxkSEQpMWhdsaU1NTREKQk8XbF9sZl9 wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGhEKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCk JOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YGlJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2VpHF9Tf gETa0hhEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXb10BZU4FThJfZHkRCnBoF2UF XlJYW3hyQ2NHEBkaEQpwaBdsWmIcTFhnYR1kcxAZGhEKcGgXbWJPAVxYf11ZUHsQGRoRCnBoF2N dZx5nHXBCfWgdEBkaEQpwaBd6aB0dG0lLQENffxAZGhEKcH0XZUFmfE5OYUFseEcQGRoRCnB/F2 UZeWZeR2kbZE9zEBsaGhEKcF8Xa1pYclhiY0JpRUIQGRoRCnBsF3ofeHlveExDX3BEEBkaEQptf hcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 suspectscore=0 mlxlogscore=999 phishscore=0 bulkscore=0 malwarescore=0 spamscore=0 adultscore=0 clxscore=180 priorityscore=0 mlxscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102120101 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------6DBCCB77F5DA2AC2E7162D57 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear, I have ran multiple setups of MW-eABF with 4 replicas. The namd ug states at https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION000126230000000000000 that one has to merge the results together using the tcl script *eabf.tcl* Do understand it correctly that this is only necessary when using the Zheng/Yang estimator of the free energy but not the CZAR estimator where this is automatically done via the "shared on" flag or does this sharing on only reflect for the standard abf output files? It confuses me a bit. Checking  one of my setups with 4 replicas ran for 20.000.000 steps with timestep of 2fs -> in total 160ns.     When calculating the number of counts in the replica0.zcount file I get a sum of 19kk (~20kk, I did not use expandBoundaries here)     While the  replica.count file results in ~80kk counts (-> already merged results) If I still need to merge I am missing the single czar files for the replicas 1-3. Are those only saved with the option `*writeCZARwindowFile **on`?* Kind regards René -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------6DBCCB77F5DA2AC2E7162D57 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Dear,


I have ran multiple setups of MW-eABF with 4 replicas.

The namd ug states at https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION000126230000000000000
that one has to merge the results together using the tcl script eabf.tcl

Do understand it correctly that this is only necessary when using the Zheng/Yang estimator of the free energy

but not the CZAR estimator where this is automatically done via the "shared on" flag or does this sharing on only reflect for the standard abf output files?

It confuses me a bit.

Checking  one of my setups with 4 replicas ran for 20.000.000 steps with timestep of 2fs -> in total 160ns.

    When calculating the number of counts in the replica0.zcount file I get a sum of 19kk (~20kk, I did not use expandBoundaries here)

    While the  replica.count file results in ~80kk counts (-> already merged results)


If I still need to merge I am missing the single czar files for the replicas 1-3.

Are those only saved with the option `writeCZARwindowFile on`?



Kind regards
René

--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="000000000000a98fc105bb23b691" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx8bEQpMehcaEQpZRBdrR35TUmRfYmhEQhEKWFgXbH9ub3B8TlN5XB0 RCnhOF25+Q3J4RwVJAR5nEQp5TBdsSRpwR0ZGQhNaRxEKQ0gXBxkcGBEKQ1kXGxgYEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcHGRpxHQYHEncGGxIbBhsaGkIbGwYaBh0fBhIfcRwQGncGGgYHGBoaB hoGBxwaBhoGGnEaEBp3BhoRClleF2hueREKSUYXX0NfSXVCRVleT04RCkNOF1t8S1NmdU5OBxlz YhxCGE4eGURHY1B4b0FafUtMTVldEQpYXBcfBBoEGBgeBRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5 ZF3JyaUBlEQpNXBcbHxoRCkxaF2l8aU1rTREKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdsa2 sRCkJPF2tBU0weElpvTxJsEQpDWhcYGhMEEh8EGxwaBBscExEKQl4XGxEKREkXGBEKQkUXZ1gZT kVCcHNkQGYRCkJOF25+Q3J4RwVJAR5nEQpCTBdsf25vcHxOU3lcHREKQmwXbmt8SX5iHBJ+eRoR CkJAF3pDfx5DGH9Gf3hcEQpCWBdnc2VzQG5hYUxdYhEKWlgXHBEKeUMXZlJgYF0aZ0VscmwRCnB nF2lDblABWXNHAR5TEBgYEQpwaBdjZU9tfXxhaWFBZhAHHhIRCnBoF2RFfmR6Xltaa3ljEAceEh EKcGgXbUlGGhtpHlkaY0gQGhEKcGgXY2Jca3pjbnsfGhkQGhEKcGgXblgTUENvGExYZBMQBx4SE QpwfRdjUGFcQmlNe1oeHhASHBEKcH0Xa2wZaFheQ0AYBWIQBxsSEQpwfxdvG0ISRUxvGEZZHxAb GxsRCnBfF20dZFtCfXNEEh4BEBIcEQpwfxdhZm9bGmdkQkgdWxAbGR8RCnBfF2NiElBIY3gffEJ 9EBsaHBEKcGwXY0RgH2xceR9QSUcQBx4SEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 mlxlogscore=897 impostorscore=0 spamscore=0 adultscore=0 priorityscore=0 clxscore=151 phishscore=0 suspectscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102120105 X-Spam-Score: 0 X-Spam-OrigSender: moura@ufscar.br X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Andre Farias de Moura --000000000000a98fc105bb23b691 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Raman, If your system is small enough, I would recommend ab initio MD to avoid the harmonic approximation issues and also possible parameterization caveats. Regards Andre On Fri, Feb 12, 2021 at 8:14 AM Raman Preet Singh < ramanpreetsingh@hotmail.com> wrote: > Thanks Andre for the info. This was indeed very useful. > > Regards, > Raman > > Get Outlook for Android > > ------------------------------ > *From:* Andre Farias de Moura > *Sent:* Friday, February 12, 2021 4:29:00 PM > *To:* namd-l@ks.uiuc.edu ; Raman Preet Singh < > ramanpreetsingh@hotmail.com> > *Subject:* Re: namd-l: Re: Infrared spectrum prediction > > Dear Raman, > > Although most people to date have relied on normal mode analysis to > predict IR features, MD simulations can be used as well, with the advanta= ge > of sampling multiple energy minima (as compared to the single minimum in > energy minimization protocols). It does not matter whether you have a lar= ge > protein or small molecule in vacuum, procedures will be pretty much the > same (maybe you might want to look at the TRAVIS program, which can handle > MD simulations to extract IR). > > Please mind that you will still need normal mode analysis to assign the IR > bands, since MD-based spectra yield only the convoluted bands. > > Regards > > Andre > > On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh < > ramanpreetsingh@hotmail.com> wrote: > > Dear All, > > I posted this earlier but received no directions. Reposting the same in > case someone who might help me missed it. > > Thanks in advance. > > RPS > > Get Outlook for Android > > > ------------------------------ > *From:* Raman Preet Singh > *Sent:* Monday, January 18, 2021 11:51:23 PM > *To:* NAMD list > *Subject:* Infrared spectrum prediction > > Dear All, > > I have come across some papers where MD has been used to predict IR > spectrum of proteins. Is it possible to predict IR spectrum of small > organic molecules from NAMD simulations? Can changes in IR spectra due to > interactions between two molecules (H-bonding, pi-pi interactions, etc ) = be > also predicted? Any papers, tutorials, scripts, etc. would be highly > appreciated. > > Thanks in advance. > > Regards, > Raman > > > --000000000000a98fc105bb23b691 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear Raman,

If your system i= s small enough, I would recommend ab initio MD to avoid the harmonic approx= imation issues and also possible parameterization caveats.

Regards

Andre

On Fri, Feb 12, 20= 21 at 8:14 AM Raman Preet Singh <ramanpreetsingh@hotmail.com> wrote:
Thanks Andre for the info. This was indeed very useful.

Regards,
Raman

<= span id=3D"gmail-m_-7995917065343334322OutlookSignature">

Fro= m: Andre Farias de Moura <moura@ufscar.br>
Sent: Friday, February 12, 2021 4:29:00 PM
To: namd-l@k= s.uiuc.edu <= namd-l@ks.uiuc.edu>; Raman Preet Singh <ramanpreetsingh@hotmail.com>=
Subject: Re: namd-l: Re: Infrared spectrum prediction
=C2=A0
Dear Raman,

Although most people to date have relied on normal mode analysis to pr= edict IR features, MD simulations can be used as well, with the advantage o= f sampling multiple energy minima (as compared to the single minimum in ene= rgy minimization protocols). It does not matter whether you have a large protein or small molecule in vacu= um, procedures will be pretty much the same (maybe you might want to look a= t the TRAVIS program, which can handle MD simulations to extract IR).

Please mind that you will still need normal mode analysis to assign th= e IR bands, since MD-based spectra yield only the convoluted bands.

Regards

Andre

On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh <ramanpreetsing= h@hotmail.com> wrote:
Dear All,

I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it.

Thanks in advance.

RPS


From: Raman Preet Singh
Sent: Monday, January 18, 2021 11:51:23 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Infrared spectrum prediction
=C2=A0
Dear All,

I have come across some papers where MD has been=C2=A0 used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


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boundary="00000000000050342905bb3164b9" X-CLX-Response: 1TFkXGxIaEQpMehcZHBoRCllEF2RDZXNsa2NuaX5iEQpYWBdjE0ZnbVxPG0l pYxEKeE4XY1Nja3sTWH4aX14RCnlMF2l5HEJ9QnMBG2QeEQpDSBcHGxIaEQpDWRcHGxsZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwacRkTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx5dQxNIUFldT2FBEhJLfF5CZRgZQF9bGloSRHJaT39TEQpYXBcfBBoEGBge BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXcnJ7H2YRCk1cFxsfGhEKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGxIYEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2ITelhYXGVMEn1BEQpCThdjU2Nre xNYfhpfXhEKQkwXYxNGZ21cTxtJaWMRCkJsF2d5bGhif29jYWB4EQpCQBdsT2MbXUJwRlpYSREK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2AefEYSUhp9c1loEQpZSxcTGRscEQpwaBd lc2MSG19GRgEZYBAZGhEKcGgXemEfQkh9Q0xDQnwQGRoRCnBoF2NBHQVtSW5EQHx4EBkaEQpwaB dvSAVwaUNjblAeTBAZGhEKcGgXYhpcBUhZAVxvXF8QGRoRCnBsF25rG2BITR1TRFBJEBkaEQptf hcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 clxscore=180 adultscore=0 mlxlogscore=742 malwarescore=0 mlxscore=0 spamscore=0 lowpriorityscore=0 priorityscore=360 impostorscore=0 bulkscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102130049 domainage_hfrom=9316 X-Spam-Score: 0 X-Spam-OrigSender: jialiwangnamd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, jiali wang --00000000000050342905bb3164b9 Content-Type: text/plain; charset="UTF-8" Dear NAMD users, I have an error when I calculate the dihedral angle, the calculation performed in the VMD. code as below, but it says "expected integer but got "$sel1" measure dihed: bad atom index". Do you know what happened? Thank you so much!! Jiali set selA [atomselect top "segname PP5 and name C"] set selB [atomselect top "segname PP5 and name CA"] set selC [atomselect top "segname PP5 and name CB"] set selD [atomselect top "segname PP5 and name CG"] set sel1 [[atomselect top "$selA"] get index] set sel2 [[atomselect top "$selB"] get index] set sel3 [[atomselect top "$selC"] get index] set sel4 [[atomselect top "$selD"] get index] set nf [molinfo top get numframes] set outfile [open dihed-cal.dat w] for {set i 0} {$i < $nf} {incr i} { puts "frame $i of $nf" set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}] puts $outfile "$i $dihedlist" --00000000000050342905bb3164b9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD users,
I have an error when I calculate the = dihedral=C2=A0angle, the calculation performed in the VMD. code as below, b= ut it says=C2=A0"expected integer but got "$sel1" measure di= hed: bad atom index". Do you know what happened?=C2=A0
Thank= you so much!!
Jiali=C2=A0

set selA [ato= mselect top "segname PP5 and name C"]
set selB [atomselect t= op "segname PP5 and name CA"]
set selC [atomselect top "s= egname PP5 and name CB"]
set selD [atomselect top "segname PP5= and name CG"]

set sel1 [[atomselect top "$selA"] get= index]
set sel2 [[atomselect top "$selB"] get index]
set s= el3 [[atomselect top "$selC"] get index]
set sel4 [[atomselect= top "$selD"] get index]

set nf [molinfo top get numframes= ]
set outfile [open dihed-cal.dat w]
for {set i 0} {$i < $nf} {inc= r i} {

=C2=A0 puts "frame $i of $nf"

=C2=A0 set dih= edlist [measure dihed {$sel1 $sel2 $sel3 $sel4}]
=C2=A0 puts $outfile &q= uot;$i $dihedlist"
--00000000000050342905bb3164b9-- From owner-namd-l@halifax.ks.uiuc.edu Sat Feb 13 18:40:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11E0eaqA004278; Sat, 13 Feb 2021 18:40:36 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11E0eaVU004277; Sat, 13 Feb 2021 18:40:36 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11E0eZFe004273; Sat, 13 Feb 2021 18:40:35 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11E0eZ1S004272; Sat, 13 Feb 2021 18:40:35 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11E0eLrh004264 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000001db4a305bb411de8" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBseEQpMehcdEhEKWUQXZ0xTRxloEmhHTHsRClhYF2NYZkF+bEhYYFJ 7EQp4ThdhfmZJQ319XFgdQBEKeUwXb09/bgEaeUsfU2URCkNIFwcYEx4RCkNZFxkRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbEx5xGx0ZEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFx1FRGZOT0Vrf0FBaW1bGW19Ull5QUdpc019fB9JHwdAEQpYXBcfBBoEGBgeBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JyQnN6EQpNXBcYEhEKTFoXeGlNTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdsexhwXkVeZEITSREKQ1oXGBoTBBIfBBgbHgQbHR 4RCkJeFxsRCkReFxkRCkJcFxsRCl5OFxsRCkJLF2F+ZklDfX1cWB1AEQpCSRdhfmZJQ319XFgdQ BEKQkUXZhgefW5gSEtmRXIRCkJOF2F+ZklDfX1cWB1AEQpCTBdjWGZBfmxIWGBSexEKQmwXbW9m HFxvfl9bY1wRCkJAF25scnlGWB4caBJ8EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUM XYB0SRlBBWhscc1gRCllLFxsYExseEQpwaBdven57Qmd4GUlaHhAZGhEKcGgXZV4aGk1IaU5iHl oQGRoRCnBoF2lZWGxjY2FfWX1PEBkaEQpwaBdvSAVwaUNjblAeTBAaEQpwaBdgfF1YbUxbbVNsa BAZGhEKcH0Xa0tzb3BYSFxCRG0QGRoRCnB/F2UZeWZeR2kbZE9zEBMaEQpwXxdiSXphH1JMQkh8 HBAZGhEKcGwXZkxhGkh4cB98Ym8QGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=78 lowpriorityscore=0 phishscore=0 impostorscore=0 adultscore=0 malwarescore=0 clxscore=214 suspectscore=0 bulkscore=0 mlxlogscore=999 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102140001 domainage_hfrom=12914 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --0000000000001db4a305bb411de8 Content-Type: text/plain; charset="UTF-8" The arguments to `measure dihed` are supposed to be atom indices, not atom selections. See https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html Best, Peter On Sat, Feb 13, 2021 at 1:56 AM jiali wang wrote: > Dear NAMD users, > I have an error when I calculate the dihedral angle, the calculation > performed in the VMD. code as below, but it says "expected integer but got > "$sel1" measure dihed: bad atom index". Do you know what happened? > Thank you so much!! > Jiali > > set selA [atomselect top "segname PP5 and name C"] > set selB [atomselect top "segname PP5 and name CA"] > set selC [atomselect top "segname PP5 and name CB"] > set selD [atomselect top "segname PP5 and name CG"] > > set sel1 [[atomselect top "$selA"] get index] > set sel2 [[atomselect top "$selB"] get index] > set sel3 [[atomselect top "$selC"] get index] > set sel4 [[atomselect top "$selD"] get index] > > set nf [molinfo top get numframes] > set outfile [open dihed-cal.dat w] > for {set i 0} {$i < $nf} {incr i} { > > puts "frame $i of $nf" > > set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}] > puts $outfile "$i $dihedlist" > --0000000000001db4a305bb411de8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
The arguments to `measure dihed` are supposed to be a= tom indices, not atom selections. See https://www.ks.uiuc.edu/Research/vmd/= vmd-1.8.6/ug/node124.html

Best,
Pete= r

On Sat, Feb 13, 2021 at 1:56 AM jiali wang <jialiwangnamd@gmail.com> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex">
Dear NAMD= users,
I have an error when I calculate the dihedral=C2=A0angle, the c= alculation performed in the VMD. code as below, but it says=C2=A0"expe= cted integer but got "$sel1" measure dihed: bad atom index".= Do you know what happened?=C2=A0
Thank you so much!!
J= iali=C2=A0

set selA [atomselect top "segname = PP5 and name C"]
set selB [atomselect top "segname PP5 and n= ame CA"]
set selC [atomselect top "segname PP5 and name CB&quo= t;]
set selD [atomselect top "segname PP5 and name CG"]
set sel1 [[atomselect top "$selA"] get index]
set sel2 [[atom= select top "$selB"] get index]
set sel3 [[atomselect top "= ;$selC"] get index]
set sel4 [[atomselect top "$selD"] ge= t index]

set nf [molinfo top get numframes]
set outfile [open dih= ed-cal.dat w]
for {set i 0} {$i < $nf} {incr i} {

=C2=A0 puts = "frame $i of $nf"

=C2=A0 set dihedlist [measure dihed {$se= l1 $sel2 $sel3 $sel4}]
=C2=A0 puts $outfile "$i $dihedlist"
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boundary="0000000000009637e005bb43ffe6" X-CLX-Response: 1TFkXGBsSEQpMehcbGhIRCllEF29cZxwBQ2hGaRN5EQpYWBdjUkVnH1t9Zkt uUxEKeE4XYXMfbUheSEReG18RCnlMF2l5HEJ9QnMBG2QeEQpDSBcHGRsYEQpDWRcSHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsTEnEbExsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XH25yZHBGRk1ybhNOaFt/B2RBRXB8XGVle3ITR0JQbVIRClhcFx8EGgQYGB4F GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdyckFwGxEKTVwXGRsYEQpMWhd7aWtdaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF20TYBMBYVprbUASEQpDWhcYGhMEEh8EGBsfBB sdHREKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXYXMfbUheSEReG18RCkJJF2FzH21IXkhEX htfEQpCRRdtHmhbE2ddfRpzRxEKQk4XYXMfbUheSEReG18RCkJMF2NSRWcfW31mS25TEQpCbBdp aUQZXkFSS2VwZREKQkAXbktcaV8YQmlcSxsRCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdrYUR nZXpGT0RnZhEKWUsXGxgZGh4RCnBnF2RGbBh8a2cYRE9oEBkaEQpwaBdsHn1ufxMYYGtpchAZGh EKcGgXYVNSZhoefEAfTWEQGRoRCnBoF2tvX2MbU2VJWEBtEBkaEQpwaBdoZGBoc3hMXUhSfBAZG hEKcGgXb0gFcGlDY25QHkwQHBoRCnB9F2tLc29wWEhcQkRtEB4SEQpwfxdlGXlmXkdpG2RPcxAT HxEKcF8XYkl6YR9STEJIfBwQHhIRCnBsF2JESWsceR5SGGljEBkaEQpwTBdtaGUZQVJ9exhFUhA ZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 clxscore=218 adultscore=0 mlxlogscore=999 malwarescore=0 mlxscore=0 spamscore=0 lowpriorityscore=0 priorityscore=108 impostorscore=0 bulkscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102140033 domainage_hfrom=12304 X-Spam-Score: 0 X-Spam-OrigSender: jwang204@binghamton.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jiali Wang --0000000000009637e005bb43ffe6 Content-Type: text/plain; charset="UTF-8" Dear Peter, Thank you for your reply. I use "set sel1 [[atomselect top "$selA"] get index]" to get index, is there something wrong here? I am very new to the script part of calculations. I appreciate your help very much. best, Jiali On Sat, Feb 13, 2021 at 7:48 PM Peter Freddolino wrote: > The arguments to `measure dihed` are supposed to be atom indices, not atom > selections. See > https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html > > Best, > Peter > > On Sat, Feb 13, 2021 at 1:56 AM jiali wang > wrote: > >> Dear NAMD users, >> I have an error when I calculate the dihedral angle, the calculation >> performed in the VMD. code as below, but it says "expected integer but got >> "$sel1" measure dihed: bad atom index". Do you know what happened? >> Thank you so much!! >> Jiali >> >> set selA [atomselect top "segname PP5 and name C"] >> set selB [atomselect top "segname PP5 and name CA"] >> set selC [atomselect top "segname PP5 and name CB"] >> set selD [atomselect top "segname PP5 and name CG"] >> >> set sel1 [[atomselect top "$selA"] get index] >> set sel2 [[atomselect top "$selB"] get index] >> set sel3 [[atomselect top "$selC"] get index] >> set sel4 [[atomselect top "$selD"] get index] >> >> set nf [molinfo top get numframes] >> set outfile [open dihed-cal.dat w] >> for {set i 0} {$i < $nf} {incr i} { >> >> puts "frame $i of $nf" >> >> set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}] >> puts $outfile "$i $dihedlist" >> > --0000000000009637e005bb43ffe6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Peter,
Thank you for your=C2=A0reply. I use "= ;set sel1 [[atomselect top "$selA"] get index]" to get index= , is there something wrong here?
=C2=A0I am very new to the scrip= t part of calculations. I appreciate your help very=C2=A0much.
be= st,
Jiali

On Sat, Feb 13, 2021 at 7:48 PM Peter Freddolino &= lt;petefred@umich.edu> wrote:<= br>
The arguments to `measure dihed` are supposed to be atom indices, not= atom selections. See https://www.ks.uiuc.edu/Research/vm= d/vmd-1.8.6/ug/node124.html

Best,
Pe= ter

On Sat, Feb 13, 2021 at 1:56 AM jiali wang <jialiwangnamd@gmail.com&g= t; wrote:
Dear NAMD users,
I have an error when I calculate the dihedr= al=C2=A0angle, the calculation performed in the VMD. code as below, but it = says=C2=A0"expected integer but got "$sel1" measure dihed: b= ad atom index". Do you know what happened?=C2=A0
Thank you s= o much!!
Jiali=C2=A0

set selA [atomselec= t top "segname PP5 and name C"]
set selB [atomselect top &qu= ot;segname PP5 and name CA"]
set selC [atomselect top "segname= PP5 and name CB"]
set selD [atomselect top "segname PP5 and n= ame CG"]

set sel1 [[atomselect top "$selA"] get index= ]
set sel2 [[atomselect top "$selB"] get index]
set sel3 [[= atomselect top "$selC"] get index]
set sel4 [[atomselect top &= quot;$selD"] get index]

set nf [molinfo top get numframes]
s= et outfile [open dihed-cal.dat w]
for {set i 0} {$i < $nf} {incr i} {=

=C2=A0 puts "frame $i of $nf"

=C2=A0 set dihedlist= [measure dihed {$sel1 $sel2 $sel3 $sel4}]
=C2=A0 puts $outfile "$i= $dihedlist"
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boundary="000000000000d094fc05bb444f52" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIdEQpMehcbGBIRCllEF2dMU0cZaBJoR0x7EQpYWBdjWGZBfmxIWGB SexEKeE4XYX5mSUN9fVxYHUARCnlMF29Pf24BGnlLH1NlEQpDSBcHGBwZEQpDWRcSHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscHXEeHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdTTExoT01SbG1zaGVaGx5fRRgdRVt4fAdrXWdYa11vbxEKWFwXHwQaBBgYHgUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3JyQV8YEQpNXBcYHB0RCkxaF2l7aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2x7GHBeRV5kQhNJEQpDWhcYGhMEEh8EGBseBB sSGhEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXYX5mSUN9fVxYHUARCkJJF2F+ZklDfX1cW B1AEQpCRRdmGB59bmBIS2ZFchEKQk4XYX5mSUN9fVxYHUARCkJMF2NYZkF+bEhYYFJ7EQpCbBdt b2YcXG9+X1tjXBEKQkAXbktcaV8YQmlcSxsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdrYURnZXpGT0RnZhEKWUsXGxgTGx4RCnBnF2IBQ0hpYGNEbF4YEBoRCnBoF2tvX2MbU2VJWE BtEBkaEQpwaBduU1BwSH58BUh/cxAaEQpwaBdlUwFbcn97RF1ERxAaEQpwaBdgcBhwRl1hUlhTf BAaEQpwaBdvSAVwaUNjblAeTBAZGhEKcH0Xa0tzb3BYSFxCRG0QHBoRCnBnF2RGbBh8a2cYRE9o EB4SEQpwfxdlGXlmXkdpG2RPcxAbGh4RCnBfF2JJemEfUkxCSHwcEBwaEQpwbBdmTGEaSHhwH3x ibxAZGhEKcEwXbWhlGUFSfXsYRVIQGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 mlxlogscore=999 malwarescore=0 phishscore=0 impostorscore=0 spamscore=0 lowpriorityscore=0 priorityscore=128 adultscore=0 mlxscore=0 clxscore=187 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102140036 domainage_hfrom=12914 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --000000000000d094fc05bb444f52 Content-Type: text/plain; charset="UTF-8" Ah my fault, I should have read more carefully, I assumed incorrectly that the variables named "$sel1", etc in the measure dihed call were atom selections. Ok, so a couple of suggestions. -Every time you make an atom selection, you need to explicitly delete it. The use of anonymous atom selections, as in your 'set sel1 ...' lines of code, will leave them hanging around and cause a memory leak. -Rather than do set selA [atomselect top "segname PP5 and name C"] ... set sel1 [[atomselect top "$selA"] get index] why not just do set selA [atomselect top "segname PP5 and name C"] set ind1 [$selA get index] (and then you'd want to add $selA delete to avoid the memory leak noted above) -at the end of the day, in tcl, using curly braces ({}) to construct a list does NOT allow substitution of variables. You'll instead want [list $ind1 $ind2 $ind3 $ind4] or some such Best, Peter On Sat, Feb 13, 2021 at 11:06 PM Jiali Wang wrote: > Dear Peter, > Thank you for your reply. I use "set sel1 [[atomselect top "$selA"] get > index]" to get index, is there something wrong here? > I am very new to the script part of calculations. I appreciate your help > very much. > best, > Jiali > > On Sat, Feb 13, 2021 at 7:48 PM Peter Freddolino > wrote: > >> The arguments to `measure dihed` are supposed to be atom indices, not >> atom selections. See >> https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html >> >> Best, >> Peter >> >> On Sat, Feb 13, 2021 at 1:56 AM jiali wang >> wrote: >> >>> Dear NAMD users, >>> I have an error when I calculate the dihedral angle, the calculation >>> performed in the VMD. code as below, but it says "expected integer but got >>> "$sel1" measure dihed: bad atom index". Do you know what happened? >>> Thank you so much!! >>> Jiali >>> >>> set selA [atomselect top "segname PP5 and name C"] >>> set selB [atomselect top "segname PP5 and name CA"] >>> set selC [atomselect top "segname PP5 and name CB"] >>> set selD [atomselect top "segname PP5 and name CG"] >>> >>> set sel1 [[atomselect top "$selA"] get index] >>> set sel2 [[atomselect top "$selB"] get index] >>> set sel3 [[atomselect top "$selC"] get index] >>> set sel4 [[atomselect top "$selD"] get index] >>> >>> set nf [molinfo top get numframes] >>> set outfile [open dihed-cal.dat w] >>> for {set i 0} {$i < $nf} {incr i} { >>> >>> puts "frame $i of $nf" >>> >>> set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}] >>> puts $outfile "$i $dihedlist" >>> >> --000000000000d094fc05bb444f52 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Ah my fault, I should have read more carefully, I ass= umed incorrectly that the variables named "$sel1", etc in the mea= sure dihed call were atom selections.
Ok, so a couple of sug= gestions.
-Every time you make an atom selection, you need to exp= licitly delete it. The use of anonymous atom selections, as in your 'se= t sel1 ...' lines of code, will leave them hanging around and cause a m= emory leak.

-Rather than do
=C2=A0 set s= elA [atomselect top "segname PP5 and name C"]
=C2=A0 ..= .
=C2=A0 set sel1 [[atomselect top "$selA"] get index]<= /div>
why not just do
=C2=A0 set selA [atomselect top &qu= ot;segname PP5 and name C"]
=C2=A0 set ind1 [$selA get index= ]
(and then you'd want to add
=C2=A0 $selA del= ete
to avoid the memory leak noted above)

-at the end of the day, in tcl, using curly braces ({}) to construct a li= st does NOT allow substitution of variables. You'll instead want
<= div>=C2=A0 [list $ind1 $ind2 $ind3 $ind4]
or some such
=
Best,
Peter



On Sat, Feb 13, 2021 at 11:06 PM Jiali Wang <jwang204@binghamton.edu> wrote:
Dear Peter,
Th= ank you for your=C2=A0reply. I use "set sel1 [[atomselect top "$s= elA"] get index]" to get index, is there something wrong here?
=C2=A0I am very new to the script part of calculations. I appreciat= e your help very=C2=A0much.
best,
Jiali

=
On Sat, Fe= b 13, 2021 at 7:48 PM Peter Freddolino <petefred@umich.edu> wrote:
The argumen= ts to `measure dihed` are supposed to be atom indices, not atom selections.= See https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/no= de124.html

Best,
Peter

On S= at, Feb 13, 2021 at 1:56 AM jiali wang <jialiwangnamd@gmail.com> wrote:
Dear N= AMD users,
I have an error when I calculate the dihedral=C2=A0angle, th= e calculation performed in the VMD. code as below, but it says=C2=A0"e= xpected integer but got "$sel1" measure dihed: bad atom index&quo= t;. Do you know what happened?=C2=A0
Thank you so much!!
Jiali=C2=A0

set selA [atomselect top "segna= me PP5 and name C"]
set selB [atomselect top "segname PP5 an= d name CA"]
set selC [atomselect top "segname PP5 and name CB&= quot;]
set selD [atomselect top "segname PP5 and name CG"]
=
set sel1 [[atomselect top "$selA"] get index]
set sel2 [[a= tomselect top "$selB"] get index]
set sel3 [[atomselect top &q= uot;$selC"] get index]
set sel4 [[atomselect top "$selD"]= get index]

set nf [molinfo top get numframes]
set outfile [open = dihed-cal.dat w]
for {set i 0} {$i < $nf} {incr i} {

=C2=A0 pu= ts "frame $i of $nf"

=C2=A0 set dihedlist [measure dihed {= $sel1 $sel2 $sel3 $sel4}]
=C2=A0 puts $outfile "$i $dihedlist"=
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charset="UTF-8" Dear Peter, Thank you so much for your suggestions. let me work on this and get back to you. best, Jiali On Sat, Feb 13, 2021 at 11:30 PM Peter Freddolino wrote: > Ah my fault, I should have read more carefully, I assumed incorrectly that > the variables named "$sel1", etc in the measure dihed call were atom > selections. > Ok, so a couple of suggestions. > -Every time you make an atom selection, you need to explicitly delete it. > The use of anonymous atom selections, as in your 'set sel1 ...' lines of > code, will leave them hanging around and cause a memory leak. > > -Rather than do > set selA [atomselect top "segname PP5 and name C"] > ... > set sel1 [[atomselect top "$selA"] get index] > why not just do > set selA [atomselect top "segname PP5 and name C"] > set ind1 [$selA get index] > (and then you'd want to add > $selA delete > to avoid the memory leak noted above) > > -at the end of the day, in tcl, using curly braces ({}) to construct a > list does NOT allow substitution of variables. You'll instead want > [list $ind1 $ind2 $ind3 $ind4] > or some such > > Best, > Peter > > > > On Sat, Feb 13, 2021 at 11:06 PM Jiali Wang > wrote: > >> Dear Peter, >> Thank you for your reply. I use "set sel1 [[atomselect top "$selA"] get >> index]" to get index, is there something wrong here? >> I am very new to the script part of calculations. I appreciate your help >> very much. >> best, >> Jiali >> >> On Sat, Feb 13, 2021 at 7:48 PM Peter Freddolino >> wrote: >> >>> The arguments to `measure dihed` are supposed to be atom indices, not >>> atom selections. See >>> https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html >>> >>> Best, >>> Peter >>> >>> On Sat, Feb 13, 2021 at 1:56 AM jiali wang >>> wrote: >>> >>>> Dear NAMD users, >>>> I have an error when I calculate the dihedral angle, the calculation >>>> performed in the VMD. code as below, but it says "expected integer but got >>>> "$sel1" measure dihed: bad atom index". Do you know what happened? >>>> Thank you so much!! >>>> Jiali >>>> >>>> set selA [atomselect top "segname PP5 and name C"] >>>> set selB [atomselect top "segname PP5 and name CA"] >>>> set selC [atomselect top "segname PP5 and name CB"] >>>> set selD [atomselect top "segname PP5 and name CG"] >>>> >>>> set sel1 [[atomselect top "$selA"] get index] >>>> set sel2 [[atomselect top "$selB"] get index] >>>> set sel3 [[atomselect top "$selC"] get index] >>>> set sel4 [[atomselect top "$selD"] get index] >>>> >>>> set nf [molinfo top get numframes] >>>> set outfile [open dihed-cal.dat w] >>>> for {set i 0} {$i < $nf} {incr i} { >>>> >>>> puts "frame $i of $nf" >>>> >>>> set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}] >>>> puts $outfile "$i $dihedlist" >>>> >>> --000000000000e2609f05bb445efa Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Peter,
Thank you so much for your suggestions. le= t me work on this and get back to you.
best,
Jiali

On Sat, Feb 13, 2021 at 11:30 PM Peter Freddolino <petefred@umich.edu> wrote:
Ah my fault, I sh= ould have read more carefully, I assumed incorrectly that the variables nam= ed "$sel1", etc in the measure dihed call were atom selections. <= br>
Ok, so a couple of suggestions.
-Every time you mak= e an atom selection, you need to explicitly delete it. The use of anonymous= atom selections, as in your 'set sel1 ...' lines of code, will lea= ve them hanging around and cause a memory leak.

-R= ather than do
=C2=A0 set selA [atomselect top "segname PP5 a= nd name C"]
=C2=A0 ...
=C2=A0 set sel1 [[atomselec= t top "$selA"] get index]
why not just do
=C2=A0 set selA [atomselect top "segname PP5 and name C"]
<= div>=C2=A0 set ind1 [$selA get index]
(and then you'd want to= add
=C2=A0 $selA delete
to avoid the memory leak = noted above)

-at the end of the day, in tcl, using= curly braces ({}) to construct a list does NOT allow substitution of varia= bles. You'll instead want
=C2=A0 [list $ind1 $ind2 $ind3 $ind= 4]
or some such

Best,
Peter



<= div dir=3D"ltr" class=3D"gmail_attr">On Sat, Feb 13, 2021 at 11:06 PM Jiali= Wang <jwan= g204@binghamton.edu> wrote:
Dear Peter,
Thank you for your=C2= =A0reply. I use "set sel1 [[atomselect top "$selA"] get inde= x]" to get index, is there something wrong here?
=C2=A0I am = very new to the script part of calculations. I appreciate your help very=C2= =A0much.
best,
Jiali

On Sat, Feb 13, 2021 at 7:48 = PM Peter Freddolino <petefred@umich.edu> wrote:
The arguments to `measure dihe= d` are supposed to be atom indices, not atom selections. See https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html

Best,
Peter

On Sat, Feb 13, 2021 at= 1:56 AM jiali wang <jialiwangnamd@gmail.com> wrote:
Dear NAMD users,
I = have an error when I calculate the dihedral=C2=A0angle, the calculation per= formed in the VMD. code as below, but it says=C2=A0"expected integer b= ut got "$sel1" measure dihed: bad atom index". Do you know w= hat happened?=C2=A0
Thank you so much!!
Jiali=C2=A0

set selA [atomselect top "segname PP5 and name C= "]
set selB [atomselect top "segname PP5 and name CA"]<= br>set selC [atomselect top "segname PP5 and name CB"]
set sel= D [atomselect top "segname PP5 and name CG"]

set sel1 [[at= omselect top "$selA"] get index]
set sel2 [[atomselect top &qu= ot;$selB"] get index]
set sel3 [[atomselect top "$selC"] = get index]
set sel4 [[atomselect top "$selD"] get index]
set nf [molinfo top get numframes]
set outfile [open dihed-cal.dat w]<= br>for {set i 0} {$i < $nf} {incr i} {

=C2=A0 puts "frame $i= of $nf"

=C2=A0 set dihedlist [measure dihed {$sel1 $sel2 $sel3= $sel4}]
=C2=A0 puts $outfile "$i $dihedlist"
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aBVkTEBkaEQpwfxdsBXpDGkBHWxMYYxAdHREKcF8XZGRMXV9HWVxIBWMQGRoRCnB/F2Fmb1saZ2 RCSB1bEBsYGREKcF8XY2ISUEhjeB98Qn0QEx4RCnBsF29JSHlZfUwFX19CEBkaEQpwQxdtG21mG E17WURrXRAbGBMRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 mlxlogscore=999 spamscore=0 adultscore=0 bulkscore=0 clxscore=189 impostorscore=0 suspectscore=0 malwarescore=0 mlxscore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102150107 domainage_hfrom=1396 X-Spam-Score: 0 X-Spam-OrigSender: msun@beamtx.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ming Sun" --_000_4D3D72747BF54FE984EA0FE21D1B6863beamtxcom_ Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Hi All, A follow-up of previous discussion on the NAMD performed performances. I=E2= =80=99m wondering if anyone has done benchmark on NAMD3 on AWS p2 instances= or another GPU workstation? What would be an optimal / okay number of CPU = per GPU ? I am using NAMD2.14 these days. I did not see improvements switc= hing from 4-GPU machine to an 8-GPU machine while the number of CPU does no= t increase, at least at my hand Any thoughts on NAMD3/ 2.14 are greatly appreciated. Thanks, Ming From: "Vermaas, Josh" > Date: Thursday, January 28, 2021 at 7:45 PM To: "namd-l@ks.uiuc.edu" >, "Ropon-Palacios G." > Subject: Re: namd-l: Improve performance For the best NAMD performance on a GPU, use NAMD 3. This blog from NVIDIA h= as been my goto for explaining the differences to folks that haven=E2=80=99= t used NAMD 3 yet. https://urldefense.com/v3/__https://developer.nvidia.com= /blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!= t0qj3lFBcdvpNQmDX-ncJjXBjvRhCU6N3PxAox6tPJy255RhbwUZMj34czWhJwpQBA$ -Josh From: > on behalf= of "Ropon-Palacios G." > Reply-To: "namd-l@ks.uiuc.edu" >, "Ropon-Palacios G." > Date: Thursday, January 28, 2021 at 7:18 PM To: "namd-l@ks.uiuc.edu" > Subject: namd-l: Improve performance Dear namd users, How can i improve namd2.14 performance on GPU? I`m using namd2.14 for run membrane protein simulation, but namd only use n= or more the 50% of GPU, as can I make to improve this performance. For other hand, if during equilibration of protein-membrane is necessary ke= ep water out membrane? Thanks, Best, Geo. Disclaimer The information contained in this communication from the sender is confiden= tial. It is intended solely for use by the recipient and others authorized = to receive it. If you are not the recipient, you are hereby notified that a= ny disclosure, copying, distribution or taking action in relation of the co= ntents of this information is strictly prohibited and may be unlawful. --_000_4D3D72747BF54FE984EA0FE21D1B6863beamtxcom_ Content-Type: text/html; charset=UTF-8 Content-ID: Content-Transfer-Encoding: base64 PGh0bWw+PGhlYWQ+DQo8bWV0YSBodHRwLWVxdWl2PSJDb250ZW50LVR5cGUiIGNvbnRlbnQ9InRl eHQvaHRtbDsgY2hhcnNldD11dGYtOCI+DQo8bWV0YSBuYW1lPSJHZW5lcmF0b3IiIGNvbnRlbnQ9 Ik1pY3Jvc29mdCBXb3JkIDE1IChmaWx0ZXJlZCBtZWRpdW0pIj4NCjxzdHlsZT48IS0tDQovKiBG b250IERlZmluaXRpb25zICovDQpAZm9udC1mYWNlDQoJe2ZvbnQtZmFtaWx5OiJDYW1icmlhIE1h dGgiOw0KCXBhbm9zZS0xOjIgNCA1IDMgNSA0IDYgMyAyIDQ7fQ0KQGZvbnQtZmFjZQ0KCXtmb250 LWZhbWlseTpEZW5nWGlhbjsNCglwYW5vc2UtMToyIDEgNiAwIDMgMSAxIDEgMSAxO30NCkBmb250 LWZhY2UNCgl7Zm9udC1mYW1pbHk6Q2FsaWJyaTsNCglwYW5vc2UtMToyIDE1IDUgMiAyIDIgNCAz IDIgNDt9DQpAZm9udC1mYWNlDQoJe2ZvbnQtZmFtaWx5OiJUaW1lcyBOZXcgUm9tYW4gXChCb2R5 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X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11G09bAd015209; Mon, 15 Feb 2021 18:09:37 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11G09aaB015208; Mon, 15 Feb 2021 18:09:36 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11G09PWJ015194 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 15 Feb 2021 18:09:26 -0600 (CST) From: David Hardy Message-Id: <164086FA-3CA9-4782-A9CA-86E51FE87C67@ks.uiuc.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_D7C8CE63-22EB-4F0B-9A99-C9AA45C8AEC8" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Re: Maximum and minimum box size Date: Mon, 15 Feb 2021 18:09:20 -0600 In-Reply-To: Cc: NAMD list To: Raman Preet Singh References: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_D7C8CE63-22EB-4F0B-9A99-C9AA45C8AEC8 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Raman, NAMD can support all-atom simulations of up to 2 billion atoms. If I=E2=80=99m doing my units conversion correctly (always my downfall), = a 50 nm cubed box would be expected to contain about 12.5 M atoms or = about 4.167 M water molecules. This is fine for NAMD but depends also on = the hardware you have available. CG using MARTINI would reduce this 1/4 = (4 AA waters for 1 CG water, right?). As to the minimum box size, each dimension of the periodic cell must be = at least pairlistdist (defaults to cutoff) plus hgroupCutoff (defaults = to 2.5 A) plus margin (defaults to 0). Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Feb 12, 2021, at 4:35 AM, Raman Preet Singh = wrote: >=20 > Dear NAMD Community, >=20 > Reposting the question in case someone might help me. >=20 > Regards, > RPS >=20 > Get Outlook for Android = > From: Raman Preet Singh > Sent: Monday, January 18, 2021 11:46:42 PM > To: NAMD list > Subject: Maximum and minimum box size > =20 > Dear All, >=20 > I am interested in performing a simulation where one of the box = dimensions is expected to reach 50 nm. I have seen publications with 20+ = nm water box sides but not sure if 50 nm or higher dimensions are = supported in NAMD. I will be using MARTINI CG models. If 50 nm is = supported, do I need to make any changes in the NAMD conf file? >=20 > A related question is: what is the minimum box size supported? A 1 nm = distance from the sides of the solute is the ideal situation. However, = if it is just a solvent box, what is the minimum supported size (for AA = and CG models)? >=20 > Thank you in advance for your time and inputs. >=20 > Regards, > Raman >=20 >=20 --Apple-Mail=_D7C8CE63-22EB-4F0B-9A99-C9AA45C8AEC8 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Raman,

NAMD can = support all-atom simulations of up to 2 billion atoms.

If I=E2=80=99m doing my = units conversion correctly (always my downfall), a 50 nm cubed box would = be expected to contain about 12.5 M atoms or about 4.167 M water = molecules. This is fine for NAMD but depends also on the hardware you = have available. CG using MARTINI would reduce this 1/4 (4 AA waters for = 1 CG water, right?).

As to the minimum box size, each dimension of the periodic = cell must be at least pairlistdist (defaults to cutoff) plus = hgroupCutoff (defaults to 2.5 A) plus margin (defaults to 0).

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Feb 12, 2021, at 4:35 AM, Raman Preet Singh <ramanpreetsingh@hotmail.com> wrote:

Dear NAMD Community,

Reposting the question in case someone might help me.

Regards,
RPS


From: = Raman Preet Singh
Sent: Monday, January 18, 2021 11:46:42 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Maximum and minimum box size
 
Dear All,

I am interested in performing a simulation where one of the box = dimensions is expected to reach 50 nm. I have seen publications with 20+ = nm water box sides but not sure if 50 nm or higher dimensions are = supported in NAMD. I will be using MARTINI CG models. If 50 nm is supported, do I need to make any changes in the NAMD conf = file?

A related question is: what is the minimum box size supported? A 1 nm = distance from the sides of the solute is the ideal situation. However, = if it is just a solvent box, what is the minimum supported size (for AA = and CG models)?

Thank you in advance for your time and inputs.

Regards,
Raman



= --Apple-Mail=_D7C8CE63-22EB-4F0B-9A99-C9AA45C8AEC8-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 15 18:25:55 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11G0Ps9q017502; Mon, 15 Feb 2021 18:25:54 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11G0Ps77017501; Mon, 15 Feb 2021 18:25:54 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11G0PsKv017497; Mon, 15 Feb 2021 18:25:54 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11G0Psl6017496; Mon, 15 Feb 2021 18:25:54 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11G0PlAB017486 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 15 Feb 2021 18:25:47 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_7241DEC9-FC3A-4CB9-9504-64D949C0D42F" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Improve performance Date: Mon, 15 Feb 2021 18:25:41 -0600 References: <5A97C027-E9C6-4763-9FA7-CD9E4F843B7C@gmail.com> <153684DA-B2E4-4FCD-9A9B-90AEEE00D2E2@ks.uiuc.edu> <4D3D7274-7BF5-4FE9-84EA-0FE21D1B6863@beamtx.com> To: namd-l@ks.uiuc.edu, Ming Sun In-Reply-To: <4D3D7274-7BF5-4FE9-84EA-0FE21D1B6863@beamtx.com> Message-Id: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_7241DEC9-FC3A-4CB9-9504-64D949C0D42F Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Ming, I see that AWS p2 uses K80 GPUs, which are now over 6 years old. The = GPU-resident integrator in NAMD 3 has been optimized for V100 or later = GPUs. It would be interesting for us to benchmark the most recent codes = on K80, but I don=E2=80=99t know that anyone has done that yet. As to your issue with running NAMD 2.14 on a 4-GPU machine versus an = 8-GPU machine, NAMD 2.14 on modern GPUs is CPU bound, so it is possible = that you saw no improvement in performance if you didn=E2=80=99t also = increase the CPU core count per GPU. In fact, this is our motivation for = developing a GPU-resident version of NAMD. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Feb 15, 2021, at 7:15 AM, Ming Sun wrote: >=20 > Hi All, > =20 > A follow-up of previous discussion on the NAMD performed performances. = I=E2=80=99m wondering if anyone has done benchmark on NAMD3 on AWS p2 = instances or another GPU workstation? What would be an optimal / okay = number of CPU per GPU ? I am using NAMD2.14 these days. I did not see = improvements switching from 4-GPU machine to an 8-GPU machine while the = number of CPU does not increase, at least at my hand > =20 > Any thoughts on NAMD3/ 2.14 are greatly appreciated. > =20 > Thanks, > Ming =20 > =20 > =20 > From: "Vermaas, Josh" > > Date: Thursday, January 28, 2021 at 7:45 PM > To: "namd-l@ks.uiuc.edu " = >, "Ropon-Palacios G." = > > Subject: Re: namd-l: Improve performance > =20 > For the best NAMD performance on a GPU, use NAMD 3. This blog from = NVIDIA has been my goto for explaining the differences to folks that = haven=E2=80=99t used NAMD 3 yet. = https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd= -v3-and-a100-gpu/ = > =20 > -Josh > =20 > From: > on = behalf of "Ropon-Palacios G." > > Reply-To: "namd-l@ks.uiuc.edu " = >, "Ropon-Palacios G." = > > Date: Thursday, January 28, 2021 at 7:18 PM > To: "namd-l@ks.uiuc.edu " = > > Subject: namd-l: Improve performance > =20 > Dear namd users,=20 > =20 > How can i improve namd2.14 performance on GPU? > =20 > I`m using namd2.14 for run membrane protein simulation, but namd only = use nor more the 50% of GPU, as can I make to improve this performance.=20= > =20 > For other hand, if during equilibration of protein-membrane is = necessary keep water out membrane?=20 > =20 > Thanks,=20 > =20 > Best,=20 > =20 > Geo.=20 > =20 >=20 >=20 > Disclaimer >=20 > The information contained in this communication from the sender is = confidential. It is intended solely for use by the recipient and others = authorized to receive it. If you are not the recipient, you are hereby = notified that any disclosure, copying, distribution or taking action in = relation of the contents of this information is strictly prohibited and = may be unlawful. >=20 --Apple-Mail=_7241DEC9-FC3A-4CB9-9504-64D949C0D42F Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Ming,

I see that AWS = p2 uses K80 GPUs, which are now over 6 years old. The GPU-resident = integrator in NAMD 3 has been optimized for V100 or later GPUs. It would = be interesting for us to benchmark the most recent codes on K80, but I = don=E2=80=99t know that anyone has done that yet.
As to your issue with running NAMD = 2.14 on a 4-GPU machine versus an 8-GPU machine, NAMD 2.14 on modern = GPUs is CPU bound, so it is possible that you saw no improvement in = performance if you didn=E2=80=99t also increase the CPU core count per = GPU. In fact, this is our motivation for developing a GPU-resident = version of NAMD.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Feb 15, 2021, at 7:15 AM, Ming Sun <msun@beamtx.com> = wrote:

Hi All,
 
A follow-up of previous discussion = on the NAMD performed performances. I=E2=80=99m wondering if anyone has = done benchmark on NAMD3 on AWS p2 instances or another GPU workstation? = What would be an optimal / okay number of CPU per GPU ?  I am using = NAMD2.14 these days. I did not see improvements switching from 4-GPU = machine to an 8-GPU machine while the number of CPU does not increase, = at least at my hand
 
Any thoughts on NAMD3/ 2.14 are = greatly appreciated.
 
Thanks,
Ming  
 
 
From: "Vermaas, Josh" <vermaasj@msu.edu>
Date: Thursday, January 28, = 2021 at 7:45 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, = "Ropon-Palacios G." <biodano.geo@gmail.com>
Subject: Re: namd-l: Improve = performance
 
For = the best NAMD performance on a GPU, use NAMD 3. This blog from NVIDIA = has been my goto for explaining the differences to folks that haven=E2=80=99= t used NAMD 3 yet. https://developer.nvidia.com/blog/delivering-up-to-9x-throughpu= t-with-namd-v3-and-a100-gpu/
 
-Josh
 
From: <owner-namd-l@ks.uiuc.edu> on = behalf of "Ropon-Palacios G." <biodano.geo@gmail.com>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, = "Ropon-Palacios G." <biodano.geo@gmail.com>
Date: Thursday, January 28, = 2021 at 7:18 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: Improve = performance
 
Dear namd users, 
 
How can i improve namd2.14 = performance on GPU?
 
I`m using namd2.14 for run membrane protein simulation, but = namd only use nor more the 50% of GPU, as can I make to improve this = performance. 
 
For other hand, if during = equilibration of protein-membrane is necessary keep water out = membrane? 
 
Thanks, 
 
Best, 
 
Geo. 
 


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The = information contained in this communication from the sender is = confidential. It is intended solely for use by the recipient and others = authorized to receive it. If you are not the recipient, you are hereby = notified that any disclosure, copying, distribution or taking action in = relation of the contents of this information is strictly prohibited and = may be unlawful.


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quoted-printable to 8bit by halifax.ks.uiuc.edu id 11K3OQQn026300 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Lorenzo Casalino Hello, I am trying to use the multiGPU version of NAMD3 (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run plain MD on 2 GPUs on a single node on a local cluster using the following command: namd3 +p 2 +setcpuaffinity +idlepoll +devices 0,1 input.conf > input.log I added the following keywords to my configuration file: - CUDASOAintegrate on - margin 4 >From the log file, it looks like the 2 GPUs are seen and activated: Info: Built with CUDA version 10010 Pe 1 physical rank 1 binding to CUDA device 1 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: 0:24:0 Pe 0 physical rank 0 binding to CUDA device 0 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: 0:1:0 The startup phase finishes smoothly, and then, when the actual MD simulation starts, the following error is generated: Info: Finished startup at 34.7205 s, 0 MB of memory in use TCL: Running for 100000 steps FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 on Pe 1 (tscc-gpu-5-0.sdsc.edu device 1 pci 0:24:0): invalid device function A single node of the cluster has 32 cpus and 8 GPUs (GeForce RTX 3090). I point out that the GPUs are NOT connected by NVlink. Finally, this is the PBS argument I use to add the GPUs to the environment: #PBS -l nodes=1:ppn=8:gpus=2:gpu3090 I was not able to work this error out. Is it possible that without NVlink I cannot use the multiGPU version? Any help or advises on this issue would be greatly appreciated. Thank you. Best regards, Lorenzo From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 16:26:11 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MMQBtZ014604; Mon, 22 Feb 2021 16:26:11 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MMQBiQ014603; Mon, 22 Feb 2021 16:26:11 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MMQABJ014599; Mon, 22 Feb 2021 16:26:10 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MMQAiE014598; Mon, 22 Feb 2021 16:26:10 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MMQ6al014590 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 22 Feb 2021 16:26:07 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_BD68A014-76D1-475E-B7C0-08B350EA744B" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: NAMD3 multiGPU: invalid device function error Date: Mon, 22 Feb 2021 16:26:01 -0600 References: To: NAMD list , Lorenzo Casalino In-Reply-To: Message-Id: <9FD2B800-CA22-4CBF-9AFD-AED126221DF7@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_BD68A014-76D1-475E-B7C0-08B350EA744B Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Lorenzo, The version of NAMD that you are running does require NVLink for = multi-GPU support (see = http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ = ). Our most recent = improvements to multi-GPU support no longer require NVLink, however, = scaling performance suffers without it. The next release (alpha 9) will = include this new multi-GPU support. Until we get new builds posted, you = will need to build from the GitLab =E2=80=9Cdevel" branch to try it out. = You can get access to the NAMD GitLab repo by following the posted = directions (https://gitlab.com/tcbgUIUC/namd = ). Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino = wrote: >=20 > Hello, >=20 > I am trying to use the multiGPU version of NAMD3 = (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run = plain MD on 2 GPUs on a single node on a local cluster using the = following command: >=20 > namd3 +p 2 +setcpuaffinity +idlepoll +devices 0,1 input.conf > = input.log >=20 > I added the following keywords to my configuration file: > - CUDASOAintegrate on > - margin 4 >=20 >> =46rom the log file, it looks like the 2 GPUs are seen and activated: > Info: Built with CUDA version 10010 > Pe 1 physical rank 1 binding to CUDA device 1 on = tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: = 0:24:0 > Pe 0 physical rank 0 binding to CUDA device 0 on = tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: = 0:1:0 >=20 > The startup phase finishes smoothly, and then, when the actual MD = simulation starts, the following error is generated: >=20 > Info: Finished startup at 34.7205 s, 0 MB of memory in use >=20 > TCL: Running for 100000 steps > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 1 (tscc-gpu-5-0.sdsc.edu device 1 pci 0:24:0): invalid device = function >=20 > A single node of the cluster has 32 cpus and 8 GPUs (GeForce RTX = 3090). > I point out that the GPUs are NOT connected by NVlink. > Finally, this is the PBS argument I use to add the GPUs to the = environment: #PBS -l nodes=3D1:ppn=3D8:gpus=3D2:gpu3090 >=20 > I was not able to work this error out. Is it possible that without = NVlink I cannot use the multiGPU version? > Any help or advises on this issue would be greatly appreciated. >=20 > Thank you. >=20 > Best regards, > Lorenzo --Apple-Mail=_BD68A014-76D1-475E-B7C0-08B350EA744B Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Lorenzo,

The version = of NAMD that you are running does require NVLink for multi-GPU support = (see http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/). = Our most recent improvements to multi-GPU support no longer require = NVLink, however, scaling performance suffers without it. The next = release (alpha 9) will include this new multi-GPU support. Until we get = new builds posted, you will need to build from the GitLab =E2=80=9Cdevel" = branch to try it out. You can get access to the NAMD GitLab repo by = following the posted directions (https://gitlab.com/tcbgUIUC/namd).
Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino <lcasalino@ucsd.edu> = wrote:

Hello,

I am trying to use the = multiGPU version of NAMD3 = (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run = plain MD on 2 GPUs on a single node on a local cluster using the = following command:

namd3 +p 2 = +setcpuaffinity +idlepoll +devices 0,1 input.conf > input.log

I added the following keywords to my = configuration file:
- CUDASOAintegrate on
- = margin 4

=46rom the log file, it looks like the 2 GPUs are seen and = activated:
Info: Built with CUDA version = 10010
Pe 1 physical rank 1 binding to CUDA device 1 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090'  Mem: = 24268MB  Rev: 8.6  PCI: 0:24:0
Pe 0 physical = rank 0 binding to CUDA device 0 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090'  Mem: = 24268MB  Rev: 8.6  PCI: 0:1:0

The = startup phase finishes smoothly, and then, when the actual MD simulation = starts, the following error is generated:

Info: Finished startup at 34.7205 s, 0 MB of memory in use

TCL: Running for 100000 steps
FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461
on Pe 1 (tscc-gpu-5-0.sdsc.edu device 1 pci 0:24:0): invalid = device function

A single node of the = cluster has 32 cpus and 8 GPUs (GeForce RTX 3090).
I point = out that the GPUs are NOT connected by NVlink.
Finally, = this is the PBS argument I use to add the GPUs to the environment: #PBS = -l nodes=3D1:ppn=3D8:gpus=3D2:gpu3090

I was = not able to work this error out. Is it possible that without NVlink I = cannot use the multiGPU version?
Any help or advises on = this issue would be greatly appreciated.

Thank you.

Best regards,
Lorenzo

= --Apple-Mail=_BD68A014-76D1-475E-B7C0-08B350EA744B-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 17:29:37 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNTb4k017775; Mon, 22 Feb 2021 17:29:37 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MNTapn017773; Mon, 22 Feb 2021 17:29:36 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNTakB017769; Mon, 22 Feb 2021 17:29:36 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MNTaOS017768; Mon, 22 Feb 2021 17:29:36 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNTU6i017760 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 22 Feb 2021 17:29:30 -0600 (CST) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 11MNTTc0006328 for ; Mon, 22 Feb 2021 23:29:29 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=ccs0019@mix.wvu.edu; dkim=pass header.s=google header.d=mix.wvu.edu Received: from mail-il1-f181.google.com (mail-il1-f181.google.com [209.85.166.181]) by mx0b-00007101.pphosted.com with ESMTP id 36u08mh444-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 22 Feb 2021 23:29:29 +0000 Received: by mail-il1-f181.google.com with SMTP id q9so12476186ilo.1 for ; Mon, 22 Feb 2021 15:29:29 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mix.wvu.edu; s=google; h=mime-version:from:date:message-id:subject:to; bh=5dxBZ5tzsBYlOW/96XcsIts+Yy1Lsgt2BfG+ez+EE7M=; b=OXnfWTqi57WRDVDu1Pf+MgkcNfpG2DgvGx7dNdJeZyFpasCDwyGDvvsvqalc52tc1B Z5IDjeoTBBOpVFAFAnPLjaafmviEkYmfkbd7p5C8KBrb5ZagdCtY+UmppwzId5+3i6k+ 0Pyh/ugbpKCG29gSJK9WQerhoA3rqQD0oM4KM= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=5dxBZ5tzsBYlOW/96XcsIts+Yy1Lsgt2BfG+ez+EE7M=; b=FWD8CuQIjD+XukkrnXxoaeGYesRDuxq9ABMJD08jpx7RN5qnTaEHZS5npCQ2yugqc4 9tXst5v2D0F1PAtaJkjpciTHrt9cu+w8lzoSD8ova0lub5rOnaXrE7KMS+8S91SP4tqz 9xWh6wSkdpkR2Y3TDOwPFNucWvWgWXC2clEmYwDDj48LBugNXSCgu+Jwmc9Xe+O6tHdu KXyUxPlsB4Yb6ijBoRWALcLJNPTiBjjn9g/lLY2M3hJ8qpsQcLoUqWS/tD9UUoyyHeXB oVU2U7uQ25wuqvFshyo7cNRIu2UgMzJbt7SpKKye0tfWRqY5khGkFjMKi+iqQYb7phhv SZrQ== X-Gm-Message-State: AOAM5323tuKjchSyr7UVSl0X7BmJGFwPFUaKeNjBTVVuNvY9oXokhvWN UaP76jz47gDzgDz+EGbs7A0jVPFnf9tnApGbJc9+2cH7n929XA== X-Google-Smtp-Source: ABdhPJxWFGi+5juw2SNC/uQH0eUIM6p9Ez2JcR701B4H+SxdQfg8+PK/Chu1ZscJ7dW8OVmw9zrUQGzlXNCynWlfr3s= X-Received: by 2002:a05:6e02:12a1:: with SMTP id f1mr3619911ilr.124.1614036547529; Mon, 22 Feb 2021 15:29:07 -0800 (PST) MIME-Version: 1.0 From: Chathuranga Siriwardhana Date: Mon, 22 Feb 2021 18:28:35 -0500 Message-ID: Subject: namd-l: Small molecule simulation error NAMD To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000001202d005bbf52b17" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRscEQpMehcaEQpZRBdoYn5NXH5YS0deQhEKWFgXYxlSeUx9QExiEl8 RCnhOF2x6UFlsfEJsRkgcEQp5TBdtQ2RTbEZFeERCXhEKQ0gXBxgbExEKQ1kXBxsfHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGxxxGwYZGHcGGBoaBhoGGgYbGhoGGnEaEBp3BhoGGgYaBhoGGgYac RoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04Xa3MeWnocX0tmb39/aF1ORhlpEkla fnppe3VjHmhmck8RClhcFx8EGgQYGB4FGxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcktPZhoRCk1 cFxkaHhEKTFoXaGlNa2sRCkxGF29ra2traxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHB wEGxIbEQpCXhcbEQpCXBcbEQpCSxdoeENjQBNIYHlaHhEKQkkXbHpQWWx8QmxGSBwRCkJFF2xDU 0cFW3B8ZFx7EQpCThdselBZbHxCbEZIHBEKQkwXYxlSeUx9QExiEl8RCkJsF25tQ25OHHJ9WEIY EQpCQBdkY3BrGHpQT0VObREKQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcYEQp5QxdiHlpHQ0l sR2JsfxEKWUsXGxoeEx0RCnBoF2lbGBtdR3hlbnxFEAcZGhEKcGgXbUxgQmBFa2xtS2MQBxkaEQ pwaBdkQkBCTXpYQR9iQxAHGRoRCnBoF2xFfxhuW25CXl1JEAcZGhEKcGgXYF56GmR6T3t6Z34QB xkaEQpwbBdiS2RuBU5pXG5HRRAHGRoRCm1+FwcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 clxscore=316 suspectscore=0 bulkscore=0 spamscore=0 mlxscore=0 mlxlogscore=589 priorityscore=0 lowpriorityscore=0 phishscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102220202 domainage_hfrom=10497 X-Spam-Score: 0 X-Spam-OrigSender: ccs0019@mix.wvu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Chathuranga Siriwardhana --0000000000001202d005bbf52b17 Content-Type: text/plain; charset="UTF-8" Hi NAMD users, I'm trying to see the interaction of a small molecule with a protein in NAMD. As the simulation starts the following error appears; ERROR: Margin is too small for 1 atoms during timestep 1004. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom 310 of 311 on patch 0 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 0 pe 1). FATAL ERROR: Exiting prematurely; see error messages above. Atom 37 is a lone pair on Chlorine in the small molecule. Any help is really appreciated. Thanks Chathuranga *Chathuranga Siriwardhana* Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 --0000000000001202d005bbf52b17 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi NAMD users,
I'm trying to see the interaction o= f a small molecule with a protein in NAMD. As the simulation starts the fol= lowing=C2=A0error appears;

ERROR: Margin is too sm= all for 1 atoms during timestep 1004.
ERROR: Incorrect nonbonded forces = and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -890= 0.08 8246.01 (limit is 12000, atom 310 of 311 on patch 0 pe 1)
ERROR: At= oms moving too fast; simulation has become unstable (1 atoms on patch 0 pe = 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecu= le. Any help is really=C2=A0appreciated.

Thanks
Chathuranga



=


Chathuranga Siriwardhana
<= font color=3D"#002855" face=3D"Helvetica Neue, Helvetica, Roboto, Arial, sa= ns-serif">Justin Legleiter Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0=
Clark Hall, Room 561
Morgantown, WV 26505
=
--0000000000001202d005bbf52b17-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 17:34:39 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNYdCm018552; Mon, 22 Feb 2021 17:34:39 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MNYdhO018551; Mon, 22 Feb 2021 17:34:39 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNYctb018547; Mon, 22 Feb 2021 17:34:38 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MNYcTE018546; Mon, 22 Feb 2021 17:34:38 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNYTjB018537 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable What version of NAMD are you using? Versions earlier than NAMD 2.14 don=E2= =80=99t support halogen lonepairs. Jeff On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana wrote: > Hi NAMD users, > I'm trying to see the interaction of a small molecule with a protein in > NAMD. As the simulation starts the following error appears; > > ERROR: Margin is too small for 1 atoms during timestep 1004. > ERROR: Incorrect nonbonded forces and energies may be calculated! > ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom > 310 of 311 on patch 0 pe 1) > ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on > patch 0 pe 1). > FATAL ERROR: Exiting prematurely; see error messages above. > > Atom 37 is a lone pair on Chlorine in the small molecule. Any help is > really appreciated. > > Thanks > Chathuranga > > > > > > > *Chathuranga Siriwardhana* > Justin Legleiter Laboratory > West Virginia University > Department of chemistry > Clark Hall, Room 561 > Morgantown, WV 26505 > --=20 =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!rrDOk0D= OYvWUezF6gBZcQhAchOUxh-pBWJ5CQg3l3Aa5zw6NmQexSwR8nuRumTCXvA$=20 --0000000000002994fd05bbf53e04 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
What version of NAMD are you=C2=A0using? Versions earlier= than NAMD 2.14 don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana &= lt;ccs0019@mix.wvu.edu> wrote= :
Hi NAMD users,I'm trying to see the interaction of a small molecule with a protein= in NAMD. As the simulation starts the following=C2=A0error appears;
<= div>
ERROR: Margin is too small for 1 atoms during timestep 1= 004.
ERROR: Incorrect nonbonded forces and energies may be calculated!ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, ato= m 310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation h= as become unstable (1 atoms on patch 0 pe 1).
FATAL ERROR: Exiting prema= turely; see error messages above.

Atom 37 is a= lone pair on Chlorine in the small molecule. Any help is really=C2=A0appre= ciated.

Thanks
Chathuranga




=


Chathuranga Siriwardhana
Justin Legleiter Laborat= ory=C2=A0
West Virginia University=C2=A0
Depart= ment of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26505<= /div>
--

=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94
Jeffrey Com= er, PhD
Associate Professor
Department of Anatomy and Physiology
K= ansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311<= br>Website: http://jeffcomer.us
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boundary="000000000000f3f07f05bbf5597b" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwbEQpMehcaEQpZRBdoYn5NXH5YS0deQhEKWFgXYxlSeUx9QExiEl8 RCnhOF2x6UFlsfEJsRkgcEQp5TBdtQ2RTbEZFeERCXhEKQ0gXBxgZExEKQ1kXBxgZEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbHHEbBhkYdwYYGhoGGgYaBgcYHwYZGnEbEBp3BhoGGgYaBgccGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdwXBpCZx1aSxp5YGxAfEtuRm1l Xk1FTGxhTn9TZRhyXREKWFwXHwQaBBgYHgUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdyS09yUhE KTVwXBx8bEQpMWhd4aU1raxEKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2 1tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBBsdGREKQl4XGxEKREkXGxEKQlwXGxEKQksXaHhDY 0ATSGB5Wh4RCkJJF2x6UFlsfEJsRkgcEQpCRRdsQ1NHBVtwfGRcexEKQk4XbHpQWWx8QmxGSBwR CkJMF2MZUnlMfUBMYhJfEQpCbBdubUNuThxyfVhCGBEKQkAXZxJTWGB4f1wZfAURCkJYF2dzZXN AbmFhTF1iEQpaWBcYEQp5QxdvUh1ifHJ9XllJRhEKWUsXGxoeEx0RCnBnF3pbbRJAUl5neEkdEB oRCnBoF21MYEJgRWtsbUtjEAceEhEKcGgXaEwScgUSHmF9YGEQGhEKcGgXZEJAQk16WEEfYkMQB xkaEQpwaBdjTX9cUltveW9QRRAaEQpwaBdgQBptGXJNZXMaYRAaEQpwfRdjQWN6a2kFHmIaWRAa EQpwfxdjQWN6a2kFHmIaWRAaEQpwbBdiS2RuBU5pXG5HRRAHHhIRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 clxscore=161 suspectscore=0 bulkscore=0 spamscore=0 mlxscore=0 mlxlogscore=907 priorityscore=0 lowpriorityscore=0 phishscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102220203 domainage_hfrom=10497 X-Spam-Score: 0 X-Spam-OrigSender: ccs0019@mix.wvu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Chathuranga Siriwardhana --000000000000f3f07f05bbf5597b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks Jeff, I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated Thanks *Chathuranga Siriwardhana* Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer wrote: > What version of NAMD are you using? Versions earlier than NAMD 2.14 don= =E2=80=99t > support halogen lonepairs. > > Jeff > > > On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana < > ccs0019@mix.wvu.edu> wrote: > >> Hi NAMD users, >> I'm trying to see the interaction of a small molecule with a protein in >> NAMD. As the simulation starts the following error appears; >> >> ERROR: Margin is too small for 1 atoms during timestep 1004. >> ERROR: Incorrect nonbonded forces and energies may be calculated! >> ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, >> atom 310 of 311 on patch 0 pe 1) >> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on >> patch 0 pe 1). >> FATAL ERROR: Exiting prematurely; see error messages above. >> >> Atom 37 is a lone pair on Chlorine in the small molecule. Any help is >> really appreciated. >> >> Thanks >> Chathuranga >> >> >> >> >> >> >> *Chathuranga Siriwardhana* >> Justin Legleiter Laboratory >> West Virginia University >> Department of chemistry >> Clark Hall, Room 561 >> Morgantown, WV 26505 >> > -- > > =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2= =80=94 > Jeffrey Comer, PhD > Associate Professor > Department of Anatomy and Physiology > Kansas State University > Office: P-213 Mosier Hall > Phone: 785-532-6311 > Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!oy19t= N7QUSKcotZH8b_xfG1SoCSjFRxtAfeYKD73jGbd_OG5PSXl7j1cR8LcY4lt7w$=20 > --000000000000f3f07f05bbf5597b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thanks=C2=A0Jeff,
I'm using NAMD 2.14. Earlier I w= as using 2.13 and got it updated=C2=A0
Thanks

<= /div>


Chathuranga Siriwardhana
=
Justin Legleiter Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer <jeffcomer@gmail.com> wrote:
What version of NAMD are= you=C2=A0using? Versions earlier than NAMD 2.14 don=E2=80=99t support halo= gen lonepairs.

Jeff


On Mon, Feb 22, 2021 at= 17:31 Chathuranga Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD users,
I&= #39;m trying to see the interaction of a small molecule with a protein in N= AMD. As the simulation starts the following=C2=A0error appears;
<= br>
ERROR: Margin is too small for 1 atoms during timestep 1004.<= br>ERROR: Incorrect nonbonded forces and energies may be calculated!
ERR= OR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom 310= of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has be= come unstable (1 atoms on patch 0 pe 1).
FATAL ERROR: Exiting prematurel= y; see error messages above.

Atom 37 is a lone= pair on Chlorine in the small molecule. Any help is really=C2=A0appreciate= d.

Thanks
Chathuranga




=

Chathuranga Siriwardhana=
Justin Legleiter Laboratory=C2=A0
West Virginia University=C2=A0=
Department of chemistry=C2=A0<= /font>
Clark Hall, Room 561=
Morgantown, WV 26505
<= /div>
--

=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and = Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone= : 785-532-6311
Website: http://jeffcomer.us
--000000000000f3f07f05bbf5597b-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 17:56:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNujvW024319; Mon, 22 Feb 2021 17:56:45 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MNujUr024318; Mon, 22 Feb 2021 17:56:45 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNuixP024314; Mon, 22 Feb 2021 17:56:44 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11MNui5P024313; Mon, 22 Feb 2021 17:56:44 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11MNucjt024303 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 22 Feb 2021 17:56:38 -0600 (CST) From: David Hardy Message-Id: Content-Type: multipart/alternative; boundary="Apple-Mail=_F6601916-2B97-433D-B47B-E3CA799DABA3" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: NAMD3 multiGPU: invalid device function error Date: Mon, 22 Feb 2021 17:56:32 -0600 In-Reply-To: <9FD2B800-CA22-4CBF-9AFD-AED126221DF7@ks.uiuc.edu> Cc: Lorenzo Casalino To: NAMD list , David Hardy References: <9FD2B800-CA22-4CBF-9AFD-AED126221DF7@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_F6601916-2B97-433D-B47B-E3CA799DABA3 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Lorenzo, Sorry, I have to follow up my previous email. I had thought that multi-GPU alpha 7 required NVLink. It happens to be = recommended, but not required. I am not sure why you are seeing an = error. If you are willing to share your data set with us, we could try = to reproduce the issue locally. Also, it would be good to have the full = log file from your failed run. Best regards, Dave > On Feb 22, 2021, at 4:26 PM, David Hardy wrote: >=20 > Hi Lorenzo, >=20 > The version of NAMD that you are running does require NVLink for = multi-GPU support (see = http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ = ). Our most recent = improvements to multi-GPU support no longer require NVLink, however, = scaling performance suffers without it. The next release (alpha 9) will = include this new multi-GPU support. Until we get new builds posted, you = will need to build from the GitLab =E2=80=9Cdevel" branch to try it out. = You can get access to the NAMD GitLab repo by following the posted = directions (https://gitlab.com/tcbgUIUC/namd = ). >=20 > Best regards, > Dave >=20 > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu , = http://www.ks.uiuc.edu/~dhardy/ >=20 >> On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino > wrote: >>=20 >> Hello, >>=20 >> I am trying to use the multiGPU version of NAMD3 = (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run = plain MD on 2 GPUs on a single node on a local cluster using the = following command: >>=20 >> namd3 +p 2 +setcpuaffinity +idlepoll +devices 0,1 input.conf > = input.log >>=20 >> I added the following keywords to my configuration file: >> - CUDASOAintegrate on >> - margin 4 >>=20 >>> =46rom the log file, it looks like the 2 GPUs are seen and = activated: >> Info: Built with CUDA version 10010 >> Pe 1 physical rank 1 binding to CUDA device 1 on = tscc-gpu-5-0.sdsc.edu : 'GeForce RTX = 3090' Mem: 24268MB Rev: 8.6 PCI: 0:24:0 >> Pe 0 physical rank 0 binding to CUDA device 0 on = tscc-gpu-5-0.sdsc.edu : 'GeForce RTX = 3090' Mem: 24268MB Rev: 8.6 PCI: 0:1:0 >>=20 >> The startup phase finishes smoothly, and then, when the actual MD = simulation starts, the following error is generated: >>=20 >> Info: Finished startup at 34.7205 s, 0 MB of memory in use >>=20 >> TCL: Running for 100000 steps >> FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 >> on Pe 1 (tscc-gpu-5-0.sdsc.edu device = 1 pci 0:24:0): invalid device function >>=20 >> A single node of the cluster has 32 cpus and 8 GPUs (GeForce RTX = 3090). >> I point out that the GPUs are NOT connected by NVlink. >> Finally, this is the PBS argument I use to add the GPUs to the = environment: #PBS -l nodes=3D1:ppn=3D8:gpus=3D2:gpu3090 >>=20 >> I was not able to work this error out. Is it possible that without = NVlink I cannot use the multiGPU version? >> Any help or advises on this issue would be greatly appreciated. >>=20 >> Thank you. >>=20 >> Best regards, >> Lorenzo >=20 --Apple-Mail=_F6601916-2B97-433D-B47B-E3CA799DABA3 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Lorenzo,

Sorry, I = have to follow up my previous email.

I had thought that multi-GPU alpha 7 = required NVLink. It happens to be recommended, but not required. I am = not sure why you are seeing an error. If you are willing to share your = data set with us, we could try to reproduce the issue locally. Also, it = would be good to have the full log file from your failed run.

Best regards,
Dave

On Feb 22, 2021, at 4:26 PM, = David Hardy <dhardy@ks.uiuc.edu> wrote:

Hi Lorenzo,

The version of NAMD that = you are running does require NVLink for multi-GPU support (see http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/). = Our most recent improvements to multi-GPU support no longer require = NVLink, however, scaling performance suffers without it. The next = release (alpha 9) will include this new multi-GPU support. Until we get = new builds posted, you will need to build from the GitLab =E2=80=9Cdevel" = branch to try it out. You can get access to the NAMD GitLab repo by = following the posted directions (https://gitlab.com/tcbgUIUC/namd).
Best regards,
Dave

--
David J. Hardy, = Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405= N. Mathews Ave., Urbana, IL 61801

On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino <lcasalino@ucsd.edu> = wrote:

Hello,

I am trying to use the = multiGPU version of NAMD3 = (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run = plain MD on 2 GPUs on a single node on a local cluster using the = following command:

namd3 +p 2 = +setcpuaffinity +idlepoll +devices 0,1 input.conf > input.log

I added the following keywords to my = configuration file:
- CUDASOAintegrate on
- = margin 4

=46rom the log file, it looks like the 2 GPUs are seen and = activated:
Info: Built with CUDA version = 10010
Pe 1 physical rank 1 binding to CUDA device 1 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090'  Mem: = 24268MB  Rev: 8.6  PCI: 0:24:0
Pe 0 physical = rank 0 binding to CUDA device 0 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX 3090'  Mem: = 24268MB  Rev: 8.6  PCI: 0:1:0

The = startup phase finishes smoothly, and then, when the actual MD simulation = starts, the following error is generated:

Info: Finished startup at 34.7205 s, 0 MB of memory in use

TCL: Running for 100000 steps
FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461
on Pe 1 (tscc-gpu-5-0.sdsc.edu device 1 pci 0:24:0): invalid = device function

A single node of the = cluster has 32 cpus and 8 GPUs (GeForce RTX 3090).
I point = out that the GPUs are NOT connected by NVlink.
Finally, = this is the PBS argument I use to add the GPUs to the environment: #PBS = -l nodes=3D1:ppn=3D8:gpus=3D2:gpu3090

I was = not able to work this error out. Is it possible that without NVlink I = cannot use the multiGPU version?
Any help or advises on = this issue would be greatly appreciated.

Thank you.

Best regards,
Lorenzo


= --Apple-Mail=_F6601916-2B97-433D-B47B-E3CA799DABA3-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 18:26:56 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0QuV2026853; Mon, 22 Feb 2021 18:26:56 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11N0QuYd026852; Mon, 22 Feb 2021 18:26:56 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0QtXv026848; Mon, 22 Feb 2021 18:26:55 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11N0QtRA026847; Mon, 22 Feb 2021 18:26:55 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0QoMh026835 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 22 Feb 2021 18:26:51 -0600 (CST) From: David Hardy Message-Id: <81604C34-A85A-42B8-9003-1611A952C444@ks.uiuc.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_65F92746-46E4-4DCD-A42D-0E3616BA9F52" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Small molecule simulation error NAMD Date: Mon, 22 Feb 2021 18:26:44 -0600 In-Reply-To: Cc: Jeff Comer To: NAMD list , Chathuranga Siriwardhana References: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_65F92746-46E4-4DCD-A42D-0E3616BA9F52 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Chathuranga, It looks to me like NAMD is not treating your atom 37 as a lone pair. = The forces on lone pairs are distributed to their support atoms and then = set to zero, so I would expect lone pairs to have zero velocity (but = I=E2=80=99m having trouble finding that in the code). If you would post the top of your log file showing the configuration of = your system before simulation begins, we could see whether or not your = simulation has any lone pairs enabled. Thanks, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana = wrote: >=20 > Thanks Jeff, > I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated=20 > Thanks >=20 >=20 >=20 > Chathuranga Siriwardhana > Justin Legleiter Laboratory=20 > West Virginia University=20 > Department of chemistry=20 > Clark Hall, Room 561 > Morgantown, WV 26505 >=20 >=20 > On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer > wrote: > What version of NAMD are you using? Versions earlier than NAMD 2.14 = don=E2=80=99t support halogen lonepairs. >=20 > Jeff >=20 >=20 > On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana = > wrote: > Hi NAMD users, > I'm trying to see the interaction of a small molecule with a protein = in NAMD. As the simulation starts the following error appears; >=20 > ERROR: Margin is too small for 1 atoms during timestep 1004. > ERROR: Incorrect nonbonded forces and energies may be calculated! > ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, = atom 310 of 311 on patch 0 pe 1) > ERROR: Atoms moving too fast; simulation has become unstable (1 atoms = on patch 0 pe 1). > FATAL ERROR: Exiting prematurely; see error messages above. >=20 > Atom 37 is a lone pair on Chlorine in the small molecule. Any help is = really appreciated. >=20 > Thanks > Chathuranga >=20 >=20 >=20 >=20 >=20 >=20 > Chathuranga Siriwardhana > Justin Legleiter Laboratory=20 > West Virginia University=20 > Department of chemistry=20 > Clark Hall, Room 561 > Morgantown, WV 26505 > --=20 >=20 > = =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 > Jeffrey Comer, PhD > Associate Professor > Department of Anatomy and Physiology > Kansas State University > Office: P-213 Mosier Hall > Phone: 785-532-6311 > Website: http://jeffcomer.us = --Apple-Mail=_65F92746-46E4-4DCD-A42D-0E3616BA9F52 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Chathuranga,

It = looks to me like NAMD is not treating your atom 37 as a lone pair. The = forces on lone pairs are distributed to their support atoms and then set = to zero, so I would expect lone pairs to have zero velocity (but I=E2=80=99= m having trouble finding that in the code).

If you would post the top of your log = file showing the configuration of your system before simulation begins, = we could see whether or not your simulation has any lone pairs = enabled.

Thanks,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <ccs0019@mix.wvu.edu>= wrote:

Thanks Jeff,
I'm using NAMD = 2.14. Earlier I was using 2.13 and got it updated 
Thanks



Chathuranga = Siriwardhana
Justin Legleiter Laboratory 
West Virginia = University 
Department of = chemistry 
Clark Hall, Room 561
Morgantown, WV = 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What = version of NAMD are you using? Versions earlier than NAMD 2.14 = don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathuranga = Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD = users,
I'm trying to see the interaction of a small = molecule with a protein in NAMD. As the simulation starts the = following error appears;

ERROR: Margin is too small for 1 atoms = during timestep 1004.
ERROR: Incorrect nonbonded forces = and energies may be calculated!
ERROR: Atom 37 velocity is = -9148.69 -8900.08 8246.01 (limit is 12000, atom 310 of 311 on patch 0 pe = 1)
ERROR: Atoms moving too fast; simulation has become = unstable (1 atoms on patch 0 pe 1).
FATAL ERROR: Exiting = prematurely; see error messages above.

Atom 37 is a lone pair = on Chlorine in the small molecule. Any help is = really appreciated.

Thanks
Chathuranga






Chathuranga = Siriwardhana
Justin Legleiter Laboratory 
West Virginia = University 
Department of = chemistry 
Clark Hall, Room 561
Morgantown, WV = 26505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2= =80=94=E2=80=94
Jeffrey Comer, PhD
Associate = Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier = Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

= --Apple-Mail=_65F92746-46E4-4DCD-A42D-0E3616BA9F52-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 18:35:46 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0Zk6K029097; Mon, 22 Feb 2021 18:35:46 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11N0ZkYa029096; Mon, 22 Feb 2021 18:35:46 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0Zj0J029092; Mon, 22 Feb 2021 18:35:45 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11N0ZjFj029091; Mon, 22 Feb 2021 18:35:45 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0ZeFr029074 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 22 Feb 2021 18:35:41 -0600 (CST) From: David Hardy Message-Id: <4FA5B33C-C9CF-4CD8-8CFD-73F44B4AFB6A@ks.uiuc.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_836891D6-2D48-4899-A9CA-2E0715CB28D7" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: NAMD3 multiGPU: invalid device function error Date: Mon, 22 Feb 2021 18:35:35 -0600 In-Reply-To: Cc: namd-l@ks.uiuc.edu, Lorenzo Casalino To: Chathuranga Siriwardhana References: <9FD2B800-CA22-4CBF-9AFD-AED126221DF7@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_836891D6-2D48-4899-A9CA-2E0715CB28D7 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Chathuranga, (It looks like you replied to Lorenzo=E2=80=99s email by mistake, but = I=E2=80=99ll go ahead and answer your lone pair question here.) By looking at your BEN_water.psf and test.log files, I can see that NAMD = is not recognizing atom 37 as a lone pair. To correctly designate a lone = pair, the PSF file has to include a !NUMLP section that specifies the = support atoms for each lone pair. Whatever you used to create the PSF = file didn=E2=80=99t produce this information. Best regards, Dave > On Feb 22, 2021, at 6:17 PM, Chathuranga Siriwardhana = wrote: >=20 > Thank you for your response=20 > Here I ve attached all the files that I used.=20 >=20 >=20 >=20 >=20 > Chathuranga Siriwardhana > Justin Legleiter Laboratory=20 > West Virginia University=20 > Department of chemistry=20 > Clark Hall, Room 561 > Morgantown, WV 26505 >=20 >=20 > On Mon, Feb 22, 2021 at 7:02 PM David Hardy > wrote: > Hi Lorenzo, >=20 > Sorry, I have to follow up my previous email. >=20 > I had thought that multi-GPU alpha 7 required NVLink. It happens to be = recommended, but not required. I am not sure why you are seeing an = error. If you are willing to share your data set with us, we could try = to reproduce the issue locally. Also, it would be good to have the full = log file from your failed run. >=20 > Best regards, > Dave >=20 >> On Feb 22, 2021, at 4:26 PM, David Hardy > wrote: >>=20 >> Hi Lorenzo, >>=20 >> The version of NAMD that you are running does require NVLink for = multi-GPU support (see = http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ = ). Our most recent = improvements to multi-GPU support no longer require NVLink, however, = scaling performance suffers without it. The next release (alpha 9) will = include this new multi-GPU support. Until we get new builds posted, you = will need to build from the GitLab =E2=80=9Cdevel" branch to try it out. = You can get access to the NAMD GitLab repo by following the posted = directions (https://gitlab.com/tcbgUIUC/namd = ). >>=20 >> Best regards, >> Dave >>=20 >> -- >> David J. Hardy, Ph.D. >> Beckman Institute >> University of Illinois at Urbana-Champaign >> 405 N. Mathews Ave., Urbana, IL 61801 >> dhardy@ks.uiuc.edu , = http://www.ks.uiuc.edu/~dhardy/ >>=20 >>> On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino > wrote: >>>=20 >>> Hello, >>>=20 >>> I am trying to use the multiGPU version of NAMD3 = (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run = plain MD on 2 GPUs on a single node on a local cluster using the = following command: >>>=20 >>> namd3 +p 2 +setcpuaffinity +idlepoll +devices 0,1 input.conf > = input.log >>>=20 >>> I added the following keywords to my configuration file: >>> - CUDASOAintegrate on >>> - margin 4 >>>=20 >>>> =46rom the log file, it looks like the 2 GPUs are seen and = activated: >>> Info: Built with CUDA version 10010 >>> Pe 1 physical rank 1 binding to CUDA device 1 on = tscc-gpu-5-0.sdsc.edu = : = 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: 0:24:0 >>> Pe 0 physical rank 0 binding to CUDA device 0 on = tscc-gpu-5-0.sdsc.edu = : = 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: 0:1:0 >>>=20 >>> The startup phase finishes smoothly, and then, when the actual MD = simulation starts, the following error is generated: >>>=20 >>> Info: Finished startup at 34.7205 s, 0 MB of memory in use >>>=20 >>> TCL: Running for 100000 steps >>> FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 >>> on Pe 1 (tscc-gpu-5-0.sdsc.edu = device = 1 pci 0:24:0): invalid device function >>>=20 >>> A single node of the cluster has 32 cpus and 8 GPUs (GeForce RTX = 3090). >>> I point out that the GPUs are NOT connected by NVlink. >>> Finally, this is the PBS argument I use to add the GPUs to the = environment: #PBS -l nodes=3D1:ppn=3D8:gpus=3D2:gpu3090 >>>=20 >>> I was not able to work this error out. Is it possible that without = NVlink I cannot use the multiGPU version? >>> Any help or advises on this issue would be greatly appreciated. >>>=20 >>> Thank you. >>>=20 >>> Best regards, >>> Lorenzo >>=20 >=20 > --Apple-Mail=_836891D6-2D48-4899-A9CA-2E0715CB28D7 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Chathuranga,

(It = looks like you replied to Lorenzo=E2=80=99s email by mistake, but I=E2=80=99= ll go ahead and answer your lone pair question here.)

By looking at your = BEN_water.psf and test.log files, I can see that NAMD is not recognizing = atom 37 as a lone pair. To correctly designate a lone pair, the PSF file = has to include a !NUMLP section that specifies the support atoms for = each lone pair. Whatever you used to create the PSF file didn=E2=80=99t = produce this information.

Best regards,
Dave

On Feb 22, 2021, at 6:17 PM, Chathuranga = Siriwardhana <ccs0019@mix.wvu.edu> wrote:

Thank you for your response 
Here I ve = attached all the files that I used. 




Chathuranga = Siriwardhana
Justin Legleiter Laboratory 
West Virginia = University 
Department of = chemistry 
Clark Hall, Room 561
Morgantown, WV = 26505


On Mon, Feb 22, 2021 at 7:02 PM David = Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Lorenzo,

Sorry, I have to follow up my previous = email.

I had = thought that multi-GPU alpha 7 required NVLink. It happens to be = recommended, but not required. I am not sure why you are seeing an = error. If you are willing to share your data set with us, we could try = to reproduce the issue locally. Also, it would be good to have the full = log file from your failed run.

Best regards,
Dave

On Feb = 22, 2021, at 4:26 PM, David Hardy <dhardy@ks.uiuc.edu> wrote:

Hi = Lorenzo,

The version = of NAMD that you are running does require NVLink for multi-GPU support = (see http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/). = Our most recent improvements to multi-GPU support no longer require = NVLink, however, scaling performance suffers without it. The next = release (alpha 9) will include this new multi-GPU support. Until we get = new builds posted, you will need to build from the GitLab =E2=80=9Cdevel" = branch to try it out. You can get access to the NAMD GitLab repo by = following the posted directions (https://gitlab.com/tcbgUIUC/namd).
Best regards,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino <lcasalino@ucsd.edu> wrote:

Hello,

I am = trying to use the multiGPU version of NAMD3 = (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run = plain MD on 2 GPUs on a single node on a local cluster using the = following command:

namd3 +p 2 = +setcpuaffinity +idlepoll +devices 0,1 input.conf > input.log

I added the following keywords to my = configuration file:
- CUDASOAintegrate on
- = margin 4

=46rom the log file, it looks like the 2 GPUs are seen and = activated:
Info: Built with CUDA version = 10010
Pe 1 physical rank 1 binding to CUDA device 1 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX = 3090'  Mem: 24268MB  Rev: 8.6  PCI: 0:24:0
Pe= 0 physical rank 0 binding to CUDA device 0 on tscc-gpu-5-0.sdsc.edu: 'GeForce RTX = 3090'  Mem: 24268MB  Rev: 8.6  PCI: 0:1:0
The startup phase finishes smoothly, and then, when the = actual MD simulation starts, the following error is generated:

Info: Finished startup at 34.7205 s, 0 MB of = memory in use

TCL: Running for 100000 = steps
FATAL ERROR: CUDA error = cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, hgi, hgi, = d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKernel.cu, = function buildRattleLists, line 4461
on Pe 1 (tscc-gpu-5-0.sdsc.edu device 1 pci = 0:24:0): invalid device function

A single = node of the cluster has 32 cpus and 8 GPUs (GeForce RTX 3090).
I point out that the GPUs are NOT connected by NVlink.
Finally, this is the PBS argument I use to add the GPUs to = the environment: #PBS -l nodes=3D1:ppn=3D8:gpus=3D2:gpu3090

I was not able to work this error out. Is it = possible that without NVlink I cannot use the multiGPU version?
Any help or advises on this issue would be greatly = appreciated.

Thank you.

Best regards,
Lorenzo


<test.conf><BEN_water.pdb><BEN_water.psf><test.log><BEN.prm>

= --Apple-Mail=_836891D6-2D48-4899-A9CA-2E0715CB28D7-- From owner-namd-l@halifax.ks.uiuc.edu Mon Feb 22 18:49:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0na2m001372; Mon, 22 Feb 2021 18:49:36 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11N0naDc001370; Mon, 22 Feb 2021 18:49:36 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0nZwR001366; Mon, 22 Feb 2021 18:49:35 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11N0nZdJ001365; Mon, 22 Feb 2021 18:49:35 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11N0nUu4001355 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 22 Feb 2021 18:49:31 -0600 (CST) From: David Hardy Message-Id: <3F1EB98D-6F5D-40DE-A026-A46687B1E94A@ks.uiuc.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_00DDCD53-FCC6-4C7B-B777-B5037C11F005" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Small molecule simulation error NAMD Date: Mon, 22 Feb 2021 18:49:25 -0600 In-Reply-To: Cc: NAMD list To: Chathuranga Siriwardhana References: <81604C34-A85A-42B8-9003-1611A952C444@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_00DDCD53-FCC6-4C7B-B777-B5037C11F005 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Chathuranga, No worries. I am replying back to the list because I don=E2=80=99t know = the answer to your question. Can anyone on list recommend how to correctly create a PSF with lone = pairs? Thanks, Dave > On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana = wrote: >=20 > Hi David, > Thank you so much for helping me with my issue. And I am really sorry = that I replied to the wrong email. I subscribed to the mailing list = today and I got confused with how it works :( =20 > Would you mind recommending a method to create the psf with lone = pairs. I used VMD psfgen. >=20 > Thanks again for helping me >=20 > Chathuranga >=20 >=20 >=20 >=20 >=20 >=20 > Chathuranga Siriwardhana > Justin Legleiter Laboratory=20 > West Virginia University=20 > Department of chemistry=20 > Clark Hall, Room 561 > Morgantown, WV 26505 >=20 >=20 > On Mon, Feb 22, 2021 at 7:26 PM David Hardy > wrote: > Hi Chathuranga, >=20 > It looks to me like NAMD is not treating your atom 37 as a lone pair. = The forces on lone pairs are distributed to their support atoms and then = set to zero, so I would expect lone pairs to have zero velocity (but = I=E2=80=99m having trouble finding that in the code). >=20 > If you would post the top of your log file showing the configuration = of your system before simulation begins, we could see whether or not = your simulation has any lone pairs enabled. >=20 > Thanks, > Dave >=20 > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu , = http://www.ks.uiuc.edu/~dhardy/ >=20 >> On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana = > wrote: >>=20 >> Thanks Jeff, >> I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated=20 >> Thanks >>=20 >>=20 >>=20 >> Chathuranga Siriwardhana >> Justin Legleiter Laboratory=20 >> West Virginia University=20 >> Department of chemistry=20 >> Clark Hall, Room 561 >> Morgantown, WV 26505 >>=20 >>=20 >> On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer > wrote: >> What version of NAMD are you using? Versions earlier than NAMD 2.14 = don=E2=80=99t support halogen lonepairs. >>=20 >> Jeff >>=20 >>=20 >> On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana = > wrote: >> Hi NAMD users, >> I'm trying to see the interaction of a small molecule with a protein = in NAMD. As the simulation starts the following error appears; >>=20 >> ERROR: Margin is too small for 1 atoms during timestep 1004. >> ERROR: Incorrect nonbonded forces and energies may be calculated! >> ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, = atom 310 of 311 on patch 0 pe 1) >> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms = on patch 0 pe 1). >> FATAL ERROR: Exiting prematurely; see error messages above. >>=20 >> Atom 37 is a lone pair on Chlorine in the small molecule. Any help is = really appreciated. >>=20 >> Thanks >> Chathuranga >>=20 >>=20 >>=20 >>=20 >>=20 >>=20 >> Chathuranga Siriwardhana >> Justin Legleiter Laboratory=20 >> West Virginia University=20 >> Department of chemistry=20 >> Clark Hall, Room 561 >> Morgantown, WV 26505 >> --=20 >>=20 >> = =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 >> Jeffrey Comer, PhD >> Associate Professor >> Department of Anatomy and Physiology >> Kansas State University >> Office: P-213 Mosier Hall >> Phone: 785-532-6311 >> Website: http://jeffcomer.us = --Apple-Mail=_00DDCD53-FCC6-4C7B-B777-B5037C11F005 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Chathuranga,

No = worries. I am replying back to the list because I don=E2=80=99t know the = answer to your question.

Can anyone on list recommend how to correctly create a PSF = with lone pairs?

Thanks,
Dave

On Feb = 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <ccs0019@mix.wvu.edu>= wrote:

Hi David,
Thank you so much = for helping me with my issue. And I am really sorry that I replied to = the wrong email. I subscribed to the mailing list today and I got = confused with how it works :(  
Would you = mind recommending a method to create the psf with lone pairs. I = used VMD psfgen.

Thanks again for helping me

Chathuranga






Chathuranga = Siriwardhana
Justin Legleiter Laboratory 
West Virginia = University 
Department of = chemistry 
Clark Hall, Room 561
Morgantown, WV = 26505


On Mon, Feb 22, 2021 at 7:26 PM David = Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Chathuranga,

It looks to me like NAMD is not = treating your atom 37 as a lone pair. The forces on lone pairs are = distributed to their support atoms and then set to zero, so I would = expect lone pairs to have zero velocity (but I=E2=80=99m having trouble = finding that in the code).

If you would post the top of your log file showing the = configuration of your system before simulation begins, we could see = whether or not your simulation has any lone pairs enabled.

Thanks,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at = Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <ccs0019@mix.wvu.edu> wrote:

Thanks Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it = updated 
Thanks



Chathuranga = Siriwardhana
Justin Legleiter Laboratory 
West Virginia = University 
Department of = chemistry 
Clark Hall, Room 561
Morgantown, WV = 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What = version of NAMD are you using? Versions earlier than NAMD 2.14 = don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathuranga = Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD = users,
I'm trying to see the interaction of a small = molecule with a protein in NAMD. As the simulation starts the = following error appears;

ERROR: Margin is too small for 1 atoms = during timestep 1004.
ERROR: Incorrect nonbonded forces = and energies may be calculated!
ERROR: Atom 37 velocity is = -9148.69 -8900.08 8246.01 (limit is 12000, atom 310 of 311 on patch 0 pe = 1)
ERROR: Atoms moving too fast; simulation has become = unstable (1 atoms on patch 0 pe 1).
FATAL ERROR: Exiting = prematurely; see error messages above.

Atom 37 is a lone pair = on Chlorine in the small molecule. Any help is = really appreciated.

Thanks
Chathuranga






Chathuranga = Siriwardhana
Justin Legleiter Laboratory 
West Virginia = University 
Department of = chemistry 
Clark Hall, Room 561
Morgantown, WV = 26505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2= =80=94=E2=80=94
Jeffrey Comer, PhD
Associate = Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier = Hall
Phone: 785-532-6311
Website: http://jeffcomer.us


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charset="utf-8" Content-Transfer-Encoding: Quoted-printable paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryland.e= du/__;!!DZ3fjg!vnVotRzugCl3ofgzMBxmMpPrbJLa9_VSrMsogKTFklbgEvU_TjExn5hFwxmU= WK8WYA$=20 Best, JC On Feb 22, 2021, at 7:49 PM, David Hardy > wrote: Hi Chathuranga, No worries. I am replying back to the list because I don=E2=80=99t know the= answer to your question. Can anyone on list recommend how to correctly create a PSF with lone pairs? Thanks, Dave On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana > wrote: Hi David, Thank you so much for helping me with my issue. And I am really sorry that = I replied to the wrong email. I subscribed to the mailing list today and I = got confused with how it works :( Would you mind recommending a method to create the psf with lone pairs. I u= sed VMD psfgen. Thanks again for helping me Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 7:26 PM David Hardy > wrote: Hi Chathuranga, It looks to me like NAMD is not treating your atom 37 as a lone pair. The f= orces on lone pairs are distributed to their support atoms and then set to = zero, so I would expect lone pairs to have zero velocity (but I=E2=80=99m h= aving trouble finding that in the code). If you would post the top of your log file showing the configuration of you= r system before simulation begins, we could see whether or not your simulat= ion has any lone pairs enabled. Thanks, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhar= dy/ On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana > wrote: Thanks Jeff, I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated Thanks Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer > wrote: What version of NAMD are you using? Versions earlier than NAMD 2.14 don=E2= =80=99t support halogen lonepairs. Jeff On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana > wrote: Hi NAMD users, I'm trying to see the interaction of a small molecule with a protein in NAM= D. As the simulation starts the following error appears; ERROR: Margin is too small for 1 atoms during timestep 1004. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1). FATAL ERROR: Exiting prematurely; see error messages above. Atom 37 is a lone pair on Chlorine in the small molecule. Any help is reall= y appreciated. Thanks Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 -- =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!vnVotRz= ugCl3ofgzMBxmMpPrbJLa9_VSrMsogKTFklbgEvU_TjExn5hFwxlbn1SV_A$ --_000_A1F9323B3F454A708175946B80ADA144physicsgatechedu_ Content-Type: text/html; charset="utf-8" Content-ID: <6A52E425B970CB4A88296061F3C228A2@namprd07.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable paramchem can do it: https://cgenff.umaryland.edu/

Best,
JC

On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy@ks.uiuc.edu> wrote:

Hi Chathuranga,

No worries. I am replying back to the list because I don=E2= =80=99t know the answer to your question.

Can anyone on list recommend how to correctly create a PSF = with lone pairs?

Thanks,
Dave

On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" class=3D"">ccs0019@mix.wvu.edu>= ; wrote:

Hi David,
Thank you so much for helping me with my issue. And I am re= ally sorry that I replied to the wrong email. I subscribed to the mailing l= ist today and I got confused with how it works :(  
Would you mind recommending a method to create the psf= with lone pairs. I used VMD psfgen.

Thanks again for helping me

Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chem= istry 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 7:26 PM David= Hardy <dhardy@ks.uiuc.= edu> wrote:
Hi Chathuranga,

It looks to me like NAMD is not treating your atom 37 as a = lone pair. The forces on lone pairs are distributed to their support atoms = and then set to zero, so I would expect lone pairs to have zero velocity (b= ut I=E2=80=99m having trouble finding that in the code).

If you would post the top of your log file showing the conf= iguration of your system before simulation begins, we could see whether or = not your simulation has any lone pairs enabled.

Thanks,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Thanks Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it up= dated 
Thanks



Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What version of NAMD are you using? Versi= ons earlier than NAMD 2.14 don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathur= anga Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD users,
I'm trying to see the interaction of a small molecule with = a protein in NAMD. As the simulation starts the following error appear= s;

ERROR: Margin is too small for 1 atoms during timestep 1004= .
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecule. A= ny help is really appreciated.

Thanks
Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us



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boundary="_000_63D6EF15F152485ABD1D097F6BE38E36physicsgatechedu_" X-OriginatorOrg: physics.gatech.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BN7PR07MB4481.namprd07.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: c0ff0ba7-f756-43e3-d0ae-08d8d79a5fef X-MS-Exchange-CrossTenant-originalarrivaltime: 23 Feb 2021 01:28:50.6483 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 482198bb-ae7b-4b25-8b7a-6d7f32faa083 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: W2gpGydFIHY/Tb/wvZjiEdYsdQK009xeGtKde0G3IGjh7jwgPnNeOP8mcTALwqi10BK6P6vq07O5LqkGnWwYDQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BN8PR07MB7170 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBofEQpMehcaEQpZRBdie05gWEVmQ09tTREKWFgXZhlwY2FScgFYG3A RCnhOF2hpBUkaRWhhHWVvEQp5TBdnbmRSR2NCG25rehEKQ0gXBxgTHhEKQ1kXBxgYEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIfcRseGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd8en1eWUhAeVJHX2NZWH9CfWIabXtpRUlSWmBBcxthThEKWFwXHwQaBBgYHgUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JLTB1SEQpNXBceHBoRCkxaF3tpa01rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29va2tsa2sRCkJPF3pec0ESTxtpHEZzEQpDWhceGgQbGh0EGBkcBB saGxEKQl4XGxEKRFgXGBEKRF4XGREKREkXGxEKQlwXGxEKQksXaBNPUBJ8YwF+c0cRCkJJF2hpB UkaRWhhHWVvEQpCRRdvbXxiTnNvTX1PfREKQk4XaGkFSRpFaGEdZW8RCkJMF2YZcGNhUnIBWBtw EQpCbBdsTUFFQE5bb1lLchEKQkAXZxJTWGB4f1wZfAURClpYFx8RCnlDF29SHWJ8cn1eWUlGEQp wZxdvXkJyf35MZ39wQRAZGhEKcGgXb0RFbl1ORHxNeEwQGRoRCnBoF2QbRW8cQkRlZBpfEBkaEQ pwaBdgfBxcGBlubGt/UxAZGhEKcGgXaB5+XBljGhkTb0IQGRoRCnBoF2RfUGNbEx5QUmFrEBkaE QpwfRdpcmtLSFkeXQVaXxAZGhEKcH0Xb2JcT2d9bHNGelIQGRoRCnBnF2tNTXxOTF96Rx5NEBwa EQpwZxd6W20SQFJeZ3hJHRAcGhEKcH0Xa2dwUFhPfkRCXBkQGRoRCnBnF2FcWHBpHE18bB5lEB4 SEQpwfRdjQWN6a2kFHmIaWRAZGhEKcH0XbH5pTERvHnMce30QGRoRCnB/F2UZeWZeR2kbZE9zEB saHhEKcF8XY0dnT2Z6YHJtE1oQGRoRCnB/F3occH4SaXxaf0VEEBsYExEKcF8XYkRYHWttBR1nX B0QGRoRCnB/F2VYchgdSRheRml8EBseGxEKcF8XaFgcY0l9e0NiXRIQHhIRCnB/F2NBY3praQUe YhpZEBkaEQpwfxdsWmBlE39nZGASRBAbGRIRCnBfF2RvaRxvR1trE05tEBseGhEKcGwXbVlrGFl 9AR8dfVkQHhIRCnBMF2VHBXhEflN+AUxsEBkaEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 spamscore=0 adultscore=0 impostorscore=0 clxscore=205 priorityscore=0 malwarescore=0 suspectscore=0 phishscore=0 lowpriorityscore=0 mlxlogscore=999 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102230007 X-Spam-Score: 0 X-Spam-OrigSender: gumbart@physics.gatech.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Gumbart, JC" --_000_63D6EF15F152485ABD1D097F6BE38E36physicsgatechedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Oops, I replied too fast. I was thinking of the parameters, not the PSF. = The latest version of PSFGen ( >=3D 2.0) can handle it: https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf It=E2=80=99s distributed with more recent VMD builds. Best, JC On Feb 22, 2021, at 8:25 PM, Gumbart, JC > wrote: paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryland.e= du/__;!!DZ3fjg!pWxsJJ6BU8ulBSozqDwkBO4YRUPpup7ygKHWurhyTZj7GzlKgzh3ZJr_dmyq= QTwguA$=20 Best, JC On Feb 22, 2021, at 7:49 PM, David Hardy > wrote: Hi Chathuranga, No worries. I am replying back to the list because I don=E2=80=99t know the= answer to your question. Can anyone on list recommend how to correctly create a PSF with lone pairs? Thanks, Dave On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana > wrote: Hi David, Thank you so much for helping me with my issue. And I am really sorry that = I replied to the wrong email. I subscribed to the mailing list today and I = got confused with how it works :( Would you mind recommending a method to create the psf with lone pairs. I u= sed VMD psfgen. Thanks again for helping me Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 7:26 PM David Hardy > wrote: Hi Chathuranga, It looks to me like NAMD is not treating your atom 37 as a lone pair. The f= orces on lone pairs are distributed to their support atoms and then set to = zero, so I would expect lone pairs to have zero velocity (but I=E2=80=99m h= aving trouble finding that in the code). If you would post the top of your log file showing the configuration of you= r system before simulation begins, we could see whether or not your simulat= ion has any lone pairs enabled. Thanks, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhar= dy/ On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana > wrote: Thanks Jeff, I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated Thanks Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer > wrote: What version of NAMD are you using? Versions earlier than NAMD 2.14 don=E2= =80=99t support halogen lonepairs. Jeff On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana > wrote: Hi NAMD users, I'm trying to see the interaction of a small molecule with a protein in NAM= D. As the simulation starts the following error appears; ERROR: Margin is too small for 1 atoms during timestep 1004. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1). FATAL ERROR: Exiting prematurely; see error messages above. Atom 37 is a lone pair on Chlorine in the small molecule. Any help is reall= y appreciated. Thanks Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 -- =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!pWxsJJ6= BU8ulBSozqDwkBO4YRUPpup7ygKHWurhyTZj7GzlKgzh3ZJr_dmxFgzx_Lg$ --_000_63D6EF15F152485ABD1D097F6BE38E36physicsgatechedu_ Content-Type: text/html; charset="utf-8" Content-ID: <43AF6FCB105A6F47B4E49EE4E72EC318@namprd07.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Oops, I replied too fast.  I was thinking of the parameters, not the P= SF.  The latest version of PSFGen ( >=3D 2.0) can handle it:

It=E2=80=99s distributed with more recent VMD builds.

Best,
JC

On Feb 22, 2021, at 8:25 PM, Gumbart, JC <gumbart@physics.gatech.edu&g= t; wrote:

paramchem can do it: https://cgenff.umaryland.edu/

Best,
JC

On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy@ks.uiuc.edu> wrote:

Hi Chathuranga,

No worries. I am replying back to the list because I don=E2= =80=99t know the answer to your question.

Can anyone on list recommend how to correctly create a PSF = with lone pairs?

Thanks,
Dave

On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" class=3D"">ccs0019@mix.wvu.edu>= ; wrote:

Hi David,
Thank you so much for helping me with my issue. And I am re= ally sorry that I replied to the wrong email. I subscribed to the mailing l= ist today and I got confused with how it works :(  
Would you mind recommending a method to create the psf= with lone pairs. I used VMD psfgen.

Thanks again for helping me

Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chem= istry 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 7:26 PM David= Hardy <dhardy@ks.uiuc.= edu> wrote:
Hi Chathuranga,

It looks to me like NAMD is not treating your atom 37 as a = lone pair. The forces on lone pairs are distributed to their support atoms = and then set to zero, so I would expect lone pairs to have zero velocity (b= ut I=E2=80=99m having trouble finding that in the code).

If you would post the top of your log file showing the conf= iguration of your system before simulation begins, we could see whether or = not your simulation has any lone pairs enabled.

Thanks,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Thanks Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it up= dated 
Thanks



Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What version of NAMD are you using? Versi= ons earlier than NAMD 2.14 don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathur= anga Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD users,
I'm trying to see the interaction of a small molecule with = a protein in NAMD. As the simulation starts the following error appear= s;

ERROR: Margin is too small for 1 atoms during timestep 1004= .
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecule. A= ny help is really appreciated.

Thanks
Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us




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charset="utf-8" Content-Transfer-Encoding: Quoted-printable You have to include the appropriate CGenFF force-field file as well. Best, JC On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana > wrote: Hi JC, Thank you for the reply. I parameterized the molecule from the same online = GUI you mentioned above. However my stream file created through the cgenff does not have bond parame= ters for CL and LPH. Do you know how to fix it FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 38 21) Thanks again for your help Chaturanga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 8:28 PM Gumbart, JC > wrote: Oops, I replied too fast. I was thinking of the parameters, not the PSF. = The latest version of PSFGen ( >=3D 2.0) can handle it: https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf It=E2=80=99s distributed with more recent VMD builds. Best, JC On Feb 22, 2021, at 8:25 PM, Gumbart, JC > wrote: paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryland.e= du/__;!!DZ3fjg!qWw5n-IteGWCR0SyAlDUHjOReMvsCCfH_Ra08P9O6Ya_gkINhwBlC314sHU9= k9qPjQ$ Best, JC On Feb 22, 2021, at 7:49 PM, David Hardy > wrote: Hi Chathuranga, No worries. I am replying back to the list because I don=E2=80=99t know the= answer to your question. Can anyone on list recommend how to correctly create a PSF with lone pairs? Thanks, Dave On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana > wrote: Hi David, Thank you so much for helping me with my issue. And I am really sorry that = I replied to the wrong email. I subscribed to the mailing list today and I = got confused with how it works :( Would you mind recommending a method to create the psf with lone pairs. I u= sed VMD psfgen. Thanks again for helping me Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 7:26 PM David Hardy > wrote: Hi Chathuranga, It looks to me like NAMD is not treating your atom 37 as a lone pair. The f= orces on lone pairs are distributed to their support atoms and then set to = zero, so I would expect lone pairs to have zero velocity (but I=E2=80=99m h= aving trouble finding that in the code). If you would post the top of your log file showing the configuration of you= r system before simulation begins, we could see whether or not your simulat= ion has any lone pairs enabled. Thanks, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhar= dy/ On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana > wrote: Thanks Jeff, I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated Thanks Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer > wrote: What version of NAMD are you using? Versions earlier than NAMD 2.14 don=E2= =80=99t support halogen lonepairs. Jeff On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana > wrote: Hi NAMD users, I'm trying to see the interaction of a small molecule with a protein in NAM= D. As the simulation starts the following error appears; ERROR: Margin is too small for 1 atoms during timestep 1004. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1). FATAL ERROR: Exiting prematurely; see error messages above. Atom 37 is a lone pair on Chlorine in the small molecule. Any help is reall= y appreciated. Thanks Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 -- =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!qWw5n-I= teGWCR0SyAlDUHjOReMvsCCfH_Ra08P9O6Ya_gkINhwBlC314sHVNwknbYw$ --_000_AD6588D56543460793E0FFEB769008C3physicsgatechedu_ Content-Type: text/html; charset="utf-8" Content-ID: <6A39F30257672E419FA5285F1B8175FF@namprd07.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable You have to include the appropriate CGenFF force-field file as well.

Best,
JC

On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" class=3D"">ccs0019@mix.wvu.edu>= ; wrote:

Hi JC,
Thank you for the reply. I parameterized the molecule from = the same online GUI you mentioned above. 
However my stream file created through the cgenff does not = have bond parameters for CL and LPH. Do you know how to fix it

FATAL ERROR: UNABLE TO FIND BOND PARAMETERS F= OR CLGR1 LPH (ATOMS 38 21)

Thanks again for your help
Chaturanga

Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chem= istry 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 8:28 PM Gumba= rt, JC <gumbart@physics.gatech.edu> wrote:
Oops, I replied too fast.  I was thinking of the param= eters, not the PSF.  The latest version of PSFGen ( >=3D 2.0) can h= andle it:

It=E2=80=99s distributed with more recent VMD builds.

Best,
JC

On Feb 22, 2021, at 8:25 PM, Gumbart, JC <gumbart@physic= s.gatech.edu> wrote:

paramchem can do it: https://cgenff.umaryland.edu/

Best,
JC

On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy@ks.uiuc.edu= > wrote:

Hi Chathuranga,

No worries. I am replying back to the list because I don=E2= =80=99t know the answer to your question.

Can anyone on list recommend how to correctly create a PSF = with lone pairs?

Thanks,
Dave

On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Hi David,
Thank you so much for helping me with my issue. And I am re= ally sorry that I replied to the wrong email. I subscribed to the mailing l= ist today and I got confused with how it works :(  
Would you mind recommending a method to create the psf= with lone pairs. I used VMD psfgen.

Thanks again for helping me

Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 7:26 PM David= Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Chathuranga,

It looks to me like NAMD is not treating your atom 37 as a = lone pair. The forces on lone pairs are distributed to their support atoms = and then set to zero, so I would expect lone pairs to have zero velocity (b= ut I=E2=80=99m having trouble finding that in the code).

If you would post the top of your log file showing the conf= iguration of your system before simulation begins, we could see whether or = not your simulation has any lone pairs enabled.

Thanks,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Thanks Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it up= dated 
Thanks



Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What version of NAMD are you using? Versi= ons earlier than NAMD 2.14 don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathur= anga Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD users,
I'm trying to see the interaction of a small molecule with = a protein in NAMD. As the simulation starts the following error appear= s;

ERROR: Margin is too small for 1 atoms during timestep 1004= .
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecule. A= ny help is really appreciated.

Thanks
Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us





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charset="utf-8" Content-Transfer-Encoding: Quoted-printable Please reply-all to keep the mailing list in your replies. As I recall, there shouldn=E2=80=99t be a bond parameter for it because it= =E2=80=99s fixed. Something is likely still wrong with your PSF. You need= to build it using PSFGen 2.0. It should be correct if you see a !NUMLP se= ction, as Dave pointed out. Best, JC On Feb 22, 2021, at 9:30 PM, Chathuranga Siriwardhana > wrote: I have included the force field files from the C36 July release. Apparently= it did not have the parameters for the CL LPH bond. Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 9:12 PM Gumbart, JC > wrote: You have to include the appropriate CGenFF force-field file as well. Best, JC On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana > wrote: Hi JC, Thank you for the reply. I parameterized the molecule from the same online = GUI you mentioned above. However my stream file created through the cgenff does not have bond parame= ters for CL and LPH. Do you know how to fix it FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 38 21) Thanks again for your help Chaturanga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 8:28 PM Gumbart, JC > wrote: Oops, I replied too fast. I was thinking of the parameters, not the PSF. = The latest version of PSFGen ( >=3D 2.0) can handle it: https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf It=E2=80=99s distributed with more recent VMD builds. Best, JC On Feb 22, 2021, at 8:25 PM, Gumbart, JC > wrote: paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryland.e= du/__;!!DZ3fjg!sAWNRPxKQeQ9Vr-YodvN7evq8h0Y95YmFj3JSN3sLcYx_RjtDj5D8PVUgq8W= NcujYg$ Best, JC On Feb 22, 2021, at 7:49 PM, David Hardy > wrote: Hi Chathuranga, No worries. I am replying back to the list because I don=E2=80=99t know the= answer to your question. Can anyone on list recommend how to correctly create a PSF with lone pairs? Thanks, Dave On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana > wrote: Hi David, Thank you so much for helping me with my issue. And I am really sorry that = I replied to the wrong email. I subscribed to the mailing list today and I = got confused with how it works :( Would you mind recommending a method to create the psf with lone pairs. I u= sed VMD psfgen. Thanks again for helping me Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 7:26 PM David Hardy > wrote: Hi Chathuranga, It looks to me like NAMD is not treating your atom 37 as a lone pair. The f= orces on lone pairs are distributed to their support atoms and then set to = zero, so I would expect lone pairs to have zero velocity (but I=E2=80=99m h= aving trouble finding that in the code). If you would post the top of your log file showing the configuration of you= r system before simulation begins, we could see whether or not your simulat= ion has any lone pairs enabled. Thanks, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhar= dy/ On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana > wrote: Thanks Jeff, I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated Thanks Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer > wrote: What version of NAMD are you using? Versions earlier than NAMD 2.14 don=E2= =80=99t support halogen lonepairs. Jeff On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana > wrote: Hi NAMD users, I'm trying to see the interaction of a small molecule with a protein in NAM= D. As the simulation starts the following error appears; ERROR: Margin is too small for 1 atoms during timestep 1004. ERROR: Incorrect nonbonded forces and energies may be calculated! ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1). FATAL ERROR: Exiting prematurely; see error messages above. Atom 37 is a lone pair on Chlorine in the small molecule. Any help is reall= y appreciated. Thanks Chathuranga Chathuranga Siriwardhana Justin Legleiter Laboratory West Virginia University Department of chemistry Clark Hall, Room 561 Morgantown, WV 26505 -- =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!sAWNRPx= KQeQ9Vr-YodvN7evq8h0Y95YmFj3JSN3sLcYx_RjtDj5D8PVUgq-9BpFQtQ$ --_000_02259C16A10747219962842BD5580A7Ephysicsgatechedu_ Content-Type: text/html; charset="utf-8" Content-ID: <67BECD951B81164495CBCCFC94A5657F@namprd07.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Please reply-all to keep the mailing list in your replies.

As I recall, there shouldn=E2=80=99t be a bond parameter fo= r it because it=E2=80=99s fixed.  Something is likely still wrong with= your PSF.  You need to build it using PSFGen 2.0.  It should be = correct if you see a !NUMLP section, as Dave pointed out.

Best,
JC

On Feb 22, 2021, at 9:30 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" class=3D"">ccs0019@mix.wvu.edu>= ; wrote:

I have included the force field files from the = C36 July release. Apparently it did not have the parameters for the CL= LPH bond.


Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chem= istry 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 9:12 PM Gumba= rt, JC <gumbart= @physics.gatech.edu> wrote:
You have to include th= e appropriate CGenFF force-field file as well.

Best,
JC

On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Hi JC,
Thank you for the reply. I parameterized the molecule from = the same online GUI you mentioned above. 
However my stream file created through the cgenff does not = have bond parameters for CL and LPH. Do you know how to fix it

FATAL ERROR: UNABLE TO FIND BOND PARAMETERS F= OR CLGR1 LPH (ATOMS 38 21)

Thanks again for your help
Chaturanga

Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 8:28 PM Gumba= rt, JC <gumbart@physics.gatech.edu> wrote:
Oops, I replied too fast.  I was thinking of the param= eters, not the PSF.  The latest version of PSFGen ( >=3D 2.0) can h= andle it:

It=E2=80=99s distributed with more recent VMD builds.

Best,
JC

On Feb 22, 2021, at 8:25 PM, Gumbart, JC <gumbart@physic= s.gatech.edu> wrote:

paramchem can do it: https://cgenff.umaryland.edu/

Best,
JC

On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy@ks.uiuc.edu= > wrote:

Hi Chathuranga,

No worries. I am replying back to the list because I don=E2= =80=99t know the answer to your question.

Can anyone on list recommend how to correctly create a PSF = with lone pairs?

Thanks,
Dave

On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Hi David,
Thank you so much for helping me with my issue. And I am re= ally sorry that I replied to the wrong email. I subscribed to the mailing l= ist today and I got confused with how it works :(  
Would you mind recommending a method to create the psf= with lone pairs. I used VMD psfgen.

Thanks again for helping me

Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 7:26 PM David= Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Chathuranga,

It looks to me like NAMD is not treating your atom 37 as a = lone pair. The forces on lone pairs are distributed to their support atoms = and then set to zero, so I would expect lone pairs to have zero velocity (b= ut I=E2=80=99m having trouble finding that in the code).

If you would post the top of your log file showing the conf= iguration of your system before simulation begins, we could see whether or = not your simulation has any lone pairs enabled.

Thanks,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <<= a href=3D"mailto:ccs0019@mix.wvu.edu" target=3D"_blank" class=3D"">ccs0019@= mix.wvu.edu> wrote:

Thanks Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it up= dated 
Thanks



Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What version of NAMD are you using? Versi= ons earlier than NAMD 2.14 don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathur= anga Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD users,
I'm trying to see the interaction of a small molecule with = a protein in NAMD. As the simulation starts the following error appear= s;

ERROR: Margin is too small for 1 atoms during timestep 1004= .
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecule. A= ny help is really appreciated.

Thanks
Chathuranga






Chathuranga Siriwardhana
Justin Legleiter Laboratory 
West Virginia University <= /span>
Department of chemis= try 
Clark Hall, Room 561
Morgantown, WV 26505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us






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boundary="000000000000e3ad5b05bc002732" X-CLX-Response: 1TFkXGxwfEQpMehcZHh8RCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHHh0TEQpDWRcHGRwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHh9xHx4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XaFtEXR1fQGJ1Z0RIR2tIUENsSXBgfW5mSUFFWmFwTn8RClhcFx8EGgQYGB4F GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdyS1pZGREKTVwXGBMfEQpMWhd4aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF21tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBB sSGxEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCR RdrExphTl9eWBgdZREKQk4XY1Nja3sTWH4aX14RCkJMF2lJSBpLfmlGG3hzEQpCbBdhHhl4Wm5s Z2NfYhEKQkAXZxJTWGB4f1wZfAURCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcSEQp5QxdvUh1 ifHJ9XllJRhEKWUsXExkYHBEKcGcXb15Ccn9+TGd/cEEQGRoRCnBoF2geZRgbehxaBRgYEBkaEQ pwaBdkG0VvHEJEZWQaXxAZGhEKcGgXZBlQX2lYZURLRU8QGRoRCnBoF2FYXwVyHUViYW4YEBkaE QpwaBdiE05EcxNaZnhfHRAZGhEKcGcXelttEkBSXmd4SR0QHRIRCnB9F2lya0tIWR5dBVpfEBka EQpwfRd6GVsTRkUfW0IfQRAZGhEKcH0Xb2JcT2d9bHNGelIQGRoRCnB9F2BEbEdoXFpbEmRZEBk aEQpwZxdrTU18TkxfekceTRASHxEKcH0Xbm5JR1prSWlOT1sQHRIRCnB9F2FhSB1lXURyElxlEB kaEQpwZxdhXFhwaRxNfGweZRAcGhEKcH0XY0FjemtpBR5iGlkQHhIRCnB9F3pNa0dIR3JfYUlLE BkaEQpwfRdpXxsBY2FMekdMbhAZGhEKcH0XbmhDax9nYkVYXXMQGRoRCnB/F2UZeWZeR2kbZE9z EBMfEQpwXxdjR2dPZnpgcm0TWhAZGhEKcH8XYWZvWxpnZEJIHVsQGxgZEQpwXxdjYhJQSGN4H3x CfRASHBEKcH8XehxwfhJpfFp/RUQQGx8dEQpwXxdiRFgda20FHWdcHRAZGhEKcH8XZVhyGB1JGF 5GaXwQGxobEQpwXxdmcEhcQHkBQR5PEhAdEhEKcH8XbURfRkVtfUh5GW4QGxkeEQpwXxdrRksTe WhpbnwTeBATGhEKcH8XY0FjemtpBR5iGlkQHhIRCnBsF24dZnsSSxp4ElxtEBkaEQptfhcbEQpY TRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 priorityscore=345 malwarescore=0 spamscore=0 clxscore=165 lowpriorityscore=0 adultscore=0 impostorscore=0 bulkscore=0 mlxlogscore=999 mlxscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102230107 domainage_hfrom=9326 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --000000000000e3ad5b05bc002732 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Somewhere in NAMD 2.13 development we dropped the use of dummy bonds to lonepairs and exclusively took that information from the PSF lonepair host section (NUMLPH). These sections were otherwise redundant at best or contradictory at worst. One thing that might still get goofed up is the "lonepairs on" command, which should be auto toggled based on the PSF header. I'm pretty sure it would be safe to add this to you config file. HTH, Brian On Mon, Feb 22, 2021, 9:42 PM Gumbart, JC wrote: > Please reply-all to keep the mailing list in your replies. > > As I recall, there shouldn=E2=80=99t be a bond parameter for it because i= t=E2=80=99s > fixed. Something is likely still wrong with your PSF. You need to build > it using PSFGen 2.0. It should be correct if you see a !NUMLP section, as > Dave pointed out. > > Best, > JC > > On Feb 22, 2021, at 9:30 PM, Chathuranga Siriwardhana > wrote: > > I have included the force field files from the C36 July release. > Apparently it did not have the parameters for the CL LPH bond. > > > *Chathuranga Siriwardhana* > Justin Legleiter Laboratory > West Virginia University > Department of chemistry > Clark Hall, Room 561 > Morgantown, WV 26505 > > > On Mon, Feb 22, 2021 at 9:12 PM Gumbart, JC > wrote: > >> You have to include the appropriate CGenFF force-field file as well. >> >> Best, >> JC >> >> On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana < >> ccs0019@mix.wvu.edu> wrote: >> >> Hi JC, >> Thank you for the reply. I parameterized the molecule from the same >> online GUI you mentioned above. >> However my stream file created through the cgenff does not have bond >> parameters for CL and LPH. Do you know how to fix it >> >> *FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 38 21)* >> >> Thanks again for your help >> Chaturanga >> >> *Chathuranga Siriwardhana* >> Justin Legleiter Laboratory >> West Virginia University >> Department of chemistry >> Clark Hall, Room 561 >> Morgantown, WV 26505 >> >> >> On Mon, Feb 22, 2021 at 8:28 PM Gumbart, JC >> wrote: >> >>> Oops, I replied too fast. I was thinking of the parameters, not the >>> PSF. The latest version of PSFGen ( >=3D 2.0) can handle it: >>> https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf >>> >>> >>> It=E2=80=99s distributed with more recent VMD builds. >>> >>> Best, >>> JC >>> >>> On Feb 22, 2021, at 8:25 PM, Gumbart, JC >>> wrote: >>> >>> paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryla= nd.edu/__;!!DZ3fjg!ryfnj3SD9J_vYHxJ8jln6BETJxv5lhVo6xyEQ84t3JSilUe5ZhC5IVe6= tHV8h3ajSA$=20 >>> >>> >>> Best, >>> JC >>> >>> On Feb 22, 2021, at 7:49 PM, David Hardy wrote: >>> >>> Hi Chathuranga, >>> >>> No worries. I am replying back to the list because I don=E2=80=99t know= the >>> answer to your question. >>> >>> Can anyone on list recommend how to correctly create a PSF with lone >>> pairs? >>> >>> Thanks, >>> Dave >>> >>> On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana < >>> ccs0019@mix.wvu.edu> wrote: >>> >>> Hi David, >>> Thank you so much for helping me with my issue. And I am really sorry >>> that I replied to the wrong email. I subscribed to the mailing list tod= ay >>> and I got confused with how it works :( >>> Would you mind recommending a method to create the psf with lone pairs. >>> I used VMD psfgen. >>> >>> Thanks again for helping me >>> >>> Chathuranga >>> >>> >>> >>> >>> >>> >>> *Chathuranga Siriwardhana* >>> Justin Legleiter Laboratory >>> West Virginia University >>> Department of chemistry >>> Clark Hall, Room 561 >>> Morgantown, WV 26505 >>> >>> >>> On Mon, Feb 22, 2021 at 7:26 PM David Hardy wrote: >>> >>>> Hi Chathuranga, >>>> >>>> It looks to me like NAMD is not treating your atom 37 as a lone pair. >>>> The forces on lone pairs are distributed to their support atoms and th= en >>>> set to zero, so I would expect lone pairs to have zero velocity (but I= =E2=80=99m >>>> having trouble finding that in the code). >>>> >>>> If you would post the top of your log file showing the configuration of >>>> your system before simulation begins, we could see whether or not your >>>> simulation has any lone pairs enabled. >>>> >>>> Thanks, >>>> Dave >>>> >>>> -- >>>> David J. Hardy, Ph.D. >>>> Beckman Institute >>>> University of Illinois at Urbana-Champaign >>>> 405 N. Mathews Ave., Urbana, IL 61801 >>>> dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ >>>> >>>> >>>> On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana < >>>> ccs0019@mix.wvu.edu> wrote: >>>> >>>> Thanks Jeff, >>>> I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated >>>> Thanks >>>> >>>> >>>> >>>> *Chathuranga Siriwardhana* >>>> Justin Legleiter Laboratory >>>> West Virginia University >>>> Department of chemistry >>>> Clark Hall, Room 561 >>>> Morgantown, WV 26505 >>>> >>>> >>>> On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer wrote: >>>> >>>>> What version of NAMD are you using? Versions earlier than NAMD 2.14 >>>>> don=E2=80=99t support halogen lonepairs. >>>>> >>>>> Jeff >>>>> >>>>> >>>>> On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana < >>>>> ccs0019@mix.wvu.edu> wrote: >>>>> >>>>>> Hi NAMD users, >>>>>> I'm trying to see the interaction of a small molecule with a protein >>>>>> in NAMD. As the simulation starts the following error appears; >>>>>> >>>>>> ERROR: Margin is too small for 1 atoms during timestep 1004. >>>>>> ERROR: Incorrect nonbonded forces and energies may be calculated! >>>>>> ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, >>>>>> atom 310 of 311 on patch 0 pe 1) >>>>>> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms >>>>>> on patch 0 pe 1). >>>>>> FATAL ERROR: Exiting prematurely; see error messages above. >>>>>> >>>>>> Atom 37 is a lone pair on Chlorine in the small molecule. Any help is >>>>>> really appreciated. >>>>>> >>>>>> Thanks >>>>>> Chathuranga >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> *Chathuranga Siriwardhana* >>>>>> Justin Legleiter Laboratory >>>>>> West Virginia University >>>>>> Department of chemistry >>>>>> Clark Hall, Room 561 >>>>>> Morgantown, WV 26505 >>>>>> >>>>> -- >>>>> >>>>> =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94= =E2=80=94 >>>>> Jeffrey Comer, PhD >>>>> Associate Professor >>>>> Department of Anatomy and Physiology >>>>> Kansas State University >>>>> Office: P-213 Mosier Hall >>>>> Phone: 785-532-6311 >>>>> Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!r= yfnj3SD9J_vYHxJ8jln6BETJxv5lhVo6xyEQ84t3JSilUe5ZhC5IVe6tHXCV2PIFQ$=20 >>>>> >>>>> >>>> >>>> >>> >>> >>> >> > --000000000000e3ad5b05bc002732 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Somewhere in NAMD 2.13 development we dropped the us= e of dummy bonds to lonepairs and exclusively took that information from th= e PSF lonepair host section (NUMLPH). These sections were otherwise redunda= nt at best or contradictory at worst.

One thing that might still get goofed up is the "lonepairs o= n" command, which should be auto toggled based on the PSF header. I= 9;m pretty sure it would be safe to add this to you config file.

HTH,=C2=A0
= Brian=C2=A0


On Mon, Feb 22, 2021, 9:42 PM Gumbart, JC <gumbart@physics.gatech.edu> wrote:<= br>
Please reply-all to keep the mailing list in your replies.

As I recall, there shouldn=E2=80=99t be a bond parameter for it becaus= e it=E2=80=99s fixed.=C2=A0 Something is likely still wrong with your PSF.= =C2=A0 You need to build it using PSFGen 2.0.=C2=A0 It should be correct if= you see a !NUMLP section, as Dave pointed out.

Best,
JC

On Feb 22, 2021, at 9:30 PM, Chathuranga Siriwardhana <ccs0019@mix= .wvu.edu> wrote:

I have included the force field files from the C36 July re= lease. Apparently=C2=A0it did not have the parameters for the CL LPH bond.


Chathuranga Siriwardhana
Justin Legleiter = Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26= 505


On Mon, Feb 22, 2021 at 9:12 PM Gumba= rt, JC <gumbart@physics.gatech.edu> wrote:
You have to include the appropriate CGenFF force-field file as well.

Best,
JC

On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana <ccs0019@mix= .wvu.edu> wrote:

Hi JC,
Thank you for the reply. I parameterized the molecule from the same on= line GUI you mentioned above.=C2=A0
However my stream file created through the cgenff does not have bond p= arameters=C2=A0for CL and LPH. Do you know how to fix it

FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 38= 21)

Thanks again for your help
Chaturanga

Chathuranga Siriwardhana
Justin Legleiter = Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26= 505


On Mon, Feb 22, 2021 at 8:28 PM Gumba= rt, JC <gumbart@physics.gatech.edu> wrote:
Oops, I replied too fast.=C2=A0 I was thinking of the parameters, not = the PSF.=C2=A0 The latest version of PSFGen ( >=3D 2.0) can handle it:

It=E2=80=99s distributed with more recent VMD builds.

Best,
JC

On Feb 22, 2021, at 8:25 PM, Gumbart, JC <gumbart@physics.g= atech.edu> wrote:

paramchem can do it:=C2=A0https://cgenff.umaryland.edu/

Best,
JC

On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy@ks.uiuc.edu>= ; wrote:

Hi Chathuranga,

No worries. I am replying back to the list because I don=E2=80=99t kno= w the answer to your question.

Can anyone on list recommend how to correctly create a PSF with lone p= airs?

Thanks,
Dave

On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <ccs0019@mix= .wvu.edu> wrote:

Hi=C2=A0David,
Thank you so much for helping me with my issue. And I am really sorry = that I replied to the wrong email. I subscribed to the mailing list today a= nd I got confused with how it works :(=C2=A0=C2=A0
Would you mind recommending=C2=A0a method to create the psf with lone = pairs. I used VMD psfgen.

Thanks again for helping me

Chathuranga






Chathuranga Siriwardhana
Justin Legleiter = Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26= 505


On Mon, Feb 22, 2021 at 7:26 PM David= Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Chathuranga,

It looks to me like NAMD is not treating your atom 37 as a lone pair. = The forces on lone pairs are distributed to their support atoms and then se= t to zero, so I would expect lone pairs to have zero velocity (but I=E2=80= =99m having trouble finding that in the code).

If you would post the top of your log file showing the configuration o= f your system before simulation begins, we could see whether or not your si= mulation has any lone pairs enabled.

Thanks,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <ccs0019@mix= .wvu.edu> wrote:

Thanks=C2=A0Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated= =C2=A0
Thanks



Chathuranga Siriwardhana
Justin Legleiter = Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26= 505


On Mon, Feb 22, 2021 at 6:34 PM Jeff = Comer <jeffcomer@gmail.com> wrote:
What version of NAMD are you=C2=A0using? Versions earlier= than NAMD 2.14 don=E2=80=99t support halogen lonepairs.

Jeff


On Mon, Feb 22, 2021 at 17:31 Chathur= anga Siriwardhana <ccs0019@mix.wvu.edu> wrote:
Hi NAMD users,
I'm trying to see the interaction of a small molecule with a prote= in in NAMD. As the simulation starts the following=C2=A0error appears;

ERROR: Margin is too small for 1 atoms during timestep 1004.
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom = 310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 0 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecule. Any help is = really=C2=A0appreciated.

Thanks
Chathuranga






Chathuranga Siriwardhana
Justin Legleiter = Laboratory=C2=A0
West Virginia University=C2=A0
Department of chemistry=C2=A0
Clark Hall, Room 561
Morgantown, WV 26= 505
--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us






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boundary="0000000000002e4dc505bc0489d9" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBoSEQpMehcZHBoRCllEF3pfQXkSS0tBQh9QEQpYWBdgHV1gS2lyR14 ZeREKeE4XY1Nja3sTWH4aX14RCnlMF2xtQ0dwUmNGG19sEQpDSBcHGRscEQpDWRcHGB4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhJxGx8bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0NwTBtrbGsdQRxoT0tue01fWmlGfElFfG1aSBgbR0VmEQpYXBcfBBoEGBge BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXcktfeRoRCk1cFxgbGREKTFoXbGlNTWsRCkxGF29ra2t raxEKQk8XYmRPXR5kfE1fUlwRCkNaFxgaEwQSHwQbHB0EHhgRCkJeFxsRCkReFxgRCkJcFxsRCl 5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXa0BwG2d7TmEYeH4RCkJOF 2NTY2t7E1h+Gl9eEQpCTBdgHV1gS2lyR14ZeREKQmwXYmNBHWFQRW0SEhMRCkJAF25IbB9iSQEd bV9bEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXZGVCe31rTRhOcwURCllLFxMZGBw RCnBoF2t+QXlEaUMYGGF/EBkaEQpwaBdrYlNYSx9GGWJAfRAZGhEKcGgXbxpmbW58HmlHem8QGR oRCnBoF25jGGcdeXxNXXMdEBkaEQpwaBdrYm9+WnBkHQUSbBAZGhEKcH0XbEdMR0xBeEhGHUMQG RoRCnB/F2tNYmFleEdoAV1vEB8cEQpwXxdsR0xHTEF4SEYdQxAZGhEKcGwXbG1YHWdeQn9hYloQ GRoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 spamscore=0 adultscore=0 impostorscore=0 clxscore=208 priorityscore=360 malwarescore=0 suspectscore=0 phishscore=0 lowpriorityscore=0 mlxlogscore=706 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102230149 domainage_hfrom=9326 X-Spam-Score: 0 X-Spam-OrigSender: eackad@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Eddie" --0000000000002e4dc505bc0489d9 Content-Type: text/plain; charset="UTF-8" Hello, I'm trying to get a small 150k system working with namd3. I am using 4 gtx1080's with the command nice -n 5 /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p4 +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_production.inp I get the error: FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0): invalid device function and CUDANBOND[2]: Allocating patch data structure with 87 patches! CUDANBOND[3]: Allocating patch data structure with 101 patches! CUDANBOND[1]: Allocating patch data structure with 89 patches! CUDANBOND[0]: Allocating patch data structure with 114 patches! FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0): invalid device function Any ideas? I know these are commerical gpus, is that an issue? Thanks, Eddie --0000000000002e4dc505bc0489d9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello,
I'm trying to get a small=C2=A0150k system = working with namd3.=C2=A0
I am using 4 gtx1080's with the com= mand
nice -n 5 /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-m= ulticore-CUDA/namd3 +p4 +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_pr= oduction.inp

I get the error:
FATAL = ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes,= hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKerne= l.cu, function buildRattleLists, line 4461
=C2=A0on Pe 0 (node10.cl.siue.edu<= /a> device 0 pci 0:2:0): invalid device function

and=

Any ideas? I k= now these are commerical=C2=A0gpus, is that an issue?
Thanks,
Eddie
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Tue, 23 Feb 2021 23:59:49 -0800 (PST) From: "=?UTF-8?Q?Jos=c3=a9_Villala=c3=adn?=" X-Google-Original-From: =?UTF-8?Q?Jos=c3=a9_Villala=c3=adn?= To: namd-l@ks.uiuc.edu Subject: Re: namd-l: Small molecule simulation error NAMD Message-ID: Date: Wed, 24 Feb 2021 08:59:49 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="------------7B6DFA843AA76FF50365216B" Content-Language: en-US X-CLX-Response: 1TFkXHhodEQpMehcaEQpZRBdvTUtjUlBgT11daREKWFgXenJiH3BhZU9bb2E RCnhOF2ljWgVPTh1HHh9PEQp5TBdibWtHYhNhWk5wexEKQ0gXBxkaGBEKQ1kXBx4YEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbGBNxHgYcHncGGxIbBhkaQAYaBhsaGgYdEnEfEBp3BhoGBx8aBhoGB xwaBhoGGnEaEBp3BhoRClleF2hueREKSUYXX0NfSXVCRVleT04RCkNOF35sHWNLfxlDTm54XWNP bkh/SVNGaE5hS214emhFHnBZEQpYXBcfBBoEGBgeBRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXcks cXX4RCk1cFxkYHxEKTFoXaX9pTWtrEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkJPF2hYXlBJBR Jce2R7EQpDWhcYGhMEEh8EGBgbBB4TEQpCXhcbEQpCRRdieV4FR0xEE0lzXBEKQk4XaWNaBU9OH UceH08RCkJMF3pyYh9wYWVPW29hEQpCbBdoZRJ+RB1uWVsTaREKQkAXZxJTWGB4f1wZfAURCkJY F2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdvUh1ifHJ9XllJRhEKcGgXbnJQBW16UEUScxkQGhEKcGg XYU9jHmhkXB5lGF0QGhEKcGgXbUZTehsFa1tlbW8QGhEKcGgXZmRhZ15HHk9zWG0QGhEKcGgXaU lgWmZLRElQeFoQGhEKcGwXYxl8Un0fTXB9TgEQGhEKcEMXa1N6QRJiR0tvS0AQGhEKbX4XGhEKW E0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 suspectscore=0 malwarescore=0 spamscore=0 clxscore=407 priorityscore=0 phishscore=0 adultscore=0 mlxscore=0 mlxlogscore=944 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102240062 X-Spam-Score: 0 X-Spam-OrigSender: jvillalain@umh.es X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "=?UTF-8?Q?Jos=c3=a9_Villala=c3=adn?=" This is a multi-part message in MIME format. --------------7B6DFA843AA76FF50365216B Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear all, First of all, sorry for any duplicate mail I might have sent, we have had some problems with our university mail in the past few days .... I have unsubscribed and subscribe again. I hope that now it is possible for me to send mails to the list. The last mail I tried to sent to the list read the following, /I have recently run into the same problem, i.e., using NAMD 2.14 and a small molecule containing a chlorine atom. In my opinion to obtain the pdb / psf pair it is best to use Charmm-Gui / Ligand Reader with the molecule previously built by using Marvin Sketch (to obtain the mol2/pdb/sdf files). I have been able to minimize my system, but it has been impossible for me to equilibrate it. The error I obtained was the always same, i.e., atom moving to fast (referring to the lone pair). It has been impossible for me to go on besides trying everything in hand ..../ // Additionally, I would like to say that the psf file I obtained through Charmm-Gui contained the " !NUMLP NUMLPH" instruction joining the chloride atom with the lone pair. Last by no least, thanks a lot to everyone for you continuous help and the owner of the list for your work on developing NAMD ¡!. José --------------7B6DFA843AA76FF50365216B Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Dear all,

First of all, sorry for any duplicate mail I might have sent, we have had some problems with our university mail in the past few days .... I have unsubscribed and subscribe again. I hope that now it is possible for me to send mails to the list.

The last mail I tried to sent to the list read the following,

I have recently run into the same problem, i.e., using NAMD 2.14 and a small molecule containing a chlorine atom. In my opinion to obtain the pdb / psf pair it is best to use Charmm-Gui / Ligand Reader with the molecule previously built by using Marvin Sketch (to obtain the mol2/pdb/sdf files). I have been able to minimize my system, but it has been impossible for me to equilibrate it. The error I obtained was the always same, i.e., atom moving to fast (referring to the lone pair). It has been impossible for me to go on besides trying everything in hand ....


Additionally, I would like to say that the psf file I obtained through Charmm-Gui contained the " !NUMLP NUMLPH" instruction joining the chloride atom with the lone pair.

Last by no least, thanks a lot to everyone for you continuous help and the owner of the list for your work on developing NAMD ¡!.

José






--------------7B6DFA843AA76FF50365216B-- From owner-namd-l@halifax.ks.uiuc.edu Wed Feb 24 11:35:23 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11OHZNIv001909; Wed, 24 Feb 2021 11:35:23 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11OHZNVR001908; Wed, 24 Feb 2021 11:35:23 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11OHZM8Y001892; Wed, 24 Feb 2021 11:35:22 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11OHZMmv001885; Wed, 24 Feb 2021 11:35:22 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11OHZFb7001850 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=L544JnTuagFyo9Y2XHn2RGQ/dKWwpBIwTWMVjySLJ9E=; b=IxZjMYgW975sBNWDNknCGUsR2D7ZorDrAIKkHyUPjj3ghNOf+7d0/PWjy9eLzQjKxO VNp6xPSltLZidPWpH1rPZg8ObCRo4NEyYh9nung9267wZGAaXv9Jp9/NWn0CWyUTuH+L il8KQy5ta9ya/6eCv1wFOGDd6I83hkfQ4MNDieiB7G6XM9puKaO4petLWyUAFCYPWGji QjBvW8HxNE4zV9mg6wCVq4HEGjHm6GqENPe/JJZu9044mx3W66hRKSiFOsR3KpY01VST f1Tn56gqa2J0BbMIwFb6Vc4JOWxvdhzWGV4ux1aPf7Rcd9WIfGWvywpcAdUAdGHRhyt2 pI3A== X-Gm-Message-State: AOAM533Mrl6E4ocIqojXuppauVkwWV07XLT7wCKWtw7wl1P7iAgLVcOI SWXpiELP0hQmjOvjUxBYZ7Z7M8gjl/dCaTOp8mnf+Vh6TPRySg== X-Google-Smtp-Source: ABdhPJyUveWhzwm6GA0vEPR3HJT9c0tYTSJAIIKqlrNOnAjNi46K4nO7LL8CtYEryFCGFFNXRVjh4AkxfH2E6j/hCFQ= X-Received: by 2002:a5d:9641:: with SMTP id d1mr24727050ios.123.1614188113956; Wed, 24 Feb 2021 09:35:13 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: Chathuranga Siriwardhana Date: Wed, 24 Feb 2021 12:34:37 -0500 Message-ID: Subject: Re: namd-l: Small molecule simulation error NAMD To: namd-l@ks.uiuc.edu, =?UTF-8?B?Sm9zw6kgVmlsbGFsYcOtbg==?= Content-Type: multipart/alternative; boundary="0000000000002225a905bc187500" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxsaEQpMehcaEQpZRBdoYn5NXH5YS0deQhEKWFgXYxlSeUx9QExiEl8 RCnhOF2x6UFlsfEJsRkgcEQp5TBdtQ2RTbEZFeERCXhEKQ0gXBxgfGBEKQ1kXBx4YEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGExpxHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZX k9OEQpDThd1G15kWmxpHnIbbBsdQBIcXkUYc2V/XE1FHElzcl4TQBEKWFwXHwQaBBgYHgUbGgQb GxoEHxoEGx4YEBseGh8aEQpeWRdySG5mXxEKTVwXGBgSEQpMWhd7aU1raxEKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh8EGxwcBB8eEQ pCXhcbEQpEXhcYEQpCXBcbEQpCSxdoeENjQBNIYHlaHhEKQkkXbHpQWWx8QmxGSBwRCkJFF2xDU 0cFW3B8ZFx7EQpCThdselBZbHxCbEZIHBEKQkwXYxlSeUx9QExiEl8RCkJsF25tQ25OHHJ9WEIY EQpCQBdnElNYYHh/XBl8BREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF29SHWJ8cn1 eWUlGEQpZSxcbGh4TExEKcGgXbUZTehsFa1tlbW8QHhIRCnBoF2l9bUxHRVxsQVBPEBkaEQpwaB d6ZmUbZk4BUlMcXxAZGhEKcGgXa0FBfRNiRhxTflgQGRoRCnBoF2xBSXNBf15oUnIaEBkaEQpwb BdiS2RuBU5pXG5HRRAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 mlxscore=0 priorityscore=0 suspectscore=0 clxscore=110 spamscore=0 mlxlogscore=999 malwarescore=0 bulkscore=0 lowpriorityscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102240136 domainage_hfrom=10499 X-Spam-Score: 0 X-Spam-OrigSender: ccs0019@mix.wvu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Chathuranga Siriwardhana --0000000000002225a905bc187500 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi all, Thank you so much for your responses for my issue. I was able to run the simulation with lone pairs. However when the psf file is generated using psfgen 2.0 it contains a bond between the lone pair and the halogen. CgenFF does not contain bond parameters for Halogen Lone pair. (May be I was doing something wrong since I'm really new to this field) I set up the simulation by generating psf files using both psfgen 1.6.4 (this version does not generate the bond between lone pair and the halogen or the NUMLP section ) and psfgen 2.0 which generates the NUMLP section. Then produced a combined psf file manually without halogen - lone pair bond but with the NUMLP section. Thanks again and I appreciate all of yours help through this mailing list Chathuranga On Wed, Feb 24, 2021 at 3:09 AM Jos=C3=A9 Villala=C3=ADn wrote: > Dear all, > > First of all, sorry for any duplicate mail I might have sent, we have had > some problems with our university mail in the past few days .... I have > unsubscribed and subscribe again. I hope that now it is possible for me t= o > send mails to the list. > The last mail I tried to sent to the list read the following, > > *I have recently run into the same problem, i.e., using NAMD 2.14 and a > small molecule containing a chlorine atom. In my opinion to obtain the pd= b > / psf pair it is best to use Charmm-Gui / Ligand Reader with the molecule > previously built by using Marvin Sketch (to obtain the mol2/pdb/sdf files= ). > I have been able to minimize my system, but it has been impossible for me > to equilibrate it. The error I obtained was the always same, i.e., atom > moving to fast (referring to the lone pair). It has been impossible for m= e > to go on besides trying everything in hand ....* > > > Additionally, I would like to say that the psf file I obtained through > Charmm-Gui contained the " !NUMLP NUMLPH" instruction joining the chlorid= e > atom with the lone pair. > > Last by no least, thanks a lot to everyone for you continuous help and th= e > owner of the list for your work on developing NAMD =C2=A1!. > > Jos=C3=A9 > > > > > > > --0000000000002225a905bc187500 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,
Thank you so much for your responses for my is= sue. I was able to run the simulation with lone pairs.=C2=A0
Howe= ver when the psf file is generated using psfgen 2.0 it contains a bond betw= een the=C2=A0lone pair and the halogen. CgenFF does not contain bond parame= ters for Halogen Lone pair. (May be I was doing something wrong since I'= ;m really new to this field)
I set up the simulation by generatin= g psf files using both psfgen 1.6.4 (this version does not generate the bon= d between lone pair and the halogen or the NUMLP section ) and psfgen 2.0 w= hich generates the NUMLP section. Then produced a combined psf file manuall= y without halogen=C2=A0- lone pair bond but with the NUMLP section.=C2=A0

Thanks again and I appreciate all of yours help thr= ough this mailing list


Chathuranga<= /div>




=


--0000000000002225a905bc187500-- From owner-namd-l@halifax.ks.uiuc.edu Wed Feb 24 13:28:32 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11OJSWlM006189; Wed, 24 Feb 2021 13:28:32 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11OJSWR5006188; Wed, 24 Feb 2021 13:28:32 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11OJSWVN006183; Wed, 24 Feb 2021 13:28:32 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 11OJSW8e006182; Wed, 24 Feb 2021 13:28:32 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 11OJSSjW006172 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Wed, 24 Feb 2021 13:28:29 -0600 (CST) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_94997F7D-1D55-4C1C-8FBB-305B312B5880" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Namd-3 alpha 7 error Date: Wed, 24 Feb 2021 13:28:23 -0600 References: To: NAMD list , "Dr. Eddie" In-Reply-To: Message-Id: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_94997F7D-1D55-4C1C-8FBB-305B312B5880 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Eddie, This looks similar to the error that Lorenzo recently reported. Would you be willing to share your data set for us to try to reproduce = this error locally? Although we don=E2=80=99t have your exact hardware = setup, we do have a few multi-GPU platforms in-house that we could try. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Feb 23, 2021, at 11:49 AM, Dr. Eddie wrote: >=20 > Hello, > I'm trying to get a small 150k system working with namd3.=20 > I am using 4 gtx1080's with the command > nice -n 5 = /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 = +p4 +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_production.inp >=20 > I get the error: > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 0 (node10.cl.siue.edu = device 0 = pci 0:2:0): invalid device function >=20 > and > CUDANBOND[2]: Allocating patch data structure with 87 patches! > CUDANBOND[3]: Allocating patch data structure with 101 patches! > CUDANBOND[1]: Allocating patch data structure with 89 patches! > CUDANBOND[0]: Allocating patch data structure with 114 patches! > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 0 (node10.cl.siue.edu = device 0 = pci 0:2:0): invalid device function >=20 > Any ideas? I know these are commerical gpus, is that an issue? > Thanks, > Eddie --Apple-Mail=_94997F7D-1D55-4C1C-8FBB-305B312B5880 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Eddie,

This looks = similar to the error that Lorenzo recently reported.

Would you be willing to = share your data set for us to try to reproduce this error locally? = Although we don=E2=80=99t have your exact hardware setup, we do have a = few multi-GPU platforms in-house that we could try.

Best regards,
Dave


On Feb 23, 2021, at 11:49 AM, Dr. Eddie <eackad@gmail.com> = wrote:

Hello,
I'm trying to get a = small 150k system working with namd3. 
I = am using 4 gtx1080's with the command
nice -n 5 = /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 = +p4 +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_production.inp

I = get the error:
FATAL ERROR: CUDA error = cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, hgi, hgi, = d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKernel.cu, = function buildRattleLists, line 4461
 on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0): invalid device = function

and
CUDANBOND[2]: Allocating patch data = structure with 87 patches!
CUDANBOND[3]: Allocating patch = data structure with 101 patches!
CUDANBOND[1]: Allocating = patch data structure with 89 patches!
CUDANBOND[0]: = Allocating patch data structure with 114 patches!
FATAL = ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, = temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file = src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461
 on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0): invalid device = function

Any ideas? I know these are commerical gpus, is that an = issue?
Thanks,
Eddie

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boundary="00000000000010c77e05bc1a3d04" X-CLX-Response: 1TFkXGxIeEQpMehcZGhEKWUQXYkZkR0dAQhp6EkMRClhYF2UbWWV5Q0tmG0N LEQp4ThdoYWsTXkR8GFxyfBEKeUwXax1HAR8bGkgbR10RCkNIFwcYEhgRCkNZFxsaEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwecR4ZEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0VPfkZca0xeZXhBEx5Nf30SHG1CTnAHGx1pcnJeZHwbEQpYXBcfBBoEGBgeBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXckhsbnsRCk1cFxgaGhEKTFoXeGtrTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXYmtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEwQbHR8RCk JeFxsRCkReFxkRCkRJFxsRCkJFF2BpaGMSH05jc0gbEQpCThdoYWsTXkR8GFxyfBEKQkwXZRtZZ XlDS2YbQ0sRCkJsF2ZLH09YSxkaGF58EQpCQBdtE2hbXBN6BVNHbBEKQlgXZ3Nlc0BuYWFMXWIR Ck1eFxsRClpYFx0RCnlDF2RYU0McaF1STX9EEQpZSxcbGBkcExEKcGcXa01NfE5MX3pHHk0QHx4 RCnBoF2sYQ3l7W09+XBNjEBkaEQpwaBdkW3l6ZExSGhp4YBAZGhEKcGgXbVlZbERyTV9zHBIQGR oRCnBoF2N8YGRFGklcZ35QEBkaEQpwaBduYGV5QmZPQXhYchAZGhEKcH0Xbm5JR1prSWlOT1sQH hIRCnB9F2BYRFpzAWd4EnttEB4SEQpwfRdoHUlbTkNGQ2xgRhAeEhEKcH8XZVhyGB1JGF5GaXwQ ExkRCnBfF2ZwSFxAeQFBHk8SEBkaEQpwfxdtRF9GRW19SHkZbhAbHhkRCnBfF2tGSxN5aGlufBN 4EBsaHhEKcH8XYWZvWxpnZEJIHVsQGxkYEQpwXxdjYhJQSGN4H3xCfRAbGhoRCnBsF2V5a0NyWH lnW1ptEBkaEQpwTBdgRRtyb05JTmh+WRAaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 suspectscore=0 bulkscore=0 malwarescore=0 mlxscore=0 adultscore=0 clxscore=184 priorityscore=30 mlxlogscore=999 lowpriorityscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102240150 domainage_hfrom=12369 X-Spam-Score: 0 X-Spam-OrigSender: bhaddad@pdx.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Bassam Haddad --00000000000010c77e05bc1a3d04 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Are all of your GPUs NV-linked? It's my understanding that you cannot use the multi-gpu NAMD 3.0 unless the GPUs are linked together. Best, Bassam On Wed, Feb 24, 2021 at 11:37 AM David Hardy wrote: > Hi Eddie, > > This looks similar to the error that Lorenzo recently reported. > > Would you be willing to share your data set for us to try to reproduce > this error locally? Although we don=E2=80=99t have your exact hardware se= tup, we do > have a few multi-GPU platforms in-house that we could try. > > Best regards, > Dave > > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > > On Feb 23, 2021, at 11:49 AM, Dr. Eddie wrote: > > Hello, > I'm trying to get a small 150k system working with namd3. > I am using 4 gtx1080's with the command > nice -n 5 > /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p4 > +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_production.inp > > I get the error: > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, > temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file > src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 0 (node10.cl.siue.edu > > device 0 pci 0:2:0): invalid device function > > and > CUDANBOND[2]: Allocating patch data structure with 87 patches! > CUDANBOND[3]: Allocating patch data structure with 101 patches! > CUDANBOND[1]: Allocating patch data structure with 89 patches! > CUDANBOND[0]: Allocating patch data structure with 114 patches! > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, > temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file > src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 0 (node10.cl.siue.edu > > device 0 pci 0:2:0): invalid device function > > Any ideas? I know these are commerical gpus, is that an issue? > Thanks, > Eddie > > > --00000000000010c77e05bc1a3d04 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Are all of your GPUs NV-linked? It's my understanding = that you cannot use the multi-gpu NAMD 3.0 unless the GPUs are linked toget= her.=C2=A0

Best,
Bassam

On Wed, Feb 24, 2= 021 at 11:37 AM David Hardy <dhard= y@ks.uiuc.edu> wrote:
Hi Eddie,

This looks similar to the error that Lorenzo recently reported.

Would you be willing to share your data set for us t= o try to reproduce this error locally? Although we don=E2=80=99t have your = exact hardware setup, we do have a few multi-GPU platforms in-house that we= could try.

Best regards,
Dave

--
D= avid J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
40= 5 N. Mathews Ave., Urbana, IL 61801

On Feb 23, 2021, at 11:49 AM, Dr. E= ddie <eackad@gmail= .com> wrote:

Hello,
I'm tryin= g to get a small=C2=A0150k system working with namd3.=C2=A0
I am = using 4 gtx1080's with the command
nice -n 5 /home/eddie/bina= ries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p4 +idlepoll +setcpu= affinity +devices 0,1,2,3 step5_production.inp

I get the error:
FATAL ERROR: CUDA error cub::DeviceSelect::If(d= _temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stre= am) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 446= 1
=C2=A0on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0)= : invalid device function

and
CUDANBOND[2]= : Allocating patch data structure with 87 patches!
CUDANBOND[3]: Allocat= ing patch data structure with 101 patches!
CUDANBOND[1]: Allocating patc= h data structure with 89 patches!
CUDANBOND[0]: Allocating patch data st= ructure with 114 patches!
FATAL ERROR: CUDA error cub::DeviceSelect::If(= d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), str= eam) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 44= 61
=C2=A0on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0= ): invalid device function

Any ideas? I know t= hese are commerical=C2=A0gpus, is that an issue?
Thanks,
Eddie

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boundary="000000000000a1949405bc1ad9e2" X-CLX-Response: 1TFkXGxwZEQpMehcZGRwRCllEF3pfQXkSS0tBQh9QEQpYWBdgHV1gS2lyR14 ZeREKeE4XY1Nja3sTWH4aX14RCnlMF2xtQ0dwUmNGG19sEQpDSBcHGBIbEQpDWRcbGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseGXEfGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdzHW9YckdBHXtyQE9tU0d4UhttfW1NRU4fWX54YwduRREKWFwXHwQaBBgYHgUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3JIbFl+EQpNXBcZHxIRCkxaF3hpa01rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGx 0TEQpCXhcbEQpEWBcYEQpEXhcYEQpESRcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQ kkXY1Nja3sTWH4aX14RCkJFF2tAcBtne05hGHh+EQpCThdjU2NrexNYfhpfXhEKQkwXYB1dYEtp ckdeGXkRCkJsF2JjQR1hUEVtEhITEQpCQBdtE2hbXBN6BVNHbBEKWlgXHREKeUMXZFhTQxxoXVJ Nf0QRCllLFxMZGB0RCnBnF2tNTXxOTF96Rx5NEB0aEQpwaBdkW3l6ZExSGhp4YBAcGhEKcGgXbV lZbERyTV9zHBIQHBoRCnBoF2FhY1oZUnx5R0tyEBkaEQpwaBdvU3N9eE5TWGYFThAZGhEKcGgXb mBleUJmT0F4WHIQHBoRCnB9F25uSUdaa0lpTk9bEB0aEQpwfRdgWERacwFneBJ7bRAcGhEKcH0X aB1JW05DRkNsYEYQHBoRCnB/F2VYchgdSRheRml8EBsYExEKcF8XZnBIXEB5AUEeTxIQHBoRCnB /F21EX0ZFbX1IeRluEBsZExEKcF8Xa0ZLE3loaW58E3gQGxoeEQpwfxdhZm9bGmdkQkgdWxAbGB 8RCnBfF2NiElBIY3gffEJ9EBMYEQpwbBdsbVgdZ15Cf2FiWhAZGhEKcEwXYEUbcm9OSU5oflkQG RoRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 suspectscore=0 bulkscore=0 malwarescore=0 mlxscore=0 adultscore=0 clxscore=163 priorityscore=336 mlxlogscore=999 lowpriorityscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102240157 domainage_hfrom=9327 X-Spam-Score: 0 X-Spam-OrigSender: eackad@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Eddie" --000000000000a1949405bc1ad9e2 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable They are notnvlinked. I say David's email which had: "I had thought that multi-GPU alpha 7 required NVLink. It happens to be recommended, but not required." so I thought I'd try. On Wed, Feb 24, 2021 at 1:42 PM Bassam Haddad wrote: > Are all of your GPUs NV-linked? It's my understanding that you cannot use > the multi-gpu NAMD 3.0 unless the GPUs are linked together. > > Best, > Bassam > > On Wed, Feb 24, 2021 at 11:37 AM David Hardy wrote: > >> Hi Eddie, >> >> This looks similar to the error that Lorenzo recently reported. >> >> Would you be willing to share your data set for us to try to reproduce >> this error locally? Although we don=E2=80=99t have your exact hardware s= etup, we do >> have a few multi-GPU platforms in-house that we could try. >> >> Best regards, >> Dave >> >> -- >> David J. Hardy, Ph.D. >> Beckman Institute >> University of Illinois at Urbana-Champaign >> 405 N. Mathews Ave., Urbana, IL 61801 >> dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ >> >> On Feb 23, 2021, at 11:49 AM, Dr. Eddie wrote: >> >> Hello, >> I'm trying to get a small 150k system working with namd3. >> I am using 4 gtx1080's with the command >> nice -n 5 >> /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p= 4 >> +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_production.inp >> >> I get the error: >> FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, >> temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file >> src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 >> on Pe 0 (node10.cl.siue.edu >> >> device 0 pci 0:2:0): invalid device function >> >> and >> CUDANBOND[2]: Allocating patch data structure with 87 patches! >> CUDANBOND[3]: Allocating patch data structure with 101 patches! >> CUDANBOND[1]: Allocating patch data structure with 89 patches! >> CUDANBOND[0]: Allocating patch data structure with 114 patches! >> FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, >> temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file >> src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 >> on Pe 0 (node10.cl.siue.edu >> >> device 0 pci 0:2:0): invalid device function >> >> Any ideas? I know these are commerical gpus, is that an issue? >> Thanks, >> Eddie >> >> >> --=20 Eddie --000000000000a1949405bc1ad9e2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
They are notnvlinked. I say David's email which had:"I had thought that multi-GPU alpha 7 required=C2=A0NVLink. It happens to be recommended, but not required.&qu= ot;=C2=A0
so I thought I'd try.

On Wed, Feb 24, 2021= at 1:42 PM Bassam Haddad <bhaddad@pdx.edu> wrote:
Are all of your GPUs NV-linked? It&= #39;s my understanding that you cannot use the multi-gpu NAMD 3.0 unless th= e GPUs are linked together.=C2=A0

Best,
Bassam=

On Wed, Feb 24, 2021 at 11:37 AM David Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Eddie,
This looks similar to the error that Lorenzo recently reported= .

Would you be willing to share your data set for = us to try to reproduce this error locally? Although we don=E2=80=99t have y= our exact hardware setup, we do have a few multi-GPU platforms in-house tha= t we could try.

Best regards,
Dave
=

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Ur= bana-Champaign
405 N. Mathews Ave., Urbana, IL 61801<= /div>

On Feb 23, 2021, at 11:49 AM, Dr. E= ddie <eackad@gmail= .com> wrote:

Hello,
I'm tryin= g to get a small=C2=A0150k system working with namd3.=C2=A0
I am = using 4 gtx1080's with the command
nice -n 5 /home/eddie/bina= ries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p4 +idlepoll +setcpu= affinity +devices 0,1,2,3 step5_production.inp

I get the error:
FATAL ERROR: CUDA error cub::DeviceSelect::If(d= _temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stre= am) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 446= 1
=C2=A0on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0)= : invalid device function

and
CUDANBOND[2]= : Allocating patch data structure with 87 patches!
CUDANBOND[3]: Allocat= ing patch data structure with 101 patches!
CUDANBOND[1]: Allocating patc= h data structure with 89 patches!
CUDANBOND[0]: Allocating patch data st= ructure with 114 patches!
FATAL ERROR: CUDA error cub::DeviceSelect::If(= d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), str= eam) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 44= 61
=C2=A0on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0= ): invalid device function

Any ideas? I know t= hese are commerical=C2=A0gpus, is that an issue?
Thanks,
Eddie



--
Eddie
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boundary="000000000000ae9f1105bc1b0880" X-CLX-Response: 1TFkXGBoaEQpMehcZHx0RCllEF3pfQXkSS0tBQh9QEQpYWBdgHV1gS2lyR14 ZeREKeE4XY1Nja3sTWH4aX14RCnlMF2xtQ0dwUmNGG19sEQpDSBcHGBkfEQpDWRcbGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsSGnEcGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdrGHVHGUREB35ZTG8cHG9dXXxGf2BuXkhYfnhfE1tuThEKWFwXHwQaBBgYHgUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JIbB5aEQpNXBcYGh8RCkxaF2l4a2tNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tia2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB 8ZEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF 2tAcBtne05hGHh+EQpCThdjU2NrexNYfhpfXhEKQkwXYB1dYEtpckdeGXkRCkJsF2JjQR1hUEVt EhITEQpCQBdufh9pcEBbR0xMQhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx0RCnlDF21JAU1 sRRkFZF1ZEQpZSxcTGRgdEQpwZxdrTU18TkxfekceTRAcHxEKcGgXbVlZbERyTV9zHBIQHBoRCn BoF2x4GXlpUHheeQUSEBoRCnBoF3oeaHIcc35fHx9zEBoRCnBoF29lbGNwX3BeeFlPEBoRCnBoF 25gZXlCZk9BeFhyEBwaEQpwfRdubklHWmtJaU5PWxAdGhEKcH0XYFhEWnMBZ3gSe20QHRoRCnB9 F2gdSVtOQ0ZDbGBGEB0aEQpwfxdlWHIYHUkYXkZpfBATHBEKcF8XZnBIXEB5AUEeTxIQHhIRCnB /F21EX0ZFbX1IeRluEBsZEhEKcF8Xa0ZLE3loaW58E3gQGxoZEQpwfxdhZm9bGmdkQkgdWxAbGB 0RCnBfF2NiElBIY3gffEJ9EBMfEQpwbBdsbVgdZ15Cf2FiWhAZGhEKcEwXbWhlGUFSfXsYRVIQG hEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 suspectscore=0 bulkscore=0 malwarescore=0 mlxscore=0 adultscore=0 clxscore=200 priorityscore=357 mlxlogscore=999 lowpriorityscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2102240159 domainage_hfrom=9327 X-Spam-Score: 0 X-Spam-OrigSender: eackad@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Eddie" --000000000000ae9f1105bc1b0880 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I'll do so privately. Thanks! Eddie On Wed, Feb 24, 2021 at 1:28 PM David Hardy wrote: > Hi Eddie, > > This looks similar to the error that Lorenzo recently reported. > > Would you be willing to share your data set for us to try to reproduce > this error locally? Although we don=E2=80=99t have your exact hardware se= tup, we do > have a few multi-GPU platforms in-house that we could try. > > Best regards, > Dave > > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > > On Feb 23, 2021, at 11:49 AM, Dr. Eddie wrote: > > Hello, > I'm trying to get a small 150k system working with namd3. > I am using 4 gtx1080's with the command > nice -n 5 > /home/eddie/binaries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p4 > +idlepoll +setcpuaffinity +devices 0,1,2,3 step5_production.inp > > I get the error: > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, > temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file > src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 0 (node10.cl.siue.edu > > device 0 pci 0:2:0): invalid device function > > and > CUDANBOND[2]: Allocating patch data structure with 87 patches! > CUDANBOND[3]: Allocating patch data structure with 101 patches! > CUDANBOND[1]: Allocating patch data structure with 89 patches! > CUDANBOND[0]: Allocating patch data structure with 114 patches! > FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, > temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file > src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461 > on Pe 0 (node10.cl.siue.edu > > device 0 pci 0:2:0): invalid device function > > Any ideas? I know these are commerical gpus, is that an issue? > Thanks, > Eddie > > > --=20 Eddie --000000000000ae9f1105bc1b0880 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I'll do so privately.
Thanks!
Eddie

On Wed, Feb 24, 2021 at 1:28 PM David Hardy <dhardy@ks.uiuc.edu> wrote:
Hi = Eddie,

This looks similar to the error that Lorenzo rece= ntly reported.

Would you be willing to share your = data set for us to try to reproduce this error locally? Although we don=E2= =80=99t have your exact hardware setup, we do have a few multi-GPU platform= s in-house that we could try.

Best regards,
<= div>Dave

--
D= avid J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
40= 5 N. Mathews Ave., Urbana, IL 61801

On Feb 23, 2021, at 11:49 AM, Dr. E= ddie <eackad@gmail= .com> wrote:

Hello,
I'm tryin= g to get a small=C2=A0150k system working with namd3.=C2=A0
I am = using 4 gtx1080's with the command
nice -n 5 /home/eddie/bina= ries/NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA/namd3 +p4 +idlepoll +setcpu= affinity +devices 0,1,2,3 step5_production.inp

I get the error:
FATAL ERROR: CUDA error cub::DeviceSelect::If(d= _temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stre= am) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 446= 1
=C2=A0on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0)= : invalid device function

and
CUDANBOND[2]= : Allocating patch data structure with 87 patches!
CUDANBOND[3]: Allocat= ing patch data structure with 101 patches!
CUDANBOND[1]: Allocating patc= h data structure with 89 patches!
CUDANBOND[0]: Allocating patch data st= ructure with 114 patches!
FATAL ERROR: CUDA error cub::DeviceSelect::If(= d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), str= eam) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 44= 61
=C2=A0on Pe 0 (node10.cl.siue.edu device 0 pci 0:2:0= ): invalid device function

Any ideas? I know t= hese are commerical=C2=A0gpus, is that an issue?
Thanks,
Eddie



--
Eddie
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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, Sorry for the spam, however I do not think my previous email went through. -Ramon ________________________________ From: Ramon Mendoza Uriarte Sent: Wednesday, February 24, 2021 7:15 PM To: NAMD list Subject: CHARMM Parameter question Hello NAMD community, I am playing with the NBFIX parameters for the interaction between a single= potassium ion and the oxygen of the TIP3P water molecule. Currently, I am = struggling to understand how the CHARMM parameters are used in a standard r= un, for instance, without the NBFIX parameters. For example, I am performin= g a minimization with the attached force field parameters. In this paramete= r file the following parameters for water and potassium ions are contained = within: OT 0.0 -0.1521 1.7682 POT 0.0 -0.0870 1.76375 and thus, from the minimization I get the following averages: pair Total Distance (K+- O) Energy (=C5) (kcal/mol) K - water -20.2 2.62 >From my understanding the Lorentz-Berthelot combination rules are used in d= etermining the LJ parameters. For instance, the parameters for the interact= ion between the oxygen and potassium ion would be as follows: Emin =3D sqrt(0.1521 * 0.0870) =3D 0.115033 Rmin =3D 0.5 * (1.7682 + 1.76375) =3D 1.7659 Now, if I were to specify this as an NBFIX parameter I get the following: pair Total Distance (K+- O) Energy (=C5) (kcal/mol) K - water -75.8 1.18 However, I do not understand why the two give different outputs for the Tot= al Energy and the distance between the potassium and oxygen atoms. So, basi= cally my question is how are the LJ parameters being combined in NAMD? I ha= ve attached my config file and the unmodified and modified parameter files = as well. Any assistance would be appreciated! Thank you, Ramon --_000_BYAPR11MB3160991A909A21BB1B6AFCBFD89E9BYAPR11MB3160namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello,

Sorry for the spam, however I do not think my previous email went through.<= /div>

-Ramon

From: Ramon Mendoza Uriarte=
Sent: Wednesday, February 24, 2021 7:15 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: CHARMM Parameter question
 
Hello NAMD community,

I am playing with the NBFIX parameters for the interaction between a single= potassium ion and the oxygen of the TIP3P water molecule. Currently, I am = struggling to understand how the CHARMM parameters are used in a standard r= un, for instance, without the NBFIX parameters. For example, I am performing a minimization with the attached = force field parameters. In this parameter file the following parameters for= water and potassium ions are contained within:

OT        0.0       -0.1521    = ;1.7682
POT      0.0       -0.0870    1.763= 75

and thus, from the minimization I get the following averages:

pair                 Total&nbs= p;              Distance (K+-= O)
                     = ;   Energy            (=C5)<= /div>
                     = ;   (kcal/mol) 
K - water        -20.2        =        2.62

>From my understanding the Lorentz-Berthelot combination rules are used= in determining the LJ parameters. For instance, the parameters for the int= eraction between the oxygen and potassium ion would be as follows:

Emin =3D sqrt(0.1521 * 0.0870) =3D 0.115033
Rmin = =3D 0.5 * (1.7682 + 1.76375) =3D 1.7= 659

Now, if I were to specify this as an NBFIX parameter I get the following:

pair        =          Total          &= nbsp;    Distance (K+- O)
         = ;               Energy    &nbs= p;       (=C5)
         = ;               (kcal/mol) 
K - water      &n= bsp; -75.8               1.18<= /span>

However, I do not understand why the two giv= e different outputs for the Total Energy and the distance between the potas= sium and oxygen atoms. So, basically my question is how are the LJ parameters being combined in= NAMD? I have attached my config file and the unmodified and modified paramete= r files as well. Any assi= stance would be appreciated!

Thank you,
Ramon
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Mon, 1 Mar 2021 08:29:01 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3703vuth5n-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 01 Mar 2021 08:29:00 +0000 Received: from [IPv6:2a02:810c:300:6724:35c2:4972:a0a5:bcb1] ([IPv6:2a02:810c:300:6724:35c2:4972:a0a5:bcb1]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 1218SpTN060583 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 1 Mar 2021 09:28:56 +0100 Subject: Re: namd-l: An running issue in eABF-replica calculations To: namd-l@ks.uiuc.edu, hua hao References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: Date: Mon, 1 Mar 2021 09:28:52 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.8.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; 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charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi,     I experience this as well.     Has there been any update regarding this? Kind regards René On 1/4/2021 5:59 PM, hua hao wrote: > Hi NAMD developers and users, > > I am learning Tutorial_QMMM_String_eABF recently, which was introduced > to be an advanced tutorial for QMMM in NAMD page > (http://www.ks.uiuc.edu/Research/qmmm/ > ). > > When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl > +stdout output_eABF/%1d/job00.%1d.log", it is strange that some > necessary files with the suffix .grad, .count, .pmf, .zcount, and > .zgrad were only present in the first replica (i..e 0), but not in > other replicas (i.e. 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were > used to perform the above calculations, and these packages were both > complied using openmpi-3.1.4 build on Intel-icc. We also tried the > pre-compiled Linux-x86_64-netlrts and Linux-x86_64-verbs, the error > was still present. > > Normally, these files should appear in each replica. > > Could you help me with this issue? Thank you very much. > > *Hua Hao* > -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------435C100DD412D19C182C52ED Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi,

    I experience this as well.

    Has there been any update regarding this?

Kind regards

René

On 1/4/2021 5:59 PM, hua hao wrote:
Hi NAMD developers and users,

I am learning Tutorial_QMMM_String_eABF recently, which was introduced to be an advanced tutorial for QMMM in NAMD page (http://www.ks.uiuc.edu/Research/qmmm/).

When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessary files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only present in the first replica (i..e 0), but not in other replicas (i.e. 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above calculations, and these packages were both complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts and Linux-x86_64-verbs, the error was still present.

Normally, these files should appear in each replica.

Could you help me with this issue? Thank you very much.

Hua Hao

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
--------------435C100DD412D19C182C52ED-- From owner-namd-l@halifax.ks.uiuc.edu Mon Mar 1 06:22:29 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 121CMTkd028190; Mon, 1 Mar 2021 06:22:29 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 121CMTwC028189; Mon, 1 Mar 2021 06:22:29 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 121CMSPx028184; Mon, 1 Mar 2021 06:22:28 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 121CMS8A028182; Mon, 1 Mar 2021 06:22:28 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 121CMFPY028174 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000e79d6105bc78aa65" X-CLX-Response: 1TFkXHhodEQpMehcYHR4RCllEF29+eBplaFx+UFh8EQpYWBdnbGEcbnpeTm8 BaBEKeE4XY1Nja3sTWH4aX14RCnlMF29EbX1+clxDaWEfEQpDSBcHGRoZEQpDWRcHGB4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsdcRsGGR53BhIfBhsaGkISBhoGHB8GGBoacRsaGhAadwYaBhoGG gYHHBoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XTkNLdQdyeHsaB3wb XBlkG0lGaWhSXU1iE2VBQEYeXmYRClhcFx8EGgQYGB8FGxoEGxsaBB8aBBseGxAbHhofGhEKXlk XcklFb3sRCk1cFxsZGxEKTFoXeGlNTWsRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbG trEQpCTxdgZGsfZ0QYcGYYWhEKQ1oXGBoTBBIfBBgYGAQfHhEKQl4XGxEKREkXGxEKQlwXGxEKX k4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdte0weRRNhRUZTXREKQk4X Y1Nja3sTWH4aX14RCkJMF2dsYRxuel5ObwFoEQpCbBdvY2VtYWdGRWNgUhEKQkAXZEESaRJnWRw aek4RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdnEmFZGmgdQl5lYxEKWUsXExkZGB EKcGcXYBlGRXtORxltXEUQGRoRCnBoF2ZQZkUYfxNdZUZAEBkaEQpwaBdnWWZhZxwaXmhgGhAZG hEKcGgXawFNbgVrExxSR0UQGRoRCnBoF2QTeF4YAU16WkJ/EBkaEQpwaBdnfFpzHWAFT3xObRAZ GhEKcH0XaHl5RENbUkNDcG8QGRoRCnB9F2RJG10SGFJPYHIZEBwaEQpwfxdlWHIYHUkYXkZpfBA bGRMRCnBfF2UcGBpjTnwZXhx5EBkaEQpwXxdmXxJ4Q2ZbemsFWhAcGhEKcGwXZFkTSRtPbX4YAR IQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 spamscore=0 clxscore=407 lowpriorityscore=0 mlxlogscore=999 phishscore=0 adultscore=0 priorityscore=274 malwarescore=0 mlxscore=0 bulkscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103010104 domainage_hfrom=9332 X-Spam-Score: 0 X-Spam-OrigSender: haohua0116@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, hua hao --000000000000e79d6105bc78aa65 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable No, I have not. Ren=C3=A9 Hafner TUK =E4=BA=8E2021=E5=B9=B43=E6= =9C=881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=883:28=E5=86=99=E9=81=93= =EF=BC=9A > Hi, > > I experience this as well. > > Has there been any update regarding this? > > Kind regards > > Ren=C3=A9 > On 1/4/2021 5:59 PM, hua hao wrote: > > Hi NAMD developers and users, > > I am learning Tutorial_QMMM_String_eABF recently, which was introduced to > be an advanced tutorial for QMMM in NAMD page ( > http://www.ks.uiuc.edu/Research/qmmm/). > > When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl > +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessary > files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only > present in the first replica (i..e 0), but not in other replicas (i.e. > 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above > calculations, and these packages were both complied using openmpi-3.1.4 > build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts > and Linux-x86_64-verbs, the error was still present. > > Normally, these files should appear in each replica. > > Could you help me with this issue? Thank you very much. > > *Hua Hao* > > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > -- *Hua Hao* --000000000000e79d6105bc78aa65 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
No, I have not.

Ren=C3=A9 Hafner TUK <hamburge@physik.uni-kl.de>=E4=BA=8E2021=E5=B9=B4= 3=E6=9C=881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=883:28=E5=86=99=E9= =81=93=EF=BC=9A
=20 =20 =20

Hi,

=C2=A0=C2=A0=C2=A0 I experience this as well.

=C2=A0=C2=A0=C2=A0 Has there been any update regarding this?

Kind regards

Ren=C3=A9

On 1/4/2021 5:59 PM, hua hao wrote:
=20
Hi NAMD developers and users,

I am learning Tutorial_QMMM_String_eABF recently, which was introduced to be an advanced tutorial for QMMM in NAMD page (http://www.ks.uiuc.edu/Research/qmmm/).

When running the eABF job by "mpirun -n 2= 8 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it i= s strange that some necessary files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only present in the first=C2=A0replica (i..e 0), but n= ot in other=C2=A0replicas (i.e. 1-13).=C2=A0NAMD-2.14 and=C2=A0NAMD-Gib-2020-12-07=C2=A0were us= ed to perform the above calculations, and these packages were both complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts and=C2=A0Linux-x86_64-verbs, the error wa= s still present.

Normally, these files should appear in each=C2=A0replica.

Could you help me with this issue? Thank you very much.

<= b>Hua Hao

--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--
Hua Hao

=
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boundary="000000000000b75a9d05bc79e630" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxgSEQpMehcZHx8RCllEF29BQ2B7QH9sE1BPEQpYWBdvT1BvWU9dGG5 TbxEKeE4XY1Nja3sTWH4aX14RCnlMF2JbTkkcUn9dHB1hEQpDSBcHGx0fEQpDWRcHGBkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGhJxGxsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWh1tT0F5GHN1ZW5IbF1yfXxdfX9yaUxCX0lHTUBZXRMRClhcFx8EGgQYGB8F GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdySVpybhEKTVwXGBkaEQpMWhd8aWtraxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh8EGxwcBB 4SEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2hOT1JYHX9uXEASEQpCThdjU2NrexNYfhpfXhEKQkwXb09Qb1lPXRhuU28RCkJsF2tl Wk8ecEJpQH9DEQpCQBdkQRJpEmdZHBp6ThEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxsaEQp 5QxdnEmFZGmgdQl5lYxEKWUsXExkZGBEKcGcXY1xQYRtSbWgcYWkQGRoRCnBoF2B9Y3pmcFJyQR NnEBkaEQpwaBdvbk9zcHpMH0tNbxAZGhEKcGgXZBN4XhgBTXpaQn8QGhEKcGgXYGtwBRlgTm9jS RwQHBwRCnBoF21GWl1iHgUeYhJfEBkaEQpwfRdvXE57aQF/Y2l/axAfGxEKcH0XaHl5RENbUkND cG8QGhEKcH0XZlpocklefkESHR4QHh0RCnB9F2ceQGBFRFNyGEZoEBwfEQpwfRdkSRtdEhhST2B yGRAZGhEKcH8XYERDE35hfFhSTU0QHR0RCnBfF2JwWE1Mck8Ff3xIEBwSEQpwfxdlWHIYHUkYXk ZpfBAbGRkRCnBfF2UcGBpjTnwZXhx5EBoRCnBfF2tbGxN4fGN+RU9mEB0aEQpwXxdmXxJ4Q2Zbe msFWhAZGhEKcGwXYx5ebn4BaFN7XXkQGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdL ESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 impostorscore=0 priorityscore=355 phishscore=0 clxscore=128 mlxscore=0 malwarescore=0 lowpriorityscore=0 mlxlogscore=990 suspectscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103010115 domainage_hfrom=9332 X-Spam-Score: 0 X-Spam-OrigSender: abhi117acharya@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Abhishek Acharya --000000000000b75a9d05bc79e630 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi, Maybe you can try something like this. mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log Abhi Virus-free. https://urldefense.com/v3/__http://www.avast.com__;!!DZ3fjg!uwTqQIwoFJrPcZw= tSdM2RwjVxn2Gtq1rTrBnDLibtrJk8t7wBd1UJPEpEE0F2J0laQ$=20 <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Mon, Jan 4, 2021 at 6:02 PM hua hao wrote: > Hi NAMD developers and users, > > I am learning Tutorial_QMMM_String_eABF recently, which was introduced to > be an advanced tutorial for QMMM in NAMD page ( > http://www.ks.uiuc.edu/Research/qmmm/). > > When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl > +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessary > files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only > present in the first replica (i..e 0), but not in other replicas (i.e. > 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above > calculations, and these packages were both complied using openmpi-3.1.4 > build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts > and Linux-x86_64-verbs, the error was still present. > > Normally, these files should appear in each replica. > > Could you help me with this issue? Thank you very much. > > *Hua Hao* > > --000000000000b75a9d05bc79e630 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi,

Maybe you can try something li= ke this.
mpirun -n 28 namd2 +replicas 14 e= ABF.tcl +stdout output_eABF/%d/job00.log
<= br>
Abhi

3D"" Virus-free. www.avast.com

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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks, Abhishek. I try to do it, but the problem is still present. Abhishek Acharya =E4=BA=8E2021=E5=B9=B43=E6=9C=88= 1=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81=93=EF=BC= =9A > Hi, > > Maybe you can try something like this. > mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log > > Abhi > > > Virus-free. > https://urldefense.com/v3/__http://www.avast.com__;!!DZ3fjg!vtVzXY1Bh5MPm= ObB6F2Kwfd0GmfBZ6lSqQpfcqGBhlh4BSHjQYhNoJJNi13m1hzxFQ$=20 > > <#m_-5299850564915384101_m_-7084929218411686926_DAB4FAD8-2DD7-40BB-A1B8-4= E2AA1F9FDF2> > > On Mon, Jan 4, 2021 at 6:02 PM hua hao wrote: > >> Hi NAMD developers and users, >> >> I am learning Tutorial_QMMM_String_eABF recently, which was introduced to >> be an advanced tutorial for QMMM in NAMD page ( >> http://www.ks.uiuc.edu/Research/qmmm/). >> >> When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl >> +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessary >> files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only >> present in the first replica (i..e 0), but not in other replicas (i.e. >> 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above >> calculations, and these packages were both complied using openmpi-3.1.4 >> build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts >> and Linux-x86_64-verbs, the error was still present. >> >> Normally, these files should appear in each replica. >> >> Could you help me with this issue? Thank you very much. >> >> *Hua Hao* >> >> --000000000000cdc46d05bc7b2cfe Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thanks, Abhishek.
<= span class=3D"gmail_default" style=3D"font-size:small;color:rgb(7,55,99)"><= br>
I try to do it,=C2=A0but the problem=C2=A0is still pre= sent.=C2=A0

Abhishek Acharya <abhi117acharya@gmail.com>=E4=BA=8E202= 1=E5=B9=B43=E6=9C=881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5= =86=99=E9=81=93=EF=BC=9A
Hi,<= /div>

Maybe you can try something like this.
mpirun -n 28 namd2 +replicas 14 eABF.= tcl +stdout output_eABF/%d/job00.log

Abhi

3D"" Virus-free. www.av= ast.com
On Mon, J= an 4, 2021 at 6:02 PM hua hao <haohua0116@gmail.com> wrote:
<= div class=3D"gmail_default" style=3D"font-size:small;color:rgb(7,55,99)">Hi= NAMD developers and users,

I am = learning Tutorial_QMMM_String_eABF recently, which was introduced to be an = advanced tutorial for QMMM in NAMD page (http://www.ks.uiuc.edu/Research/qmmm/= ).

When running the eABF job= by "mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/= job00.%1d.log", it is strange that some necessary files with the suffi= x .grad, .count, .pmf, .zcount, and .zgrad were only present in the first= =C2=A0replica (i..e 0), but not in other=C2=A0replicas (i.e. 1-13).=C2=A0NA= MD-2.14 and=C2=A0NAMD-Gib-2020-12-07=C2=A0were used to perform the above ca= lculations, and these packages were both complied using openmpi-3.1.4 build= on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts and=C2= =A0Linux-x86_64-verbs, the error was still present.

Normally, = these files should appear in each=C2=A0replica.

Could you = help me with this issue? Thank you very much.

<= div dir=3D"ltr">
Hua Hao<= /font>

<= /div>
--000000000000cdc46d05bc7b2cfe-- From owner-namd-l@halifax.ks.uiuc.edu Mon Mar 1 20:02:19 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12222JEG018671; Mon, 1 Mar 2021 20:02:19 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12222JdL018670; Mon, 1 Mar 2021 20:02:19 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12222InY018666; Mon, 1 Mar 2021 20:02:18 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12222IhW018665; Mon, 1 Mar 2021 20:02:18 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12221wR0018656 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 1 Mar 2021 20:02:03 -0600 (CST) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 1221wBaV003885 for ; Tue, 2 Mar 2021 02:01:58 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=randall.hall@dominican.edu; dkim=pass header.s=google header.d=dominican.edu Received: from mail-pf1-f175.google.com (mail-pf1-f175.google.com [209.85.210.175]) by mx0b-00007101.pphosted.com with ESMTP id 3703vv5sud-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Tue, 02 Mar 2021 02:01:58 +0000 Received: by mail-pf1-f175.google.com with SMTP id l7so8586209pfd.3 for ; Mon, 01 Mar 2021 18:01:57 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=dominican.edu; s=google; h=from:mime-version:subject:message-id:date:to; bh=TJCvD7BnWAOTF5zdXSVC0oyXhyw7GcEG/Z2DOeVzY1w=; b=HwM4AXuNJGLAcAqBxifDSsIBpmeHYyiXgL/w0n8QovLPAMwLctOmFpG5ux0JDgNDo2 TXPYkznBcGfQzaGbR8eRDPl4YrsPyW4pSDNJP0CMiQ6KU54NTgEbWzdIH0ekuI+Q0z/R yOBBbW+plukMyG51PJXvQypFqZjsXTA8MmcJA= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:mime-version:subject:message-id:date:to; bh=TJCvD7BnWAOTF5zdXSVC0oyXhyw7GcEG/Z2DOeVzY1w=; b=IsunP0uIofKn4kn6A3AEVv9DwtReHrP8B2IK/Y3fvo7hBsXc8GA84JEihucYcuhI/x mLb+wUiiQdj1OcWTxLk/QrPnSSgmEWlmzq7vW4SS91dNOZtRXSH+/Z3ppp69fNDsU0ml 9IJt7cZpzsLycz7OasqAm3kFpMDebP3Vb+QMn/cyEkfGYVhxyeXGOc5ge+oOHSQUskLd JUDfI85Nhcsm1cMqtNV5pP06QPpeyXS1gLvIJrLdq43ePfMPqVvjtwQ3eny4dNft717r C3DZHI93sQe/TUEdalSd+ALXfz+CWoWDE+rJ8klhJGwC2JHYfxIELeFUrsDpLaVKas9d 2eJg== X-Gm-Message-State: AOAM530eb5Ht1lM2D7g1l7bsUc+UlddRiww3zXI76cIh+ghBS/QshU98 wyvAoj8/un0bcKvyGkWIoqZNP84mYFSP8Q== X-Google-Smtp-Source: ABdhPJzWyieFKYQShrQaj2vIQYN5kJNE6yok+SWtomCZoSh1HO+qxxXvQ+eu76+Gtx6wvg8LyeJV3w== X-Received: by 2002:a63:e554:: with SMTP id z20mr16226308pgj.448.1614650516448; Mon, 01 Mar 2021 18:01:56 -0800 (PST) Received: from mac5100026-18.lan (76-218-116-20.lightspeed.sntcca.sbcglobal.net. [76.218.116.20]) by smtp.gmail.com with ESMTPSA id 9sm17365646pgw.61.2021.03.01.18.01.55 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 01 Mar 2021 18:01:55 -0800 (PST) From: Randall Hall Content-Type: multipart/alternative; boundary="Apple-Mail=_BCE2182E-5F79-465C-A803-B1297E6D1E95" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.17\)) Subject: namd-l: Dual topology questions Message-Id: <93B393D8-52C2-48C6-81CD-EFA299C569A4@dominican.edu> Date: Mon, 1 Mar 2021 18:01:52 -0800 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3445.104.17) X-CLX-Response: 1TFkXGxwSEQpMehcaEQpZRBdiZx1NHVhGYUEBfhEKWFgXbk4bGU5vTR0cQng RCnhOF25fTUlubGAcQB9DEQp5TBd6S2JsZVwZWlpZexEKQ0gXBxgcExEKQ1kXBxsTHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseEnEYExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdNdWBOQ3tAY2tTHlpOH19sUht4eW9uRXV4E2QbRn97QxEKWFwXHwQaBBgYHwUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdySRpvUhEKTVwXGBIYEQpMWhdsaU1NaxEKTEYXb2tra2t rEQpCTxdiZ1sfUBlTYHscExEKQ1oXGBoTBBIfBBgbGgQbHR8RCkJeFxsRCkJcFxsRCl5OFxsRCk JLF25fTUlubGAcQB9DEQpCSRduX01JbmxgHEAfQxEKQkUXZWIFH3N+bWJSQAURCkJOF25fTUlub GAcQB9DEQpCTBduThsZTm9NHRxCeBEKQmwXbGBQUm9SZVBhZEYRCkJAF2gaX1xAE0BHfEl/EQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUMXellhUHlLEnNsaG0RCllLFxMdGhsRCnBoF2J +GGlJbEhFb2UdEBseHBEKcGgXaW9aRk1bXmUFQ3wQGRoRCnBoF2l6bnJJW21QYExNEBkaEQpwaB d6ThxMaHgbEklcYhAZGhEKcGgXbUcaU08FfnxIQmkQGRoRCnBsF2FlG0RfExsBBUhsEB4SEQpwQ xdoeBoYQV17T2NLXxAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 spamscore=0 clxscore=168 lowpriorityscore=0 mlxlogscore=765 phishscore=0 adultscore=0 priorityscore=0 malwarescore=0 mlxscore=0 bulkscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103020012 domainage_hfrom=9701 X-Spam-Score: 0 X-Spam-OrigSender: randall.hall@dominican.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Randall Hall --Apple-Mail=_BCE2182E-5F79-465C-A803-B1297E6D1E95 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Greetings, I want to make sure I understand a detail of the NAMD implementation = of the dual topology FEP algorithm. With alchDecouple off, is the = following correct? 1) all bonds, dihedrals, angles, and impropers are not scaled for any = value of lambda 2) non-bonded interactions between atoms in annihilated are scaled with = lambda Thanks in advance for helping me understand these details. Randy Randall Hall (he/him) Lillian L.Y. Wang Yin, Ph.D. Endowed Professor of Chemistry Dominican University of California randall.hall@dominican.edu 220 Science Center Phone: 415-482-1911 Fax: 415-482-1972 --Apple-Mail=_BCE2182E-5F79-465C-A803-B1297E6D1E95 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Greetings,
  I want to make sure I = understand a detail of the NAMD implementation of the dual topology FEP = algorithm.   With alchDecouple off, is the following = correct?

1) = all bonds, dihedrals, angles, and impropers are not scaled for any value = of lambda

2) = non-bonded interactions between atoms in annihilated are scaled with = lambda

Thanks = in advance for helping me understand these details.

Randy


Randall Hall (he/him)
Lillian L.Y. Wang = Yin, Ph.D. Endowed Professor of Chemistry
Dominican = University of California
randall.hall@dominican.edu
220 Science = Center
Phone: 415-482-1911
Fax: = 415-482-1972




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boundary="000000000000fe93ad05bc9c03bd" X-CLX-Response: 1TFkXGBgaEQpMehcZGxsRCllEF29HYBkeHE0ZYFxOEQpYWBdnTEcdHnlhXHA SbBEKeE4XY1Nja3sTWH4aX14RCnlMF2FoWGhtWhpbBRkTEQpDSBcHHh0bEQpDWRcHGx8cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGBoacRgaGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdyfBocYW4fbUdGX3tiUnNLbkZoYFhnb3pmaWdcQ0QSTBEKWFwXHwQaBBgY HwUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdyTmRjSREKTVwXHxMYEQpMWhdoaU1NaxEKTEYXb2t ra2trEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGwQfHhEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdpRn9AGlpmTmtEHBEKQk4XY1Nja 3sTWH4aX14RCkJMF2dMRx0eeWFccBJsEQpCbBdgbElSaFB/GEIeWREKQkAXZwVPRFN/QVtjWx0R CkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5QxdnYnsbR3gBe39OcxEKWUsXExkZHhEKcGgXbV5mZlx QSRhZZ2YQGRoRCnBoF2BOAUVnWFJSQ1McEBkaEQpwaBdmYF0aT0Zwe2ZPbRAZGhEKcGgXYmRwHk NnchJMZGsQGRoRCnBoF2hcYlBNR3xAaWhLEBkaEQpwfRd6Z2hzcllgbV4fYRAZGhEKcH0XaQV+Q F1rW3BJHxIQGRoRCnB/F2RIQmIaQXxQaE1rEBsbHhEKcF8Xb21JY19QSWZ+c08QGRoRCnBsF2IB fV9hXHlsQhNuEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 bulkscore=0 clxscore=220 mlxscore=0 suspectscore=0 impostorscore=0 spamscore=0 lowpriorityscore=0 malwarescore=0 mlxlogscore=783 priorityscore=311 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103030049 domainage_hfrom=9334 X-Spam-Score: 0 X-Spam-OrigSender: soumadwipghosh@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, soumadwip ghosh --000000000000fe93ad05bc9c03bd Content-Type: text/plain; charset="UTF-8" Hi, I have simulated an MSPA protein pore in lipid for 1 ns using steered MD as shown in the tutorial https://bionano.physics.illinois.edu/sites/default/files/nanopore-protocols.pdf. I followed the protocol described in section 3.10 (page 29) for 0.05 V external field and 1M KCl. However, the current I am getting has negative values in some of the frames. Is it happening because the system may not be well equilibrated in such a short time or am I getting such an ambiguous current because the external field is only 50 mV ? I am showing below the current_electric.dat file that was produced after executing the currentTraj.tcl on page 30. Is there anything wrong with the procedure I am following? 0.075 -16.300602643139975 0.12499999999999999 0.5290047015453344 0.175 1.464401254746031 0.22499999999999998 -0.7136776318778846 0.27499999999999997 -0.01999234528800148 0.32499999999999996 1.2573843539474363 0.37499999999999994 -1.4266596705622407 0.425 -0.3222860406576734 0.475 -0.3000825571992549 0.5249999999999999 -1.2037490289372796 0.575 -1.8169851733662754 0.625 -0.33687052745937707 0.6749999999999999 1.0995286022674309 0.725 0.2529037773776375 0.7749999999999999 2.0539884190047886 0.825 -0.5471836863775636 0.8749999999999999 -0.5362299610804959 0.9249999999999999 0.3134277024231096 0.9749999999999999 2.616593249612792 1.025 0.3470090546120108 1.075 0.590928539300756 1.125 -0.7080767926283599 Thank you for your help in advance. Best Soumadwip Ghosh La Jolla, CA United States --000000000000fe93ad05bc9c03bd Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I have simulated an MSPA protein po= re in lipid for 1 ns using steered MD as shown in the tutorial=C2=A0https://bionano.physics.illinois.edu/sites/default/files/nanopore= -protocols.pdf. I followed=C2=A0the protocol described=C2=A0in section = 3.10 (page 29) for 0.05 V external field and 1M KCl. However, the current I= am getting has negative values in some of the frames. Is it happening beca= use the system may not be well equilibrated in such a short time or am I ge= tting such an ambiguous=C2=A0current because the external field is only 50 = mV ? I am showing below the current_electric.dat file that was produced aft= er executing the currentTraj.tcl on page 30. Is there anything wrong with t= he procedure I am following?=C2=A0

0.075 -16.30060= 2643139975
0.12499999999999999 0.5290047015453344
0.175 1.46440125474= 6031
0.22499999999999998 -0.7136776318778846
0.27499999999999997 -0.0= 1999234528800148
0.32499999999999996 1.2573843539474363
0.37499999999= 999994 -1.4266596705622407
0.425 -0.3222860406576734
0.475 -0.3000825= 571992549
0.5249999999999999 -1.2037490289372796
0.575 -1.81698517336= 62754
0.625 -0.33687052745937707
0.6749999999999999 1.099528602267430= 9
0.725 0.2529037773776375
0.7749999999999999 2.0539884190047886
0= .825 -0.5471836863775636
0.8749999999999999 -0.5362299610804959
0.924= 9999999999999 0.3134277024231096
0.9749999999999999 2.6165932496127921.025 0.3470090546120108
1.075 0.590928539300756
1.125 -0.7080767926= 283599

Thank you for your help in advance.

Best
Soumadwip Ghosh
La Jolla, CA=
United States
--000000000000fe93ad05bc9c03bd-- From owner-namd-l@halifax.ks.uiuc.edu Wed Mar 3 15:12:44 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 123LCiBV004157; Wed, 3 Mar 2021 15:12:44 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 123LCipV004156; Wed, 3 Mar 2021 15:12:44 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 123LChoo004152; Wed, 3 Mar 2021 15:12:43 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 123LCh71004151; Wed, 3 Mar 2021 15:12:43 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 123LCTcI004138 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 3 Mar 2021 15:12:29 -0600 (CST) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 123L8R2f000401 for ; Wed, 3 Mar 2021 21:12:29 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qt1-f175.google.com (mail-qt1-f175.google.com [209.85.160.175]) by mx0a-00007101.pphosted.com with ESMTP id 372cpucryx-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 03 Mar 2021 21:12:28 +0000 Received: by mail-qt1-f175.google.com with SMTP id v3so18771769qtw.4 for ; Wed, 03 Mar 2021 13:12:28 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=L5F+ksyyPU9FljPmWMTMG0S6mQNTrzG6zSVq/Ox1e5A=; b=W9QG5w7Pod5sMAp19srzm1UuuDQP4ebbCJJ4T1s83CyMAnfeyYWnnxOGjRKVXvp5LV 44BC6sg60LdiNqQGF6Ge/fnqvOfEK9aHR7J3lE5YtSQ4hHFP77wqPMpNc5jKAXRaeVhq RzlO8/3vrMwetD86RS1SuRv6iuTklxou7iFiIC23hIU/uUA1R8kKxHG4603IATX07blz DohGgvm3jQpjxLodCZD4S6O371mNuuUJlpixgaKqnLLCeAZ/4sFiwYSOiCrFEXSaAO6B 8UooYKH0VRAPqEKP59XotQrXanQFYQ9dhtNgxNEEcJYgxCCzRdLWwDaldcSbwGtbWTT2 B4hA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=L5F+ksyyPU9FljPmWMTMG0S6mQNTrzG6zSVq/Ox1e5A=; b=cYX+xLOw86Gq6N8OQKOchnG6cr9rKCwez2Z3cn87tfLyIXW9N6JstPvE+wdPaNU1Oq weby2VX8sZIVsub9zTOQgyzXRINV7RS1H7pHvEfRiVkimmAcoZFGA02/u/Oen8560rNF 1wg7SmTaZei5gS8ZmM90a2VcOMyubwCudkwiO7pYG8Ul1XkPs75Ymelqiv+43g0a/WvN tsZAZ57nQR66zhw/46efT5bsh8nKMxhoZOLc64/rq7rlRK6hmtpWNsjhRp5Nwc9cX0Hm ctzXMzU9AJW+3MKz/pfIWcm+SVktZlqhd/CvA64OPVd3mNnWcqdEHBMZUMApG3sdr34K u+aw== X-Gm-Message-State: AOAM533X3hUhYWhb+arCqvKLTLvhG9SZKtn+y6ajf7jh4I/Lq/LV3tT9 iezFsB+XZDsEXpJcRiu1TxoROIPn8q+ddQ== X-Google-Smtp-Source: ABdhPJxNKEKiepQcmt/0i0tWeD5roNbPlq+pKYqGlhfjMP0suGT1uFo/xxXVQgyxQbo6SeIqyJgrAw== X-Received: by 2002:ac8:7a94:: with SMTP id x20mr378542qtr.51.1614805947591; Wed, 03 Mar 2021 13:12:27 -0800 (PST) Received: from [192.168.1.34] ([181.64.230.185]) by smtp.gmail.com with ESMTPSA id z7sm8983911qkf.136.2021.03.03.13.12.25 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Wed, 03 Mar 2021 13:12:26 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Wed, 03 Mar 2021 16:12:23 -0500 Subject: namd-l: Compile NAMD with AMD GPU From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: <07C51C81-3B53-4DDE-8BF3-3DFB210CD3A1@gmail.com> Thread-Topic: Compile NAMD with AMD GPU Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3697632745_1565125168" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIaEQpMehcZGhgRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGBkZEQpDWRcHHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGnEZExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdiUFN/RX5rSENMcmZCUnVgWkV8fGZvRhhCU3xPZ2RkYhEKWFwXHwQaBBgYHwUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3JOS2hzEQpNXBcYGhkRCkxaF2xpTU1rEQpMRhdva2tra2s RCkJPF2tBU0weElpvTxJsEQpDWhcYGhMEEh8EGxwaBBsdHxEKQl4XGxEKRF4XGBEKQlwXGxEKXk 4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY 1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXek0fZ0NCUH5z GV8RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdtHktOaFJuXmtocBEKWUsXExkZHhE KcGgXYk5yZmB9QEhzGHAQGRoRCnBoF25CBWxec055QEZpEBkaEQpwaBdiSFwdYU8fR1B4ExAZGh EKcGgXYl1GbUZ/Z3l/TEgQGRoRCnBoF2lucAVGQxxaZlxhEBsfGxEKcGwXekdAaxhZeX8eG0gQG RoRCnBDF2ZER3tmfRtmQlJYEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 malwarescore=0 spamscore=0 impostorscore=0 mlxscore=0 clxscore=180 phishscore=0 lowpriorityscore=0 adultscore=0 mlxlogscore=349 bulkscore=0 priorityscore=302 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103030151 domainage_hfrom=9334 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3697632745_1565125168 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear namd users,=20 =20 How can I compile NAMD with Radeon o similar AMD GPU? =C2=A0 =20 Best,=20 =20 Geo.=20 --B_3697632745_1565125168 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dea= r namd users,

 

How can I compile NAMD with Radeon o similar AMD GPU? =C2=A0=

 

Be= st,

=  

Geo.

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Subject: Re: namd-l: Compile NAMD with AMD GPU Thread-Topic: namd-l: Compile NAMD with AMD GPU Thread-Index: AQHXEHTizkSxUPO5YECYybcMJnG9Jg== Date: Wed, 3 Mar 2021 21:33:43 +0000 Message-ID: <539B869C-38AE-4AC8-9D78-2E8D8E74280A@msu.edu> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/16.46.21021202 authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=msu.edu; x-originating-ip: [52.144.34.248] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 3ea1b0b1-88af-4b03-841d-08d8de8c0509 x-ms-traffictypediagnostic: CY4PR12MB1351: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:7691; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:CY4PR12MB1351.namprd12.prod.outlook.com;PTR:;CAT:NONE;SFS:(4636009)(376002)(366004)(136003)(39860400002)(396003)(346002)(166002)(71200400001)(6486002)(316002)(2906002)(966005)(478600001)(786003)(36756003)(6506007)(53546011)(110136005)(2616005)(6512007)(8676002)(33656002)(5660300002)(66476007)(66446008)(66946007)(66556008)(8936002)(91956017)(83380400001)(75432002)(76116006)(86362001)(64756008)(26005)(186003)(4744005)(45980500001);DIR:OUT;SFP:1101; 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boundary="_000_539B869C38AE4AC89D782E8D8E74280Amsuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 3ea1b0b1-88af-4b03-841d-08d8de8c0509 X-MS-Exchange-CrossTenant-originalarrivaltime: 03 Mar 2021 21:33:43.3582 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: o5c8vdssnjMVC14JBtXSRXFk/BZGrTHQeXlbyxWzuwm8GGRoFIcOrREXB0l9ncLFmsWjnI0qUPNIjBomAtwAYw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR12MB1351 X-CLX-Response: 1TFkXGxIYEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxsSEhEKQ1kXBxsZEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwYcR4bEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0RyXFhwRH1uQR9EZ1JGWXtiGkhwZmVZUk5pWRlnRG0eEQpYXBcfBBoEGBgfBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXck5LfH4RCk1cFxkeGxEKTFoXeGlNTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2tra2traxEKQk8XZ2BaT3sBenkeZEARCkNaFx4aBBsaHQQYGBoEHh oRCkJeFxsRCkReFxkRCkJFF2hta2B5EktAWh59EQpCThdob0xmAXJmZEtdEhEKQkwXb2FYExpLX RtDQWURCkJsF2F5HB8SXHtPWmlCEQpCQBdicwFDexxYBXAabREKQlgXZ3Nlc0BuYWFMXWIRClpY Fx8RCnlDF29ETE0eTkVbQnBhEQpZSxcbGBkfHxEKcGcXbUdha01jGUxTaW4QGRoRCnBoF2NeUm5 /S0l6emdLEBkaEQpwaBdoTH9uSHlLHGtGUxAbHh4RCnBoF2sYTWthHBIcEnliEBkaEQpwaBduZG JkYBxkWk1eHhAZGhEKcGgXYh0TcFJ6GxhpHX8QGx8YEQpwfRd6e1xua24YW25dGRAZGhEKcH0XY lxtR21zck4dR0wQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwfxdlWHIYHUkYXkZpfBAbGhMRCnBf F2hPeWVORFtcQ2FzEBkaEQpwfxdrHWseU3tnY0ttehAbGhsRCnBfF2t9E1BOGEAZS1lOEBkaEQp wbBdneBpAYhhJGn55TRAZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 priorityscore=0 lowpriorityscore=0 clxscore=182 impostorscore=0 phishscore=0 mlxlogscore=889 mlxscore=0 bulkscore=0 suspectscore=0 spamscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103030153 domainage_hfrom=12355 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_539B869C38AE4AC89D782E8D8E74280Amsuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable This exists, but is super alpha at the moment (apparently it doesn=E2=80=99= t entirely conserve energy. My bad!). See http://www.ks.uiuc.edu/Research/n= amd/alpha/2.15_amdhip/, especially the source tarball, which has building i= nstructions. The requirements are basically that you need an AMD GPU that is compatible = with HIP, which is some but not all Radeon cards, and basically none of the= common consumer cards a typical computational scientist is likely to have = laying around. https://urldefense.com/v3/__https://github.com/RadeonOpenCom= pute/ROCm*Hardware-and-Software-Support__;Iw!!DZ3fjg!vF2k_mcreXXti7f1gNtf6Z= 7wuXLAhCjyJPFrv_xfhg1tHFAwHjMbUDAQ9IylFSCvKg$=20 -Josh From: on behalf of "Ropon-Palacios G." Reply-To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." Date: Wednesday, March 3, 2021 at 4:22 PM To: "namd-l@ks.uiuc.edu" Subject: namd-l: Compile NAMD with AMD GPU Dear namd users, How can I compile NAMD with Radeon o similar AMD GPU? Best, Geo. --_000_539B869C38AE4AC89D782E8D8E74280Amsuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <05F9785145415C4B86EE328017AF11DD@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable

This exists, but is= super alpha at the moment (apparently it doesn=E2=80=99t entirely conserve= energy. My bad!). See http://= www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/, especially the source= tarball, which has building instructions.

 

The requirements ar= e basically that you need an AMD GPU that is compatible with HIP, which is = some but not all Radeon cards, and basically none of the common consumer ca= rds a typical computational scientist is likely to have laying around. https://github.com/RadeonOpenCompute/ROCm#Hardware-and-Software-Support=

 

-Josh

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of "= ;Ropon-Palacios G." <biodano.geo@gmail.com>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>,= "Ropon-Palacios G." <biodano.geo@gmail.com>
Date: Wednesday, March 3, 2021 at 4:22 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: Compile NAMD with AMD GPU

 

Dear na= md users,

 <= /span>

How can I compile N= AMD with Radeon o similar AMD GPU?  

 <= /o:p>

Best, <= /o:p>

 <= /o:p>

Geo.

--_000_539B869C38AE4AC89D782E8D8E74280Amsuedu_-- From owner-namd-l@halifax.ks.uiuc.edu Fri Mar 5 11:11:51 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 125HBpbj024904; Fri, 5 Mar 2021 11:11:51 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 125HBp0X024903; Fri, 5 Mar 2021 11:11:51 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 125HBoYR024899; Fri, 5 Mar 2021 11:11:50 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 125HBo1B024898; Fri, 5 Mar 2021 11:11:50 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 125HBWwv024888 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 5 Mar 2021 11:11:38 -0600 (CST) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 125H8aTF007173 for ; Fri, 5 Mar 2021 17:11:32 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=zdorevskyi@bitp.kiev.ua Received: from mail.bitp.kiev.ua (mail.bitp.kiev.ua [194.44.37.244]) by mx0a-00007101.pphosted.com with ESMTP id 3731r0cwb1-1 (version=TLSv1 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 05 Mar 2021 17:11:31 +0000 Received: from localhost ([127.0.0.1] helo=mail.bitp.kiev.ua) by mail.bitp.kiev.ua with esmtp (Exim 4.76) (envelope-from ) id 1lIDz7-0006KG-Jb for namd-l@ks.uiuc.edu; Fri, 05 Mar 2021 19:11:29 +0200 Received: from 185.190.149.1 (SquirrelMail authenticated user zdorevskyi) by mail.bitp.kiev.ua with HTTP; Fri, 5 Mar 2021 19:11:29 +0200 Message-ID: Date: Fri, 5 Mar 2021 19:11:29 +0200 Subject: namd-l: simulations under a periodic electric field - possible bug From: "Oleksii Zdorevskyi" To: namd-l@ks.uiuc.edu User-Agent: SquirrelMail/1.4.22 MIME-Version: 1.0 Content-Type: text/plain;charset=utf-8 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxgaEQpMehcaEQpZRBduYG19U1MTSXBFQxEKWFgXaERsXR9EQlxPYBI RCnhOF2QbZhlSYAFreBxYEQp5TBdkRkRYYHofa2ZbcxEKQ0gXBxkbGxEKQ1kXBxsaEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsaGnETEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0F4QU0Hc2hdThNBW2l8YUFobUt9TVkYGEgdXkR8bWlAEQpYXBcfBBoEGBgfBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXck9rWEwRCk1cFxkaGREKTFoXaGlNa2sRCkJPF21gQWlNQ35 QXm4fEQpDWhcbEx4EHh4EGR0EGB4eEQpCXhcbEQpCRRdhWEFcfRlQHG5mexEKQk4XZBtmGVJgAW t4HFgRCkJMF2hEbF0fREJcT2ASEQpCbBdnBRkZc3B/Rh5MZhEKQkAXbEtaQmlMU2kBXxwRCkJYF 2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxdla0Mce0IeHm9rHBEKcGgXYERJXUxyQkgST28QGRoRCnBo F2FPWEljQ0xOZEMTEBkaEQpwaBdiRXJgH11rZWxyEhAZGhEKcGgXYhJ9WFphbVl6GnsQGRoRCnB oF2xyYn0eWmFdemhgEBkaEQpwfRdhf2Bcfh4BZ0hObRAZGhEKcH8XZRl5Zl5HaRtkT3MQEhoRCn BfF2keR2lsYEgBZnhMEBkaEQpwbBdvX3N5W1xrXxhgfRAZGhEKcEMXa218XFhGEmBuTUsQGRoRC m1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 suspectscore=0 adultscore=0 mlxscore=0 spamscore=0 malwarescore=0 priorityscore=0 clxscore=120 impostorscore=0 phishscore=0 mlxlogscore=999 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103050087 X-Spam-Score: 0 X-Spam-OrigSender: zdorevskyi@bitp.kiev.ua X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Oleksii Zdorevskyi" Dear NAMD developers, I am performing all-atom simulations of DNA dodecamer neutralized by potassium ions in a water box under an external periodic electric field. When the frequency of the electric field is high enough, the simulation works fine. That is, under 1Ghz (eFieldFreq is 0.001 1/ps), the ionic current changes its sign every quarter of the period (in this case every 0.25 ns). But when reducing the frequency by one order of magnitude, namely to 0.1 GHz (eFieldFreq is 0.0001 1/ps), the current must change its sign every 2.5 ns. However, during the whole 10-ns simulation the system experiences a constant ionic current. It is seen from visual examinations as well as from the explicit calculation of ionic current within a Tcl script. Could you give me an idea if NAMD has some limits to eFieldFreq? That is, could it be that when this parameter is, for instance 0.0001 (1/ps), the program just equals it to zero? In both cases (for frequencies 1Ghz and 0.1 GHz) the initial electric field vector was: eField -0.522 0 0 If it is necessary, I can provide you with all the configuration files and simulation results. Unfortunately, I have not found any documentation about the implementation of a periodic field in NAMD. I have seen only this post (https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/1278.html), however, it does not discuss any limitations of the eFieldFreq parameter. Best regards, Oleksii From owner-namd-l@halifax.ks.uiuc.edu Fri Mar 5 16:05:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 125M5e8s000989; Fri, 5 Mar 2021 16:05:40 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 125M5e1v000988; Fri, 5 Mar 2021 16:05:40 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 125M5dQa000983; Fri, 5 Mar 2021 16:05:39 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 125M5dJZ000982; Fri, 5 Mar 2021 16:05:39 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 125M5TBh000973 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 5 Mar 2021 16:05:30 -0600 (CST) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 125M45rO028542 for ; Fri, 5 Mar 2021 22:05:29 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qk1-f178.google.com (mail-qk1-f178.google.com [209.85.222.178]) by mx0a-00007101.pphosted.com with ESMTP id 372f6qs9ua-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 05 Mar 2021 22:05:29 +0000 Received: by mail-qk1-f178.google.com with SMTP id z190so3559246qka.9 for ; Fri, 05 Mar 2021 14:05:29 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=r0JgPIzO2DlhaKPBviUv9BlH+Zm8FSweC7lzp99aUVg=; b=mJyXzLY5XeJxfg+63lOe+NfzfJ6HP8b+PUgXQfvtLD7gRqPjo8sW6rXbRNAXxWcXbp y7TNP9nyvU9nanQ+n4BFhzni1Z7DgWoXvuxRSJnWcRkj5OG+N/uO3zza3Z98M0E65vlN wtlLcjl2Q90rnKRFlzJz2w0JM5l+js/HO1VKUKTYG8aqM4C4wh0YCAqWLJ6JoCqg0Vfk XvnKAL1bSeSt4qgz1m2B7DYzengz+fKXePvyEnbHEalN/trwN8x16iPcG21B8rOQZNE8 D82ETRUBSIUGXCBiylQiWtt6r1KLyeLi1bR5/fclyEV4uQ5M+E3ZEFGMneRywKA4vKN8 k/7w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=r0JgPIzO2DlhaKPBviUv9BlH+Zm8FSweC7lzp99aUVg=; b=chRrPx4RjJbrjqqEXcYLw7XrWj/8je7tIZ96dMkifOVT9bBjV/3UtJhJVcERkIFctQ tibkKxcDAjlo0c7peLbzEj3lvyhTV9RlgeJq6hc7FowpyNPyLIi6pStRguXKtENOeZpI icPFt9yU6PIJPj3vYXOVazn17Tv7UrlhpmAwtsO3Lb+RN7NnHEy/FDDeaWQXMO0et3KP NMok48zv+UqvlC3Knf1n1P7Mo0zDx9GoHoZqxJnFOZ0tGwfbxvd3ICac6hqM2F8rFRB7 eH63V5HPE30e3Ct1fA5fMwtoBkkE2sSn2NVihgmY+rj2A5N4w1gPGdKPRZJzOff8fHHL pn2A== X-Gm-Message-State: AOAM531uhk8Uj/g4/u9tOCaZXK8RPcUOqlUfMrB9UFL/Pnnek9jtSRDk DtuGD5Em1r2lNMdVzSs1xnCeZ5nExad8Ow== X-Google-Smtp-Source: ABdhPJz1wZUWtgff2xX7QKdqviNiCOw7pHVqBDAIB+ohHzKHOqTxMY9+y+WnfANco6iTxao+MEHbgA== X-Received: by 2002:ae9:c00e:: with SMTP id u14mr10896342qkk.482.1614981927682; Fri, 05 Mar 2021 14:05:27 -0800 (PST) Received: from [192.168.1.34] ([181.64.230.253]) by smtp.gmail.com with ESMTPSA id l186sm2674424qke.92.2021.03.05.14.05.25 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Fri, 05 Mar 2021 14:05:26 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 05 Mar 2021 17:05:22 -0500 Subject: namd-l: Placed random molecules into Box From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: Thread-Topic: Placed random molecules into Box Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3697808725_487474133" X-CLX-Response: 1TFkXGxwSEQpMehcZGRsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGBsdEQpDWRcZGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseEnEYExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdaB3x6HUUZcH1nYG5rX3xCXFMeSEtwTE8HGGx4GWFzfREKWFwXHwQaBBgYHwUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JPbwVvEQpNXBcbHRoRCkxaF2xpTU1rEQpMRhdva2tra2s RCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBBsdEhEKQl4XGxEKRF4XGBEKQlwXGxEKXk 4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY 1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXZR4dUHt7H3lP X3kRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdpYBl/QUZrSF5dUhEKWUsXExkZHBE KcGgXZklGa1p5ewFFHWEQGRoRCnBoF2lucAVGQxxaZlxhEBsYHREKcGgXbE5hTx1bEl1ibQEQGR oRCnBoF21MHGdLRX4Bb2FnEBkaEQpwaBdhAWFlcm1GX1h5cxAZGhEKcGwXekdAaxhZeX8eG0gQG RoRCnBDF3oZR3tmfFlGZWcdEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 priorityscore=331 lowpriorityscore=0 clxscore=168 impostorscore=0 phishscore=0 mlxlogscore=415 mlxscore=0 bulkscore=0 suspectscore=0 spamscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103050112 domainage_hfrom=9336 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3697808725_487474133 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear namd users,=20 =20 I=E2=80=99ve a questions:=20 =20 I have a system that is an membrane protein solvated and ionized, an like a= dd ligand placed random in extracellular side to an given concentration (10 = micromolar):=20 =20 Q1: How can calculate number of ligands to add into given concentration?=20 Q1: How placed ligand random ?=20 =20 =20 Best,=20 =20 Geo.=20 --B_3697808725_487474133 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear namd u= sers,

 

I=E2=80=99ve a questions:

 

I have a system that is an membrane protein solvated a= nd ionized, an like add ligand placed random in extracellular side to an giv= en concentration (10 micromolar):

<= span style=3D'font-size:11.0pt'> 

Q1: How can calculate number of ligands to a= dd into given concentration?

Q1: How placed ligand random ?

 =

 

Best,

 <= /span>

Geo. =

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boundary="_000_BY3PR09MB81316D2329C4B0EEEAC5C20CF6969BY3PR09MB8131namp_" MIME-Version: 1.0 X-OriginatorOrg: llnl.gov X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BY3PR09MB8131.namprd09.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 790324b5-c334-4da3-bfab-08d8e02e8ab2 X-MS-Exchange-CrossTenant-originalarrivaltime: 05 Mar 2021 23:29:37.2226 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: a722dec9-ae4e-4ae3-9d75-fd66e2680a63 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 1OIHbkzprfqhS7rbTB/yReILHoFVGWT5laAnVoWHxM2RqA6YbbR/3iKyfa+X/cJCzbocF1zRYGR1Gr961quzXQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SJ0PR09MB6208 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGB4ZEQpMehcdGhEKWUQXYW4aQk18Y3pgQEARClhYF2lpY0weUEtnQR5 cEQp4ThdnemMSQEQeWWtGHREKeUwXYFhgb18dGB1mWGgRCkNIFwcZGBwRCkNZFx8RCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYYGBlxGxwTEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF1kecktpE1NgcGRZcB1fYn5PeHN5ZXl6fhJlS1xtbXJhEQpYXBcfBBoEGBgfBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXck9tZAURCk1cFxscHxEKTFoXaWhpTU1rEQpMRhdvb2trbGt rEQpCTxdpSBlJS1lYaUdMRREKQ1oXGxgSBBsfBBseGQQbEhkRCkJeFxsRCkReFxgRCkJcFxsRCl 5OFxsRCkJLF2d6YxJARB5Za0YdEQpCSRdnemMSQEQeWWtGHREKQkUXZXAbck8YTWleWU4RCkJOF 2d6YxJARB5Za0YdEQpCTBdpaWNMHlBLZ0EeXBEKQmwXZl5dRGlBQmRIb1wRCkJAF2dfGFNIQX99 QV5YEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUMXYBNne1IZYksSSEERCnBnF21HYWt NYxlMU2luEBoRCnBoF29kGGBCaBN/Z1oSEBoRCnBoF2dIQ1xtb2lQcm9JEBoRCnBoF2dbZEsSWG 9ZckABEBoRCnBoF20fe1NfUGxuWBgcEBoRCnBoF3peBV5DAXgcHFx5EB0ZEQpwZxdoZ3MFcB1ye l9haBAaEQpwZxdpQ25QAVlzRwEeUxAaEQpwbBdkf25rTG1AQHteHRAZGhEKcEMXbV5rZhhCTERD XWkQGxsSEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 spamscore=0 impostorscore=0 mlxscore=0 lowpriorityscore=0 priorityscore=70 suspectscore=0 mlxlogscore=704 bulkscore=0 phishscore=0 clxscore=243 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103050121 X-Spam-Score: 0 X-Spam-OrigSender: bennion1@llnl.gov X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Bennion, Brian" --_000_BY3PR09MB81316D2329C4B0EEEAC5C20CF6969BY3PR09MB8131namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable mole fractions are probably the best thing to use. You might be able to le= arn how the psfgen plugin in vmd replaces water with ions in a random way..= --_000_BY3PR09MB81316D2329C4B0EEEAC5C20CF6969BY3PR09MB8131namp_-- From owner-namd-l@halifax.ks.uiuc.edu Sat Mar 6 02:12:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1268CdtX013132; Sat, 6 Mar 2021 02:12:39 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1268CdZv013131; Sat, 6 Mar 2021 02:12:39 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1268CcQV013126; Sat, 6 Mar 2021 02:12:38 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1268Ccg7013125; Sat, 6 Mar 2021 02:12:38 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1268CO9m013112 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000009450eb05bcd9c268" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBkSEQpMehccEx0RCllEF29HYBkeHE0ZYFxOEQpYWBdnTEcdHnlhXHA SbBEKeE4XY1Nja3sTWH4aX14RCnlMF2FoWGhtWhpbBRkTEQpDSBcHGR4dEQpDWRcHGx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYYGxJxGRoaEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0xjH2t7e1tLclJ6bx1ebk15cGdsH39vcEB/QlNiHkJeEQpYXBcfBBoEGBgf BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXck9kHm4RCk1cFxsTEhEKTFoXfGlNUmsRCkVZF2gRCkx fF3oFBQUFBQUFBQVSEQpNThdpaxEKTEYXb2tra2trEQpCTxdofUFgQ1p9c0dBExEKQ1oXGBoTBB IfBBsYEgQeEhEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdpRn9AGlpmTmtEHBEKQk4XY1Nja3sTWH4aX14RCkJMF2dMRx0eeWFccBJsEQpCbBdg bElSaFB/GEIeWREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCllLFxMZGR0RCnBoF21vaVx JS3MSHx1wEBkaEQpwaBdnW1xaW0NoWVJ/eBAZGhEKcGgXYkxaaWdpb11yG2MQGRoRCnBoF2gZTm BmQkRhaUB+EBkaEQpwaBdnWVJhW2ljG2JNUBAZGhEKcH0XYmJ+e09kZXpceUEQGRoRCnB/F2BsZ kZ8eWNTchprEBsYGBEKcF8XZ0Qfa0hAWGYaH1gQGRoRCnBsF2IBfV9hXHlsQhNuEBkaEQptfhcb EQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 lowpriorityscore=0 adultscore=0 mlxlogscore=513 spamscore=0 priorityscore=697 suspectscore=0 clxscore=238 bulkscore=0 phishscore=0 impostorscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103060050 domainage_hfrom=9337 X-Spam-Score: 0 X-Spam-OrigSender: soumadwipghosh@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, soumadwip ghosh --0000000000009450eb05bcd9c268 Content-Type: text/plain; charset="UTF-8" Hi folks. I have done steered MD simulation of DNA+mspa to calculate the average electrostatic potential of the system. However, we need to add the applying external field (120 mV in this case) to get the complete electrostatic potential. It is also the first step to study accelerated translocation (grid-steered MD) of DNA through the pore under applied external field. I have followed the NAMD tutorial below: http://bionano.physics.illinois.edu/sites/default/files/nanopore-protocols.pdf . I am applying the following command: ../grid/gridExternalForce electric_raw.dx 0.02585 1.2 electric.dx (you can find the procedure on page # 25 of the tutorial attached) . But it is not working since the script is a .C script and I am unable to compile it properly. Have you run this utility before and help me troubleshoot this? I tried using gcc for compilation but to no use. Could someone provide some insights into how to make it work? Soumadwip Ghosh --0000000000009450eb05bcd9c268 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi folks.

=C2=A0

I have done steered MD simulation of DNA+mspa to calculate the average electrostatic potential of the system. However, we need to add = the applying external field (120 mV in this case) =C2=A0to get the complete electrostatic potential. It is also the first step to study accelerated translocation (grid-steered MD) of DNA through the pore under applied exter= nal field. I have followed the NAMD tutorial below:

http://bionano.physics.illinois.edu/sites/default/files/nanopore-p= rotocols.pdf.=C2=A0I am applying the following command:

=C2=A0../grid/gridExternalFor= ce electric_raw.dx 0.02585 1.2 electric.dx (you can find the procedure on page # 25 of the tutorial attach= ed) . But it is not working since the script is a .C script and I am unable to compile it properly. Have you run this utility before and help me troublesh= oot this? I tried using gcc for compilation but to no use.

=C2=A0

Coul= d someone provide some insights into how to make it work?=C2=A0

Soumadwip Ghosh

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charset="UTF-8" Hi folks. I have done steered MD simulation of DNA+mspa to calculate the average electrostatic potential of the system. However, we need to add the applying external field (120 mV in this case) to get the complete electrostatic potential. It is also the first step to study accelerated translocation (grid-steered MD) of DNA through the pore under applied external field. I have followed the NAMD tutorial below: http://bionano.physics.illinois.edu/sites/default/files/nanopore-protocols.pdf . I am applying the following command: ../grid/gridExternalForce electric_raw.dx 0.02585 1.2 electric.dx (you can find the procedure on page # 25 of the tutorial attached) . But it is not working since the script is a .C script and I am unable to compile it properly. Have you run this utility before and help me troubleshoot this? I tried using gcc for compilation but to no use. Could someone provide some insights into how to make it work? Soumadwip Ghosh --00000000000076576f05bcd9c640 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi folks.

=C2=A0

I have done steered MD simulation of DNA+ms= pa to calculate the average electrostatic potential of the system. However,= we need to add the applying external field (120 mV in this case) =C2=A0to = get the complete electrostatic potential. It is also the first step to stud= y accelerated translocation (grid-steered MD) of DNA through the pore under= applied external field. I have followed the NAMD tutorial below:

http://bionano.physics.illinois.= edu/sites/default/files/nanopore-protocols.pdf.=C2=A0I am applying the following command:

= =C2=A0../grid/gridExternalForce electric_raw= .dx 0.02585 1.2 electric.dx (you can find the procedure on page # 25 of the= tutorial attached) . But it is not working since the script is a .C script= and I am unable to compile it properly. Have you run this utility before a= nd help me troubleshoot this? I tried using gcc for compilation but to no= =C2=A0use.

= =C2=A0

Could someone provi= de some insights into how to make it work?=C2=A0

Soumadwip Gho= sh


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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear NAMD Community, I was attempting to use NAMD3 alpha7 MultiGPU version but keep bumping into= errors. My system has Ubuntu 20.04 LTS with CUDA 11.2 and three GTX 1050 T= i GPUs (Pascal architecture). I can run the NAMD conf file NAMD3 alpha8 SingleGPU (with "CUDASOAintegrate= on" + "margin 4") as well as NAMD 2.14 (both, "CUDASOAintegrate on" and "m= argin 4" deleted from conf file) without any errors. However, when trying t= o run the same input file with multiGPU flavor, I keep bumping into errors.= So, I guess this is a problem with the specific NAMD flavor. When I used 3 GPUs and 3 cores "namd3 +p3 +devices 0,1,2 ",= I get error as appended below. The same error appears if use "+p2" with di= fferent combinations of +devices arguments (0,1 or 0,2 or 1,2). I was wondering if I am doing it the right way or this has something to do = with the old architecture of my GPUs. Thanks in advance for help. Regards, Raman PS: A few lines (at the end) in the console are: Info: Startup phase 2 took 0.0116317 s, 0 MB of memory in use Info: Startup phase 3 took 7.2254e-05 s, 0 MB of memory in use Info: Startup phase 4 took 0.000177379 s, 0 MB of memory in use Info: Startup phase 5 took 3.4625e-05 s, 0 MB of memory in use Info: PATCH GRID IS 9 (PERIODIC) BY 2 (PERIODIC) BY 1 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file step4_equilibration.vel Info: REMOVING COM VELOCITY -0.0219164 -0.0463273 -0.043283 Info: LARGEST PATCH (10) HAS 2867 ATOMS Info: TORUS A SIZE 1 USING 0 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0113036 s, 0 MB of memory in use Info: Use 3D box decompostion in PME FFT. Info: PME using 1 x 1 x 1 pencil grid for FFT and reciprocal sum. Info: Startup phase 7 took 0.000145019 s, 0 MB of memory in use Info: Updated CUDA force table with 4096 elements. Info: Updated CUDA LJ table with 704 x 704 elements. Info: Updated CUDA force table with 4096 elements. Info: Updated CUDA LJ table with 704 x 704 elements. Info: Startup phase 8 took 0.0145335 s, 0 MB of memory in use Info: Startup phase 9 took 7.8326e-05 s, 0 MB of memory in use Info: Startup phase 10 took 3.0677e-05 s, 0 MB of memory in use Info: Startup phase 11 took 0.00250443 s, 0 MB of memory in use LDB: Central LB being created... Info: Startup phase 12 took 0.00139309 s, 0 MB of memory in use Info: CREATING 394 COMPUTE OBJECTS CUDANBOND[0]: Allocating patch data structure with 12 patches! CUDANBOND[1]: Allocating patch data structure with 12 patches! Info: Found 564 unique exclusion lists needing 21824 bytes Info: Found 564 unique exclusion lists needing 21824 bytes Info: useSync: 0 useProxySync: 0 Info: Startup phase 13 took 0.0858623 s, 0 MB of memory in use Info: Startup phase 14 took 7.2114e-05 s, 0 MB of memory in use Info: Startup phase 15 took 3.5726e-05 s, 0 MB of memory in use Info: Finished startup at 11.7413 s, 0 MB of memory in use TCL: Running for 25000000 steps FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_= bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUD= AKernel.cu, function buildRattleLists, line 4461 on Pe 0 (raman device 0 pci 0:3:0): invalid device function FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_= bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUD= AKernel.cu, function buildRattleLists, line 4461 on Pe 0 (raman device 0 pci 0:3:0): invalid device function [Partition 0][Node 0] End of program --_000_BMXPR01MB352673D7A7AEECDB77F955E0B39C9BMXPR01MB3526INDP_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear NAMD Community,

I was attempting to use NAMD3 alpha7 MultiGPU version but keep bumping into= errors. My system has Ubuntu 20.04 LTS with CUDA 11.2 and three GTX 1050 T= i GPUs (Pascal architecture).

I can run the NAMD conf file NAMD3 alpha8 SingleGPU (with &qu= ot;CUDASOAintegrate on" + "margin 4") as well as NAMD 2.14&n= bsp;(both, "CUDASOAintegrate on" and "margin 4" deleted= from conf file) without any errors. However, when trying to run the same input = file with multiGPU flavor, I keep bumping into errors. So, I guess this is = a problem with the specific NAMD flavor.

When I used 3 GPUs and 3 cores "namd3 +p3 +devices 0,1,2 <NAMD conf= file>", I get error as appended below. The same error appears if u= se "+p2" with different combinations of +devices arguments (0,1 o= r 0,2 or 1,2). 

I was wondering if I am doing it the right way or this has something to do = with the old architecture of my GPUs.

Thanks in advance for help.

Regards,
Raman

PS: A few lines (at the end) in the console are:
Info: Startup phase 2 took 0.0116317 s, 0 MB of memory in use
Info: Startup phase 3 took 7.2254e-05 s, 0 MB of memory in use
Info: Startup phase 4 took 0.000177379 s, 0 MB of memory in use
Info: Startup phase 5 took 3.4625e-05 s, 0 MB of memory in use
Info: PATCH GRID IS 9 (PERIODIC) BY 2 (PERIODIC) BY 1 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file step4_equilibration.vel
Info: REMOVING COM VELOCITY -0.0219164 -0.0463273 -0.043283
Info: LARGEST PATCH (10) HAS 2867 ATOMS
Info: TORUS A SIZE 1 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0113036 s, 0 MB of memory in use
Info: Use 3D box decompostion in PME FFT.
Info: PME using 1 x 1 x 1 pencil grid for FFT and reciprocal sum.
Info: Startup phase 7 took 0.000145019 s, 0 MB of memory in use
Info: Updated CUDA force table with 4096 elements.
Info: Updated CUDA LJ table with 704 x 704 elements.
Info: Updated CUDA force table with 4096 elements.
Info: Updated CUDA LJ table with 704 x 704 elements.
Info: Startup phase 8 took 0.0145335 s, 0 MB of memory in use
Info: Startup phase 9 took 7.8326e-05 s, 0 MB of memory in use
Info: Startup phase 10 took 3.0677e-05 s, 0 MB of memory in use
Info: Startup phase 11 took 0.00250443 s, 0 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 12 took 0.00139309 s, 0 MB of memory in use
Info: CREATING 394 COMPUTE OBJECTS
CUDANBOND[0]: Allocating patch data structure with 12 patches!
CUDANBOND[1]: Allocating patch data structure with 12 patches!
Info: Found 564 unique exclusion lists needing 21824 bytes
Info: Found 564 unique exclusion lists needing 21824 bytes
Info: useSync: 0 useProxySync: 0
Info: Startup phase 13 took 0.0858623 s, 0 MB of memory in use
Info: Startup phase 14 took 7.2114e-05 s, 0 MB of memory in use
Info: Startup phase 15 took 3.5726e-05 s, 0 MB of memory in use
Info: Finished startup at 11.7413 s, 0 MB of memory in use

TCL: Running for 25000000 steps
FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_sto= rage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/Sequenc= erCUDAKernel.cu, function buildRattleLists, line 4461
 on Pe 0 (raman device 0 pci 0:3:0): invalid device function
FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_sto= rage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/Sequenc= erCUDAKernel.cu, function buildRattleLists, line 4461
 on Pe 0 (raman device 0 pci 0:3:0): invalid device function
[Partition 0][Node 0] End of program



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To: "namd-l@ks.uiuc.edu" Message-ID: Thread-Topic: N-glycosylation bond not view after patching Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3697985731_1376435401" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMaEQpMehcZHh8RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGxIaEQpDWRcHGx8fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxxgenltYUtMHVtZelMaGHJkTnN7aWR+dXx5QF1bU2FTEQpYXBcfBBoEGBgf BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JPXWdQEQpNXBcbGxsRCkxaF2hpTU1rEQpMRhdva2t ra2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBBscExEKQl4XGxEKRF4XGBEKQlwXGx EKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQ k4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXeltncGxz flBMWxIRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdvTF9OGBN8eWB+RREKWUsXExk ZEhEKcGgXaGdAch1nXmFnHxoQGRoRCnBoF2BOaGJaeGQZfAFiEBkaEQpwaBdtHR1DX0dFHm5IeB AZGhEKcGgXbUJLE0B4QX1sZGMQGRoRCnBoF25AElxjRBlQZnIBEBkaEQpwbBd6R0BrGFl5fx4bS BAeEhEKcEMXZnpHe2Z/XWZwbmAQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=83 mlxlogscore=759 lowpriorityscore=0 spamscore=0 clxscore=190 malwarescore=0 priorityscore=345 impostorscore=0 bulkscore=0 suspectscore=0 phishscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103070128 domainage_hfrom=9338 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3697985731_1376435401 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear namd users,=20 I have generated the PSF file for my system, patching the N-glycosylation a= s follows:=20 patch NGLB PROA:343 CARA:1=20 Where PROA is my protein and CARA is the sugar.=20 My script for building the PSF runs perfectly with no errors, but when I op= en the new PSF and PDB files I cannot see the bond between the protein and t= he sugar. I noticed that the correct Hydrogen and Oxygen atoms have been del= eted, but somehow the bond is not there.=20 Has anyone else have an issue like this before? Am I missing something?=20 My script :=20 =20 ;# Script for generate topology if {1} { package require psfgen=20 =20 ;# Fix topology=20 topology ../../toppar_c36_jul20/top_all36_prot.rtf topology ../../toppar_c36_jul20/top_all36_na.rtf topology ../../toppar_c36_jul20/toppar_water_ions.str topology ../../toppar_c36_jul20/top_all36_lipid.rtf=C2=A0 ; ## lipids=20 topology ../../toppar_c36_jul20/top_all36_carb.rtf=20 topology ../../toppar_c36_jul20/stream/carb/toppar_all36_carb_glycopeptide.= str=20 } =20 ;# Protein select=C2=A0=C2=A0=20 mol new step1_pdbreader.pdb type pdb waitfor all set sel [atomselect top "protein"] set segnames [lsort -unique [$sel get segname]] foreach segname $segnames { =C2=A0=C2=A0=C2=A0 puts "Adding protein segname $segname to psfgen" =C2=A0=C2=A0=C2=A0 #pdbalias residue HIS HSD =C2=A0=C2=A0=C2=A0 #pdbalias residue CYSP CYS=20 =C2=A0=C2=A0=C2=A0=C2=A0pdbalias atom ILE CD1 CD =C2=A0=C2=A0=C2=A0 set seg ${segname}=20 =C2=A0=C2=A0=C2=A0=C2=A0set sel [atomselect top "protein and segname $segname"] =C2=A0=C2=A0=C2=A0 $sel set segid $seg=20 =C2=A0=C2=A0=C2=A0=C2=A0$sel writepdb tmp.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0segment $seg {pdb tmp.pdb} =C2=A0=C2=A0=C2=A0 #regenerate dihedrals=C2=A0=20 =C2=A0=C2=A0=C2=A0=C2=A0coordpdb tmp.pdb $seg=20 =C2=A0=C2=A0=C2=A0=C2=A0guesscoord=C2=A0=C2=A0 ;## adiciona, H, y algunos atomos perdidos.=20 }=C2=A0=C2=A0=C2=A0=20 =20 if {1} { ;# Glycan select=C2=A0=C2=A0=20 set sel [atomselect top "hetero and not protein"] set segnames [lsort -unique [$sel get segname]] foreach segname $segnames { =C2=A0=C2=A0=C2=A0 puts "Adding glycan segname $segname to psfgen" =C2=A0=C2=A0=C2=A0 pdbalias residue ANE ANE5AC=C2=A0=C2=A0 ; ## carbohydrates =C2=A0=C2=A0=C2=A0 pdbalias residue BGL=C2=A0 BGLCNA=C2=A0=C2=A0 ; ## carbohydrates =C2=A0=C2=A0=C2=A0 #pdbalias residue BGL NGLA=20 =C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue AMA=C2=A0 AMAN=C2=A0=C2=A0=20 =C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue BMA=C2=A0 BMAN=20 =C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue BGA=C2=A0 BGAL=20 =C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue AFU=C2=A0 AFUC =C2=A0=C2=A0=C2=A0 pdbalias residue AGA=C2=A0 AGALNA =C2=A0=C2=A0=C2=A0 set seg ${segname} =C2=A0=C2=A0=C2=A0 set sel [atomselect top "hetero and not protein and segname $segname= "] =C2=A0=C2=A0=C2=A0 $sel set segid $seg =C2=A0=C2=A0=C2=A0 $sel writepdb tmp.pdb =C2=A0=C2=A0=C2=A0 segment $seg {pdb tmp.pdb} =C2=A0=C2=A0=C2=A0 coordpdb tmp.pdb $seg=20 =C2=A0=C2=A0=C2=A0=C2=A0#regenerate angles=20 =C2=A0=C2=A0=C2=A0=C2=A0guesscoord=C2=A0=C2=A0 ;## adiciona, H, y algunos atomos perdidos.=20 } } =20 if {0} {=20 ##; Patching Disulfide bonds=20 patch DISU PROA:131 PROA:166=20 patch DISU PROA:291 PROA:301=20 }=20 =20 ##; Patching glycans ##; information was get from: step1_pdbreader_glycan.str charmm-gui=C2=A0=20 ##; forward=20 patch NGLB PROA:343 CARA:1=20 patch NGLB PROB:90 CARB:1 patch NGLB PROB:103 CARC:1 patch NGLB PROB:53 CARD:1 patch NGLB PROB:322 CARE:1 patch NGLB PROB:546 CARF:1=C2=A0=20 =20 ;# Escribiendo los output writepsf wildtype_top.psf ; # Output PSF writepdb --B_3697985731_1376435401 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear namd users,

I have generated the PS= F file for my system, patching the N-glycosylation as follows:

patch NGLB PROA:343 CARA:1

Where PROA is my protein a= nd CARA is the sugar.

My script for building the PSF runs = perfectly with no errors, but when I open the new PSF and PDB files I cannot= see the bond between the protein and the sugar. I noticed that the correct = Hydrogen and Oxygen atoms have been deleted, but somehow the bond is not the= re.

Has anyone else have an issue like this before? Am I m= issing something?

My script :

 

;# Script for generate topology

if {1} {

package require psfgen =

&nbs= p;

;# Fix = topology

topology ../../toppar_c36_jul20/top_all36_prot.rtf

topology ../../toppar_c36= _jul20/top_all36_na.rtf

topology ../../toppar_c36_jul20/toppar_water_ions.str

topology= ../../toppar_c36_jul20/top_all36_lipid.rtf=C2=A0 ; ## lipids =

topology ../../toppar_= c36_jul20/top_all36_carb.rtf

topology ../../toppar_c36_jul20/stream/carb/toppar_= all36_carb_glycopeptide.str

}

 

;# Protein select=C2=A0=C2=A0

mol new step1_pdbreader.pdb type pd= b waitfor all

set sel [atomselect top "protein"]

<= p class=3DMsoNormal>set segnames [lsort -unique= [$sel get segname]]

foreach segname $segnames {

=C2=A0=C2=A0=C2=A0 puts "Adding protein segn= ame $segname to psfgen"

=C2=A0=C2=A0=C2=A0 #pdbalias residue HIS HSD

=C2=A0=C2=A0=C2=A0 #pdbalias residue= CYSP CYS

=C2=A0=C2=A0=C2=A0=C2=A0pdbalias atom ILE CD1 CD

=C2=A0=C2=A0=C2=A0 set seg ${segname}

=C2=A0=C2=A0=C2=A0=C2=A0set sel [ato= mselect top "protein and segname $segname"]

<= p class=3DMsoNormal>=C2=A0=C2=A0=C2=A0 $sel set segid $seg =

=C2=A0=C2=A0= =C2=A0=C2=A0$sel writepdb tmp.pdb

=C2=A0=C2=A0=C2=A0=C2=A0segment $seg {pdb tmp.pdb}

=C2=A0=C2=A0=C2=A0 #regenerate dihed= rals=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0coordpdb tmp.pdb $seg

=C2=A0=C2=A0=C2=A0=C2=A0guesscoord=C2=A0=C2=A0 ;## adiciona, H, y algunos atomos perdidos.

}=C2=A0=C2=A0=C2=A0 <= /o:p>

 = ;

if {1} {=

;# G= lycan select=C2=A0=C2=A0

set sel [atomselect top "hetero and not protein"]

set segn= ames [lsort -unique [$sel get segname]]

foreach segname $segnames {

=C2=A0=C2=A0=C2=A0 puts "= Adding glycan segname $segname to psfgen"

=C2=A0=C2=A0=C2=A0 pdbalias residue ANE ANE5AC= =C2=A0=C2=A0 ; ## carbohydrates

=C2=A0=C2=A0=C2=A0 pdbalias residue BGL=C2=A0 BGLCNA=C2=A0=C2=A0 ; ## carbohydrat= es

=C2=A0= =C2=A0=C2=A0 #pdbalias residue BGL NGLA

=C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue AMA=C2=A0 AMAN=C2=A0=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0pdba= lias residue BMA=C2=A0 BMAN

=C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue BGA=C2=A0 BGAL

=C2=A0=C2=A0=C2=A0=C2=A0pdbalias residue= AFU=C2=A0 AFUC

=C2=A0=C2=A0=C2=A0 pdbalias residue AGA=C2=A0 AGALNA

=C2=A0=C2=A0=C2=A0 set seg ${segname}<= /span>

=C2=A0=C2=A0=C2=A0 set sel [= atomselect top "hetero and not protein and segname $segname"]=

=C2=A0=C2=A0=C2=A0 $s= el set segid $seg

=C2=A0=C2=A0=C2=A0 $sel writepdb tmp.pdb

=C2=A0=C2=A0=C2=A0 segment $seg {pdb tmp.pdb}<= /o:p>

=C2=A0=C2=A0=C2=A0 coo= rdpdb tmp.pdb $seg

=C2=A0=C2=A0=C2=A0=C2=A0#regenerate angles

=C2=A0=C2=A0=C2=A0=C2=A0guesscoord=C2=A0=C2=A0 ;## adiciona, H= , y algunos atomos perdidos.

}

}

 

if {0} {

##; Patching Disulfide bonds

patch DISU PROA:131 PROA:= 166

= patch DISU PROA:291 PROA:301

}

 

##; Patching glycans

##; information was get from: step1= _pdbreader_glycan.str charmm-gui=C2=A0

= ##; forward

patch NGLB PROA:343 CARA:1

patch NGLB PRO= B:90 CARB:1

patch NGLB PROB:103 CARC:1

patch NGLB PROB:53 CARD:1

=

patch NGLB PROB:322 CARE:1=

patc= h NGLB PROB:546 CARF:1=C2=A0

 

;# Escribiendo los output

writepsf wildtype_top.psf ; # Ou= tput PSF

writepdb

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cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Sun, 07 Mar 2021 21:33:15 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Mon, 08 Mar 2021 00:33:10 -0500 Subject: namd-l: NAMD and VMD on AMAZON instances From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: Thread-Topic: NAMD and VMD on AMAZON instances Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3698008394_573234248" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxISEQpMehcYExgRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGx8cEQpDWRcHGxoeEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwScR4dEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0NueX5TaBhgTRNoZxIcfl4cWXgHQxtjXhJhX1JDWVh7EQpYXBcfBBoEGBgf BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JPG18eEQpNXBcZHBEKTFoXbGlNTU0RCkxGF29ra2t raxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx0SEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hPHWFFcFlwBU0aEQpCT hdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2NpWW96Tx1yR09/EQpCQBdgZltcTW5S G2hDQBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2d+XBhZRXJoWhxaEQpZSxcTGRk TEQpwaBdiSFwdYU8fR1B4ExAZGhEKcGgXaU8SY1xzYR1nRWcQGRoRCnBoF2lucAVGQxxaZlxhEB sYGREKcGgXekdBWH0bbX9aTWwQGRoRCnBoF2dEe01vWBx9fGF9EBkaEQpwbBd6R0BrGFl5fx4bS BAbEhEKcEMXZnpHe2Z/XWZwbmAQHhIRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 bulkscore=0 adultscore=0 impostorscore=0 priorityscore=292 clxscore=188 malwarescore=0 suspectscore=0 phishscore=0 mlxlogscore=603 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103080027 domainage_hfrom=9339 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698008394_573234248 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear NAMD users,=20 =20 I=E2=80=99ve an system with 200K atoms and want purchase amazon instances, please= suggest me and instance for purchase. I like get 100 ns/day into this insta= nce.=20 =20 Suggest me best setup.=20 =20 Best,=20 =20 Geo.=20 --B_3698008394_573234248 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dea= r NAMD users,

 

I=E2=80=99ve an system with 200K atoms and want purchase amazo= n instances, please suggest me and instance for purchase. I like get 100 ns/= day into this instance.

 

Suggest me best setup.

 

Best,

 

Geo.

--B_3698008394_573234248-- From owner-namd-l@halifax.ks.uiuc.edu Mon Mar 8 03:12:11 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1289CB7l010030; Mon, 8 Mar 2021 03:12:11 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1289CBHA010029; Mon, 8 Mar 2021 03:12:11 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1289CArr010025; Mon, 8 Mar 2021 03:12:10 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1289CAfE010024; Mon, 8 Mar 2021 03:12:10 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1289BvZj009983 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000004096f005bd02d3c3" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxgZEQpMehcZGhMRCllEF2dGZ2F9ZG0TbkdNEQpYWBdrT29semAfW0k eHREKeE4XY1Nja3sTWH4aX14RCnlMF2dYWFBoXUVpG0NfEQpDSBcHGxIcEQpDWRcHGx8bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcYGHEbBh4edwYSHgYaBhoGHB0GGnEaEBp3BhoGBx8aBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdFG3geQFJyf1NvW2Z6aU14bRhi UFplT3tjYkhPHH5mXBEKWFwXHwQaBBgYHwUbGgQbGxoEHxoEGx4YEBseGh8aEQpeWRdyTx4dHhE KTVwXGxkeEQpMWhdsaU1raxEKTEYXb2tra2trEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBB gYGwQfGxEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eE QpCRRdrZwFLW0BASVBoEhEKQk4XY1Nja3sTWH4aX14RCkJMF2tPb2x6YB9bSR4dEQpCbBdkR1B/ a0t5RH0ZfxEKQkAXbkNMe2FYcB5Sf3kRCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGBEKeUM XZkdQXG96Ek4Ze20RCllLFxMZGRMRCnBoF2B6RWUZQ1pPH2ZBEAcZGhEKcGgXaFxnT09EQ1NkU3 sQBxkaEQpwaBdiS2waSVBsHRhnTRAHGRoRCnBoF2tQcBtOAQFAX01NEAcZGhEKcGgXZl5JS2xLR mwcHE8QBxkaEQpwbBdncFlha3NBW1MFRhAHGRoRCm1+FwcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxlogscore=268 lowpriorityscore=0 spamscore=0 clxscore=123 malwarescore=0 priorityscore=309 impostorscore=0 bulkscore=0 suspectscore=0 phishscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103080048 domainage_hfrom=9339 X-Spam-Score: 0 X-Spam-OrigSender: rabiulgazi876@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Rabiul Gazi --0000000000004096f005bd02d3c3 Content-Type: text/plain; charset="UTF-8" Dear Experts, I am dealing with a chlorobenzene derivative molecules water system. The system contains 10 molecules. After energy minimization it has been observed that lone pairs of chlorine atoms disconnected for few chlorobenzene derivative molecules. I am using NAMD2.14 for the water system . The psf files were built using psfgen 2.0. Please help me in this regard. Thank you. Rabiul --0000000000004096f005bd02d3c3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Experts,
I am dealing with a chlorobenzene deriva= tive molecules water system. The system contains 10=C2=A0 molecules. After = energy=20 minimization it has been observed that lone pairs of chlorine atoms=20 disconnected for few chlorobenzene derivative=C2=A0 molecules.=C2=A0=C2=A0<= /div>

I am using NAMD2.14 for the water system . The psf= files were built using psfgen 2.0.

Please hel= p me in=C2=A0this regard.

Thank you.
=C2=A0Rabiul
--0000000000004096f005bd02d3c3-- From owner-namd-l@halifax.ks.uiuc.edu Mon Mar 8 16:41:50 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 128MfoZ9025612; Mon, 8 Mar 2021 16:41:50 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 128MfoEY025611; Mon, 8 Mar 2021 16:41:50 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 128MfnMd025607; Mon, 8 Mar 2021 16:41:49 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 128Mfnbw025606; Mon, 8 Mar 2021 16:41:49 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 128MfgU8025592 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Hua Hao and Ren=C3=A9, I was not aware of that use of eABF in multiple-walker form in the tutorial. That is not a documented/supported feature, and there is a little work to properly combine the data. Anyway, I have just pushed a commit that partly reverts the previous one. What remains is that ABF files are written after sharing, so the plain ABF data should be the same for all replicas. Best regards, J=C3=A9r=C3=B4me On Mon, 1 Mar 2021 at 16:28, hua hao wrote: > Thanks, Abhishek. > > I try to do it, but the problem is still present. > > Abhishek Acharya =E4=BA=8E2021=E5=B9=B43=E6=9C= =881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81=93=EF= =BC=9A > >> Hi, >> >> Maybe you can try something like this. >> mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log >> >> Abhi >> >> >> Virus-free. >> https://urldefense.com/v3/__http://www.avast.com__;!!DZ3fjg!siwtr1uSfIo8= ipuBPVvVF31XUPzn788_H5Ti9srFIEyqK7nR6g9nqHn3M1GP7b8TFA$=20 >> >> <#m_-4492801418626280070_m_-498203762167974806_m_-5299850564915384101_m_= -7084929218411686926_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> On Mon, Jan 4, 2021 at 6:02 PM hua hao wrote: >> >>> Hi NAMD developers and users, >>> >>> I am learning Tutorial_QMMM_String_eABF recently, which was introduced >>> to be an advanced tutorial for QMMM in NAMD page ( >>> http://www.ks.uiuc.edu/Research/qmmm/). >>> >>> When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl >>> +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessa= ry >>> files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only >>> present in the first replica (i..e 0), but not in other replicas (i.e. >>> 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above >>> calculations, and these packages were both complied using openmpi-3.1.4 >>> build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts >>> and Linux-x86_64-verbs, the error was still present. >>> >>> Normally, these files should appear in each replica. >>> >>> Could you help me with this issue? Thank you very much. >>> >>> *Hua Hao* >>> >>> --0000000000002ff33d05bd0e238e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Hua Hao and Ren=C3=A9,

I was not a= ware of that use of eABF in multiple-walker form in the tutorial. That is n= ot a documented/supported feature, and there is a little work to properly c= ombine the data.
Anyway, I have just pushed a commit that partly = reverts the previous one. What remains is that ABF files are written after = sharing, so the plain ABF data should be the same for all replicas.

Best regards,
J=C3=A9r=C3=B4me

<= div class=3D"gmail_quote">
On Mon, 1 M= ar 2021 at 16:28, hua hao <haohua0116@gmail.com> wrote:
Tha= nks, Abhishek.

I try to do it,=C2=A0= but the problem=C2=A0is still present.=C2=A0

Abhishek Acharya &l= t;abhi117acha= rya@gmail.com>=E4=BA=8E2021=E5=B9=B43=E6=9C=881=E6=97=A5 =E5=91=A8= =E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81=93=EF=BC=9A
Hi,

Maybe you can try= something like this.
mpiru= n -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log
<= div class=3D"gmail_default" style=3D"font-family:"times new roman"= ;,serif;font-size:small;color:rgb(0,0,0)">
Abhi

3D"" Virus-free. www.av= ast.com

On Mon, Jan 4, 2021 at 6:02 PM hua hao = <haohua0116@gm= ail.com> wrote:
=
Hi NAMD developers and users,

I am learning Tutorial_QMMM_String_= eABF recently, which was introduced to be an advanced tutorial for QMMM in = NAMD page (http://www.ks.uiuc.edu/Research/qmmm/).

When running the eABF job by "mpirun -n 28 namd2 += replicas 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it is str= ange that some necessary files with the suffix .grad, .count, .pmf, .zcount= , and .zgrad were only present in the first=C2=A0replica (i..e 0), but not = in other=C2=A0replicas (i.e. 1-13).=C2=A0NAMD-2.14 and=C2=A0NAMD-Gib-2020-1= 2-07=C2=A0were used to perform the above calculations, and these packages w= ere both complied using openmpi-3.1.4 build on Intel-icc. We also tried the= pre-compiled Linux-x86_64-netlrts and=C2=A0Linux-x86_64-verbs, the error w= as still present.

Normally, these files should appear in each= =C2=A0replica.

Could you help me with this issue? Thank yo= u very much.

Hua Hao

--0000000000002ff33d05bd0e238e-- From owner-namd-l@halifax.ks.uiuc.edu Mon Mar 8 17:21:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 128NLK1K028261; Mon, 8 Mar 2021 17:21:20 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 128NLKfj028260; Mon, 8 Mar 2021 17:21:20 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 128NLJFJ028256; Mon, 8 Mar 2021 17:21:19 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 128NLJFu028255; Mon, 8 Mar 2021 17:21:19 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 128NL9pU028246 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 8 Mar 2021 17:21:09 -0600 (CST) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 128NIQG8021066 for ; Mon, 8 Mar 2021 23:21:09 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 37403sr0n1-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 08 Mar 2021 23:21:08 +0000 Received: from [IPv6:2a02:810c:300:6724:1421:308c:77c9:b3b4] ([IPv6:2a02:810c:300:6724:1421:308c:77c9:b3b4]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 128NL4S5149131 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Tue, 9 Mar 2021 00:21:04 +0100 Subject: Re: namd-l: An running issue in eABF-replica calculations To: namd-l@ks.uiuc.edu Cc: Abhishek Acharya , hua hao References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <61971be9-e361-61a4-6c79-270b9047f83a@physik.uni-kl.de> Date: Tue, 9 Mar 2021 00:21:02 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.8.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------EC8F3C6FA4958CA2ACB9730B" Content-Language: de-DE X-Spam-Status: No, hits=5.956, tests=FREEMAIL_FORGED_REPLYTO=2.503,HELO_MISC_IP=0.001,HELO_NO_DOMAIN=1.443,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.001,T_REMOTE_IMAGE=0.01,URI_DOTEDU=1.999 X-Spam-Score: ***** (5.956) X-Spam-Flag: NO X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0YEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxkTHBEKQ1kXBxseEQpDXhcbGx EKXloXGxoYHhEKQ0kXGgQaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGHEcHxAadwYYGgYaEQpZX hdobnkRCklGF19DX0l1QkVZXk9OEQpDThdde0BvH3tLQnNzEmN9YWkbHxoebnIYWWZ+fkd5B0Vz fxEKWFwXHwQaBBgYHwUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdyTGxzaxEKTVwXHh8TEQpMWhd 4aVJNTREKRVkXaG9rEQpMXxd6BQUFBQUFBQUBBREKTU4XaBEKTEYXe2tka2sRCkJPF2xfbGZfcE xLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGBoRCkJeFxsRCkRJFxgRCkJFF2wdWHJFHxxHSQVuEQpCT hdkGkluenp4GmR9XBEKQkwXYGAbUhkdGBpScgURCkJsF2ZrYmQYWWJtSH5sEQpCQBdkQRJpEmdZ HBp6ThEKQlgXZ3Nlc0BuYWFMXWIRClpYFx8RCnlDF2cSYVkaaB1CXmVjEQpwZxdjXFBhG1JtaBx haRAaEQpwaBdsS3puGH1SbmAfARAZGhEKcGgXaB5heHlpGUMab0QQGRoRCnBoF2BzYGxCUmNNXF t6EBkaEQpwaBdlHGt5bXpNWEBrRhAZGhEKcGgXZHpBWm55U3xYa2wQGhEKcGcXbkB6fXtuZWdES BsQGhEKcH0Xb1NnfUNDSxlQHmYQGhEKcH0XZEkbXRIYUk9gchkQGhEKcGcXY0JJYmRkfVxCGB0Q GRoRCnB9F2BveGBDHB15RWgbEBoRCnB/F2Fmb1saZ2RCSB1bEBsYGxEKcF8XY2ISUEhjeB98Qn0 QEhMRCnB/F2VYchgdSRheRml8EBsaGREKcF8XZl8SeENmW3prBVoQGhEKcGwXeh94eW94TENfcE QQGRoRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 bulkscore=0 adultscore=0 impostorscore=0 priorityscore=0 clxscore=172 malwarescore=0 suspectscore=0 phishscore=0 mlxlogscore=999 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103080123 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------EC8F3C6FA4958CA2ACB9730B Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Thanks a lot J=C3=A9r=C3=B4me! To understand this correctly: * This means that when using MW-ABF the walkers are benefitting from each other (as gradient counts are shared, well reflected in the files) * but in case of MW-eABF sharing of eABF data is not (and was never?) shared (as it was not reflected in the files before and therefore also not internally?!) or do/did the walkers still benefit from each other? =C2=A0=C2=A0=C2=A0 * Then latest literature would be a bit mislead= ing when stating usage of MW-eABF. Best regards Ren=C3=A9 On 3/8/2021 11:41 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote: > Dear Hua Hao and Ren=C3=A9, > > I was not aware of that use of eABF in multiple-walker form in the=20 > tutorial. That is not a documented/supported feature, and there is a=20 > little work to properly combine the data. > Anyway, I have just pushed a commit that partly reverts the previous=20 > one. What remains is that ABF files are written after sharing, so the=20 > plain ABF data should be the same for all replicas. > > Best regards, > J=C3=A9r=C3=B4me > > On Mon, 1 Mar 2021 at 16:28, hua hao > wrote: > > Thanks,Abhishek. > > I try to do it,=C2=A0but the problem=C2=A0is still present. > > Abhishek Acharya >=E4=BA=8E2021=E5=B9=B43=E6=9C=881= =E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81=93=EF=BC= =9A > > Hi, > > Maybe you can try something like this. > mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout > output_eABF/%d/job00.log > > Abhi > > > Virus-free. https://urldefense.com/v3/__http://www.avast.com__;!= !DZ3fjg!t9PBDglPJzc1GGiBP9pEpxn_82qS0d5hkm7qYimFV1-3JVeXB8MiiVN0b_cL24JUSA$= =20 > > > > > On Mon, Jan 4, 2021 at 6:02 PM hua hao > wrote: > > Hi NAMD developers and users, > > I am learning Tutorial_QMMM_String_eABF recently, which > was introduced to be an advanced tutorial for QMMM in NAMD > page (http://www.ks.uiuc.edu/Research/qmmm/ > ). > > When running the eABF job by "mpirun -n 28 namd2 +replicas > 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it is > strange that some necessary files with the suffix .grad, > .count, .pmf, .zcount, and .zgrad were only present in the > first=C2=A0replica (i..e 0), but not in other=C2=A0replicas (= i.e. > 1-13).=C2=A0NAMD-2.14 and=C2=A0NAMD-Gib-2020-12-07=C2=A0were = used to > perform the above calculations, and these packages were > both complied using openmpi-3.1.4 build on Intel-icc. We > also tried the pre-compiled Linux-x86_64-netlrts > and=C2=A0Linux-x86_64-verbs, the error was still present. > > Normally, these files should appear in each=C2=A0replica. > > Could you help me with this issue? Thank you very much. > > *Hua Hao* > --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------EC8F3C6FA4958CA2ACB9730B Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Thanks a lot Jérôme!

To understand this correctly:

* This means that when using MW-ABF the walkers are benefitting from each other (as gradient counts are shared, well reflected in the files)

* but in case of MW-eABF sharing of eABF data is not (and was never?) shared (as it was not reflected in the files before and therefore also not internally?!) or do/did the walkers still benefit from each other?

    * Then latest literature would be a bit misleading when stating usage of MW-eABF.

Best regards

René

On 3/8/2021 11:41 PM, Jérôme Hénin wrote:
Dear Hua Hao and René,

I was not aware of that use of eABF in multiple-walker form in the tutorial. That is not a documented/supported feature, and there is a little work to properly combine the data.
Anyway, I have just pushed a commit that partly reverts the previous one. What remains is that ABF files are written after sharing, so the plain ABF data should be the same for all replicas.

Best regards,
Jérôme

On Mon, 1 Mar 2021 at 16:28, hua hao <haohua0116@gmail.com> wrote:
Thanks, Abhishek.

I try to do it, but the problem is still present. 

Abhishek Acharya <abhi117acharya@gmail.com>于2021å¹´3月1æ—¥ 周一上åˆ8:50写é“:
Hi,

Maybe you can try something like this.
mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log

Abhi

Virus-free. www.avast.com

On Mon, Jan 4, 2021 at 6:02 PM hua hao <haohua0116@gmail.com> wrote:
Hi NAMD developers and users,

I am learning Tutorial_QMMM_String_eABF recently, which was introduced to be an advanced tutorial for QMMM in NAMD page (http://www.ks.uiuc.edu/Research/qmmm/).

When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necessary files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only present in the first replica (i..e 0), but not in other replicas (i.e. 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above calculations, and these packages were both complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts and Linux-x86_64-verbs, the error was still present.

Normally, these files should appear in each replica.

Could you help me with this issue? Thank you very much.

Hua Hao

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="0000000000007b412f05bd3339b5" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBsdEQpMehcbHxgRCllEF2JgH2F9ekdpXxl/EQpYWBdkG1xLZh5PBR5 jGhEKeE4XYGx6Em4BGRwTZB0RCnlMF3pvfXlCGm5mSGJvEQpDSBcHGxwaEQpDWRcHGxIfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxMdcRsSHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdHfkFSWUMZWW0eWFtCZURna35tYUZlU1tAH2RfHl0eSBEKWFwXHwQaBBgY HwUbGgQbGxoEHxoEGx4YEBseGh8aEQpeWRdyTFhYHxEKTVwXGxEKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8XekxDSXNpeQFbQHsRCkNaFxgaEwQSHwQYGxoEHhkRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2BsehJuARkcE2QdEQpCSRdgbHoSbgEZHBNkHREKQkUXaxxSX2QfQktnRkERCkJOF2BsehJuA RkcE2QdEQpCTBdkG1xLZh5PBR5jGhEKQmwXZF9Ofn9oT0RFfm0RCkJAF2FpBWVsQntiQ2FHEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaV5lRBtmEgFhZRIRCllLFxsYGR4SEQpwaBd sfWEfAUFjaBtuWxAZGhEKcGgXZB96ZU9HGmVobUQQGRoRCnBoF2VhfUcabhsTbRNuEBkaEQpwaB dnUG1SXRtISF1MSxAZGhEKcGwXZE97c0JffkdATFgQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=690 spamscore=0 impostorscore=0 suspectscore=0 clxscore=217 bulkscore=0 lowpriorityscore=0 adultscore=0 phishscore=0 malwarescore=0 priorityscore=152 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103100089 domainage_hfrom=12348 X-Spam-Score: 0 X-Spam-OrigSender: sowaheed@mtu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Sodiq Waheed --0000000000007b412f05bd3339b5 Content-Type: text/plain; charset="UTF-8" Hello NAMD Users, I want to calculate the helical axis of an alpha-helix of a protein and I want to rotate that particular axis with respect to one of the domains of the protein. Is there a way to implement and perform this in NAMD? Thank you Sodiq --0000000000007b412f05bd3339b5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello NAMD Users,

I want to = calculate the helical axis of an alpha-helix of a protein and I want to rot= ate that particular=C2=A0axis with respect to one of the domains of the pro= tein. Is there a way to implement and perform this in NAMD?

<= /div>
Thank you
Sodiq
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Thu, 11 Mar 2021 08:21:42 -0800 (PST) Content-Type: text/plain; charset=utf-8 From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: Axis Definition in Metadynamics Date: Thu, 11 Mar 2021 11:21:32 -0500 Message-Id: <7A5A030D-7313-44A8-B8A5-FBAB73281A39@gmail.com> References: In-Reply-To: To: namd-l@ks.uiuc.edu, Sodiq Waheed X-Mailer: iPhone Mail (18B92) X-CLX-Response: 1TFkXGBobEQpMehcZHxoRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGRgSEQpDWRcHHhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhtxGxgTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF10bbV1sT31+H15Tb0VeQxJjR2xrTU5ARUF7bX5jbR9rEQpYXBcfBBoEGBgc BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXckwBTVARCk1cFx4fEQpMWhd8aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF21ScxJBW2lEEx5MEQpDWhcYGhMEEh8EGBsTBB 4SEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2ZLbVhGGE9jRUNAEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF29P ZEFaQlBtZmtZEQpCQBdlXmdMZ29vQUdPThEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnl DF3pgTGJhS0JTfE57EQpZSxcTGR4YEQpwaBdocF1gXHh+HWVlQRAZGhEKcGgXaR5ZW3pISFwTfU MQGRoRCnBoF2JEZ3xJeEZmBWxAEBkaEQpwbBdnaENrcxJ5GE1iXBAZGhEKcEMXYnwYWWZycFtwZ kQQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 bulkscore=0 impostorscore=0 mlxlogscore=838 mlxscore=0 adultscore=0 suspectscore=0 priorityscore=350 clxscore=201 phishscore=0 spamscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103110086 domainage_hfrom=9342 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 12BGLj5h007423 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Yes, you can applied torque using Tclforces. Search in NAMD tutorial there is an best example. Geo Enviado desde mi iPhone > El 10 mar. 2021, a la(s) 1:58 p. m., Sodiq Waheed escribió: > >  > Hello NAMD Users, > > I want to calculate the helical axis of an alpha-helix of a protein and I want to rotate that particular axis with respect to one of the domains of the protein. Is there a way to implement and perform this in NAMD? > > Thank you > Sodiq From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 11 18:43:33 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C0hXoc018145; Thu, 11 Mar 2021 18:43:33 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C0hXaP018144; Thu, 11 Mar 2021 18:43:33 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C0hW4D018140; Thu, 11 Mar 2021 18:43:32 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C0hWp4018139; Thu, 11 Mar 2021 18:43:32 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C0hMuU018129 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 11 Mar 2021 18:43:23 -0600 (CST) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12C0P2A5029826 for ; Fri, 12 Mar 2021 00:43:22 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=mvondoma@uci.edu; dkim=pass header.d=uci-edu.20150623.gappssmtp.com header.s=20150623 Received: from mail-oi1-f169.google.com (mail-oi1-f169.google.com [209.85.167.169]) by mx0b-00007101.pphosted.com with ESMTP id 3773gu6jkt-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 12 Mar 2021 00:43:22 +0000 Received: by mail-oi1-f169.google.com with SMTP id y131so22273205oia.8 for ; Thu, 11 Mar 2021 16:43:22 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=uci-edu.20150623.gappssmtp.com; s=20150623; h=mime-version:from:date:message-id:subject:to; bh=vuuMdV+lBt4jMa71k+dFVb8wSX6iuF/stDEtWsqSFIw=; b=D/JmFG1DG1jlCBGOfylm4AI7uzZKJp584SIhC/In11WMkHkVZ/gbRI1+q2qmh4Xo5f 4KA03fSLmGtZBqbXaBgp0u8okTIfGImNcaQiRRhO/0YlMtAPePqCT37WV3c4CX07u2TK 1yWZkUmqShIKUkdfmHNI91rTFRXMqbGKPN+KJZDhu1abHV1fKDzWAiBWF9hkEHp/uVZf B2WFUE5cik3fFV0bximfi/jhT6QnXCMYuIYLnA7jW/mqFHcKkwhuL7Urdh1/K9Or/UEf nLS2ZYEwVXLvO6u1hLZrah9/KV1eCDA8ShdZx9r5REJT37IwMl2mkbs4i6QGo/SXL0Qg UH0g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=vuuMdV+lBt4jMa71k+dFVb8wSX6iuF/stDEtWsqSFIw=; b=nA456r6wSe2TK7luMcpopyoyWz+3M0Uss6BFk1eJTSqaeBgRvOeBBVbd6i3XUVbnFm UbyarAZ9/qhWbPOmFcoPdESVV4MfDHPOj6CPILMptkHoiRxKrs7InUA/l401/YLboCNB Slo7rwSkjR7ZQ1NX0+lZoN6YkEpdKNeNTEwRyP3kRcguTeUspXs5LNHziZohIL9IuuOw XRS68HmzwgehCg1FBsOQlhEk8hHFZ4II+t0E/PcZiTc39rL8BqqlP8dNkKjShTGwEvDn 95N7OpaYikYi3+ydyR4+HH1dNB4KL7HaoN/CUcXn5kqmJJxdFn33Eod2EhRqMDr8zbqb uR3A== X-Gm-Message-State: AOAM533MeByaR+zq5fUo/2fjuSaGkU9jAY+LGNAvfHum0pmct4l4We+Z g88WF44zMjkmCxZK2UFQOdbOr5gcuAtApbvvEVERflWErKP/ X-Google-Smtp-Source: ABdhPJyz7IQxg6xRVsVpOOCAO7v0hst0oqBFoeTOb1U/cuUldRHLG2xvbXZTRKhLw/2soZGKesnnCA/p0A7aYFxgqXI= X-Received: by 2002:aca:578b:: with SMTP id l133mr8381286oib.96.1615509801521; Thu, 11 Mar 2021 16:43:21 -0800 (PST) MIME-Version: 1.0 From: Michael Von Domaros Date: Thu, 11 Mar 2021 16:42:23 -0800 Message-ID: Subject: namd-l: 3.0alpha9 CUDA version To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000d9e77005bd4c2f3d" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBgaEQpMehcaEQpZRBdkf2AffUBwZBwdfxEKWFgXZl5laFtDbXJ6aEI RCnhOF2QfUwFPXWNZeRoYEQp5TBdnT0l6f05sfWhMThEKQ0gXBxIbEQpDWRcHHB4RCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYYGhpxGxMdEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF19mYXBOG0cdUh5zYntlR1xgeH9AQEFlYWhDGUN1QUR+EQpYXBcfBBoEGBgcBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3JNbBlsEQpNXBcZEhMRCkxaF2xpTU1rEQpCTxdmTB9NaW1 BQB8TcxEKQ1oXGBoTBBIfBBscHQQbHBMRCkJeFxsRCkJFF2JYGFNkcHgdQl0dEQpCThdkH1MBT1 1jWXkaGBEKQkwXZl5laFtDbXJ6aEIRCkJsF2cbE1xmHl5pc3JaEQpCQBdrR31iR3t8aH1/GREKQ lgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2RGWh9uUlNSe15FEQpwaBdgYBl5b058Yl59ehAZGhEK cGgXYhwbch94c1h6f2AQGRoRCnBoF2NQRX9mZB5wRkIcEBkaEQpwaBdmYWhhRB1lW1IcHBAZGhE KcGgXYk1oc35+e0duRBIQGRoRCnBsF24fZUgFXUJFbm9eEBkaEQptfhcaEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=999 spamscore=0 impostorscore=0 suspectscore=0 clxscore=220 bulkscore=0 lowpriorityscore=0 adultscore=0 phishscore=0 malwarescore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120000 X-Spam-Score: 0 X-Spam-OrigSender: mvondoma@uci.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Von Domaros --000000000000d9e77005bd4c2f3d Content-Type: text/plain; charset="UTF-8" Hi everyone, It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or something even newer? not sure.) Is this absolutely necessary? I'm asking because our compute cluster is stuck with CUDA 10 and CUDA 10 compatible device drivers, because a pretty substantial software stack has been compiled against this version. The admins are somewhat hesitant to update the device drivers, because they don't think that running CUDA 10 apps with newer device drivers will be flawless. So, long story short: Could NAMD3 be compiled against CUDA 10? If so, is there any way to access the source code? As far as I can tell, only source codes for the 2.x series and nightly snapshots are available. Thanks a bunch, Michael --000000000000d9e77005bd4c2f3d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi everyone,

It appears that= the namd 3 alpha 9 builds now require CUDA 11.0 (or something even newer? = not sure.) Is this absolutely necessary? I'm asking because our compute= cluster is stuck with CUDA 10 and CUDA 10 compatible device drivers, becau= se a pretty substantial software stack has been compiled against this versi= on. The admins are somewhat hesitant to update the device drivers, because = they don't think that running CUDA 10 apps with newer device drivers wi= ll be flawless.

So, long story short: Could NAMD3 = be compiled against CUDA 10? If so, is there any way to access the source c= ode? As far as I can tell, only source codes for the 2.x series and nightly= snapshots are available.

Thanks a bunch,
Michael
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charset="utf-8" Content-ID: X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 234bf7ba-94bf-48d7-4848-08d8e4f60f00 X-MS-Exchange-CrossTenant-originalarrivaltime: 12 Mar 2021 01:27:53.6300 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: Dv+f9ctEk/8lCYdMbYDaTN1kyYr7bXVtzpZNBkEquny+lqwthwLnQ2SDThI7uSA3P7aMvaiCbDyxJ0Hfcmv9Jw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR12MB1223 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxsZGxEKQ1kXGxEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhseGXEfGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1QkVZX k9OEQpDThdMYBNFTkJSfmlZbUtgQxxLTGlwWB5+RW9Se24ZbFJgZxEKWFwXHwQaBBgYHAUbGgQb GxoEHxoEGx4bEBseGh8aEQpeWRdyTW1NGBEKTVwXGBIfEQpMWhd4aU1NTREKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxd6XnNBEk8baRxGcxEKQ1oXHhoEGxodBBsaGgQeGB EKQl4XGxEKRF4XGREKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCTBdvYVgTGktdG 0NBZREKQmwXYXkcHxJce09aaUIRCkJAF2FgEkhLUmZBGGhEEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXHxEKeUMXbEcaaVkdaX9TGmMRCllLFxsYGRweEQpwaBd6bRlOfk98UBNISBAZGhEKcGg XY1BFf2ZkHnBGQhwQHhIRCnBoF2QYRUBwWwFzGxwFEBkaEQpwaBdvUGkcbUNLeRIdaxAZGhEKcG gXYh1lEkBscG5ablIQGRoRCnB9F3pzfmZPHkN7SUdGEBkaEQpwfRdlS2dAT1Jvc2RvYBAZGhEKc H0Xa3ocYFMZGG9QRWAQGRoRCnB/F2BCU3pubVh6ZAETEBISEQpwXxdkW09zQUdDfVt5eBAZGhEK cH8Xax1rHlN7Z2NLbXoQGxsaEQpwXxduRER8QXgaZF5vexAZGhEKcH8Xbh9nXX1eQBN4ZHkQGxs dEQpwXxdkY2htHn1Qa0xQYBAZGhEKcGwXZ3gaQGIYSRp+eU0QGRoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 impostorscore=0 adultscore=0 lowpriorityscore=0 phishscore=0 mlxlogscore=999 spamscore=0 mlxscore=0 bulkscore=0 suspectscore=0 clxscore=163 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120006 domainage_hfrom=12364 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 12C1Rur1020750 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Hi Michael, I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the source from gitlab. https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!oGE0nGoRal7nV7lEzLdJsLjX376iV7WJNvSe9ZFp002XAcmFUzLWKQHR4L21njhdHA$ It is in the devel branch, and it tagged as 3.0a9. I have compilation instructions that are what I used (or at least what I think I used from memory) on github. https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!DZ3fjg!oGE0nGoRal7nV7lEzLdJsLjX376iV7WJNvSe9ZFp002XAcmFUzLWKQHR4L3sGWKUNA$ Compilation with NAMD3 from there is basically the same as it would be anywhere else. You need charm++ compiled, followed by NAMD itself. The hardest part for me was actually sorting out which of the many openMPI implementations installed on the cluster had the PMI backend so I could just call srun if I wanted to do replica exchange stuff. -Josh On 3/11/21 7:42 PM, Michael Von Domaros wrote: > Hi everyone, > > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or > something even newer? not sure.) Is this absolutely necessary? I'm > asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > compatible device drivers, because a pretty substantial software stack > has been compiled against this version. The admins are somewhat > hesitant to update the device drivers, because they don't think that > running CUDA 10 apps with newer device drivers will be flawless. > > So, long story short: Could NAMD3 be compiled against CUDA 10? If so, > is there any way to access the source code? As far as I can tell, only > source codes for the 2.x series and nightly snapshots are available. > > Thanks a bunch, > Michael -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!oGE0nGoRal7nV7lEzLdJsLjX376iV7WJNvSe9ZFp002XAcmFUzLWKQHR4L3lIBscZA$ From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 11 20:50:43 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C2ohDU024273; Thu, 11 Mar 2021 20:50:43 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C2ohhB024272; Thu, 11 Mar 2021 20:50:43 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C2ognc024268; Thu, 11 Mar 2021 20:50:42 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C2ogSR024266; Thu, 11 Mar 2021 20:50:42 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C2oYsB024255 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 11 Mar 2021 20:50:35 -0600 (CST) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12C2h4Zw016492 for ; Fri, 12 Mar 2021 02:50:34 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qv1-f49.google.com (mail-qv1-f49.google.com [209.85.219.49]) by mx0a-00007101.pphosted.com with ESMTP id 3775e57ewd-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 12 Mar 2021 02:50:34 +0000 Received: by mail-qv1-f49.google.com with SMTP id 30so3616616qva.9 for ; Thu, 11 Mar 2021 18:50:34 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=6qeQEi6PQYdKK84iSZqEZmkEumdReS0Y3akq3Ry8xic=; b=SUPGOX1R3DKIq/E2Cqs5OxDYnHuqDKMFVLRhUzxF1owvzuRux830be0ByAqfwIYN2G XiPoK/gSvw1yLvvCkFBqmoBZ2KhghUgDnogjhaco0u6EkpIi8iO3ukWcmZ4yd4kQPjAI BsyVnucZziha/mzg61wNM0MMYD/f8GekOdmb2pVZSgOGASXFYeL4E+RyedW/LN5QBep/ 7sRJhEhS9nDDFzo61emSObHb5oTawMoSaSHD1yALNhZwRNxfo0bfgPw/W+tL+Ncvsl7K oRpxiA06IKjw4W/wf/UemPT6h6ibssech8/RZrYg0FWl+OeRUkOBTLnQS1SK75S4DLMB mPLA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=6qeQEi6PQYdKK84iSZqEZmkEumdReS0Y3akq3Ry8xic=; b=RJlThhFVmx3PUIMZ1WhnyMsaUhHAQ/1x4yj6TOi5nkkpdTj0zUuBQcEQMhMHhJJXd4 BEWUVnMjEKko2xswNQ/8optzPnWyP9q6fe0m4NY8KtqOGnnU2eh6+B52mOPUWIGm4ZvQ yuRIaExuKq7dggg6qdt4a6hnqdm7lMfH96T03Ct6Po4MlBgI5Uj/gsF5R21u6ePkazoG gMcm+B2BcVxWoD5GKpDspzoxGqJAslfiQGYgf6kdhmt4xViQpez7WD5aUPR5spqOhstM OZeJQR52oA/f0u1fXq1itiXsb/02+R1a4HO7GGoYGZXMlz1e44NfEGtJlDdWTlv4Uczx Bn/w== X-Gm-Message-State: AOAM532B1yKPJNSFf2upAW9TSm+g6VyqNrTIz1UBBfgivJiWqS0e/g4T d1oh4BX2TiQGIB5dBh7DcDDrNope/YASQQ== X-Google-Smtp-Source: ABdhPJzyjxMygxbw+Z4WYpnTVKoKUamHk70UaAWQWf1MW9LZTLPFYLy1EZxP7+fwS0mdY7cxd3Mx/g== X-Received: by 2002:a0c:b66c:: with SMTP id q44mr10534717qvf.3.1615517432807; Thu, 11 Mar 2021 18:50:32 -0800 (PST) Received: from [192.168.1.44] ([181.64.230.110]) by smtp.gmail.com with ESMTPSA id q125sm3500022qkf.68.2021.03.11.18.50.31 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 11 Mar 2021 18:50:32 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 11 Mar 2021 21:50:28 -0500 Subject: namd-l: Ligand concentration From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: Thread-Topic: Ligand concentration Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3698344231_169665419" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwTEQpMehcZHh0RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHRMRCkNZFwcfGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseE3EZGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdmcnV5GHpCU0UZBxxQZHlEcHtIXhxdQ0hFUGhzGX57YREKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JNYl98EQpNXBcbHRIRCkxaF2hpTU1rEQpMRhdva2tra2s RCkJPF21ScxJBW2lEEx5MEQpDWhcYGhMEEh8EGBsTBB4TEQpCXhcbEQpEXhcYEQpCXBcbEQpeTh cbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU 2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2NpWW96Tx1yR09/EQpCQBdrc1plUxx5E2J8 cxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2RtZkRcQmQSBUV6EQpZSxcTGR4ZEQp waBdpb1ldHG9jf2hGfRAZGhEKcGgXb1BPSF4FWBIZR2AQGRoRCnBoF2JIXB1hTx9HUHgTEBkaEQ pwaBdrcGhZa18FGn5JbBAZGhEKcGgXaW5wBUZDHFpmXGEQGxgdEQpwbBd6R0BrGFl5fx4bSBAZG hEKcEMXbR1He2Z8HnxDaQUQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 phishscore=0 adultscore=0 lowpriorityscore=0 mlxscore=0 malwarescore=0 spamscore=0 bulkscore=0 mlxlogscore=432 clxscore=169 impostorscore=0 priorityscore=347 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120017 domainage_hfrom=9343 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698344231_169665419 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear namd users, How calculate number of ligand to placing into box with concentration of 100 mM? Best, Geo. --B_3698344231_169665419 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear namd u= sers,

 

How calculate number of ligand to placing into box with concentration of= 100 mM?

 

Best,

 

Geo.

--B_3698344231_169665419-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 11 20:54:00 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C2s0an025015; Thu, 11 Mar 2021 20:54:00 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C2s0ot025014; Thu, 11 Mar 2021 20:54:00 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C2rxW6025010; Thu, 11 Mar 2021 20:53:59 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C2rxwS025009; Thu, 11 Mar 2021 20:53:59 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C2rnJM024999 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000005fd31a05bd4e02cd" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBgZEQpMehcaEQpZRBdkf2AffUBwZBwdfxEKWFgXZl5laFtDbXJ6aEI RCnhOF2QfUwFPXWNZeRoYEQp5TBdnT0l6f05sfWhMThEKQ0gXBxkcHxEKQ1kXGxEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhgaGXEbGh0QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XXmV8eX1rYE5fYEBEdXpYThtuYGxbWAdLchJiWBtQH24RClhcFx8EGgQYGBwFGxoE GxsaBB8aBBseHxAbHhofGhEKXlkXck1iUnMRCk1cFx8fExEKTFoXeGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxd6TENJc2l5AVtAexEKQ1oXGBoTBBIfBBgbGgQfGBEKQl 4XGxEKREkXGBEKQkUXYlgYU2RweB1CXR0RCkJOF2QfUwFPXWNZeRoYEQpCTBdmXmVoW0NtcnpoQ hEKQmwXZxsTXGYeXmlzcloRCkJAF2FgEkhLUmZBGGhEEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxEK eUMXbEcaaVkdaX9TGmMRCnBoF2FlWx4fbxJHBVt4EBoRCnBoF29QaRxtQ0t5Eh1rEBkaEQpwaBd pYXl4b2NgQHNPWRAaEQpwaBdiHWUSQGxwblpuUhAaEQpwaBdvQEtMUxlSE35caRAaEQpwfRd6c3 5mTx5De0lHRhAaEQpwfRdlS2dAT1Jvc2RvYBAaEQpwfRdrehxgUxkYb1BFYBAZGhEKcH8XYEJTe m5tWHpkARMQGxobEQpwXxdkW09zQUdDfVt5eBAaEQpwfxdrHWseU3tnY0ttehAbGxsRCnBfF25E RHxBeBpkXm97EBoRCnB/F24fZ119XkATeGR5EBsYHhEKcF8XZGNobR59UGtMUGAQGRoRCnBsF24 fZUgFXUJFbm9eEB4SEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=999 spamscore=0 impostorscore=0 suspectscore=0 clxscore=223 bulkscore=0 lowpriorityscore=0 adultscore=0 phishscore=0 malwarescore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120018 X-Spam-Score: 0 X-Spam-OrigSender: mvondoma@uci.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Von Domaros --0000000000005fd31a05bd4e02cd Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks, Josh! That's quite encouraging. Does that mean it's possible to request Gitlab access for this reason? I was operating under the assumption that this is just for developers. Michael On Thu, Mar 11, 2021 at 5:28 PM Vermaas, Josh wrote: > Hi Michael, > > I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the > source from gitlab. > > https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!u= W5z2anQvBXI7OPMObXMeUCjFslS1-ugHNIGKaN36MZwiAg1XsI_IZXgpIHdgk2pKg$=20 > > It is in the devel branch, and it tagged as 3.0a9. I have compilation > instructions that are what I used (or at least what I think I used from > memory) on github. > > https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building= -Instructions/blob/main/NAMD.md__;!!DZ3fjg!uW5z2anQvBXI7OPMObXMeUCjFslS1-ug= HNIGKaN36MZwiAg1XsI_IZXgpIH_dYoZXQ$=20 > > Compilation with NAMD3 from there is basically the same as it would be > anywhere else. You need charm++ compiled, followed by NAMD itself. The > hardest part for me was actually sorting out which of the many openMPI > implementations installed on the cluster had the PMI backend so I could > just call srun if I wanted to do replica exchange stuff. > > -Josh > > On 3/11/21 7:42 PM, Michael Von Domaros wrote: > > Hi everyone, > > > > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or > > something even newer? not sure.) Is this absolutely necessary? I'm > > asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > > compatible device drivers, because a pretty substantial software stack > > has been compiled against this version. The admins are somewhat > > hesitant to update the device drivers, because they don't think that > > running CUDA 10 apps with newer device drivers will be flawless. > > > > So, long story short: Could NAMD3 be compiled against CUDA 10? If so, > > is there any way to access the source code? As far as I can tell, only > > source codes for the 2.x series and nightly snapshots are available. > > > > Thanks a bunch, > > Michael > > -- > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of > Biochemisty and Molecular Biology > vermaasj@msu.edu > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/__;!!DZ3fjg!uW5z2anQvBXI7OPMObXMeUCjFslS1-ugHNIGKaN36MZwiAg1XsI_I= ZXgpIEJUk8k9Q$=20 > > --0000000000005fd31a05bd4e02cd Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thanks, Josh! That&= #39;s quite encouraging. Does that mean it's=20 possible to request Gitlab access for this reason? I was operating under the assumption that this is just for developers.

Michael

On Thu, Mar 11, 202= 1 at 5:28 PM Vermaas, Josh <vermaasj= @msu.edu> wrote:
Hi Michael,

I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the
source from gitlab.

https://gitlab.com/tcbgUIUC/namd=

It is in the devel branch, and it tagged as 3.0a9. I have compilation
instructions that are what I used (or at least what I think I used from
memory) on github.
https://github.com/jvermaas/Software-Building-Instructions/blob/mai= n/NAMD.md

Compilation with NAMD3 from there is basically the same as it would be
anywhere else. You need charm++ compiled, followed by NAMD itself. The
hardest part for me was actually sorting out which of the many openMPI
implementations installed on the cluster had the PMI backend so I could
just call srun if I wanted to do replica exchange stuff.

-Josh

On 3/11/21 7:42 PM, Michael Von Domaros wrote:
> Hi everyone,
>
> It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or
> something even newer? not sure.) Is this absolutely necessary? I'm=
> asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > compatible device drivers, because a pretty substantial software stack=
> has been compiled against this version. The admins are somewhat
> hesitant to update the device drivers, because they don't think th= at
> running CUDA 10 apps with newer device drivers will be flawless.
>
> So, long story short: Could NAMD3 be compiled against CUDA 10? If so,<= br> > is there any way to access the source code? As far as I can tell, only=
> source codes for the 2.x series and nightly snapshots are available. >
> Thanks a bunch,
> Michael

--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology
vermaasj@msu.edu<= br> https://prl.n= atsci.msu.edu/people/faculty/josh-vermaas/

--0000000000005fd31a05bd4e02cd-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 11 21:09:50 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C39oQL028941; Thu, 11 Mar 2021 21:09:50 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C39nAD028940; Thu, 11 Mar 2021 21:09:49 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C39nIE028935; Thu, 11 Mar 2021 21:09:49 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C39nEP028934; Thu, 11 Mar 2021 21:09:49 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C39aKM028920 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 11 Mar 2021 21:09:36 -0600 (CST) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12C32hJQ013375 for ; Fri, 12 Mar 2021 03:09:36 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qv1-f41.google.com (mail-qv1-f41.google.com [209.85.219.41]) by mx0b-00007101.pphosted.com with ESMTP id 376j07rmj6-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 12 Mar 2021 03:09:36 +0000 Received: by mail-qv1-f41.google.com with SMTP id a14so3634194qvj.7 for ; Thu, 11 Mar 2021 19:09:36 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=UxuRiuJeWL7ha1K01je92GXbypNuIohZH+D/b2x+XoY=; b=odtUZvY7o9xu0iMiu/QDWjo+hmTFXA6MpbM4w2zzNm9ECFSzU/XmGgTW7lz4RbZ6S2 VuRJEw02VIk+rina/8YB+EFAUXe8JuuULSjEbmgx3b3E4SfBt/RGr7B6aRHJzFg36Mgr OKa2+uOSFkNHUMciGQxpUd0HAp3fcebLvEOvKiGNxWDZCNeyq/wZhUZNXGG1CHSpcMrI ONpdhLrL79lFxKLfRugsO3IXY8L6ZoDclP6qwiXhVsIlyGHubEcCU2Gqjxk86iOQH2mX fLSoVhH2mvogygSg//LJ/1q7ZMeqknJGd6bXtfH0sppwZx2y1Mk5jmn/Igq4il2cVSKN 4fqw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=UxuRiuJeWL7ha1K01je92GXbypNuIohZH+D/b2x+XoY=; b=ZskmKKrd8nZv+puGJYzLLLn34Y50tjqCCR/ZQ2eBeUMucvt/Am2KtPG6MIhapeIEgM Oxe944zQH/lbvpkrwiIKiBWY27DXKpPS9+h6Nbnn6qKMV7gxOFyx81Iyh9MYUvYiwqa9 OWbYGnIu95hQJ2AWrneDM4szzSrDyXJfQPo1IgbPL8A+EBYR41L4E3otu/k+9id9KjQg fG3FXazmDs5hlETZ53MXJ8P8whQYNRQz8t0w3VZH5Vn44t03GgaIxjtRHNmsVadq8sJt ScG4Gsqt3nNgMkscjQmqyk2IUIfVu6QNrfBYJV2sFYqh9ScTysNxg1baBf1Ky+MROErm 0G6w== X-Gm-Message-State: AOAM53237de+YnWKW5AypM57Yc9xumeG6VxNjS/0fJOCNANsJ6jHfbMS ytlFVKXxJdx6jMMFYQyoDRnfcfSGZ6Lw0g== X-Google-Smtp-Source: ABdhPJwDtvIwA/abXfr3cIG6g4m+tt3cruyJq/EmzV08n8gRusts3mfRiQ5d8sKH32Wf4eHFP3n7/g== X-Received: by 2002:a0c:9a04:: with SMTP id p4mr10745745qvd.38.1615518575581; Thu, 11 Mar 2021 19:09:35 -0800 (PST) Received: from [192.168.1.44] ([181.64.230.110]) by smtp.gmail.com with ESMTPSA id k24sm3150289qtu.35.2021.03.11.19.09.33 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 11 Mar 2021 19:09:35 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 11 Mar 2021 22:09:31 -0500 Subject: namd-l: Ligand concentration From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: <41E35A43-E815-4953-B8A1-0FBA9E332E1D@gmail.com> Thread-Topic: Ligand concentration Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3698345374_1749408154" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwbEQpMehcZHBsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGx8SEQpDWRcHHxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhtxHxoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XRxx+X3NbY21SdRlua2RkS0ZvBxhTbG9GGx8eHklaa2gRClhcFx8EGgQYGBwF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXck1ja2YRCk1cFxMcEQpMWhdsaU1NaxEKTEYXb2tra2t rEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEwQeGxEKQl4XGxEKRF4XGBEKQlwXGxEKXk 4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY 1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXa3NaZVMceRNi fHMRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdkbWZEXEJkEgVFehEKWUsXExkeGRE KcGgXYwVoQhhEXWtraGMQGxofEQpwaBdgXWhtcGNJYR5GfxAZGhEKcGgXax17X2x7bRNGc3oQGR oRCnBoF3ocHVxZGW9yAWNBEBkaEQpwaBdiGHgeXQF5AX1fRRAZGhEKcGwXekdAaxhZeX8eG0gQG xIRCnBDF20dR3tmfB58Q2kFEB4SEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 phishscore=0 mlxlogscore=352 lowpriorityscore=0 malwarescore=0 clxscore=161 priorityscore=361 suspectscore=0 spamscore=0 impostorscore=0 adultscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120020 domainage_hfrom=9343 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698345374_1749408154 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear namd users,=20 =20 How calculate number of ligand to placing into box with concentration of 10= 0 mM? =20 And how impose repulsive forcer based into equation below with Tclforces:=20 =20 LJ 12 6 E (r) =3D 4=CE=B5[(=CF=83/r) =E2=88=92 (=CF=83/r) ]=20 where =CE=B5 =3D 10=E2=88=923 kJ/mol, =CF=83 =3D 20 A=CC=8A, and r is the distance between the ce= nters of mass of the ligands=20 =20 refrence: ColDock: Concentrated Ligand Docking with All-Atom Molecular=20 Dynamics Simulation . 10.1021=20 =20 =20 --B_3698345374_1749408154 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear namd users, 

 

How calculate number of ligand to placing= into box with concentration of 100 mM?

&nb= sp;

And ho= w impose repulsive forcer based into equation below with Tclforces:

 

LJ 12 6= E (r) =3D 4=CE=B5[(=CF=83/r) =E2=88=92 (=CF=83/r) ]

where =CE=B5 =3D 10=E2=88=923 kJ/mol, =CF=83 =3D 20 A=CC=8A, and r is the distance between the c= enters of mass of the ligands

 

refrence: ColDock: Concentrated Ligand Do= cking with All-Atom Molecular

Dynamics Simulation . 10.1021

 

 

<= /div> --B_3698345374_1749408154-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 11 21:29:33 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C3TXad001624; Thu, 11 Mar 2021 21:29:33 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C3TXUq001623; Thu, 11 Mar 2021 21:29:33 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C3TW5m001619; Thu, 11 Mar 2021 21:29:32 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C3TWfZ001618; Thu, 11 Mar 2021 21:29:32 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C3TMOA001606 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 11 Mar 2021 21:29:22 -0600 (CST) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12C3SlYl014229 for ; Fri, 12 Mar 2021 03:29:22 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=zhangyuzhou15@mails.ucas.edu.cn Received: from cstnet.cn (smtp37.cstnet.cn [159.226.251.37]) by mx0b-00007101.pphosted.com with ESMTP id 3775bceka1-1 for ; Fri, 12 Mar 2021 03:29:21 +0000 Received: by ajax-webmail-APP-12 (Coremail) ; Fri, 12 Mar 2021 11:29:17 +0800 (GMT+08:00) X-Originating-IP: [106.120.127.15] Date: Fri, 12 Mar 2021 11:29:17 +0800 (GMT+08:00) X-CM-HeaderCharset: UTF-8 From: =?UTF-8?B?5byg6amt5rSy?= To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Subject: Re: Re: namd-l: 3.0alpha9 CUDA version X-Priority: 3 X-Mailer: Coremail Webmail Server Version XT5.0.13 build 20201118(d3a44678) Copyright (c) 2002-2021 www.mailtech.cn cnic.cn In-Reply-To: <48a9706a-aed3-1a68-6bb5-5f7642411134@msu.edu> References: <48a9706a-aed3-1a68-6bb5-5f7642411134@msu.edu> Content-Type: text/plain; charset=UTF-8 MIME-Version: 1.0 Message-ID: <1e982de.3a8df.178247b34c3.Coremail.zhangyuzhou15@mails.ucas.edu.cn> X-Coremail-Locale: zh_CN X-CM-TRANSID: tgCowACX2vgN4EpgLtADAA--.37177W X-CM-SenderInfo: x2kd0wx1x2x0rxrvqzpdlo2hpxfd2hldfou0/1tbiCwkSElz4j4wG 0AACsx X-Coremail-Antispam: 1Ur529EdanIXcx71UUUUU7IcSsGvfJ3iIAIbVAYjsxI4VWxJw CS07vEb4IE77IF4wCS07vE1I0E4x80FVAKz4kxMIAIbVAFxVCaYxvI4VCIwcAKzIAtYxBI daVFxhVjvjDU= X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIeEQpMehcaEQpZRBdpEh4cT2JwHF5IUhEKWFgXYmdJS15re2BJXhk RCnhOF2tdeGNoHxpSWWJjEQp5TBdpbF1ZZRNmR3tzQBEKQ0gXBxgbGREKQ1kXGRgRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHB5xHhkQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XfH1Ic2UZZHVMUhh1YBh+cnNibRt6UmEcfkRuenVLXWcRClhcFx8EGgQYGBwFGxoE GxsaBB8aBBseGBAbHhofGhEKXlkXck1jeV4RCk1cFxsdHxEKTFoXeGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdgY2tPY3pQe0VrBREKQ1oXGx8TBBgYHAQYHxsEGR0RCk JeFxsRCkReFxgRCkJFF2hmWEBJXn5SY3pEEQpCThdrXXhjaB8aUlliYxEKQkwXYmdJS15re2BJX hkRCkJsF2dvGFlOcEtbSE5SEQpCQBdiRkl4G01SaU5zGREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsR ClpYFxkRCnlDF2IFWVJCc1pvTxNMEQpwZxdpQ25QAVlzRwEeUxAZGhEKcGgXb0ZfSF9pTUsSE14 QGRoRCnBoF3peXHtTGAUYTUQeEBwaEQpwaBdjGXkeRXtLHEBhYxAZGhEKcGgXb0hNHW1gc28BWA UQGRoRCnBoF2RPYGtwf3NdfVBcEBkaEQpwZxdpfgF6Q3JOf0JTexAeEhEKcH0Xb1JNUGZsYGdbS FoQHBoRCnB9F2FCGV5ERGsTSExGEBwaEQpwfRdhSFxgZmZPUEV9HxAcGhEKcGcXYUh6YF0feENj fh8QGRoRCnBnF2RkZ35vc3x7QhtTEBkaEQpwZxdpGW9jWURgfnhzQhAZGhEKcH8XYWZvWxpnZEJ IHVsQGxgeEQpwXxdjYhJQSGN4H3xCfRAbGhgRCnBsF2JIeBNIRXpfAVlPEBkaEQptfhcbEQpYTR dLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 impostorscore=0 adultscore=0 lowpriorityscore=0 phishscore=0 mlxlogscore=999 spamscore=0 mlxscore=0 bulkscore=0 suspectscore=0 clxscore=184 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120022 X-Spam-Score: 0 X-Spam-OrigSender: zhangyuzhou15@mails.ucas.edu.cn X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by halifax.ks.uiuc.edu id 12C3TMO9001607 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?B?5byg6amt5rSy?= Hello, I wonder if there is any release of HIP version of the namd 3 ? -zhang > -----原始邮件----- > å‘件人: "Vermaas, Josh" > å‘é€æ—¶é—´: 2021-03-12 09:27:53 (星期五) > 收件人: "namd-l@ks.uiuc.edu" , "Michael Von Domaros" > 抄é€: > 主题: Re: namd-l: 3.0alpha9 CUDA version > > Hi Michael, > > I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the > source from gitlab. > > https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!oGE0nGoRal7nV7lEzLdJsLjX376iV7WJNvSe9ZFp002XAcmFUzLWKQHR4L21njhdHA$ > > It is in the devel branch, and it tagged as 3.0a9. I have compilation > instructions that are what I used (or at least what I think I used from > memory) on github. > https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!DZ3fjg!oGE0nGoRal7nV7lEzLdJsLjX376iV7WJNvSe9ZFp002XAcmFUzLWKQHR4L3sGWKUNA$ > > Compilation with NAMD3 from there is basically the same as it would be > anywhere else. You need charm++ compiled, followed by NAMD itself. The > hardest part for me was actually sorting out which of the many openMPI > implementations installed on the cluster had the PMI backend so I could > just call srun if I wanted to do replica exchange stuff. > > -Josh > > On 3/11/21 7:42 PM, Michael Von Domaros wrote: > > Hi everyone, > > > > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or > > something even newer? not sure.) Is this absolutely necessary? I'm > > asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > > compatible device drivers, because a pretty substantial software stack > > has been compiled against this version. The admins are somewhat > > hesitant to update the device drivers, because they don't think that > > running CUDA 10 apps with newer device drivers will be flawless. > > > > So, long story short: Could NAMD3 be compiled against CUDA 10? If so, > > is there any way to access the source code? As far as I can tell, only > > source codes for the 2.x series and nightly snapshots are available. > > > > Thanks a bunch, > > Michael > > -- > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology > vermaasj@msu.edu > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!oGE0nGoRal7nV7lEzLdJsLjX376iV7WJNvSe9ZFp002XAcmFUzLWKQHR4L3lIBscZA$ > From owner-namd-l@halifax.ks.uiuc.edu Fri Mar 12 00:10:08 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12C6A8qi008381; Fri, 12 Mar 2021 00:10:08 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12C6A8Y3008380; Fri, 12 Mar 2021 00:10:08 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu 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X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 4a52a478-a812-4a64-cfa7-08d8e55e63a5 X-MS-Exchange-CrossTenant-originalarrivaltime: 12 Mar 2021 13:54:43.2963 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: dFS95L4br4VnMlGqcawH4mj8BYEGYrqvTFSk2Rh/mCgAv11Rh79KWk2w4o0YszoU2kB5UQ679BDF1bmHVPNIXA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR12MB1142 X-CLX-Response: 1TFkXGxwTEQpMehcZGhEKWUQXaXtSfmRsGVBgYWQRClhYF29hWBMaS10bQ0F lEQp4Thdob0xmAXJmZEtdEhEKeUwXYGVTYE0dTx5nGFwRCkNIFwcbGRoRCkNZFxsRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHhNxGRoQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04Xb1xrHGFue0EcU0YZfHJQRRoHbUFcbnNrXkd6dUVsaRwRClhcFx8EGgQYGBwFGxoE 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bulkscore=0 impostorscore=0 mlxlogscore=999 mlxscore=0 adultscore=0 suspectscore=0 priorityscore=30 clxscore=169 phishscore=0 spamscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120099 domainage_hfrom=12364 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_73a47451b78558dbed952e54aed3d09amsuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Michael, Developers are certainly one audience, but really the reason behind the git= lab wall is due to needing to be able to track users for reporting usage st= atistics back to funding agencies, and to make sure folks have agreed to th= e NAMD license. That is why the user registration form is one of the prereq= uisites, so that the developers can report back to NIH the percentage of us= ers that have NIH funding. Being able to download the source so you can com= pile it on your own hardware is totally a legit reason to get access throug= h gitlab IMHO. I believe this opinion is shared by the folks that actually = have decision making power. -Josh On 3/11/21 9:52 PM, Michael Von Domaros wrote: Thanks, Josh! That's quite encouraging. Does that mean it's possible to req= uest Gitlab access for this reason? I was operating under the assumption th= at this is just for developers. Michael On Thu, Mar 11, 2021 at 5:28 PM Vermaas, Josh > wrote: Hi Michael, I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the source from gitlab. https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!raz= e168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyEzJmbEwHA$ It is in the devel branch, and it tagged as 3.0a9. I have compilation instructions that are what I used (or at least what I think I used from memory) on github. https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-I= nstructions/blob/main/NAMD.md__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR= 2t5nQdeDtoqT8L_6DAspneyEy1mAqwHw$ Compilation with NAMD3 from there is basically the same as it would be anywhere else. You need charm++ compiled, followed by NAMD itself. The hardest part for me was actually sorting out which of the many openMPI implementations installed on the cluster had the PMI backend so I could just call srun if I wanted to do replica exchange stuff. -Josh On 3/11/21 7:42 PM, Michael Von Domaros wrote: > Hi everyone, > > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or > something even newer? not sure.) Is this absolutely necessary? I'm > asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > compatible device drivers, because a pretty substantial software stack > has been compiled against this version. The admins are somewhat > hesitant to update the device drivers, because they don't think that > running CUDA 10 apps with newer device drivers will be flawless. > > So, long story short: Could NAMD3 be compiled against CUDA 10? If so, > is there any way to access the source code? As far as I can tell, only > source codes for the 2.x series and nightly snapshots are available. > > Thanks a bunch, > Michael -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspn= eyExZF2KpHQ$=20 -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspn= eyExZF2KpHQ$=20 --_000_73a47451b78558dbed952e54aed3d09amsuedu_ Content-Type: text/html; charset="utf-8" Content-ID: Content-Transfer-Encoding: Quoted-printable Hi Michael,

Developers are certainly one audience, but really the reason behind the git= lab wall is due to needing to be able to track users for reporting usage st= atistics back to funding agencies, and to make sure folks have agreed to th= e NAMD license. That is why the user registration form is one of the prerequisites, so that the developers= can report back to NIH the percentage of users that have NIH funding. Bein= g able to download the source so you can compile it on your own hardware is= totally a legit reason to get access through gitlab IMHO. I believe this opinion is shared by the folks that ac= tually have decision making power.

-Josh

On 3/11/21 9:52 PM, Michael Von Domaros wrot= e:
Thanks, Josh! That's quite encouraging. Does that mean it's possible t= o request Gitlab access for this reason? I was operating under the assumpti= on that this is just for developers.

Michael

On Thu, Mar 11, 2021 at 5:28 PM Verma= as, Josh <v= ermaasj@msu.edu> wrote:
Hi Michael,

I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the
source from gitlab.

https://gitla= b.com/tcbgUIUC/namd

It is in the devel branch, and it tagged as 3.0a9. I have compilation
instructions that are what I used (or at least what I think I used from
memory) on github.
https://github.com/jvermaas/Software-Buildin= g-Instructions/blob/main/NAMD.md

Compilation with NAMD3 from there is basically the same as it would be
anywhere else. You need charm++ compiled, followed by NAMD itself. The
hardest part for me was actually sorting out which of the many openMPI
implementations installed on the cluster had the PMI backend so I could
just call srun if I wanted to do replica exchange stuff.

-Josh

On 3/11/21 7:42 PM, Michael Von Domaros wrote:
> Hi everyone,
>
> It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or
> something even newer? not sure.) Is this absolutely necessary? I'm
> asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > compatible device drivers, because a pretty substantial software stack=
> has been compiled against this version. The admins are somewhat
> hesitant to update the device drivers, because they don't think that > running CUDA 10 apps with newer device drivers will be flawless.
>
> So, long story short: Could NAMD3 be compiled against CUDA 10? If so,<= br> > is there any way to access the source code? As far as I can tell, only=
> source codes for the 2.x series and nightly snapshots are available. >
> Thanks a bunch,
> Michael

--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="000000000000b0871b05bd5b95ae" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxkfEQpMehcZGxMRCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHHxoRCkNZFwcZHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsbH3EbGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd9TEVuTh1ra2FQRW0SHFtSeUVLE1BvZxIYHX94ElN+YREKWFwXHwQaBBgYHAUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdyTX1rSxEKTVwXGBsSEQpMWhdsaU1raxEKTEYXb2tra2t rEQpCTxdtbVJNa2xbb0hsbREKQ1oXGBoTBBIfBBscHAQbHR4RCkJeFxsRCkReFxgRCkJcFxsRCl 5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaFpwGEkfZngeQF4RCkJOF 2NTY2t7E1h+Gl9eEQpCTBdsH15ZWm5MYWBbQREKQmwXb0Jpf25OW1IZeBoRCkJAF2IFAUdhcGdS TEkdEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXZFlAYVwZUnl8XEQRCllLFxMZHhk RCnBoF2JuSVwfeEldWmxNEBkaEQpwaBdsfwUeeVtLeBxsWhAZGhEKcGgXY0tkQk4aXkB6AXsQGR oRCnBsF2d4c3NCR1xbfUZLEB4SEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=613 spamscore=0 impostorscore=0 suspectscore=0 clxscore=135 bulkscore=0 lowpriorityscore=0 adultscore=0 phishscore=0 malwarescore=0 priorityscore=319 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120138 domainage_hfrom=9343 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000b0871b05bd5b95ae Content-Type: text/plain; charset="UTF-8" Dear Colleges, Recently, our docked ligand-complexes have been showing unfavorable interactions. How to avoid them in AutodockVina? We are using AutodockVina through the PyRx platform Any comment will be highly appreciated! Dr. Mi --000000000000b0871b05bd5b95ae Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleges,
Recently, our docked ligand-complexes h= ave been showing unfavorable interactions. How to avoid=C2=A0them in Autodo= ckVina? We are using AutodockVina through the PyRx platform
Any c= omment will be highly appreciated!

Dr. Mi
--000000000000b0871b05bd5b95ae-- From owner-namd-l@halifax.ks.uiuc.edu Fri Mar 12 14:54:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12CKsH4n000054; Fri, 12 Mar 2021 14:54:17 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12CKsHMc000053; Fri, 12 Mar 2021 14:54:17 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12CKsGL7000048; Fri, 12 Mar 2021 14:54:16 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12CKsGbj000047; Fri, 12 Mar 2021 14:54:16 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12CKs7ZO000013 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 12 Mar 2021 14:54:08 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12CKrsEI029686 for ; Fri, 12 Mar 2021 20:54:07 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qt1-f181.google.com (mail-qt1-f181.google.com [209.85.160.181]) by mx0a-00007101.pphosted.com with ESMTP id 3772njvf4d-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 12 Mar 2021 20:54:07 +0000 Received: by mail-qt1-f181.google.com with SMTP id 94so4899542qtc.0 for ; Fri, 12 Mar 2021 12:54:06 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=LAFUjsG/JOmBRr0VVurX2b4NwSmaZyBLJT7uXucgKS4=; b=K1VQmmyoCZA9Vyg8Vr+VC5S9D33Qz+m2JiPXSFT25Y8epK3KewKAxPjIx3RhXTIOvg 2mjvoo8f70yoExr83av08yf6DyvGVEBeULPm/4/vj6bC1FlVo23YUvEXy9INfLL0PrKO y0II+97FHY7aSeaOSu/czopt6UUZPRk9f46Q486vCFDNY/El9X66O+9rVPWSg2poyaHF J2iWs72BUhMPA5bxYKAqV0cALZ/quuJOaP53qd7LrnXfP4dRkUhFRaDr+c5cLddqvjp7 pxHVAzRA/BJn+Ehn8KFCFE0//32foUm+ANrVY6ZV9mc+rnwZm45kXKIEEMGBvnM2cS4K HvaA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=LAFUjsG/JOmBRr0VVurX2b4NwSmaZyBLJT7uXucgKS4=; b=ctxDZuCrJHoquvdy7bCnoLp3t6Ungm/z+Y/Qi/PP19xDCv6CZETBqTRzpom+UHRksH Gow89JXXeMXZ4CG55My7lAPa6Cl5S1bOMlG3/TqamK3g5Mwg0ZOdSmehys853ekcYkdE b7tNeJg7aSRQQQO1H1+janym+TICme8LEzCrXa+nnkpGlunigNZ49aHp33c+dvzDud1U Jw0dlFLv4Mhop23Nf8yevcaxLOW8La+VmJtPZelzGy6pM5wQl67tVNzFpggkjn06ysD5 CFeQGQGmK8ymotBWeYuYj6wQfTVxZH26ay4XkajX5nOuHV5S3+DaVJx/guoO3108ed2b uO4Q== X-Gm-Message-State: AOAM532dqhNunJJLwC07lQdBZogACH3gVQYQaGYJor9FOHY0D30SAVMp oUMraJ8prpvALopO7pDf494DM7X9ilFHfg== X-Google-Smtp-Source: ABdhPJzZMnk3ZHcutZdqrNyJfyp+E5495LSatqH7c7GtbkQMTUo7k7+Pwt9trTctjkwqOhbWjLDIsw== X-Received: by 2002:ac8:664a:: with SMTP id j10mr13499087qtp.119.1615582445692; Fri, 12 Mar 2021 12:54:05 -0800 (PST) Received: from [192.168.1.44] ([181.64.230.122]) by smtp.gmail.com with ESMTPSA id c186sm5271433qkb.107.2021.03.12.12.54.03 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Fri, 12 Mar 2021 12:54:05 -0800 (PST) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 12 Mar 2021 15:54:01 -0500 Subject: namd-l: Add repulsive potential with dummy atom From: "Ropon-Palacios G." To: "namd-l@ks.uiuc.edu" Message-ID: <16255591-6B19-4EA9-91CC-24A14D04CC58@gmail.com> Thread-Topic: Add repulsive potential with dummy atom Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3698409243_946113340" X-CLX-Response: 1TFkXGxIbEQpMehcZHxIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGB4ZEQpDWRcHHxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBtxHhoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XeWx5S0VcQGscZmNMYklzB3BTGWsTfm9QWFt/GXtaQW0RClhcFx8EGgQYGBwF GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdyTXJHYREKTVwXGxIZEQpMWhdsaU1NaxEKTEYXb2tra2t rEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGgQbEhsRCkJeFxsRCkReFxgRCkJcFxsRCl 5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF 2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXY2lZb3pPHXJHT38RCkJAF29sbx9LG2Af TWxFEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXYhkdU0VwfBJME0ARCllLFxMZHhk RCnBoF2FiHH5IfBpieFxoEBkaEQpwaBdiSFwdYU8fR1B4ExAZGhEKcGgXaW5wBUZDHFpmXGEQGx 4fEQpwaBdoThlAZl9Ne0hPHRAZGhEKcGgXY3NMekloRhpnZ0kQGRoRCnBsF3pHQGsYWXl/HhtIE BkaEQpwQxdiWEd7ZnxIa2dAZxAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 bulkscore=0 impostorscore=0 mlxlogscore=363 mlxscore=0 adultscore=0 suspectscore=0 priorityscore=358 clxscore=181 phishscore=0 spamscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103120153 domainage_hfrom=9343 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698409243_946113340 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear namd user,=20 =20 How can add LJ 12 6 E (r) =3D 4=CE=B5[(=CF=83/r) =E2=88=92 (=CF=83/r) ] this respulsive potenti= al where =CE=B5 =3D 10=E2=88=923 kJ/mol, =CF=83 =3D 20 A=CC=8A, and r is the distance between the = centers of mass of the ligands?=20 =20 How add this in rtf or parm files?=20 =20 Best,=20 =20 Geo.=20 --B_3698409243_946113340 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dea= r namd user,

 

How can add LJ 12 6&n= bsp;(r) =3D 4=CE=B5[(=CF=83/r) =E2=88=92 (=CF=83/r) ] this respulsive potentia= l where =CE=B5 =3D 10=E2=88=923 kJ/mol, =CF=83 =3D 20 A=CC=8A, and r is = the distance between the centers of mass of the ligands? <= /span>

 

How add this i= n rtf or parm files?

 

Best,

 

Geo.

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charset="UTF-8" Dear Experts, I am dealing with a chlorobenzene derivative molecules water system. The system contains 10 molecules. After energy minimization it has been observed that lone pairs of chlorine atoms disconnected for few chlorobenzene derivative molecules. I am using NAMD2.14 for the water system . The psf files were built using psfgen 2.0. Please help me in this regard. Thank you Rabiul --0000000000003532a205bd90196a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Experts,
I am dealing with a chlorobenzene deriva= tive molecules water system. The system contains 10=C2=A0 molecules. After = energy=20 minimization it has been observed that lone pairs of chlorine atoms=20 disconnected for few chlorobenzene derivative=C2=A0 molecules.=C2=A0=C2=A0<= /div>

I am using NAMD2.14 for the water system . The psf= files were built using psfgen 2.0.

Please hel= p me in=C2=A0this regard.

Thank you
=C2=A0Rabiul
--0000000000003532a205bd90196a-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 05:06:43 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GA6hM9017388; Tue, 16 Mar 2021 05:06:43 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GA6gXN017387; Tue, 16 Mar 2021 05:06:42 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GA6g96017383; Tue, 16 Mar 2021 05:06:42 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GA6gFC017382; Tue, 16 Mar 2021 05:06:42 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GA6SaL017372 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 16 Mar 2021 05:06:29 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12G9h7X8026025 for ; Tue, 16 Mar 2021 10:06:28 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=yasser.almeida-hernandez@uni-due.de Received: from mailoutzim.uni-due.de (mailoutzim.uni-due.de [134.91.56.37]) by mx0b-00007101.pphosted.com with ESMTP id 378pu4xev0-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 16 Mar 2021 10:06:28 +0000 Received: from EX4.win.uni-due.de (ns2-owa.uni-duisburg-essen.de [134.91.18.67]) by mailoutzim.uni-due.de (8.14.7/8.14.7) with ESMTP id 12GA6Qv8002344 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 16 Mar 2021 11:06:26 +0100 Received: from EX3.win.uni-due.de (134.91.18.65) by EX4.win.uni-due.de (134.91.18.66) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2106.2; Tue, 16 Mar 2021 11:06:25 +0100 Received: from EX3.win.uni-due.de ([134.91.18.65]) by EX3.win.uni-due.de ([134.91.18.65]) with mapi id 15.01.2106.013; Tue, 16 Mar 2021 11:06:25 +0100 From: =?iso-8859-1?Q?Almeida-Hern=E1ndez=2C_Yasser=2C_Dr=2E?= To: "namd-l@ks.uiuc.edu" Subject: namd-l: AMBER99bsc1 force field for NAMD Thread-Topic: AMBER99bsc1 force field for NAMD Thread-Index: AQHXGkoZan9iuSwySkmfldVNBHdCuw== Date: Tue, 16 Mar 2021 10:06:25 +0000 Message-ID: <04a9555dd32d4e3ab233ceb72f471513@uni-due.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [132.252.183.35] Content-Type: multipart/alternative; boundary="_000_04a9555dd32d4e3ab233ceb72f471513uniduede_" X-Virus-Scanned: Clam Anti Virus - http://www.clamav.net X-Spam-Scanned: SpamAssassin: 3.004000 - http://www.spamassassin.org X-Scanned-By: MIMEDefang 2.84 X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBduS39HeRJcWF5AQxEKWFgXaHxGZ05ucAFZWVI RCnhOF298QmxwTUJneFxZEQp5TBdvRHljckNZflxafBEKQ0gXBxsfGhEKQ1kXBxMcEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ZcR8ZEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF3JwYHJucEBjRXMHX3lcRWRzW2ReeG9MHxxre0RzaBpfEQpYXBcfBBoEGBgcBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JCQ08FEQpNXBcbHBsRCkxaF3xpTU1NEQpFWRd7axEKTF8 XegUFBQUFBQUFBUMRCkxGF2lrEQpCTxd6Ql1SbGAbGllsbREKQ1oXGxkeBBMbBB8cBBkdEQpCXh cbEQpEXhcYEQpCRRdhRBsSZU57bBhYGBEKQk4Xb3xCbHBNQmd4XFkRCkJMF2h8RmdObnABWVlSE QpCbBdsRmtcfHNjUxp5aBEKQkAXel9ubxNublhca0gRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpa WBcYEQp5QxdiTkseWEVJc0lkbREKcGcXbkB5HXtiHX1BemwQGRoRCnBoF2V/S256WhwbQ0MfEB4 SEQpwaBdmUH9cU0ZrQkdbTxAZGhEKcGgXbGBBUGx9UGhCSW0QGRoRCnBoF2d8RlBFAR5tRnsYEB kaEQpwaBdlE39paGtlXhgFWRAZGhEKcH0Xbn5Mc01YWVsbTVMQGRoRCnB9F21wQF5dQFNpW0huE BkaEQpwfxdmHG1wZHxsXWleHRAfHBEKcF8XYFxeaERpXllGWHMQGRoRCnBsF25hXG14QmsaAQEB EBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 bulkscore=0 clxscore=163 phishscore=0 mlxscore=0 malwarescore=0 impostorscore=0 mlxlogscore=453 lowpriorityscore=0 priorityscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103160066 X-Spam-Score: 0 X-Spam-OrigSender: yasser.almeida-hernandez@uni-due.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?iso-8859-1?Q?Almeida-Hern=E1ndez=2C_Yasser=2C_Dr=2E?= --_000_04a9555dd32d4e3ab233ceb72f471513uniduede_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Hi, Where can I find the force field files for AMBER99bsc1 in CHARMM format to = run with NAMD? I could locate the AMBER99bsc0 prm and rtf files (https://urldefense.com/v3= /__http://alma.karlov.mff.cuni.cz/bio/VMD/toppar/non_charmm/__;!!DZ3fjg!pEC= TcxqCHzch2iPWL2fpZBCbX82TACrEmH-JNOfavr_FTSM55bPUmjnHAcmjBq2ogg$ ), but not= bsc1. Any help will be appreciated. Best, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universit=E4tsstr. 2, 45117 Essen Email: yasser.almeida-hernandez@uni-due.de Phone: +49 201 183 2457 --_000_04a9555dd32d4e3ab233ceb72f471513uniduede_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable

Hi,


Where can I find the force field files for AMBER99bsc1 in CHARMM format = to run with NAMD?


I could locate the AMBER99bsc0 prm and rtf files (http://alma.karlov.mff.cuni.cz/bio/VMD/toppar/non_charmm/), but not bsc1.


Any help will be appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=E4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" target=3D"_blank" = rel=3D"noopener noreferrer" id=3D"LPNoLP" title=3D"Ctrl+Click or tap to= follow the link"> yasser.almeida-hernan= dez@uni-due.de

--_000_04a9555dd32d4e3ab233ceb72f471513uniduede_-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 13:20:39 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIKdJP026876; Tue, 16 Mar 2021 13:20:39 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GIKdUR026875; Tue, 16 Mar 2021 13:20:39 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIKcpl026871; Tue, 16 Mar 2021 13:20:38 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GIKcoW026870; Tue, 16 Mar 2021 13:20:38 -0500 (CDT) Received: from wirelessprv-10-195-186-140.near.illinois.edu ([10.195.186.140]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIKNRd026859 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 16 Mar 2021 13:20:24 -0500 (CDT) From: David Hardy Message-Id: <7831F286-3614-449D-89D7-25D40E7D747C@ks.uiuc.edu> Content-Type: multipart/alternative; boundary="Apple-Mail=_98021BCF-1044-4133-84AA-F55EBA7DBE73" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: 3.0alpha9 CUDA version Date: Tue, 16 Mar 2021 13:20:22 -0500 In-Reply-To: <73a47451-b785-58db-ed95-2e54aed3d09a@msu.edu> Cc: Michael Von Domaros To: namd-l@ks.uiuc.edu, "Vermaas, Josh" References: <48a9706a-aed3-1a68-6bb5-5f7642411134@msu.edu> <73a47451-b785-58db-ed95-2e54aed3d09a@msu.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_98021BCF-1044-4133-84AA-F55EBA7DBE73 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Michael, I just wanted to follow up in support of what Josh said. The NAMD = License that we developed years ago with the university legal department = allows much freedom to users, including monetarily free access to run = the software and view the source code, along with some amount of reuse = of the code. However, in order for us to not to be in violation of our = own license when distributing NAMD, the license must be presented to the = user in a =E2=80=9Cclick-through=E2=80=9D form, which is why access to = the GitLab repository is protected in the way that it is. As Josh stated, it is fine for you to obtain the NAMD source code = through GitLab, even when your intention is simply to build NAMD = yourself. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 12, 2021, at 7:54 AM, Vermaas, Josh wrote: >=20 > Hi Michael, >=20 > Developers are certainly one audience, but really the reason behind = the gitlab wall is due to needing to be able to track users for = reporting usage statistics back to funding agencies, and to make sure = folks have agreed to the NAMD license. That is why the user registration = form is one of the prerequisites, so that the developers can report back = to NIH the percentage of users that have NIH funding. Being able to = download the source so you can compile it on your own hardware is = totally a legit reason to get access through gitlab IMHO. I believe this = opinion is shared by the folks that actually have decision making power. >=20 > -Josh >=20 > On 3/11/21 9:52 PM, Michael Von Domaros wrote: >> Thanks, Josh! That's quite encouraging. Does that mean it's possible = to request Gitlab access for this reason? I was operating under the = assumption that this is just for developers. >>=20 >> Michael >>=20 >> On Thu, Mar 11, 2021 at 5:28 PM Vermaas, Josh > wrote: >> Hi Michael, >>=20 >> I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the >> source from gitlab. >>=20 >> https://gitlab.com/tcbgUIUC/namd = >>=20 >> It is in the devel branch, and it tagged as 3.0a9. I have compilation >> instructions that are what I used (or at least what I think I used = from >> memory) on github. >> = https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.= md = >>=20 >> Compilation with NAMD3 from there is basically the same as it would = be >> anywhere else. You need charm++ compiled, followed by NAMD itself. = The >> hardest part for me was actually sorting out which of the many = openMPI >> implementations installed on the cluster had the PMI backend so I = could >> just call srun if I wanted to do replica exchange stuff. >>=20 >> -Josh >>=20 >> On 3/11/21 7:42 PM, Michael Von Domaros wrote: >> > Hi everyone, >> > >> > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or >> > something even newer? not sure.) Is this absolutely necessary? I'm >> > asking because our compute cluster is stuck with CUDA 10 and CUDA = 10 >> > compatible device drivers, because a pretty substantial software = stack >> > has been compiled against this version. The admins are somewhat >> > hesitant to update the device drivers, because they don't think = that >> > running CUDA 10 apps with newer device drivers will be flawless. >> > >> > So, long story short: Could NAMD3 be compiled against CUDA 10? If = so, >> > is there any way to access the source code? As far as I can tell, = only >> > source codes for the 2.x series and nightly snapshots are = available. >> > >> > Thanks a bunch, >> > Michael >>=20 >> --=20 >> Josh Vermaas >> Assistant Professor, MSU-DOE Plant Research Lab and Department of = Biochemisty and Molecular Biology >> vermaasj@msu.edu >> https://prl.natsci.msu.edu/people/faculty/josh-vermaas/ = >>=20 >=20 > --=20 > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of = Biochemisty and Molecular Biology > vermaasj@msu.edu > https://prl.natsci.msu.edu/people/faculty/josh-vermaas/ = --Apple-Mail=_98021BCF-1044-4133-84AA-F55EBA7DBE73 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Michael,

I just = wanted to follow up in support of what Josh said. The NAMD License that = we developed years ago with the university legal department allows much = freedom to users, including monetarily free access to run the software = and view the source code, along with some amount of reuse of the code. = However, in order for us to not to be in violation of our own license = when distributing NAMD, the license must be presented to the user in a = =E2=80=9Cclick-through=E2=80=9D form, which is why access to the GitLab = repository is protected in the way that it is.

As Josh stated, it is fine for you to = obtain the NAMD source code through GitLab, even when your intention is = simply to build NAMD yourself.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Mar 12, 2021, at 7:54 AM, Vermaas, Josh <vermaasj@msu.edu> = wrote:

Hi Michael,

Developers are certainly one audience, but really the reason behind the = gitlab wall is due to needing to be able to track users for reporting = usage statistics back to funding agencies, and to make sure folks have = agreed to the NAMD license. That is why the user registration form is one of the prerequisites, so that the = developers can report back to NIH the percentage of users that have NIH = funding. Being able to download the source so you can compile it on your = own hardware is totally a legit reason to get access through gitlab IMHO. I believe this opinion is shared by the folks that = actually have decision making power.

-Josh

On 3/11/21 9:52 PM, Michael Von Domaros = wrote:
Thanks, Josh! That's quite encouraging. Does that mean = it's possible to request Gitlab access for this reason? I was operating = under the assumption that this is just for developers.

Michael

On Thu, Mar 11, 2021 at 5:28 PM = Vermaas, Josh <vermaasj@msu.edu> wrote:
Hi Michael,

I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the
source from gitlab.

https://gitlab.com/tcbgUIUC/namd

It is in the devel branch, and it tagged as 3.0a9. I have compilation
instructions that are what I used (or at least what I think I used = from
memory) on github.
https://github.com/jvermaas/Software-Building-Instructions/blob= /main/NAMD.md

Compilation with NAMD3 from there is basically the same as it would = be
anywhere else. You need charm++ compiled, followed by NAMD itself. = The
hardest part for me was actually sorting out which of the many = openMPI
implementations installed on the cluster had the PMI backend so I = could
just call srun if I wanted to do replica exchange stuff.

-Josh

On 3/11/21 7:42 PM, Michael Von Domaros wrote:
> Hi everyone,
>
> It appears that the namd 3 alpha 9 builds now require CUDA 11.0 = (or
> something even newer? not sure.) Is this absolutely necessary? = I'm
> asking because our compute cluster is stuck with CUDA 10 and CUDA = 10
> compatible device drivers, because a pretty substantial software = stack
> has been compiled against this version. The admins are somewhat
> hesitant to update the device drivers, because they don't think = that
> running CUDA 10 apps with newer device drivers will be flawless.
>
> So, long story short: Could NAMD3 be compiled against CUDA 10? If = so,
> is there any way to access the source code? As far as I can tell, = only
> source codes for the 2.x series and nightly snapshots are = available.
>
> Thanks a bunch,
> Michael

--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of = Biochemisty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of =
Biochemisty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/people/faculty/josh-ver=
maas/

= --Apple-Mail=_98021BCF-1044-4133-84AA-F55EBA7DBE73-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 13:31:57 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIVvw0029177; Tue, 16 Mar 2021 13:31:57 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GIVvvQ029176; Tue, 16 Mar 2021 13:31:57 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIVvqX029170; Tue, 16 Mar 2021 13:31:57 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GIVuhO029169; Tue, 16 Mar 2021 13:31:56 -0500 (CDT) Received: from wirelessprv-10-195-186-140.near.illinois.edu ([10.195.186.140]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIVs2q029161 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 16 Mar 2021 13:31:54 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_AC59C2E1-A54F-4697-A259-236257D2A53E" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Add repulsive potential with dummy atom Date: Tue, 16 Mar 2021 13:31:53 -0500 References: <16255591-6B19-4EA9-91CC-24A14D04CC58@gmail.com> To: NAMD list , "Ropon-Palacios G." In-Reply-To: <16255591-6B19-4EA9-91CC-24A14D04CC58@gmail.com> Message-Id: <07810365-E4F5-4100-B087-93DFEF79AA24@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_AC59C2E1-A54F-4697-A259-236257D2A53E Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Geo, Introducing an external force between the centers of mass of various = subsets of atoms is possible through the Colvars module. There is good = documentation available = https://www.ks.uiuc.edu/Research/namd/2.14/ug/node53.html = . Since this force is being applied to centers of mass, there is no = mechanism for calculating what you want by simply changing the force = field parameter files. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 12, 2021, at 2:54 PM, Ropon-Palacios G. = wrote: >=20 > Dear namd user,=20 > =20 > How can add LJ 12 6 E (r) =3D 4=CE=B5[(=CF=83/r) =E2=88=92 (=CF=83/r) = ] this respulsive potential where =CE=B5 =3D 10=E2=88=923 kJ/mol, =CF=83 = =3D 20 A=CC=8A, and r is the distance between the centers of mass of the = ligands?=20 > =20 > How add this in rtf or parm files?=20 > =20 > Best,=20 > =20 > Geo.=20 --Apple-Mail=_AC59C2E1-A54F-4697-A259-236257D2A53E Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear = Geo,

Introducing an = external force between the centers of mass of various subsets of atoms = is possible through the Colvars module. There is good documentation = available https://www.ks.uiuc.edu/Research/namd/2.14/ug/node53.html.<= /div>

Since this = force is being applied to centers of mass, there is no mechanism for = calculating what you want by simply changing the force field parameter = files.

Best = regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Mar 12, 2021, at 2:54 PM, Ropon-Palacios G. <biodano.geo@gmail.com> wrote:

Dear namd user, 
 
How can add LJ 12 6 (r) =3D 4=CE=B5[= (=CF=83/r) =E2=88=92 (=CF=83/r) ] this respulsive = potential where =CE=B5 =3D 10=E2=88=923 kJ/mol, =CF=83 =3D = 20 A=CC=8A, and r is the distance between the centers of mass of the = ligands? 
 
How add this in = rtf or parm files? 
 
Best, 
 
Geo. 

= --Apple-Mail=_AC59C2E1-A54F-4697-A259-236257D2A53E-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 13:40:34 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIeYMW001443; Tue, 16 Mar 2021 13:40:34 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GIeYwB001442; Tue, 16 Mar 2021 13:40:34 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIeY5Q001438; Tue, 16 Mar 2021 13:40:34 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GIeXpJ001437; Tue, 16 Mar 2021 13:40:33 -0500 (CDT) Received: from wirelessprv-10-195-186-140.near.illinois.edu ([10.195.186.140]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GIeVim001429 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 16 Mar 2021 13:40:31 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_D4AEC136-8FAE-4950-BC3B-3370AB1FEA61" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Applying an external field to the electrostatic potential map Date: Tue, 16 Mar 2021 13:40:29 -0500 References: To: NAMD list , soumadwip ghosh In-Reply-To: Message-Id: <6E9B6EB0-4397-4F1B-B375-61DFBD256AEB@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_D4AEC136-8FAE-4950-BC3B-3370AB1FEA61 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Soumadwip, This tutorial is doing potential map manipulation external to either = NAMD or VMD. On page 3, point 6, they mention the external tools = provided and how to compile them. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 6, 2021, at 2:13 AM, soumadwip ghosh = wrote: >=20 > Hi folks. > =20 > I have done steered MD simulation of DNA+mspa to calculate the average = electrostatic potential of the system. However, we need to add the = applying external field (120 mV in this case) to get the complete = electrostatic potential. It is also the first step to study accelerated = translocation (grid-steered MD) of DNA through the pore under applied = external field. I have followed the NAMD tutorial below: > = http://bionano.physics.illinois.edu/sites/default/files/nanopore-protocols= .pdf = . I am applying the following command: > ../grid/gridExternalForce electric_raw.dx 0.02585 1.2 electric.dx = (you can find the procedure on page # 25 of the tutorial attached) . But = it is not working since the script is a .C script and I am unable to = compile it properly. Have you run this utility before and help me = troubleshoot this? I tried using gcc for compilation but to no use. > =20 > Could someone provide some insights into how to make it work?=20 > Soumadwip Ghosh >=20 --Apple-Mail=_D4AEC136-8FAE-4950-BC3B-3370AB1FEA61 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = Soumadwip,

This = tutorial is doing potential map manipulation external to either NAMD or = VMD. On page 3, point 6, they mention the external tools provided and = how to compile them.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Mar 6, 2021, at 2:13 AM, soumadwip ghosh <soumadwipghosh@gmail.com> wrote:

Hi folks.

 <= /p>

I have done steered MD simulation of DNA+mspa to = calculate the average electrostatic potential of the system. However, we = need to add the applying external field (120 mV in this case)  to = get the complete electrostatic potential. It is also the first step to = study accelerated translocation (grid-steered MD) of DNA through the = pore under applied external field. I have followed the NAMD tutorial = below:
 ../grid/gridExternalForce = electric_raw.dx 0.02585 1.2 electric.dx (you can find the procedure on = page # 25 of the tutorial attached) . But it is not working since the = script is a .C script and I am unable to compile it properly. Have you = run this utility before and help me troubleshoot this? I tried using gcc = for compilation but to no use.

 <= /p>

Could = someone provide some insights into how to make it work? 
Soumadwip = Ghosh


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boundary="000000000000b5f2ad05bdacfbd0" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxkSEQpMehcZHx8RCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHExoRCkNZFwcbHh8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGxJxGx4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XREd1GF5hTGVjSGYabWxgH11GT3V8W0wbfWVAfxlvdWMRClhcFx8EGgQYGBwF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXckJYfQURCk1cFxsdGREKTFoXbGlNa2sRCkxGF29ra2t raxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHBwEGx0YEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hacBhJH2Z4HkBeEQpCT hdjU2NrexNYfhpfXhEKQkwXbB9eWVpuTGFgW0ERCkJsF29CaX9uTltSGXgaEQpCQBdrbV5vTRx7 Rll9cxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2V4EhNkTWdMYXhoEQpZSxcTGR4 dEQpwaBdtTRh9WXtbGXJSQxAZGhEKcGgXZXhzH2tMb11/eV8QGRoRCnBoF2tIbx5/b1xPUBxiEB kaEQpwaBdiSRJcTngZbxkffxAZGhEKcGwXZ3hzc0JHXFt9RksQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 lowpriorityscore=0 clxscore=138 mlxlogscore=411 priorityscore=355 phishscore=0 mlxscore=0 suspectscore=0 adultscore=0 malwarescore=0 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103160126 domainage_hfrom=9347 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000b5f2ad05bdacfbd0 Content-Type: text/plain; charset="UTF-8" Dear Colleagues, What is the best time step for getting less fluctuations during NAMD simulations? Is there any rule of thumb for Protein alone or Ligand-protein complex inputs? Any comment will be highly appreciating! Dr. Mi --000000000000b5f2ad05bdacfbd0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
What is the best time step for gettin= g less fluctuations during NAMD simulations?
Is there any rule of= thumb for Protein alone or Ligand-protein complex inputs?
Any co= mment will be highly appreciating!

Dr. Mi
--000000000000b5f2ad05bdacfbd0-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 16:23:28 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GLNSxc008314; Tue, 16 Mar 2021 16:23:28 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GLNR7H008313; Tue, 16 Mar 2021 16:23:27 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GLNRXt008309; Tue, 16 Mar 2021 16:23:27 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GLNRUW008308; Tue, 16 Mar 2021 16:23:27 -0500 (CDT) Received: from wirelessprv-10-195-186-140.near.illinois.edu ([10.195.186.140]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GLNMOQ008301 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 16 Mar 2021 16:23:22 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_0B1FDAB9-2697-4311-866B-E16FE4BEE2D7" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Rule of thumb for choosing time step in MD Date: Tue, 16 Mar 2021 16:23:21 -0500 References: To: NAMD list , Mi Yang In-Reply-To: Message-Id: <14629019-374E-4DFB-BF5C-D8F2FB33527B@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_0B1FDAB9-2697-4311-866B-E16FE4BEE2D7 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Dr. Mi, Are you talking about energy fluctuations? The energy is expected to = fluctuate. There are known stability limits on the step size. Specifically, the = time step should be no more than about 1/5 the period of the fastest = oscillations present in the system (see = https://bionum.cs.purdue.edu/03aMaIS.pdf = ). This is the big motivation = for constraining bonds to hydrogen atoms (=E2=80=9CrigidBonds all=E2=80=9D= ) in order to eliminate what would otherwise be the fastest = oscillations, permitting use of multiple time stepping with a base time = step of up to 2 fs and a longest time step of 4 fs for the long-range = electrostatics. Simulating without constraints, you probably shouldn=E2=80= =99t exceed a base time step of 1 fs and a longest time step of 2 fs for = the long-range electrostatics. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 16, 2021, at 3:12 PM, Mi Yang wrote: >=20 > Dear Colleagues, > What is the best time step for getting less fluctuations during NAMD = simulations? > Is there any rule of thumb for Protein alone or Ligand-protein complex = inputs? > Any comment will be highly appreciating! >=20 > Dr. Mi --Apple-Mail=_0B1FDAB9-2697-4311-866B-E16FE4BEE2D7 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear = Dr. Mi,

Are you = talking about energy fluctuations? The energy is expected to = fluctuate.

There= are known stability limits on the step size. Specifically, the time = step should be no more than about 1/5 the period of the fastest = oscillations present in the system (see https://bionum.cs.purdue.edu/03aMaIS.pdf). This is the = big motivation for constraining bonds to hydrogen atoms (=E2=80=9CrigidBon= ds all=E2=80=9D) in order to eliminate what would otherwise be the = fastest oscillations, permitting use of multiple time stepping with a = base time step of up to 2 fs and a longest time step of 4 fs for the = long-range electrostatics. Simulating without constraints, you probably = shouldn=E2=80=99t exceed a base time step of 1 fs and a longest time = step of 2 fs for the long-range electrostatics.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Mar 16, 2021, at 3:12 PM, Mi Yang <drmiyang2019@gmail.com> wrote:

Dear Colleagues,
What is the best time step = for getting less fluctuations during NAMD simulations?
Is there any rule of thumb for Protein alone or = Ligand-protein complex inputs?
Any comment will be = highly appreciating!

Dr. Mi

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([2001:1388:3cc3:fa64:2805:767f:8d4b:448b]) by smtp.gmail.com with ESMTPSA id e3sm14080362qtj.28.2021.03.16.14.29.20 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Tue, 16 Mar 2021 14:29:21 -0700 (PDT) Content-Type: text/plain; charset=utf-8 From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Date: Tue, 16 Mar 2021 16:23:22 -0500 Subject: Re: namd-l: Add repulsive potential with dummy atom Message-Id: <20760B7C-5CC1-4C32-9964-00F260B01276@gmail.com> Cc: NAMD list To: David Hardy X-Mailer: iPhone Mail (18B92) X-CLX-Response: 1TFkXGxITEQpMehcZGR4RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGxMbEQpDWRcHGxwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBNxHhIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XfkRdR19oX2BTXXVYWVxAT09/SXBeGhxhQHJmB0thHkkRClhcFx8EGgQYGBwF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXckJZTGQRCk1cFxsYGxEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb29ra2traxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGB gEGx0dEQpCXhcbEQpEWBcYEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY 1Nja3sTWH4aX14RCkJFF2ZLbVhGGE9jRUNAEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwf cksRCkJsF29PZEFaQlBtZmtZEQpCQBdoSwFzRGxlbHB6ExEKTV4XGxEKWlgXGREKeUMXb3BIZBJ NXRtcRH0RCllLFxMZHh0RCnBnF2tNTXxOTF96Rx5NEBwaEQpwaBdvaR9oZRlhQWEeaBAZGhEKcG gXYEZdZW5EcmRYYn0QGRoRCnBsF2doQ2tzEnkYTWJcEBkaEQpwTBdgRRtyb05JTmh+WRAZGhEKb X4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 bulkscore=0 clxscore=189 phishscore=0 mlxscore=0 malwarescore=0 impostorscore=0 mlxlogscore=720 lowpriorityscore=0 priorityscore=334 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103160137 domainage_hfrom=9347 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 12GLTNfE009167 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Dear David, I have a box with 84 small molecules and not like that they make agregation. You can give an example of as make this with colvar please. Best, Geo. Enviado desde mi iPhone > El 16 mar. 2021, a la(s) 1:31 p. m., David Hardy escribió: > From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 16:52:16 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GLqGtJ012830; Tue, 16 Mar 2021 16:52:16 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GLqG0W012829; Tue, 16 Mar 2021 16:52:16 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GLqFIf012825; Tue, 16 Mar 2021 16:52:15 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GLqF9F012824; Tue, 16 Mar 2021 16:52:15 -0500 (CDT) Received: from wirelessprv-10-195-186-140.near.illinois.edu ([10.195.186.140]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GLqDOW012815 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 16 Mar 2021 16:52:13 -0500 (CDT) From: David Hardy Content-Type: text/plain; charset=utf-8 Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Add repulsive potential with dummy atom Date: Tue, 16 Mar 2021 16:52:13 -0500 References: <20760B7C-5CC1-4C32-9964-00F260B01276@gmail.com> To: NAMD list , =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= In-Reply-To: <20760B7C-5CC1-4C32-9964-00F260B01276@gmail.com> Message-Id: <5A518617-A888-4ADF-BF61-AD993E2D5809@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 12GLqDOV012816 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy Dear Geo, That does seem to be a lot of molecules for use with Colvars. That would require defining 84 center-of-mass CVs, and then there would be 3486 pairwise interactions between those centers. I don’t personally have expertise with using Colvars, but this seems larger than what might be reasonable. I’ll leave it to someone with Colvars expertise to further advise you. Best regards, Dave > On Mar 16, 2021, at 4:23 PM, ROPÓN-PALACIOS G. wrote: > > Dear David, > > I have a box with 84 small molecules and not like that they make agregation. > > You can give an example of as make this with colvar please. > > Best, > > Geo. > > Enviado desde mi iPhone > >> El 16 mar. 2021, a la(s) 1:31 p. m., David Hardy escribió: >> From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 17:02:06 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GM26p5015021; Tue, 16 Mar 2021 17:02:06 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GM26iC015020; Tue, 16 Mar 2021 17:02:06 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GM25c9015016; Tue, 16 Mar 2021 17:02:05 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GM25ek015015; 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Tue, 16 Mar 2021 15:01:51 -0700 (PDT) References: <20760B7C-5CC1-4C32-9964-00F260B01276@gmail.com> <5A518617-A888-4ADF-BF61-AD993E2D5809@ks.uiuc.edu> In-Reply-To: <5A518617-A888-4ADF-BF61-AD993E2D5809@ks.uiuc.edu> From: Giacomo Fiorin Date: Tue, 16 Mar 2021 18:01:15 -0400 Message-ID: Subject: Re: namd-l: Add repulsive potential with dummy atom To: NAMD list , David Hardy Cc: =?UTF-8?B?Uk9Qw5NOLVBBTEFDSU9TIEcu?= Content-Type: multipart/alternative; boundary="0000000000007e52be05bdae83fb" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIZEQpMehcZHxMRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHRsZEQpDWRcHGxwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBlxEh8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYFlJUmRAHQdYZn58ZE5DdRodf2FaYH19WhhvbmVBX1wRClhcFx8EGgQYGBwF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyQlkTWREKTVwXHxoTEQpMWhd4a2tNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tia2sRCkJPF2FZHHkYSAUSG0J4EQpDWhcYGhMEEh8EGBsTBB sSGBEKQl4XGxEKRFgXGBEKRF4XGBEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RC kJJF2NTY2t7E1h+Gl9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3Id bmxPWHhgEQpCbBdhX3pTGUNEGnobfhEKQkAXaEsBc0RsZWxwehMRClpYFxkRCnlDF29wSGQSTV0 bXER9EQpZSxcTGR4dEQpwZxdrTU18TkxfekceTRATGhEKcGgXaUJQQ359GWkdbEIQGRoRCnBoF2 17X05cYh1gHklaEBkaEQpwaBdmbmAcaVMFGktzXhAZGhEKcGgXa3pQQ14cfVpSUHgQGRoRCnBoF 2RMTmN6cG5JXn5TEBkaEQpwfRdvYXJyYWt/XXppehAZGhEKcH0Xbh5DWWZPHF8bUF8QGRoRCnB/ F2JOBQFwRF5pRHtlEBsaExEKcF8XYhpfUExGAUYcGlIQGRoRCnBfF2RDHktYekJHfVgcEBkaEQp wbBdmH3tYXGIFS1hkHxAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=183 bulkscore=0 impostorscore=0 malwarescore=0 suspectscore=0 spamscore=0 phishscore=0 priorityscore=359 mlxscore=0 adultscore=0 lowpriorityscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103160139 domainage_hfrom=9347 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --0000000000007e52be05bdae83fb Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Geo, the documentation at the Colvars website is a bit richer than what is included in the NAMD manual: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html__;!!DZ3fjg!qyo_tG5E3pBOtceAeUUlmOgzvZhE-ISTyqmxGzMq= 3Q7N6md_JUVoSGd9o1sZkrRtJg$=20 and there are specific examples listed on the top page: https://urldefense.com/v3/__https://colvars.github.io/__;!!DZ3fjg!qyo_tG5E3= pBOtceAeUUlmOgzvZhE-ISTyqmxGzMq3Q7N6md_JUVoSGd9o1sQEdszXg$=20 However, there isn't likely to be an input file that is just ready to be reused, though, for several reasons: 1. There are details of your system that you didn't describe, but would be needed to prepare a good input. 2. The version of NAMD that you are using is important, as it affects the Colvars features available to you. In principle it is possible to build a more recent version of Colvars with older versions of NAMD, but this is not supported (meaning, it will likely work but taking more work on your part). 3. The Lennard-Jones potential is not present as a pre-compiled function for Colvars, although there are provisions to add custom functions at runtime listed in the Colvars doc. 4. If I understand correctly what Dave also understood, you have many pairs of molecules, which would mean a lot of variables that aren't really "collective". Without resorting to advanced features/packages, why not simply pick one atom for each molecule, and apply forces between them with tclBC? It is slower than C++ code (like e.g. the force field functions from NAMD or the collective variables from Colvars), but it would be at least parallelized over nodes, and probably result in small overhead. Giacomo On Tue, Mar 16, 2021 at 5:53 PM David Hardy wrote: > Dear Geo, > > That does seem to be a lot of molecules for use with Colvars. That would > require defining 84 center-of-mass CVs, and then there would be 3486 > pairwise interactions between those centers. I don=E2=80=99t personally h= ave > expertise with using Colvars, but this seems larger than what might be > reasonable. > > I=E2=80=99ll leave it to someone with Colvars expertise to further advise= you. > > Best regards, > Dave > > > On Mar 16, 2021, at 4:23 PM, ROP=C3=93N-PALACIOS G. > wrote: > > > > Dear David, > > > > I have a box with 84 small molecules and not like that they make > agregation. > > > > You can give an example of as make this with colvar please. > > > > Best, > > > > Geo. > > > > Enviado desde mi iPhone > > > >> El 16 mar. 2021, a la(s) 1:31 p. m., David Hardy > escribi=C3=B3: > >> > > > --0000000000007e52be05bdae83fb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Geo, the documentation at the Colvars website is a bit = richer than what is included in the NAMD manual:
and there are specific ex= amples listed on the top page:

However, there isn't likely to be a= n input file that is just ready to be reused, though, for several reasons:<= /div>
1. There are details of your system that you didn't describe,= but would be needed to prepare a good input.
2. The version of N= AMD that you are using is important, as it affects the Colvars features ava= ilable to you.=C2=A0 In principle it is possible to build a more recent ver= sion of Colvars with older versions of NAMD, but this is not supported (mea= ning, it will likely work but taking more work on your part).
3. = The Lennard-Jones potential is not present as a pre-compiled function for C= olvars, although there are provisions to add custom functions at runtime li= sted in the Colvars doc.
4. If I understand correctly what Dave a= lso understood, you have many pairs of molecules, which would mean a lot of= variables that aren't really "collective".

Without resorting to advanced features/packages, why not simply pic= k one atom for each molecule, and apply forces between them with tclBC?=C2= =A0 It is slower than C++ code (like e.g. the force field functions from NA= MD or the collective variables from Colvars), but it would be at least para= llelized over nodes, and probably result in small overhead.

<= /div>
Giacomo

On Tue, Mar 16, 2021 at 5:53 PM David Hardy <dhardy@ks.uiuc.edu&= gt; wrote:
Dear = Geo,

That does seem to be a lot of molecules for use with Colvars. That would re= quire defining 84 center-of-mass CVs, and then there would be 3486 pairwise= interactions between those centers. I don=E2=80=99t personally have expert= ise with using Colvars, but this seems larger than what might be reasonable= .

I=E2=80=99ll leave it to someone with Colvars expertise to further advise y= ou.

Best regards,
Dave

> On Mar 16, 2021, at 4:23 PM, ROP=C3=93N-PALACIOS G. <biodano.geo@gmail.com> = wrote:
>
> Dear David,
>
> I have a box with 84 small molecules and not like that they make agreg= ation.
>
> You can give an example of as make this with colvar please.
>
> Best,
>
> Geo.
>
> Enviado desde mi iPhone
>
>> El 16 mar. 2021, a la(s) 1:31 p. m., David Hardy <dhardy@ks.uiuc.edu> escri= bi=C3=B3:
>>


--0000000000007e52be05bdae83fb-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 16 17:24:06 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GMO6a9017345; Tue, 16 Mar 2021 17:24:06 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GMO6q4017344; Tue, 16 Mar 2021 17:24:06 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GMO5x1017340; Tue, 16 Mar 2021 17:24:05 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12GMO527017339; Tue, 16 Mar 2021 17:24:05 -0500 (CDT) Received: from wirelessprv-10-195-186-140.near.illinois.edu ([10.195.186.140]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12GMO0Y9017332 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 16 Mar 2021 17:24:01 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_FB00C2BA-6CB6-44AA-8A30-9FE241D9A3C5" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Lone pair disconnected after minimization Date: Tue, 16 Mar 2021 17:23:59 -0500 References: To: NAMD list , Rabiul Gazi In-Reply-To: Message-Id: <695E6AE1-46A0-4332-8F0C-2C216C739B2C@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_FB00C2BA-6CB6-44AA-8A30-9FE241D9A3C5 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Rabiul, This sounds suspiciously that NAMD was not actually aware of the lone = pairs, i.e., your PSF file might be wrong. First, can you please verify = that your PSF file actually has lone pairs properly defined in it (e.g., = grep for the NUMLP section of your PSF)? When you list out the NUMLP = section of your PSF file, do you see the supporting atom definitions for = all of the lone pairs listed in your NATOM section? Finally, near the = top of your log file output, do you see LONE PAIRS listed under = STRUCTURE SUMMARY? Is it the same number of lone pairs that you defined = in your PSF file? Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 15, 2021, at 4:36 AM, Rabiul Gazi = wrote: >=20 > Dear Experts, > I am dealing with a chlorobenzene derivative molecules water system. = The system contains 10 molecules. After energy minimization it has been = observed that lone pairs of chlorine atoms disconnected for few = chlorobenzene derivative molecules. =20 >=20 > I am using NAMD2.14 for the water system . The psf files were built = using psfgen 2.0. >=20 > Please help me in this regard. >=20 > Thank you > Rabiul --Apple-Mail=_FB00C2BA-6CB6-44AA-8A30-9FE241D9A3C5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = Rabiul,

This sounds = suspiciously that NAMD was not actually aware of the lone pairs, i.e., = your PSF file might be wrong. First, can you please verify that your PSF = file actually has lone pairs properly defined in it (e.g., grep for the = NUMLP section of your PSF)? When you list out the NUMLP section of your = PSF file, do you see the supporting atom definitions for all of the lone = pairs listed in your NATOM section? Finally, near the top of your log = file output, do you see LONE PAIRS listed under STRUCTURE SUMMARY? Is it = the same number of lone pairs that you defined in your PSF = file?

Best = regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Mar 15, 2021, at 4:36 AM, Rabiul Gazi <rabiulgazi876@gmail.com> wrote:

Dear Experts,
I am dealing with a = chlorobenzene derivative molecules water system. The system contains = 10  molecules. After energy=20 minimization it has been observed that lone pairs of chlorine atoms=20 disconnected for few chlorobenzene derivative  = molecules.  

I am using NAMD2.14 for the water system . The psf files were = built using psfgen 2.0.

Please help me in this regard.

Thank you
 Rabiul

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To: Giacomo Fiorin , NAMD list , David Hardy Message-ID: <68EDF00E-2EC6-4698-926D-47E47169D29A@gmail.com> Thread-Topic: namd-l: Add repulsive potential with dummy atom References: <20760B7C-5CC1-4C32-9964-00F260B01276@gmail.com> <5A518617-A888-4ADF-BF61-AD993E2D5809@ks.uiuc.edu> In-Reply-To: Content-type: multipart/alternative; boundary="B_3698761504_699680641" X-CLX-Response: 1TFkXGx0ZEQpMehcZHhoRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHBgfEQpDWRcHGxwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxlxGRkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XbEFEXG5JY3gbXEt1fEltQ1BNEhJ7eHlLU14dZFgac3kRClhcFx8EGgQYGBwF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyQl5HZBEKTVwXHh4ZEQpMWhdpe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGA QbEhoRCkJeFxsRCkRYFxgRCkReFxkRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9y SxEKQmwXY2lZb3pPHXJHT38RCkJAF2hLAXNEbGVscHoTEQpaWBcZEQp5QxdvcEhkEk1dG1xEfRE KWUsXExkeHREKcGcXaUNuUAFZc0cBHlMQGhEKcGgXaHJvWHx8YG99QXsQGhEKcGgXbEFHQ1pwR1 AFRFkQGhEKcGgXZnNta01vcgV4Hh4QGhEKcGgXbnp5WGhpR38ZE1oQGhEKcGgXZ1BAf0R8bxxOR l8QGhEKcGcXa01NfE5MX3pHHk0QGxoaEQpwfRdvYXJyYWt/XXppehAZGhEKcH0Xbh5DWWZPHF8b UF8QGRoRCnB/F2JOBQFwRF5pRHtlEBsaExEKcF8XYhpfUExGAUYcGlIQGRoRCnBfF2RDHktYekJ HfVgcEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCnBDF25eZWEdHl xHQ31HEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 priorityscore=340 malwarescore=0 suspectscore=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 clxscore=173 adultscore=0 spamscore=0 mlxscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103160146 domainage_hfrom=9347 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698761504_699680641 Content-type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Giacomo,=20 =20 I have not had any rapprochement with tclBC, I don't know if you could give= me an example that I can start with please. =20 On the other hand, I found in the example of colvar one called "02_aggregat= ion.colvars.in", basically what I want is that the molecules (84 ligands pl= aced around my protein at random), I don't know how to add, forming a clust= er of itself, already I have a high number and many authors have mentioned = this phenomenon. This script (02_aggregtion_colvars.in) that I found in the= examples might help me. =20 Greetings, =20 geo. =20 From: Giacomo Fiorin Date: Tuesday, March 16, 2021 at 5:01 PM To: NAMD list , David Hardy Cc: "ROP=C3=93N-PALACIOS G." Subject: Re: namd-l: Add repulsive potential with dummy atom =20 Hi Geo, the documentation at the Colvars website is a bit richer than what = is included in the NAMD manual: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html__;!!DZ3fjg!rTvkcxHZMdgD-cSj2vJjRDsVB3nInQ8zcezbiQHE= dvI4YOC9Ey0P3AABAShYYhq8VA$=20 and there are specific examples listed on the top page: https://urldefense.com/v3/__https://colvars.github.io/__;!!DZ3fjg!rTvkcxHZM= dgD-cSj2vJjRDsVB3nInQ8zcezbiQHEdvI4YOC9Ey0P3AABASinxQtBcw$=20 =20 However, there isn't likely to be an input file that is just ready to be re= used, though, for several reasons: 1. There are details of your system that you didn't describe, but would be = needed to prepare a good input. 2. The version of NAMD that you are using is important, as it affects the C= olvars features available to you. In principle it is possible to build a m= ore recent version of Colvars with older versions of NAMD, but this is not = supported (meaning, it will likely work but taking more work on your part). 3. The Lennard-Jones potential is not present as a pre-compiled function fo= r Colvars, although there are provisions to add custom functions at runtime= listed in the Colvars doc. 4. If I understand correctly what Dave also understood, you have many pairs= of molecules, which would mean a lot of variables that aren't really "coll= ective". =20 Without resorting to advanced features/packages, why not simply pick one at= om for each molecule, and apply forces between them with tclBC? It is slow= er than C++ code (like e.g. the force field functions from NAMD or the coll= ective variables from Colvars), but it would be at least parallelized over = nodes, and probably result in small overhead. =20 Giacomo --B_3698761504_699680641 Content-type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

Dear Giacomo,

 

I have not had any r= approchement with tclBC, I don't know if you could give me an example that = I can start with please.

 

On the other hand, I found in the example of col= var one called "02_aggregation.colvars.in", basically what I want= is that the molecules (84 ligands placed around my protein at random), I d= on't know how to add, forming a cluster of itself, already I have a high nu= mber and many authors have mentioned this phenomenon. This script (02_aggre= gtion_colvars.in) that I found in the examples might help me.

 

Greetings,<= o:p>

 

geo.

 

<= p class=3DMsoNormal>From: <= /span>Giacomo Fiorin <g= iacomo.fiorin@gmail.com>
Date: Tuesday, March 16, 2021 at 5:01= PM
To: NAMD list <namd-l@ks.uiuc.edu>, David Hardy <dha= rdy@ks.uiuc.edu>
Cc: "ROP=C3=93N-PALACIOS G." <bi= odano.geo@gmail.com>
Subject: Re: namd-l: Add repulsive potent= ial with dummy atom

 

Hi Geo, the documentat= ion at the Colvars website is a bit richer than what is included in the NAM= D manual:

an= d there are specific examples listed on the top page:

=

 

<= p class=3DMsoNormal>However, there isn't likely to be an input file that is just read= y to be reused, though, for several reasons:

1. There are details of your system that you didn't describe, = but would be needed to prepare a good input.

2. The version of NAMD that you are using is important, as it = affects the Colvars features available to you.  In principle it is pos= sible to build a more recent version of Colvars with older versions of NAMD= , but this is not supported (meaning, it will likely work but taking more w= ork on your part).

3. The Lennar= d-Jones potential is not present as a pre-compiled function for Colvars, al= though there are provisions to add custom functions at runtime listed in th= e Colvars doc.

4. If I understan= d correctly what Dave also understood, you have many pairs of molecules, wh= ich would mean a lot of variables that aren't really "collective"= .

 

Without resorting to advanced features/packages, why no= t simply pick one atom for each molecule, and apply forces between them wit= h tclBC?  It is slower than C++ code (like e.g. the force field functi= ons from NAMD or the collective variables from Colvars), but it would be at= least parallelized over nodes, and probably result in small overhead.=

 

Giacomo

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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=ds35bRs9nL3A5vy9JHV6plXnzggA79VxWJ95QlRiR4o=; b=GtXqDYcJaFZbaCXq7tNoA037Da4Q4aO4Vm6NPDdtUMArM8RRt5GFhmc/D97wfUXVG6 18NPsCeVSsZcMwp3NTFF7uGCUPW7U70+NJBlg9IisFeMjTlNDoQOTLTzmBd1GeRW6DMr SV9ZsQvGzoIpwiHNsFOTtKHxjdMxR8/GDSMwOOIZKz1N1VbmQoQYeqamPQzgRb6OrYhb ahMPK+zwoSXqtLtZuftvryU+yT6Vmkgehtd5Xp7ZV03B7M6iqBjpaB+uyivOIezfzvrW kK1JDbx/OhHXIjgS6ZmAdjMtK1FX9LY7vJMSZf/yOKt12dP+unkEGrKWXQVqrNyDOfb2 XcZA== X-Gm-Message-State: AOAM531UY5O/oEHB4QToFsU3iQayVi/4aMUYMX+BfB/wx+s1+ccEa67+ vTrLDLBhvOOPcyHOmARA6C1wWvuwRsMb35yki+JH2GpPog== X-Google-Smtp-Source: ABdhPJy4taZW8j45qGgt5DrcB+d7P6Twa4Ca8cMqVnbFFXpWoJ6PXvW3Z9J6uHToppLiMA0p/gvkn83cVHRkh0Htc+g= X-Received: by 2002:aca:4fc1:: with SMTP id d184mr1106315oib.31.1615945706683; Tue, 16 Mar 2021 18:48:26 -0700 (PDT) References: <48a9706a-aed3-1a68-6bb5-5f7642411134@msu.edu> <73a47451-b785-58db-ed95-2e54aed3d09a@msu.edu> <7831F286-3614-449D-89D7-25D40E7D747C@ks.uiuc.edu> In-Reply-To: <7831F286-3614-449D-89D7-25D40E7D747C@ks.uiuc.edu> From: Michael Von Domaros Date: Tue, 16 Mar 2021 18:47:26 -0700 Message-ID: Subject: Re: namd-l: 3.0alpha9 CUDA version To: David Hardy Cc: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000d2d52e05bdb1ad9c" X-CLX-Response: 1TFkXGxwfEQpMehceEhEKWUQXZH9gH31AcGQcHX8RClhYF2ZeZWhbQ21yemh CEQp4ThdkH1MBT11jWXkaGBEKeUwXZ09Jen9ObH1oTE4RCkNIFwcfGx8RCkNZFwcbGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseH3EYHRAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThccTWBwWnpyWGR8TmwfHWl7Xh1MGHBNYXJ8YQdMXEBvexEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JCXXltEQpNXBceHhIRCkxaF3tra01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2JraxEKQk8XZkwfTWltQUAfE3MRCkNaFxgaEwQSHwQbHB0EGx0bEQ pCXhcbEQpESRcbEQpCRRdiWBhTZHB4HUJdHREKQk4XZB9TAU9dY1l5GhgRCkJMF2ZeZWhbQ21ye mhCEQpCbBdnGxNcZh5eaXNyWhEKQkAXYWASSEtSZkEYaEQRCkJYF2dzZXNAbmFhTF1iEQpaWBcS EQp5QxdsRxppWR1pf1MaYxEKcGcXa01NfE5MX3pHHk0QHRIRCnBoF2hEHGIZelJiEkxcEBkaEQp waBdkWxtDZVJJZUhgeBAZGhEKcGgXY3lBHBJtG01lBUIQGRoRCnBoF2ZDUkVuXEdbZ0kFEBkaEQ pwaBdnXXAbe0xeRntMUxAZGhEKcH0Xbm5JR1prSWlOT1sQGRoRCnBnF2V9XUEaXH5Ea0VrEBkaE QpwfRd6c35mTx5De0lHRhAZGhEKcH0XZVxjXH9uY2hTRHMQGRoRCnB9F2VLZ0BPUm9zZG9gEBka EQpwfRd6TBtlfH9+YmVgRhAZGhEKcH0Xa3ocYFMZGG9QRWAQGRoRCnB9F2IBbmRpW2BFcnkfEBk aEQpwZxdgHkVsQmZrRxpfYBAZGhEKcH8XZVhyGB1JGF5GaXwQHRwRCnBfF2ZwSFxAeQFBHk8SEB kaEQpwfxdgQlN6bm1YemQBExASGBEKcF8XZFtPc0FHQ31beXgQGRoRCnB/F2Fmb1saZ2RCSB1bE BsYHREKcF8XY2ISUEhjeB98Qn0QGxocEQpwfxdrHWseU3tnY0ttehAbGx8RCnBfF25ERHxBeBpk Xm97EBkaEQpwfxduH2ddfV5AE3hkeRATHBEKcF8XZGNobR59UGtMUGAQGRoRCnBsF24fZUgFXUJ Fbm9eEBkaEQpwTBdgRRtyb05JTmh+WRAZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 priorityscore=48 malwarescore=0 suspectscore=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 clxscore=165 adultscore=0 spamscore=0 mlxscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103170010 X-Spam-Score: 0 X-Spam-OrigSender: mvondoma@uci.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Von Domaros --000000000000d2d52e05bdb1ad9c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks for clarifying this, Dave! And thanks to everyone else for their help, too. I have it working now and our admins are relieved :) On Tue, Mar 16, 2021 at 11:21 AM David Hardy wrote: > Hi Michael, > > I just wanted to follow up in support of what Josh said. The NAMD License > that we developed years ago with the university legal department allows > much freedom to users, including monetarily free access to run the softwa= re > and view the source code, along with some amount of reuse of the code. > However, in order for us to not to be in violation of our own license when > distributing NAMD, the license must be presented to the user in a > =E2=80=9Cclick-through=E2=80=9D form, which is why access to the GitLab r= epository is > protected in the way that it is. > > As Josh stated, it is fine for you to obtain the NAMD source code through > GitLab, even when your intention is simply to build NAMD yourself. > > Best regards, > Dave > > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > > On Mar 12, 2021, at 7:54 AM, Vermaas, Josh wrote: > > Hi Michael, > > Developers are certainly one audience, but really the reason behind the > gitlab wall is due to needing to be able to track users for reporting usa= ge > statistics back to funding agencies, and to make sure folks have agreed to > the NAMD license. That is why the user registration form is one of the > prerequisites, so that the developers can report back to NIH the percenta= ge > of users that have NIH funding. Being able to download the source so you > can compile it on your own hardware is totally a legit reason to get acce= ss > through gitlab IMHO. I believe this opinion is shared by the folks that > actually have decision making power. > > -Josh > > On 3/11/21 9:52 PM, Michael Von Domaros wrote: > > Thanks, Josh! That's quite encouraging. Does that mean it's possible to > request Gitlab access for this reason? I was operating under the assumpti= on > that this is just for developers. > > Michael > > On Thu, Mar 11, 2021 at 5:28 PM Vermaas, Josh wrote: > >> Hi Michael, >> >> I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the >> source from gitlab. >> >> https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!= srKSpjcmbaw8r4qFlcV6ANlGmRzm2eWt-nIUQ2RDvcTTbX1_otEf3LsT7SJm_3qAQQ$=20 >> >> >> It is in the devel branch, and it tagged as 3.0a9. I have compilation >> instructions that are what I used (or at least what I think I used from >> memory) on github. >> >> https://urldefense.com/v3/__https://github.com/jvermaas/Software-Buildin= g-Instructions/blob/main/NAMD.md__;!!DZ3fjg!srKSpjcmbaw8r4qFlcV6ANlGmRzm2eW= t-nIUQ2RDvcTTbX1_otEf3LsT7SJZ7lghhQ$=20 >> >> >> Compilation with NAMD3 from there is basically the same as it would be >> anywhere else. You need charm++ compiled, followed by NAMD itself. The >> hardest part for me was actually sorting out which of the many openMPI >> implementations installed on the cluster had the PMI backend so I could >> just call srun if I wanted to do replica exchange stuff. >> >> -Josh >> >> On 3/11/21 7:42 PM, Michael Von Domaros wrote: >> > Hi everyone, >> > >> > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or >> > something even newer? not sure.) Is this absolutely necessary? I'm >> > asking because our compute cluster is stuck with CUDA 10 and CUDA 10 >> > compatible device drivers, because a pretty substantial software stack >> > has been compiled against this version. The admins are somewhat >> > hesitant to update the device drivers, because they don't think that >> > running CUDA 10 apps with newer device drivers will be flawless. >> > >> > So, long story short: Could NAMD3 be compiled against CUDA 10? If so, >> > is there any way to access the source code? As far as I can tell, only >> > source codes for the 2.x series and nightly snapshots are available. >> > >> > Thanks a bunch, >> > Michael >> >> -- >> Josh Vermaas >> Assistant Professor, MSU-DOE Plant Research Lab and Department of >> Biochemisty and Molecular Biology >> vermaasj@msu.edu >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!srKSpjcmbaw8r4qFlcV6ANlGmRzm2eWt-nIUQ2RDvcTTbX1_otEf= 3LsT7SJw-8BqoA$=20 >> >> >> > -- > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochem= isty and Molecular Biologyvermaasj@msu.eduhttps://prl.natsci.msu.edu/people= /faculty/josh-vermaas/ > > > --000000000000d2d52e05bdb1ad9c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thanks for clarifying this, Dave! And thanks to every= one else for their help, too. I have it working now and our admins are reli= eved :)



On Tue, Mar 16, 2021 at 11:21 AM= David Hardy <dhardy@ks.uiuc.edu> wrote:
Hi Michael,

I ju= st wanted to follow up in support of what Josh said. The NAMD License that = we developed years ago with the university legal department allows much fre= edom to users, including monetarily free access to run the software and vie= w the source code, along with some amount of reuse of the code. However, in= order for us to not to be in violation of our own license when distributin= g NAMD, the license must be presented to the user in a =E2=80=9Cclick-throu= gh=E2=80=9D form, which is why access to the GitLab repository is protected= in the way that it is.

As Josh stated, it is fine= for you to obtain the NAMD source code through GitLab, even when your inte= ntion is simply to build NAMD yourself.

Best regar= ds,
Dave


On Mar 12, 2021, at 7:54 AM, Vermaa= s, Josh <vermaasj@= msu.edu> wrote:

Hi Michael,

Developers are certainly one audience, but really the reason behind the git= lab wall is due to needing to be able to track users for reporting usage st= atistics back to funding agencies, and to make sure folks have agreed to th= e NAMD license. That is why the user registration form is one of the prerequisites, so that the developers= can report back to NIH the percentage of users that have NIH funding. Bein= g able to download the source so you can compile it on your own hardware is= totally a legit reason to get access through gitlab IMHO. I believe this opinion is shared by the folks that ac= tually have decision making power.

-Josh

On 3/11/21 9:52 PM, Michael Von Domaros wrote:
Thanks, Josh! That's quite encouraging. Does that mean it's po= ssible to request Gitlab access for this reason? I was operating under the = assumption that this is just for developers.

Michael

On Thu, Mar 11, 2021 at 5:28 PM Verma= as, Josh <vermaasj= @msu.edu> wrote:
Hi Michael,

I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the
source from gitlab.

https://gitlab.com/tcbgUIUC/namd
It is in the devel branch, and it tagged as 3.0a9. I have compilation
instructions that are what I used (or at least what I think I used from
memory) on github.
https://github.com/jvermaas/Software-Building-Instructions/blob/main/= NAMD.md

Compilation with NAMD3 from there is basically the same as it would be
anywhere else. You need charm++ compiled, followed by NAMD itself. The
hardest part for me was actually sorting out which of the many openMPI
implementations installed on the cluster had the PMI backend so I could
just call srun if I wanted to do replica exchange stuff.

-Josh

On 3/11/21 7:42 PM, Michael Von Domaros wrote:
> Hi everyone,
>
> It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or > something even newer? not sure.) Is this absolutely necessary? I'm=
> asking because our compute cluster is stuck with CUDA 10 and CUDA 10 > compatible device drivers, because a pretty substantial software stack=
> has been compiled against this version. The admins are somewhat
> hesitant to update the device drivers, because they don't think th= at
> running CUDA 10 apps with newer device drivers will be flawless.
>
> So, long story short: Could NAMD3 be compiled against CUDA 10? If so,<= br> > is there any way to access the source code? As far as I can tell, only=
> source codes for the 2.x series and nightly snapshots are available. >
> Thanks a bunch,
> Michael

--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology
vermaasj@msu.edu<= br> https://prl.n= atsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/

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boundary="000000000000d008aa05bdbbcd1f" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxgeEQpMehcZGhIRCllEF2R+YBkeS29lZ10cEQpYWBdrRm0dHmlzUB1 +GBEKeE4XY1Nja3sTWH4aX14RCnlMF21vaExoaE0SH0xkEQpDSBcHGR4SEQpDWRcHGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsaHnEbGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThcSZ0REcGUaYE9TcnlncB5oZR0Sa3VjYRNve1xMQmZgQxEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3JCHB9GEQpNXBcfGBkRCkxaF3xpa2trEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XekxDSXNpeQFbQHsRCkNaFxgaEwQSHwQYGxoEHh IRCkJeFxsRCkReFxgRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2Nre xNYfhpfXhEKQkUXZ0BOeAFNXkdZTnsRCkJOF2NTY2t7E1h+Gl9eEQpCTBdrRm0dHmlzUB1+GBEK QmwXYRIST09MTX9PHgURCkJAF2RBEmkSZ1kcGnpOEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxEKeUM XZxJhWRpoHUJeZWMRCllLFxMZHhIRCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdkegFJTUJnQWtMeR AZGhEKcGgXekliHH5iT3NNfFgQGRoRCnBoF2tQfEVhYG5wWUVPEBkaEQpwaBdoX1t/GGNHaHBtQ xAZGhEKcGgXZxJgHExjZx0cfH0QGRoRCnBnF2NcUGEbUm1oHGFpEBkaEQpwZxduQHp9e25lZ0RI GxAZGhEKcH0Xb1NnfUNDSxlQHmYQGRoRCnB9F2h5eURDW1JDQ3BvEBkaEQpwfRdgb3hgQxwdeUV oGxAZGhEKcH0XZEkbXRIYUk9gchkQGRoRCnB/F2Fmb1saZ2RCSB1bEBsZHxEKcF8XY2ISUEhjeB 98Qn0QGxobEQpwfxdlWHIYHUkYXkZpfBAbGB4RCnBfF2UcGBpjTnwZXhx5EBkaEQpwXxdmXxJ4Q 2ZbemsFWhAZGhEKcGwXaHtGWGJ/emZ9HGUQGRoRCnBMF2YaXhJOZE1DeGRYEBkaEQptfhcaEQpY TRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=124 bulkscore=0 impostorscore=0 malwarescore=0 suspectscore=0 spamscore=0 phishscore=0 priorityscore=308 mlxscore=0 adultscore=0 lowpriorityscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103170104 domainage_hfrom=9348 X-Spam-Score: 0 X-Spam-OrigSender: heninj@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= --000000000000d008aa05bdbbcd1f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable On Tue, 9 Mar 2021 at 00:26, Ren=C3=A9 Hafner TUK wrote: > Thanks a lot J=C3=A9r=C3=B4me! > > To understand this correctly: > > * This means that when using MW-ABF the walkers are benefitting from each > other (as gradient counts are shared, well reflected in the files) > > Yes. > * but in case of MW-eABF sharing of eABF data is not (and was never?) > shared (as it was not reflected in the files before and therefore also not > internally?!) or do/did the walkers still benefit from each other? > > MW-eABF is not that different from ABF, it's just that the ABF quantities (mainly the biasing force itself) pertain to the extended coordinate. Those are shared exactly as in standard mwABF, because they are represented the same way in the implementation. The data for the *unbiased free energy estimators* is a separate question: it is not shared in the current state of the code, and in a sense it does not need to be shared during the simulation, as these estimators are really a matter of post-processing. Anything that is done on the fly is just for convenience. * Then latest literature would be a bit misleading when stating usage > of MW-eABF. > > Is there something else than the QM/MM tutorial that mentions it? Best, Jerome > On 3/8/2021 11:41 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote: > > Dear Hua Hao and Ren=C3=A9, > > I was not aware of that use of eABF in multiple-walker form in the > tutorial. That is not a documented/supported feature, and there is a litt= le > work to properly combine the data. > Anyway, I have just pushed a commit that partly reverts the previous one. > What remains is that ABF files are written after sharing, so the plain ABF > data should be the same for all replicas. > > Best regards, > J=C3=A9r=C3=B4me > > On Mon, 1 Mar 2021 at 16:28, hua hao wrote: > >> Thanks, Abhishek. >> >> I try to do it, but the problem is still present. >> >> Abhishek Acharya =E4=BA=8E2021=E5=B9=B43=E6=9C= =881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81=93=EF= =BC=9A >> >>> Hi, >>> >>> Maybe you can try something like this. >>> mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.l= og >>> >>> Abhi >>> >>> >>> Virus-free. >>> https://urldefense.com/v3/__http://www.avast.com__;!!DZ3fjg!sevlfjQ6JGJ= uVU9XpERk00JW3ppf3VaHSmqjskAT9ZlEVUI_HsrREErAxJBGQwPcvg$=20 >>> >>> >>> On Mon, Jan 4, 2021 at 6:02 PM hua hao wrote: >>> >>>> Hi NAMD developers and users, >>>> >>>> I am learning Tutorial_QMMM_String_eABF recently, which was introduced >>>> to be an advanced tutorial for QMMM in NAMD page ( >>>> http://www.ks.uiuc.edu/Research/qmmm/). >>>> >>>> When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl >>>> +stdout output_eABF/%1d/job00.%1d.log", it is strange that some necess= ary >>>> files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were on= ly >>>> present in the first replica (i..e 0), but not in other replicas (i.e. >>>> 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were used to perform the above >>>> calculations, and these packages were both complied using openmpi-3.1.4 >>>> build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts >>>> and Linux-x86_64-verbs, the error was still present. >>>> >>>> Normally, these files should appear in each replica. >>>> >>>> Could you help me with this issue? Thank you very much. >>>> >>>> *Hua Hao* >>>> >>>> -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --000000000000d008aa05bdbbcd1f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
On Tue, 9 Mar 2021 at 00:26, Ren=C3=A9 Ha= fner TUK <hamburge@physik.uni-kl.de> wrote:
=20 =20 =20

Thanks a lot J=C3=A9r=C3=B4me!

To understand this correctly:

* This means that when using MW-ABF the walkers are benefitting from each other (as gradient counts are shared, well reflected in the files)

<= /blockquote>
Yes.=C2=A0

* but in case of MW-eABF sharing of eABF data is not (and was never?) shared (as it was not reflected in the files before and therefore also not internally?!) or do/did the walkers still benefit from each other?

MW-eABF is not that different from ABF, it's just th= at the ABF quantities (mainly the biasing force itself) pertain to the exte= nded coordinate. Those are shared exactly as in standard mwABF, because the= y are represented the same way in the implementation.
The data fo= r the *unbiased free energy estimators* is a separate question: it is not s= hared in the current state of the code, and in a sense it does not need to = be shared during the simulation, as these estimators are really a matter of= post-processing. Anything that is done on the fly is just for convenience.=

=C2=A0=C2=A0=C2=A0 * Then latest literature would be a bit misle= ading when stating usage of MW-eABF.

Is there something else than the QM/MM tutorial that=C2=A0men= tions it?

Best,
Jerome
=C2=A0<= /div>
=C2=A0
=C2=A0

On 3/8/2021 11:41 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote:
=20
Dear Hua Hao and Ren=C3=A9,

I was not aware of that use of eABF in multiple-walker form in the tutorial. That is not a documented/supported feature, and there is a little work to properly combine the data.
Anyway, I have just pushed a commit that partly reverts the previous one. What remains is that ABF files are written after sharing, so the plain ABF data should be the same for all replicas.

Best regards,
J=C3=A9r=C3=B4me

On Mon, 1 Mar 2021 at 16:28, hua hao <haohua0116@gmail.com> wrote:
Thanks, Abhishek.

I try to do it,=C2=A0but the problem=C2=A0is still present.=C2=A0

Abhishek Acharya <abhi117acharya@gmail.com>=E4=BA=8E2021=E5=B9=B43=E6=9C= =881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81= =93=EF=BC=9A
Hi,

Maybe you can try something like this.
mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log

Abhi
3D""
Virus-free. www.avast.com

On Mon, Jan 4, 2021 at 6:02 PM hua hao <haohua0116@gmail.com> wrote:
Hi NAMD developers and users,

I am learning Tutorial_QMMM_String_eABF recently, which was introduced to be an advanced tutorial for QMMM in NAMD page (http://www.ks= .uiuc.edu/Research/qmmm/).

When running the eABF job by "mpirun -n 28 namd= 2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/job00.%= 1d.log", it is strange that some necessary files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only present in the first=C2=A0replica (i..e 0), but not in other=C2=A0replicas (i.= e. 1-13).=C2=A0NAMD-2.14 and=C2=A0NAMD-Gib-2020-= 12-07=C2=A0were used to perform the above calculations, and these packages were both complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netlrts and=C2=A0Linux-x86_64-verbs, the error was still present.

Normally, these files should appear in each=C2=A0replica.

Could you help me with this issue? Thank you very much.

= Hua Hao

--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--000000000000d008aa05bdbbcd1f-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 18 12:17:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12IHHeSi003839; Thu, 18 Mar 2021 12:17:40 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12IHHeSL003838; Thu, 18 Mar 2021 12:17:40 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12IHHdmd003834; Thu, 18 Mar 2021 12:17:39 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12IHHd7L003833; Thu, 18 Mar 2021 12:17:39 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12IHHUbA003820 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 18 Mar 2021 12:17:30 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12IHFbNA000681 for ; Thu, 18 Mar 2021 17:17:29 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=abalaeff@polarisqb.com; dkim=pass header.s=google header.d=polarisqb.com Received: from mail-il1-f177.google.com (mail-il1-f177.google.com [209.85.166.177]) by mx0a-00007101.pphosted.com with ESMTP id 37bn2658vp-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 18 Mar 2021 17:17:29 +0000 Received: by mail-il1-f177.google.com with SMTP id v3so5571032ilj.12 for ; Thu, 18 Mar 2021 10:17:29 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=polarisqb.com; s=google; h=mime-version:from:date:message-id:subject:to; bh=26C69CeGlC/VLFmYlGXhpWAC0mujwBaEAbocNv+pEXQ=; b=GiSFZUeHGlCDk6bQtoJgEYau+5whXONqkjisQOwMt4jvanvh6yCJubKDLtJRYbG8t7 xoaJBiT+AedqZcWS1jGajS497DIhOkEY6jHQzb9pG8SJkqSqsMB8YoCzMHcseajdPdIb 9YOaLX2rA/xG/HyVjU8wTTUKw+nxCc1xptwuE= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=26C69CeGlC/VLFmYlGXhpWAC0mujwBaEAbocNv+pEXQ=; b=S7me2tvY6bQ2gEq2+86uhmfd3xyAnGrhpLaIQe4ak+QwAH0OeH4yykmgi5wLxGb3Cn BZwt4JBAaRoHbnqEgaov9IIkU3+omsvh5SVsqwwX7IdGa1HOWNdqtGZk/wj8MOo1qx8y 60irhZ4aD6SE+I8onefGyHdUz2RAAtvyZuW5rOkTLDhYH05n3pNcHkTL7T3L4L6adeuv DH7xBJmDj2Q1S9zYEPpnSzHmDei3HF7IAFyeBrzFcxfpMELzYyhDQ1vdXFXjpSP+ruQJ nnhTzccInNwBgn7c1PIVfbSm7YR885ZAAdpo2xOFP0RRZOliqJDrOv7H46ck4CvYrL0f 8udg== X-Gm-Message-State: AOAM533Jp0ikxWT1VJ46O4esnE3zBmI0e+Jd72gAJF65m9g27I9Umw+S z2B4y+/20EMNK9lcP4wnVgkuE6HTlEfj5nyldNLFyr/Wa2cf5twr X-Google-Smtp-Source: ABdhPJyAGdPY/xQ2GHq2kSWJpX6/9Q5sPAHCvP9aCAJ9rSICZkqXNBfi/T/Pu2T7LeOBqIx0U47F61pzYXIkKmF1Qho= X-Received: by 2002:a92:d0c3:: with SMTP id y3mr11727014ila.303.1616087848423; Thu, 18 Mar 2021 10:17:28 -0700 (PDT) From: Alex Balaeff Date: Thu, 18 Mar 2021 13:17:11 -0400 Message-ID: Subject: namd-l: NAMD QMMM: Electrostatic energy and PMECORRENERGY To: namd-l Content-Type: text/plain; charset="UTF-8" X-CLX-Response: 1TFkXGxwTEQpMehcaEQpZRBdtUxlYUGFnGBhERxEKWFgXYntJfh4eYR0efH4 RCnhOF2tBT3NsGlNpZ0toEQp5TBdvQRJJTh1sfhMSSREKQ0gXBxkeHBEKQ1kXBxkRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHhNxGRoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XGERkYHVmS0hAQXV+chNcc1lYa2FGQ1pjZ3BkQxJsY08RClhcFx8EGgQYGBwFGxoE GxoaBB4SBBgYEBseGh8aEQpeWRdyQ3kFbxEKTVwXGBIaEQpMWhdoaU1BTREKTEYXb2tra2trEQp CTxdtbVJNa2xbb0hsbREKQ1oXGBoTBBIfBBscHAQbHR0RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2 tBT3NsGlNpZ0toEQpCSRdrQU9zbBpTaWdLaBEKQkUXZ2JoWxlTQxhiYlkRCkJOF2tBT3NsGlNpZ 0toEQpCTBdie0l+Hh5hHR58fhEKQmwXb0R+ZmNaWUV6cBgRCkJAF2NSRGJ/fW9wcGYTEQpCWBdn c2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaWNHbEttSWxCSx0RCnBoF2t5E09ZQGBuSEljEBk aEQpwaBdgUEdnbHxEXkJdXRAZGhEKcGgXaHAbTx5Zc09jWF8QGRoRCnBoF2hOR2BaehkfXmtlEB kaEQpwaBdjXFxBa2wcUGZcHhAZGhEKcH0XZn16W0VrUHNha00QGRoRCnB/F29EYVASE38bHBJ+E BMEHxEKcF8XaUNPXWweRUhffl4QGRoRCnBsF2YSa1lwRVAYQxkFEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 spamscore=0 impostorscore=0 mlxlogscore=999 clxscore=169 suspectscore=0 mlxscore=0 malwarescore=0 bulkscore=0 priorityscore=0 phishscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180121 X-Spam-Score: 0 X-Spam-OrigSender: abalaeff@polarisqb.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 12IHHVb9003823 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alex Balaeff Dear NAMD developers and QMMM gurus: Could you kindly advise what terms the printed out NAMD electrostatic energy includes in a QMMM simulation? Here's the link to an "ultimate" example: https://urldefense.com/v3/__https://drive.google.com/drive/folders/1mFKQ7eLQYOzH7pwFKsGJ9377FI9twKBO?usp=sharing__;!!DZ3fjg!tLywrT9Ies8ueIfslWWFnhAUUlorpX5Uy8hCjwaJkBaf6QG-NoUGlK73B295Mn-_Gw$ where the system consists of a QM ligand only and no classical part. >From the NAMD QMMM calculation (cf. energy_ligand_only_1.{namd,log}) it appears that ELEC = QMENERGY - PMECORRENERGY. So... what is PMECORRENERGY? The NAMD QMMM paper (nihms947830.pdf) gives a vague explanation that "corrections are calculated to subtract from the PME forces all interactions already calculated by the QM package between QM-QM atom pairs, and by NAMD QM module between QM-point charge atom pairs". The latter part is absent from my test system (no point charges!) so only the former part remains. So it sounds like the PMECORRENERGY could be the PME interaction energy between the QM-generated point charges. However, when I literally substitute those charges into my PSF file (Ligand_test.psf_new) and redo the calculation with the ligand as a classical MM system, the electrostatic energy comes out different from PMECORRENERGY (184.55 kcal/mol vs. 111.05 kcal/mol, respectively: cf. energy_ligand_only_1.log and energy_ligand_only_MM.log). Moreover, when I redo the MM calculation without the PME term (and with a large cutoff, to get the actual all-with-all interaction), I am getting the electrostatic energy very similar to the PME one (184.53 kcal/mol: cf energy_ligand_only_MM_noPME.log) Which means that the electrostatic interaction with the ligand copies is minuscule and the PMECORRENERGY term cannot be that, either. So, if someone could kindly explain what the PMECORRENERGY term includes, that would be much appreciated :-) Thank you very much, Alexander. ----- Dr. Alexander Balaeff Polaris Quantum Biotech https://urldefense.com/v3/__http://www.PolarisQB.com__;!!DZ3fjg!tLywrT9Ies8ueIfslWWFnhAUUlorpX5Uy8hCjwaJkBaf6QG-NoUGlK73B2-1KqG5pQ$ (919)-270-5772 From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 18 16:26:15 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12ILQFrx009387; Thu, 18 Mar 2021 16:26:15 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12ILQFru009386; Thu, 18 Mar 2021 16:26:15 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12ILQExv009380; Thu, 18 Mar 2021 16:26:14 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12ILQE9Y009379; Thu, 18 Mar 2021 16:26:14 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12ILQ6ZE009372 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 18 Mar 2021 16:26:06 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12ILNxfn013673 for ; Thu, 18 Mar 2021 21:26:05 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qt1-f173.google.com (mail-qt1-f173.google.com [209.85.160.173]) by mx0a-00007101.pphosted.com with ESMTP id 37bnuuye00-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 18 Mar 2021 21:26:05 +0000 Received: by mail-qt1-f173.google.com with SMTP id f12so5267135qtq.4 for ; Thu, 18 Mar 2021 14:26:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=SZxU+utPJLchAlHyJp3SzTDu9jHhVRjXUFlTo+v6eFk=; b=Rq1LXi08nz27aH+YhZ5VNNXHzyrHjf8A7EGWTgaf0UCN+sfGeua98c1diCspWG18Ev 71NNc5Di74d1eTL7UQ27G4hPqQdS2N9mTFRrD2vbOUH4UId2PTuoVEZ5VGXL6sAo9+D5 YnqpplSmyjRZsoYdiQVlj8rBGrYrktmnxDJDZZQQCPH5FFRPBOfWKIfFxHezN7vliz5z m4grS3mw33b9AIdaXy+OIfkgaUIak1oOKRNw50IwY/lL5aneCyek8C9nNR8jw5Amtmbc 5xRLyKaNM3M7iirqCYAes6udsgn63Jz/0vlca8ssC5jpK22h1bcCmQl6T1U98YNfrKWD EjJA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=SZxU+utPJLchAlHyJp3SzTDu9jHhVRjXUFlTo+v6eFk=; b=mGUAEa+QCSV2Y8Ky8Obk2nSOYqgsJ0pWnISpTtV61DENYMjOAEOYtokMlxCAsUTwRt X4QJ+aGlzGaeSKdQer/BkPNJRRPC14Z7idYZf34oiLFriot9WpoEx+0OaRxVmjnb/lOE tdQqPbxVgLlixVm9BDij8TnjbqjxTa/387hxRClmbrKMbPkkSA+n8qF0SpurE5bR7d0u n5GAmZcThBIYMJ21tfxY1Iq6tWIPNqjYwbxS5gJkRFturxOk7uUxo+15apwQN65YePdC hfTldujV4kyX3d8wYQMtP5amw49Czba2fX28QQriTySU4I/O8cn+cDKPUUwPtFf7G+c4 nY0g== X-Gm-Message-State: AOAM531XXdNgJj7fyg1XiZnCGrpEd+AnWVTm1IGySXMOcJS6pIGy193U 3uALUmEs6dtNXWSDuvj9RYitIsGz4bnmcg== X-Google-Smtp-Source: ABdhPJw1rB3Ini8srSjPmJ4XcHj5xn/hoCk6kiZFG5jXvWubTmRipYuKfpe+hkzdGoKiKeoXjmZ2qg== X-Received: by 2002:ac8:70d8:: with SMTP id g24mr5648107qtp.389.1616102763980; Thu, 18 Mar 2021 14:26:03 -0700 (PDT) Received: from [192.168.1.37] ([181.64.231.211]) by smtp.gmail.com with ESMTPSA id b2sm2203987qtb.54.2021.03.18.14.26.02 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 18 Mar 2021 14:26:03 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 18 Mar 2021 16:25:59 -0500 Subject: namd-l: Lipid into sphere From: "Ropon-Palacios G." To: NAMD list Message-ID: Thread-Topic: Lipid into sphere Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3698929562_1919115847" X-CLX-Response: 1TFkXGx0cEQpMehcYHB0RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGBkYEQpDWRcbEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFxJQH0ZbehpmfUQab2N/aHxyZ2B5clgfZmNdZx9uQxlZEQpYXBcfBBoEGBgcBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXckN9RWMRCk1cFxsZEQpMWhdsaWtNaxEKTEYXb2tra2trEQp CTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGgQbHRkRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2 NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E1h+G l9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXY2lZb3pPHXJHT38RCkJAF2RvR39PaEleUG96EQpCWBdn c2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUMXa2hkfFJ+S2lAYVARCllLFxMZHhMRCnBoF2BDRk1 NYxJdRh9oEBseEhEKcGgXYkNjUHxwR3N/chwQGRoRCnBoF2JIXB1hTx9HUHgTEBkaEQpwaBdpbn AFRkMcWmZcYRAbGB8RCnBoF2AeHUITT30YWGxwEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEwXb WhlGUFSfXsYRVIQGRoRCnBDF2R6RHtmfVtOa1NuEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 lowpriorityscore=0 priorityscore=267 mlxlogscore=380 mlxscore=0 clxscore=176 spamscore=0 phishscore=0 adultscore=0 bulkscore=0 suspectscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180153 domainage_hfrom=9349 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698929562_1919115847 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear NAMD users, How can calculate lipid (POPE) number to be placed into an sphere the 425 Angstrom. Best, Geo. --B_3698929562_1919115847 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear NAMD u= sers,

 

How can calculate lipid (POPE) number to be placed into an sphere the 42= 5 Angstrom.

 

Best,

 

Geo.

--B_3698929562_1919115847-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 18 17:13:41 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12IMDfeU012146; Thu, 18 Mar 2021 17:13:41 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12IMDfxS012145; Thu, 18 Mar 2021 17:13:41 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12IMDeIK012141; Thu, 18 Mar 2021 17:13:40 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12IMDeZx012140; Thu, 18 Mar 2021 17:13:40 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12IMDUfv012130 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 18 Mar 2021 17:13:30 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12IMDQgk017827 for ; Thu, 18 Mar 2021 22:13:30 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=mmccallum@PACIFIC.EDU; dkim=pass header.d=pacificedu.onmicrosoft.com header.s=selector2-PacificEdu-onmicrosoft-com Received: from nam10-dm6-obe.outbound.protection.outlook.com (mail-dm6nam10on2070.outbound.protection.outlook.com [40.107.93.70]) by mx0b-00007101.pphosted.com with ESMTP id 37bpq1y2y7-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Thu, 18 Mar 2021 22:13:30 +0000 ARC-Seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=fP3wBPrN1ehcLIBmh7tBmKYEhQcbKalK42Es9fjCSOYR1n8a8dJdMLP7c1vDAbJ32aeyASrwBMt/DU+W5tvICOkQWDHLOi0BpY0lgd01asBfhEXVOHVYKOVP5+pdgQ3NxQdFkh7GsKhyZ0p0EXMqpDs3DCXvVMkUxwRucC0mfML/f8acLQJEBYztZEzcWBAZxqSqWx3vz/b2fGgf9xl79BsUq12LAHSk3H8KGnA/SL7mifkO8qOesQcMnMiAbXEkwBHQomiUxqcO03r7JuYvAbrFUePl2imDM1EbO6Ro9jqkNBGVqi/upYDef814awjhMzaLMO4fWjt31dNWkX36Nw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=uo5vBq4ivOAnLIIv1d4smxS7J1n4a95UznZJ4eDwO1M=; b=dj9PiIqswbYMZ08SKrICSdoA9GJ43dA0Ek6Bl+eM1K0YJM4i/hzSqiWRwDb7UDDnafiCvSq/yLJp7RzIfFZf4t6YhICqkwETNRr7piPPdBwhrriFABh1eZsyHbRCCy5zVhjROw1O+QRzwb0aOeLVWMYWQ8OMsYknIUUTFGZJo1z+20qnCH5TYxVdUpd4RVF8ah9JRXjf1Xm5sr0D/ZbjTsUVRsBBl0fowsaZiC/vSWbLH4xICQg/J2e/5PP0D53Nl7dYkZOUqYMRsQpoGQAHcyAObQKIWoLHINA8SGUa1QD3mwNa9820kFz0Lijlfosas1gvE4CSLqrC9pOLuAEb7g== ARC-Authentication-Results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=pacific.edu; dmarc=pass action=none header.from=pacific.edu; dkim=pass header.d=pacific.edu; arc=none DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=PacificEdu.onmicrosoft.com; s=selector2-PacificEdu-onmicrosoft-com; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=uo5vBq4ivOAnLIIv1d4smxS7J1n4a95UznZJ4eDwO1M=; b=ZYGA7TzjSc55Y1qDq5yOo3mdciyZm7QnusSPUrddulA63UrBzaifkDCJspVjdJdwLd7jDCMRDhvp4jKFkg5MANLzBFOPiQtE15dWbccGprDlaSGKKInTXeHhxjlxtoxO+tgRBN04MVc/+R8uA8oGa1iXzJxpQ8n8h3hdtg0HDPA= Received: from SJ0PR06MB7440.namprd06.prod.outlook.com (2603:10b6:a03:319::19) by BYAPR06MB5063.namprd06.prod.outlook.com (2603:10b6:a03:7e::16) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.3933.32; Thu, 18 Mar 2021 22:13:26 +0000 Received: from SJ0PR06MB7440.namprd06.prod.outlook.com ([fe80::524:bc95:c19:f7d1]) by SJ0PR06MB7440.namprd06.prod.outlook.com ([fe80::524:bc95:c19:f7d1%4]) with mapi id 15.20.3955.018; Thu, 18 Mar 2021 22:13:26 +0000 From: Mike McCallum To: KS UIUC , "Ropon-Palacios G." Subject: Re: namd-l: Lipid into sphere Thread-Topic: namd-l: Lipid into sphere Thread-Index: AQHXHD5f8Nw8pOqfU0yYJVkJ/qDsWaqKT1kA Date: Thu, 18 Mar 2021 22:13:26 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=PACIFIC.EDU; x-originating-ip: [2601:205:4080:4190:6080:7175:ceaa:5ce1] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: f6fa782c-2da9-40bc-7d00-08d8ea5b0dd0 x-ms-traffictypediagnostic: BYAPR06MB5063: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:7691; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:SJ0PR06MB7440.namprd06.prod.outlook.com;PTR:;CAT:NONE;SFS:(4636009)(396003)(346002)(376002)(39850400004)(136003)(366004)(8676002)(186003)(166002)(110136005)(86362001)(83380400001)(8936002)(33656002)(36756003)(71200400001)(478600001)(966005)(6486002)(4744005)(76116006)(75432002)(66476007)(66556008)(64756008)(2906002)(6506007)(53546011)(6512007)(66446008)(5660300002)(2616005)(786003)(66946007)(316002)(38100700001)(45980500001);DIR:OUT;SFP:1101; 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boundary="_000_FEE03906FF59449FB1BFFBC6D62E4F54pacificedu_" X-OriginatorOrg: pacific.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SJ0PR06MB7440.namprd06.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: f6fa782c-2da9-40bc-7d00-08d8ea5b0dd0 X-MS-Exchange-CrossTenant-originalarrivaltime: 18 Mar 2021 22:13:26.6062 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: f81ceafa-e5d9-48b3-bc2e-066d171f7d18 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: y7eNy13RHgXbotKoPwhY23/LkXjIMijpYqPi0QpHRPDYsDN6CHF5c9/HHzT1zWSGbtp5PKH2N2FxMwUzsq5zmA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BYAPR06MB5063 X-CLX-Response: 1TFkXGxgaEQpMehcaEQpZRBd6HEdzf0ISW3hZbREKWFgXYQVNc3NFG3BlGWY RCnhOF2FMG3pITRpsXE9OEQp5TBdpSHlZWxJiXxtpaREKQ0gXBxsYGBEKQ1kXGBgRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbGhpxExAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1QkVZX k9OEQpDThdHck15aV5zUltneVsfQGBPH0diW2Ief3x8QhhZa3NNQxEKWFwXHwQaBBgYHAUbGgQb GhoEHhIEGBkQGx4aHxoRCl5ZF3JDcn9GEQpNXBceEh4RCkxaF3hpa2trEQpFWRdvaxEKTF8XegU FBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF3oef2ZvQh9Tcmt9EQpDWhceGgQbGh0EExkEHRoRCk JeFxsRCkReFxgRCkJFF2kcQWUcXmdNXn1OEQpCThdhTBt6SE0abFxPThEKQkwXYQVNc3NFG3BlG WYRCkJsF29HWWR4bBJSHU9uEQpCQBdpZXBZb0hNfm0FTBEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4R CnlDF2tlfF1vGwVYZhJnEQpwaBdrS2V5WltBUx5DfxAZGhEKcGgXeh5SWUZNaU9cRksQGRoRCnB oF3pTRW0cARhAenpwEBkaEQpwaBdkckMfBWxwG1NMGhAZGhEKcGgXbHpmf3xlTElzX2AQGRoRCn B9F24BU0lBBXtMR2EZEBkaEQpwfxdhHx1lRBkZfnp9eBAbGhoRCnBfF2dNYEZYQBsdRx5eEBkaE QpwbBdoZEVGXWhiBV9iaxASHxEKcEwXZ35QfU1rUE9PRmIQGRoRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=120 malwarescore=0 suspectscore=0 priorityscore=0 bulkscore=0 mlxscore=0 lowpriorityscore=0 adultscore=0 spamscore=0 impostorscore=0 mlxlogscore=829 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180158 X-Spam-Score: 0 X-Spam-OrigSender: mmccallum@PACIFIC.EDU X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mike McCallum --_000_FEE03906FF59449FB1BFFBC6D62E4F54pacificedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Geo., I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!vN3b0_NdPh5BT7rcX_-5j5yftnuHzXMrcCEnGPxkfsc3Fv59SXT_qI5pGg= Zrq-Jbyg$=20 Best Mike On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. > wrote: Dear NAMD users, How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom. Best, Geo. -- C. Michael McCallum Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax --_000_FEE03906FF59449FB1BFFBC6D62E4F54pacificedu_ Content-Type: text/html; charset="utf-8" Content-ID: <9759B002088417488109DF194A0756AE@namprd06.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Hi Geo.,
I=E2=80=99d look into PACKMOL.  It should be able to d= o exactly this for you, and it is easy to use.


Best
Mike

On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. <biodano.geo@gmail.com> = wrote:

Dear NAMD users, 
 
How can calculate lipid (POPE) = number to be placed into an sphere the 425 Angstrom. 
 
Best, 
 
Geo. 

--
C. Michael McCallum           = ;
Professor               =          
Department of Chemistry, UOP    
mmccallum .at. pacific .dot. edu       =         (209) 946-2636 v  / (209) 946-2607 fax




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To: Mike McCallum , KS UIUC Message-ID: Thread-Topic: namd-l: Lipid into sphere References: In-Reply-To: Content-type: multipart/alternative; boundary="B_3698932716_434393431" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcYHxwRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHhIbEQpDWRcYGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfG3EZGxAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThcZc3xwc2BgbH18XhtiZ05eB0NYQGweWl0dSHNdH3UTbhEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JDcnBwEQpNXBcYHRkRCkxaF39pa01rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGxMEHh 8RCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXY2lZ b3pPHXJHT38RCkJAF2llcFlvSE1+bQVMEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUM Xa2V8XW8bBVhmEmcRCllLFxMZHhMRCnBnF2lDblABWXNHAR5TEBkaEQpwaBdrTm0bRhJzR25fRR AZGhEKcGgXbFB5XkBzHxsbUnMQGRoRCnBoF2V+BW5MYF5HAWsYEBkaEQpwaBduf2lCBWN8eF0BZ xAZGhEKcGgXellkflpAHl1QXwEQGRoRCnB9F24BU0lBBXtMR2EZEB4SEQpwfxdhHx1lRBkZfnp9 eBAbGhgRCnBfF2dNYEZYQBsdRx5eEB4SEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEwXZ35QfU1rUE9 PRmIQHhIRCnBDF2R6RHtmfVtOa1NuEBwaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 phishscore=0 spamscore=0 mlxlogscore=657 malwarescore=0 mlxscore=0 clxscore=171 impostorscore=0 lowpriorityscore=0 adultscore=0 priorityscore=256 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180159 domainage_hfrom=9349 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698932716_434393431 Content-type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Yes, but I want calculate number of lipid to placed given an radius of sphe= re in my case is 425 angstrom=20 =20 From: Mike McCallum Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC , "Ropon-Palacios G." Subject: Re: namd-l: Lipid into sphere =20 Hi Geo.,=20 I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. =20 https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!tEJyvrvToC26sOR6PHbYrgfoYR45N1eLtftgToUwnflxGDY0Qrw8HU6arV= iDo6iSjg$=20 =20 Best Mike On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. wrot= e: =20 Dear NAMD users,=20 =20 How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom.=20 =20 Best,=20 =20 Geo.=20 =20 -- C. Michael McCallum=20=20=20=20=20=20=20=20=20=20=20 Professor=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20= =20=20 Department of Chemistry, UOP=20=20=20=20 mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax =20 =20 =20 --B_3698932716_434393431 Content-type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

Yes, but I want calculate number of li= pid to placed given an radius of sphere in my case is 425 angstrom

 

From: Mike McCallum <mmccallum@PACIFIC.= EDU>
Date: Thursday, March 18, 2021 at 5:13 PM
To: K= S UIUC <namd-l@ks.uiuc.edu>, "Ropon-Palacios G." <biodan= o.geo@gmail.com>
Subject: Re: namd-l: Lipid into sphere

 

<= p class=3DMsoNormal>Hi Geo.,

I=E2= =80=99d look into PACKMOL.  It should be able to do exactly this for y= ou, and it is easy to use.

 

=

 

Best

Mike

<= div>



On Mar 18, 2021, = at 2:25 PM, Ropon-Palacios G. <= biodano.geo@gmail.com> wrote:

 

Dear NAMD users, 

 

How can calculate lipid (POPE) number to be placed into an sphere the 425 = Angstrom. 

 = ;

Best, 

 

Geo. =

 

--

C. Michael Mc= Callum           

=

Professor              =          

Department of Chemistry, UOP    

=

mmccallum .at. pacific .dot. edu       = ;         (209) 946-2636 v  / (209) 946-2607 fax

 

<= o:p> 



 

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boundary="_000_DM6PR11MB45948E77D1BB2D2A05F6A36DAA699DM6PR11MB4594namp_" X-OriginatorOrg: wayne.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: DM6PR11MB4594.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 7bd3fc0d-0619-45c1-a015-08d8ea5cf90c X-MS-Exchange-CrossTenant-originalarrivaltime: 18 Mar 2021 22:27:10.7766 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: e51cdec9-811d-471d-bbe6-dd3d8d54c28b X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: VNxXPJO+3Xn5mBF3kc+mHg2kHbf9wK8Spyw38GZqkFUEcE6gYcXX1fUotgQxRw8TAGPqkIqEH1+0aAqLp7P/sQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: DM6PR11MB2571 X-CLX-Response: 1TFkXGBsdEQpMehcaEQpZRBdoeBkeAR8bGmJkfxEKWFgXZHlrX1lbfEF7c2I RCnhOF2JYXmZ6SxMfehwZEQp5TBdjYmRuaEFHEmdnEhEKQ0gXBxsTGxEKQ1kXGBgRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbEx1xGxIeEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF2teUEhYXRscW0xzHV9yEn5IbV5Nb3xLGWRySF5iQRt7EQpYXBcfBBoEGBgcBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXckNyQkgRCk1cFwcbGB4RCkxaF3tpTU1vEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29va2tsa2sRCkJPF3pec0ESTxtpHEZzEQpDWhceGgQbGh0EGBkdBB MZEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdiWF5meksTH3ocGREKQkkXYlheZnpLEx96H BkRCkJFF2VgBW9+eHB5b3NdEQpCThdiWF5meksTH3ocGREKQkwXZHlrX1lbfEF7c2IRCkJsF2UF H318eU9Aa2UYEQpCQBdpZXBZb0hNfm0FTBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnl DF2tlfF1vGwVYZhJnEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXaXNbYGtfaW0eaUYQGRoRCnBoF2 UbUFIbenBgeE1tEBkaEQpwaBdmAX9meUVTeUZ/eBAZGhEKcGgXZU1meWFOG31rSx8QGRoRCnBoF 3pmXVhfZkMeREl4EBkaEQpwZxdvTkdffX5YbElPaBAZGhEKcGcXaUNuUAFZc0cBHlMQHhIRCnBn F2hncwVwHXJ6X2FoEBkaEQpwfRdmfUtZQlxhAU96GhAZGhEKcH0XaUkSextdbWtDfW8QGRoRCnB /F2EfHWVEGRl+en14EBsaHhEKcF8XZ01gRlhAGx1HHl4QHBoRCnB/F2Fmb1saZ2RCSB1bEBsbHh EKcF8Xa0tvcm59ZkBYH1gQHhIRCnBsF2dge00dRF4bYUFnEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 mlxscore=0 malwarescore=0 phishscore=0 adultscore=0 bulkscore=0 mlxlogscore=794 spamscore=0 lowpriorityscore=0 impostorscore=0 suspectscore=0 clxscore=217 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180160 X-Spam-Score: 0 X-Spam-OrigSender: jpotoff@wayne.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeffrey Potoff --_000_DM6PR11MB45948E77D1BB2D2A05F6A36DAA699DM6PR11MB4594namp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable If you know the area per lipid for the lipid of interest, couldn=E2=80=99t = you calculate the surface area of your sphere and divide by the area per li= pid to get the (approximate) number of lipids required? --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: owner-namd-l@ks.uiuc.edu On Behalf Of Ropo= n-Palacios G. Sent: Thursday, March 18, 2021 6:19 PM To: Mike McCallum ; KS UIUC Subject: Re: namd-l: Lipid into sphere [EXTERNAL] Yes, but I want calculate number of lipid to placed given an radius of sphe= re in my case is 425 angstrom From: Mike McCallum > Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC >, "Ropon-Palacio= s G." > Subject: Re: namd-l: Lipid into sphere Hi Geo., I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!r6lC50g0XjgTZFN17r7ozq7ybNmR9XiXYuKs_ZyNtI7N-vB9liFsYeGYs4= HT4YWRQw$ Best Mike On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. > wrote: Dear NAMD users, How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom. Best, Geo. -- C. Michael McCallum Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax --_000_DM6PR11MB45948E77D1BB2D2A05F6A36DAA699DM6PR11MB4594namp_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PGh0bWwgeG1sbnM6dj0idXJuOnNjaGVtYXMtbWljcm9zb2Z0LWNvbTp2bWwiIHhtbG5zOm89InVy bjpzY2hlbWFzLW1pY3Jvc29mdC1jb206b2ZmaWNlOm9mZmljZSIgeG1sbnM6dz0idXJuOnNjaGVt YXMtbWljcm9zb2Z0LWNvbTpvZmZpY2U6d29yZCIgeG1sbnM6bT0iaHR0cDovL3NjaGVtYXMubWlj cm9zb2Z0LmNvbS9vZmZpY2UvMjAwNC8xMi9vbW1sIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcv VFIvUkVDLWh0bWw0MCI+DQo8aGVhZD4NCjxtZXRhIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSIg Y29udGVudD0idGV4dC9odG1sOyBjaGFyc2V0PXV0Zi04Ij4NCjxtZXRhIG5hbWU9IkdlbmVyYXRv ciIgY29udGVudD0iTWljcm9zb2Z0IFdvcmQgMTUgKGZpbHRlcmVkIG1lZGl1bSkiPg0KPHN0eWxl PjwhLS0NCi8qIEZvbnQgRGVmaW5pdGlvbnMgKi8NCkBmb250LWZhY2UNCgl7Zm9udC1mYW1pbHk6 SGVsdmV0aWNhOw0KCXBhbm9zZS0xOjIgMTEgNiA0IDIgMiAyIDIgMiA0O30NCkBmb250LWZhY2UN 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X-Google-Smtp-Source: ABdhPJxJtVgVY40KV15gz/hVtMLs03im6LmCY0TjW77FWwOfVVGi4i9cdWRonq6c5VOu8rIwU66btw== X-Received: by 2002:a05:620a:12da:: with SMTP id e26mr6485452qkl.92.1616107657210; Thu, 18 Mar 2021 15:47:37 -0700 (PDT) Received: from [192.168.1.37] ([181.64.231.211]) by smtp.gmail.com with ESMTPSA id t188sm2937332qke.91.2021.03.18.15.47.35 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 18 Mar 2021 15:47:36 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 18 Mar 2021 17:47:33 -0500 Subject: Re: namd-l: Lipid into sphere From: "Ropon-Palacios G." To: , Jeffrey Potoff Message-ID: <6A9AFCFE-5DAF-4FA1-BCF5-565D47B4FDFE@gmail.com> Thread-Topic: namd-l: Lipid into sphere References: In-Reply-To: Content-type: multipart/alternative; boundary="B_3698934456_1293613766" X-CLX-Response: 1TFkXGx0dEQpMehcYHxsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHh0aEQpDWRcYGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfHXEZHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd/Hn51WEgdQWl/c0xPUxhYHGFmGwcaeUlnX1p1GWFveBEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3JDchpGEQpNXBccGxoRCkxaF3hpTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx wTEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2Np WW96Tx1yR09/EQpCQBdpZXBZb0hNfm0FTBEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF2tlfF1 vGwVYZhJnEQpZSxcTGR4TEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXZRtQUht6cGB4TW0QGRoRCn BoF2FlRU5kc2FfQnh6EBoRCnBoF2h8bGNHR0NsWWtIEBoRCnBoF2hdc3xZZHxZSUdAEBoRCnBoF 2NjG1IBEltETFhYEBoRCnBnF2lDblABWXNHAR5TEBkaEQpwZxdvTkdffX5YbElPaBAZGhEKcH0X bgFTSUEFe0xHYRkQGhEKcH0XaUkSextdbWtDfW8QGRoRCnB/F2EfHWVEGRl+en14EBsYGREKcF8 XZ01gRlhAGx1HHl4QGhEKcH8XYWZvWxpnZEJIHVsQGxseEQpwXxdrS29ybn1mQFgfWBAaEQpwbB d6R0BrGFl5fx4bSBAdEhEKcEMXZHpEe2Z9W05rU24QHRIRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 spamscore=0 impostorscore=0 mlxlogscore=627 clxscore=177 suspectscore=0 mlxscore=0 malwarescore=0 bulkscore=0 priorityscore=251 phishscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180164 domainage_hfrom=9349 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698934456_1293613766 Content-type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Have lipid POPE take from CHARMM-GUI into it and column section named =E2= =80=9CSurface Area=E2=80=9D indicate 58.8 Angstrom^3. This can be right to = area per lipid?=20 =20 From: on behalf of Jeffrey Potoff Reply-To: , Jeffrey Potoff Date: Thursday, March 18, 2021 at 5:28 PM To: "namd-l@ks.uiuc.edu" Subject: RE: namd-l: Lipid into sphere =20 If you know the area per lipid for the lipid of interest, couldn=E2=80=99t = you calculate the surface area of your sphere and divide by the area per li= pid to get the (approximate) number of lipids required?=20 =20 --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University =20 From: owner-namd-l@ks.uiuc.edu On Behalf Of Ropo= n-Palacios G. Sent: Thursday, March 18, 2021 6:19 PM To: Mike McCallum ; KS UIUC Subject: Re: namd-l: Lipid into sphere =20 [EXTERNAL]=20 Yes, but I want calculate number of lipid to placed given an radius of sphe= re in my case is 425 angstrom=20 =20 From: Mike McCallum Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC , "Ropon-Palacios G." Subject: Re: namd-l: Lipid into sphere =20 Hi Geo.,=20 I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. =20 https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!pYJGZx5Hii4X_Bki_ifac8TGWApCZuKngMwmkK-ePDM2fEmeeRdXzEZOCv= rcgeuUeQ$=20 =20 Best Mike =20 On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. wrot= e: =20 Dear NAMD users,=20 =20 How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom.=20 =20 Best,=20 =20 Geo.=20 =20 -- C. Michael McCallum=20=20=20=20=20=20=20=20=20=20=20 Professor=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20= =20=20 Department of Chemistry, UOP=20=20=20=20 mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax =20 =20 =20 =20 --B_3698934456_1293613766 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Have lipid POPE take from CHARMM-GUI into it and c= olumn section named =E2=80=9CSurface Area=E2=80=9D indicate 58.8 Angstrom^3. This can be= right to area per lipid?

 

= From: <owner-namd-l= @ks.uiuc.edu> on behalf of Jeffrey Potoff <jpotoff@wayne.edu>
Reply-To: <namd-l@ks.uiuc.edu>, Jeffrey Potoff <jpotoff@wayne.= edu>
Date: Thursday, March 18, 2021 at 5:28 PM
To: &q= uot;namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: R= E: namd-l: Lipid into sphere

 

If you know the area per lipid for the lipid of interest, couldn=E2=80=99t you c= alculate the surface area of your sphere and divide by the area per lipid to= get the (approximate) number of lipids required?

 

=

---

Jeffrey Potoff<= /p>

Interim Chair, Department = of Chemical Engineering and Materials Science

College of Engineering

Wayne State University<= /span>

&n= bsp;

From: owner-n= amd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.edu> On Behalf Of Ropon= -Palacios G.
Sent: Thursday, March 18, 2021 6:19 PM
To: = Mike McCallum <mmccallum@PACIFIC.EDU>; KS UIUC <namd-l@ks.uiuc.edu&= gt;
Subject: Re: namd-l: Lipid into sphere

 

[EXTERNAL]

Yes= , but I want calculate number of lipid to placed given an radius of sphere i= n my case is 425 angstrom

 

= From: Mike McCallum &l= t;mmccallum@PACIFIC.EDU>
Date: Thursday, March 18, 2021 at 5:13 PM
To: KS UIUC <namd-l@ks.uiuc.edu>, "Ropon-Pal= acios G." <biodano.geo@gmail.= com>
Subject: Re: namd-l: Lipid into sphere

 

Hi Geo.,

I=E2=80=99d look into PACKMO= L.  It should be able to do exactly this for you, and it is easy to use= .

 

http://leandro.iqm.unicamp.br/m3g/pack= mol/home.shtml

 

Best

Mike

 

On Mar 18, 2021, at 2:25 PM, Ropon-Palacios= G. <biodano.geo@gmail.com>= wrote:

 

Dear NAMD users, = ;

 

How can calculate lipid (POPE) number to be plac= ed into an sphere the 425 Angstrom. <= /span>

 

Best, 

 

Geo. 

 

--

C. Michael McCallum           

Professor           &n= bsp;            

Department of Chemistry, UOP    

mmccallum .at. pacific .dot. edu        =         (209) 946-2636 v  / (209) 946-2607 fax

 

 

 

 

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boundary="_000_DM6PR11MB459477A43B5A85847945B01FAA699DM6PR11MB4594namp_" X-OriginatorOrg: wayne.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: DM6PR11MB4594.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: dfde6c1e-a4c8-4f87-9d6d-08d8ea605b9d X-MS-Exchange-CrossTenant-originalarrivaltime: 18 Mar 2021 22:51:24.6745 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: e51cdec9-811d-471d-bbe6-dd3d8d54c28b X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: PxVr2LPUr8uRcnwg11cFNzt5Xt6ArdiCMrJX8oe3oeNdW3+uqmPD2F3FWnEkuZw9gZc10k5RGNi75oU15DbOjw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: DM5PR11MB0075 X-CLX-Response: 1TFkXGBsTEQpMehcaEQpZRBdoeBkeAR8bGmJkfxEKWFgXZHlrX1lbfEF7c2I RCnhOF2JYXmZ6SxMfehwZEQp5TBdjYmRuaEFHEmdnEhEKQ0gXBxsZEhEKQ1kXGBsRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbExNxGxMZEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF197eh1hSx5CfmxiGRxCX2MZclwbQnhDG0F+GX1HG15+EQpYXBcfBBoEGBgcBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXckNyHmYRCk1cFxgfHxEKTFoXfGlNTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb29ra2xraxEKQk8XbntEGFt5ZhpHeAERCkNaFx4aBBsaHQQdGgQbGx kRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2JYXmZ6SxMfehwZEQpCSRdiWF5meksTH3ocG REKQkUXZWAFb354cHlvc10RCkJOF2JYXmZ6SxMfehwZEQpCTBdkeWtfWVt8QXtzYhEKQmwXZQUf fXx5T0BrZRgRCkJAF2llcFlvSE1+bQVMEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUM Xa2V8XW8bBVhmEmcRCnBnF2hncwVwHXJ6X2FoEB4SEQpwaBdvU1JdXGcaeXhkYhAZGhEKcGgXZg F/ZnlFU3lGf3gQHhIRCnBoF2tTG2Z+fnNHaFIfEBkaEQpwaBdlTWZ5YU4bfWtLHxAeEhEKcGgXZ kcZGkAeY1BlHloQGRoRCnBnF2lDblABWXNHAR5TEB4SEQpwZxdtR2FrTWMZTFNpbhAeEhEKcGcX b05HX31+WGxJT2gQHhIRCnB9F2Z9S1lCXGEBT3oaEBkaEQpwfRdpSRJ7G11ta0N9bxAeEhEKcH8 XYR8dZUQZGX56fXgQGxsbEQpwXxdnTWBGWEAbHUceXhAZGhEKcH8XYWZvWxpnZEJIHVsQGxsSEQ pwXxdrS29ybn1mQFgfWBAeEhEKcGwXZ2B7TR1EXhthQWcQHhIRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 spamscore=0 impostorscore=0 mlxlogscore=626 clxscore=219 suspectscore=0 mlxscore=0 malwarescore=0 bulkscore=0 priorityscore=0 phishscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180164 X-Spam-Score: 0 X-Spam-OrigSender: jpotoff@wayne.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeffrey Potoff --_000_DM6PR11MB459477A43B5A85847945B01FAA699DM6PR11MB4594namp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable If it were me, I would start here: Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation o= n Six Lipid Types Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O=E2= =80=99Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, A= lexander D. MacKerell, and Richard W. Pastor The Journal of Physical Chemistry B 2010 114 (23), 7830-7843 DOI: 10.1021/jp101759q --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: Ropon-Palacios G. Sent: Thursday, March 18, 2021 6:48 PM To: namd-l@ks.uiuc.edu; Jeffrey Potoff Subject: Re: namd-l: Lipid into sphere Have lipid POPE take from CHARMM-GUI into it and column section named =E2= =80=9CSurface Area=E2=80=9D indicate 58.8 Angstrom^3. This can be right to = area per lipid? From: > on behalf= of Jeffrey Potoff > Reply-To: >, Jeffrey Potoff <= jpotoff@wayne.edu> Date: Thursday, March 18, 2021 at 5:28 PM To: "namd-l@ks.uiuc.edu" > Subject: RE: namd-l: Lipid into sphere If you know the area per lipid for the lipid of interest, couldn=E2=80=99t = you calculate the surface area of your sphere and divide by the area per li= pid to get the (approximate) number of lipids required? --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: owner-namd-l@ks.uiuc.edu > On Behalf Of Ropon-Palacio= s G. Sent: Thursday, March 18, 2021 6:19 PM To: Mike McCallum >; KS= UIUC > Subject: Re: namd-l: Lipid into sphere [EXTERNAL] Yes, but I want calculate number of lipid to placed given an radius of sphe= re in my case is 425 angstrom From: Mike McCallum > Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC >, "Ropon-Palacio= s G." > Subject: Re: namd-l: Lipid into sphere Hi Geo., I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!uNKm95xfIozq7j_mmJz6fAPe3QgU-a-YXftOoFEYnne1TSoj_1N2DCxAcm= 81nqwnsg$ Best Mike On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. > wrote: Dear NAMD users, How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom. Best, Geo. -- C. Michael McCallum Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax --_000_DM6PR11MB459477A43B5A85847945B01FAA699DM6PR11MB4594namp_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PGh0bWwgeG1sbnM6dj0idXJuOnNjaGVtYXMtbWljcm9zb2Z0LWNvbTp2bWwiIHhtbG5zOm89InVy bjpzY2hlbWFzLW1pY3Jvc29mdC1jb206b2ZmaWNlOm9mZmljZSIgeG1sbnM6dz0idXJuOnNjaGVt YXMtbWljcm9zb2Z0LWNvbTpvZmZpY2U6d29yZCIgeG1sbnM6bT0iaHR0cDovL3NjaGVtYXMubWlj cm9zb2Z0LmNvbS9vZmZpY2UvMjAwNC8xMi9vbW1sIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcv VFIvUkVDLWh0bWw0MCI+DQo8aGVhZD4NCjxtZXRhIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSIg Y29udGVudD0idGV4dC9odG1sOyBjaGFyc2V0PXV0Zi04Ij4NCjxtZXRhIG5hbWU9IkdlbmVyYXRv ciIgY29udGVudD0iTWljcm9zb2Z0IFdvcmQgMTUgKGZpbHRlcmVkIG1lZGl1bSkiPg0KPHN0eWxl PjwhLS0NCi8qIEZvbnQgRGVmaW5pdGlvbnMgKi8NCkBmb250LWZhY2UNCgl7Zm9udC1mYW1pbHk6 SGVsdmV0aWNhOw0KCXBhbm9zZS0xOjIgMTEgNiA0IDIgMiAyIDIgMiA0O30NCkBmb250LWZhY2UN 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To: , Jeffrey Potoff Message-ID: <14CB4794-7C37-4CB0-BBE6-26E4F5E70F51@gmail.com> Thread-Topic: namd-l: Lipid into sphere References: <6A9AFCFE-5DAF-4FA1-BCF5-565D47B4FDFE@gmail.com> In-Reply-To: Content-type: multipart/alternative; boundary="B_3698935714_644830704" X-CLX-Response: 1TFkXGx0YEQpMehcZGhkRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGR0dEQpDWRcYGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGHEZGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdeZH9YaH5MS30eflJ/GH9BdVteGmFlRUtwYFNdB00dGhEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JDc2N7EQpNXBcZHB8RCkxaF3tpTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHBoEGx 0YEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2Np WW96Tx1yR09/EQpCQBdpZXBZb0hNfm0FTBEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF2tlfF1 vGwVYZhJnEQpZSxcTGR4TEQpwZxdtR2FrTWMZTFNpbhAbEhEKcGgXbWYfYUN5UmVdaW0QGhEKcG gXbkgSQGJzE2tjQEgQGhEKcGgXZhgZaXgFQmRvTkIQGhEKcGgXaHxsY0dHQ2xZa0gQGhEKcGgXY 2MbUgESW0RMWFgQGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnBnF29OR199flhsSU9oEBsSEQpwfRdu AVNJQQV7TEdhGRAeEhEKcH0XaUkSextdbWtDfW8QGxIRCnB/F2EfHWVEGRl+en14EBsaHhEKcF8 XZ01gRlhAGx1HHl4QHBoRCnB/F2Fmb1saZ2RCSB1bEBsbHhEKcF8Xa0tvcm59ZkBYH1gQGRoRCn BsF3pHQGsYWXl/HhtIEBkaEQpwQxdkekR7Zn1bTmtTbhAcGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=172 malwarescore=0 suspectscore=0 priorityscore=303 bulkscore=0 mlxscore=0 lowpriorityscore=0 adultscore=0 spamscore=0 impostorscore=0 mlxlogscore=565 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180164 domainage_hfrom=9349 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698935714_644830704 Content-type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable One last question dear Jeffrey , packmol can run in parallel?=20 =20 Best,=20 =20 Geo.=20 =20 From: on behalf of Jeffrey Potoff Reply-To: , Jeffrey Potoff Date: Thursday, March 18, 2021 at 5:52 PM To: "namd-l@ks.uiuc.edu" Subject: RE: namd-l: Lipid into sphere =20 If it were me, I would start here: =20 Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation o= n Six Lipid Types Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O=E2= =80=99Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, A= lexander D. MacKerell, and Richard W. Pastor The Journal of Physical Chemistry B 2010 114 (23), 7830-7843 DOI: 10.1021/jp101759q =20 --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University =20 From: Ropon-Palacios G. =20 Sent: Thursday, March 18, 2021 6:48 PM To: namd-l@ks.uiuc.edu; Jeffrey Potoff Subject: Re: namd-l: Lipid into sphere =20 Have lipid POPE take from CHARMM-GUI into it and column section named =E2= =80=9CSurface Area=E2=80=9D indicate 58.8 Angstrom^3. This can be right to = area per lipid?=20 =20 From: on behalf of Jeffrey Potoff Reply-To: , Jeffrey Potoff Date: Thursday, March 18, 2021 at 5:28 PM To: "namd-l@ks.uiuc.edu" Subject: RE: namd-l: Lipid into sphere =20 If you know the area per lipid for the lipid of interest, couldn=E2=80=99t = you calculate the surface area of your sphere and divide by the area per li= pid to get the (approximate) number of lipids required?=20 =20 --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University =20 From: owner-namd-l@ks.uiuc.edu On Behalf Of Ropo= n-Palacios G. Sent: Thursday, March 18, 2021 6:19 PM To: Mike McCallum ; KS UIUC Subject: Re: namd-l: Lipid into sphere =20 [EXTERNAL]=20 Yes, but I want calculate number of lipid to placed given an radius of sphe= re in my case is 425 angstrom=20 =20 From: Mike McCallum Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC , "Ropon-Palacios G." Subject: Re: namd-l: Lipid into sphere =20 Hi Geo.,=20 I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. =20 https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!uWh88g9gQHZKORAzHObqSSE5sPVsOvNNpjpUZvH_y0zYUTY-bRyfLbwyZy= bo3gf0Dg$=20 =20 Best Mike =20 On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. wrot= e: =20 Dear NAMD users,=20 =20 How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom.=20 =20 Best,=20 =20 Geo.=20 =20 -- C. Michael McCallum=20=20=20=20=20=20=20=20=20=20=20 Professor=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20= =20=20 Department of Chemistry, UOP=20=20=20=20 mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax =20 =20 =20 =20 --B_3698935714_644830704 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

One last question dear Jeffrey , packmol can run i= n parallel?

 

Best,

 

Geo.

 

From: <= /span><owner-namd-l@ks.uiu= c.edu> on behalf of Jeffrey Potoff <jpotoff@wayne.edu>
Reply-= To: <namd-l@ks.uiuc.edu>, Jeffrey Potoff <jpotoff@wayne.edu>=
Date: Thursday, March 18, 2021 at 5:52 PM
To: "nam= d-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: RE: namd= -l: Lipid into sphere

 

If it= were me, I would start here:

 

Update of the CHARMM All-Atom Additive Force Field for = Lipids: Validation on Six Lipid Types

Jeffery B. Klauda, Richard M. Venable, J. Alfr= edo Freites, Joseph W. O=E2=80=99Connor, Douglas J. Tobias, Carlos Mondragon-Ramir= ez, Igor Vorobyov, Alexander D. MacKerell, and Richard W. Pastor=

The Journal of Phys= ical Chemistry B 2010 114 (23), 7830-7843

DOI: 10.1021/jp101759q

 

---

Jeffrey Potoff<= /o:p>

Interim Chair, Depar= tment of Chemical Engineering and Materials Science

College of Engineering

Wayne State Unive= rsity

 

From: R= opon-Palacios G. <biodano.geo@gmail.com>
Sent: Thursday, Ma= rch 18, 2021 6:48 PM
To: namd-l@ks.uiuc.edu; Jeffrey Potoff <jp= otoff@wayne.edu>
Subject: Re: namd-l: Lipid into sphere

 

Have lipid POPE take from CHARMM-GUI into it and column section named =E2=80=9CS= urface Area=E2=80=9D indicate 58.8 Angstrom^3. This can be right to area per lipid= ?

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of Jeffrey Potoff <jpotoff@wayne.edu>
Reply-To: = <namd-l@ks.uiuc.edu>, Jeffrey = Potoff <jpotoff@wayne.edu>
<= b>Date: Thursday, March 18, 2021 at 5:28 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: RE: namd-= l: Lipid into sphere

&nbs= p;

If you= know the area per lipid for the lipid of interest, couldn=E2=80=99t you calculate= the surface area of your sphere and divide by the area per lipid to get the= (approximate) number of lipids required?

 

---

Jeffrey Potoff

Interim Chair, Department of Chemi= cal Engineering and Materials Science

College of Engineering

Wayne State University

 

From: owner-namd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.edu> On Behalf Of <= /b>Ropon-Palacios G.
Sent: Thursday, March 18, 2021 6:19 PM
= To: Mike McCallum <mmccallum@P= ACIFIC.EDU>; KS UIUC <namd-l@k= s.uiuc.edu>
Subject: Re: namd-l: Lipid into sphere

 

[EXTERNAL]

Yes, but I want calculate number of lipid to placed given an rad= ius of sphere in my case is 425 angstrom

&= nbsp;

From: M= ike McCallum <mmccallum@PACIFIC.ED= U>
Date: Thursday, March 18, 2021 at 5:13 PM
To: = KS UIUC <namd-l@ks.uiuc.edu>, = "Ropon-Palacios G." <bio= dano.geo@gmail.com>
Subject: Re: namd-l: Lipid into sphere<= /span>

 

Hi Geo.,

I=E2=80=99d l= ook into PACKMOL.  It should be able to do exactly this for you, and it= is easy to use.

 

 

Best

Mike

 

On Mar 18, 2021, at 2:25 PM,= Ropon-Palacios G. <biodano.geo@gm= ail.com> wrote:

 

Dear NAMD users, 

 

How can calculate lipid (POPE) nu= mber to be placed into an sphere the 425 Angstrom. 

 

Best, 

 

Geo.&= nbsp;

 

--

C. Michael McCallum          &n= bsp;

Professor       &= nbsp;                

Department of Chemistry, UOP    

mmccallum .at. pacific .dot. edu   =             (209) 946-2636 v  / (209) 94= 6-2607 fax

 

=  

 

 

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boundary="_000_DM6PR11MB4594B94D08E3E38FC096149DAA699DM6PR11MB4594namp_" X-OriginatorOrg: wayne.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: DM6PR11MB4594.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 5a5b6408-a372-474d-3118-08d8ea634891 X-MS-Exchange-CrossTenant-originalarrivaltime: 18 Mar 2021 23:12:21.1897 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: e51cdec9-811d-471d-bbe6-dd3d8d54c28b X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 7vBq2MClXa1Ds0e5r780jZmBLA9wPyNrBOb2nDoSU3YfP8RONDzYDekrTHp2lbrCkd1XLxSUKApvT0iYb4rkFQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: DM5PR11MB1468 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMfEQpMehcaEQpZRBdoeBkeAR8bGmJkfxEKWFgXZHlrX1lbfEF7c2I RCnhOF2JYXmZ6SxMfehwZEQp5TBdjYmRuaEFHEmdnEhEKQ0gXBxsfHBEKQ1kXGBsRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHR9xGxsbEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFxpBcmd7GkF4Qx1+GR1hQV9fYmcfR09Sc0VdUAdBeGZIEQpYXBcfBBoEGBgcBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXckNzZlMRCk1cFxkcHREKTFoXeGlNTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb29ra2xraxEKQk8Xel5zQRJPG2kcRnMRCkNaFx4aBBsaHQQYGR0EGx gSEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdiWF5meksTH3ocGREKQkkXYlheZnpLEx96H BkRCkJFF2VgBW9+eHB5b3NdEQpCThdiWF5meksTH3ocGREKQkwXZHlrX1lbfEF7c2IRCkJsF2UF H318eU9Aa2UYEQpCQBdpZXBZb0hNfm0FTBEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF2tlfF1 vGwVYZhJnEQpwZxdoZ3MFcB1yel9haBAeEhEKcGgXaGATZ2ROGnsFX2IQGRoRCnBoF2ITRklAZ3 wFaGlDEBkaEQpwaBduWFx5HUlwT0x/ThAZGhEKcGgXaXxBQUEbbFNAYGcQGRoRCnBoF2BJZnJ8U GlbXGRjEBkaEQpwfRdjW3pzWGl5YUZJQhAZGhEKcGcXaUNuUAFZc0cBHlMQHBoRCnBnF21HYWtN YxlMU2luEBwaEQpwZxdvTkdffX5YbElPaBAcGhEKcH0XZn1LWUJcYQFPehoQGRoRCnB/F21mH2V SBU1gH1IFEB0SEQpwXxdgAX1AHXl+Yh1zTBAZGhEKcH8XYR8dZUQZGX56fXgQGxgcEQpwXxdnTW BGWEAbHUceXhAZGhEKcGwXZ2B7TR1EXhthQWcQHhIRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 phishscore=0 spamscore=0 mlxlogscore=754 malwarescore=0 mlxscore=0 clxscore=195 impostorscore=0 lowpriorityscore=0 adultscore=0 priorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180165 X-Spam-Score: 0 X-Spam-OrigSender: jpotoff@wayne.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeffrey Potoff --_000_DM6PR11MB4594B94D08E3E38FC096149DAA699DM6PR11MB4594namp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Apparently, yes. https://urldefense.com/v3/__http://vision.ime.usp.br/*randrade/parpackmol/i= ndex.html__;fg!!DZ3fjg!tbpgGsC5OnBK7umyVD3j_z3Cm9TffFZWk-MzGBR6iYNzims6fKvq= KVD0JOfp2DQABQ$=20 --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: Ropon-Palacios G. Sent: Thursday, March 18, 2021 7:09 PM To: namd-l@ks.uiuc.edu; Jeffrey Potoff Subject: Re: namd-l: Lipid into sphere One last question dear Jeffrey , packmol can run in parallel? Best, Geo. From: > on behalf= of Jeffrey Potoff > Reply-To: >, Jeffrey Potoff <= jpotoff@wayne.edu> Date: Thursday, March 18, 2021 at 5:52 PM To: "namd-l@ks.uiuc.edu" > Subject: RE: namd-l: Lipid into sphere If it were me, I would start here: Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation o= n Six Lipid Types Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O=E2= =80=99Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, A= lexander D. MacKerell, and Richard W. Pastor The Journal of Physical Chemistry B 2010 114 (23), 7830-7843 DOI: 10.1021/jp101759q --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: Ropon-Palacios G. > Sent: Thursday, March 18, 2021 6:48 PM To: namd-l@ks.uiuc.edu; Jeffrey Potoff > Subject: Re: namd-l: Lipid into sphere Have lipid POPE take from CHARMM-GUI into it and column section named =E2= =80=9CSurface Area=E2=80=9D indicate 58.8 Angstrom^3. This can be right to = area per lipid? From: > on behalf= of Jeffrey Potoff > Reply-To: >, Jeffrey Potoff <= jpotoff@wayne.edu> Date: Thursday, March 18, 2021 at 5:28 PM To: "namd-l@ks.uiuc.edu" > Subject: RE: namd-l: Lipid into sphere If you know the area per lipid for the lipid of interest, couldn=E2=80=99t = you calculate the surface area of your sphere and divide by the area per li= pid to get the (approximate) number of lipids required? --- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: owner-namd-l@ks.uiuc.edu > On Behalf Of Ropon-Palacio= s G. Sent: Thursday, March 18, 2021 6:19 PM To: Mike McCallum >; KS= UIUC > Subject: Re: namd-l: Lipid into sphere [EXTERNAL] Yes, but I want calculate number of lipid to placed given an radius of sphe= re in my case is 425 angstrom From: Mike McCallum > Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC >, "Ropon-Palacio= s G." > Subject: Re: namd-l: Lipid into sphere Hi Geo., I=E2=80=99d look into PACKMOL. It should be able to do exactly this for yo= u, and it is easy to use. https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.= shtml__;!!DZ3fjg!tbpgGsC5OnBK7umyVD3j_z3Cm9TffFZWk-MzGBR6iYNzims6fKvqKVD0JO= eO-6tQEQ$ Best Mike On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. > wrote: Dear NAMD users, How can calculate lipid (POPE) number to be placed into an sphere the 425 A= ngstrom. Best, Geo. -- C. Michael McCallum Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 9= 46-2607 fax --_000_DM6PR11MB4594B94D08E3E38FC096149DAA699DM6PR11MB4594namp_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: Quoted-printable

Apparently, yes. =

 

http://vision.ime.usp.br/~randrade/parpackmol/index.html

 

---<= /p>

Jeffrey Potoff

Interim Chair, Departm= ent of Chemical Engineering and Materials Science

College of Engineering=

Wayne State University=

 

From: Ropon-Palacios G. <biodano.geo@gmail= .com>
Sent: Thursday, March 18, 2021 7:09 PM
To: namd-l@ks.uiuc.edu; Jeffrey Potoff <jpotoff@wayne.edu>
Subject: Re: namd-l: Lipid into sphere

 

One last question dear Jeffrey , packmol can run in = parallel?

 

Best,

 

Geo.

 

From= : <owner-namd-l@ks.uiuc.edu> on behalf o= f Jeffrey Potoff <jpotoff@wayne.edu= >
Reply-To: <namd-l@ks.uiuc.e= du>, Jeffrey Potoff <jpotoff= @wayne.edu>
Date: Thursday, March 18, 2021 at 5:52 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu&g= t;
Subject: RE: namd-l: Lipid into sphere

 

If it were me, I would= start here:

 

Update of the CHARMM A= ll-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Jeffery B. Klauda, Ric= hard M. Venable, J. Alfredo Freites, Joseph W. O=E2=80=99Connor, Douglas J.= Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, a= nd Richard W. Pastor

The Journal of Physica= l Chemistry B 2010 114 (23), 7830-7843

DOI: 10.1021/jp101759q=

 

---<= /p>

Jeffrey Potoff<= o:p>

Interim Chair, Departm= ent of Chemical Engineering and Materials Science

College of Engineering=

Wayne State University=

 

From: Ropon-Palacios G. <biodano.geo@gmail.com>
Sent: Thursday, March 18, 2021 6:48 PM
To: namd-l@ks.uiuc.edu; Je= ffrey Potoff <jpotoff@wayne.edu= >
Subject: Re: namd-l: Lipid into sphere

 

Have lipid POPE take from CHARMM-GUI into it and col= umn section named =E2=80=9CSurface Area=E2=80=9D indicate 58.8 Angstrom^3. = This can be right to area per lipid?

 

From= : <owner-namd-l@ks.uiuc.edu> on behalf o= f Jeffrey Potoff <jpotoff@wayne.edu= >
Reply-To: <namd-l@ks.uiuc.e= du>, Jeffrey Potoff <jpotoff= @wayne.edu>
Date: Thursday, March 18, 2021 at 5:28 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu&g= t;
Subject: RE: namd-l: Lipid into sphere

 

If you know the area p= er lipid for the lipid of interest, couldn=E2=80=99t you calculate the surf= ace area of your sphere and divide by the area per lipid to get the (approx= imate) number of lipids required?

 

---<= /p>

Jeffrey Potoff<= o:p>

Interim Chair, Departm= ent of Chemical Engineering and Materials Science

College of Engineering=

Wayne State University=

 

From: owner-namd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.edu> On Behalf Of Ropon-Palacios G.
Sent: Thursday, March 18, 2021 6:19 PM
To: Mike McCallum <mmcca= llum@PACIFIC.EDU>; KS UIUC <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: Lipid into sphere

 

[EXTERNAL]

Yes, but I want calculate number of lipid to placed = given an radius of sphere in my case is 425 angstrom

 

From= : Mike McCallum <= ;mmccallum@PACIFIC.EDU>
Date: Thursday, March 18, 2021 at 5:13 PM
To: KS UIUC <namd-l@ks.uiuc= .edu>, "Ropon-Palacios G." <biodano.geo@gmail.com>
Subject: Re: namd-l: Lipid into sphere

 

Hi Geo.,

I=E2=80=99d look into PACKMOL.  It should be ab= le to do exactly this for you, and it is easy to use.

 

 

Best

Mike

 

On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. <<= a href=3D"mailto:biodano.geo@gmail.com">biodano.geo@gmail.com> wrote= :

 

Dear NAMD users, 

 

How can calculate lipid (POPE) number to be placed i= nto an sphere the 425 Angstrom. =

 

Best, 

 

Geo. 

 

--

C. Michael McCallum     &nbs= p;     

Professor         =                

Department of Chemistry, UOP   &n= bsp;

mmccallum .at. pacific .dot. edu =               (209) 946-2636 v  / = (209) 946-2607 fax

 

 

 

 

--_000_DM6PR11MB4594B94D08E3E38FC096149DAA699DM6PR11MB4594namp_-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 18 18:25:14 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12INPEoi027505; Thu, 18 Mar 2021 18:25:14 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12INPE2n027504; Thu, 18 Mar 2021 18:25:14 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12INPDpt027499; Thu, 18 Mar 2021 18:25:13 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12INPDQU027498; Thu, 18 Mar 2021 18:25:13 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12INP6Fw027491 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 18 Mar 2021 18:25:07 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12INHTNv030438 for ; Thu, 18 Mar 2021 23:25:06 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qk1-f172.google.com (mail-qk1-f172.google.com [209.85.222.172]) by mx0b-00007101.pphosted.com with ESMTP id 37bny9g9mj-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 18 Mar 2021 23:25:06 +0000 Received: by mail-qk1-f172.google.com with SMTP id q3so1101206qkq.12 for ; Thu, 18 Mar 2021 16:25:06 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic:references :in-reply-to:mime-version; bh=O9O6A40+cOIw2xovDjT/YhtaYxFW6Bn/qr0YbCQ0gP8=; b=gNbzA+FihRYbUf/vAZkRGtu0HZIEUqMkUgOyI3e8YQ+EJqWs8r09Buo27VS2uXcAMk YNouH5hhZBnjwcrtpluprpDJjDY6b6kFUyE+06PFpinLLF2J5thNsmAFLndPESV5W054 XT4d6Uxkx/Y+qYGXnMR6FUP+wsIeEjFvL8cXkEnjKHptZL/S7GI2c6qapLWrUPeFN7bw ki2EOCVKhqys567mwfTFPl7iIIqKWNqA1qlwos5RyHw5DnRmEaG98SSJS9YMlfEZMDN2 HSbb9n4BF+9UKxMMA2H50rmQn0MJjVnOBaHboYFwOxpzTEsDGgxeVeP8hlCzGxi5fLFK Un/w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:references:in-reply-to:mime-version; bh=O9O6A40+cOIw2xovDjT/YhtaYxFW6Bn/qr0YbCQ0gP8=; b=rpZtSYfTDqJkuQdDHIcJ0zAYhilNsXUMB3IdjVlFjc5MPUi6+jd0JgEWRwWjzb9zEO DC0I86cdqhv7qJMW3QCDgAAdD/f3FhX6keuMaRu6EHw1ggi4YH8X0IrJrPb5B8PQiSrG 0QcSvF6dX/AkE5YYKsp6BCxYerslLxo4NEjqrTNCvYm+k+gtxkwReVXA+JzaqUCwRlY7 em2nBoNsGk7XZIqEAKECQNd7CbXFmwyAubs39tQs4jSiXFWPU2ZyuflHz0ET1ZecK8+R QevEH6OcGc2o0z0ma0QdsyT+4YwdkZffJToYlbWJlqk5kZRUQfMifYt8d5FbRpfZvlYH NbXw== X-Gm-Message-State: AOAM530Kv9/WqTBP0javqs2ZGcnt8FvUOM61WLymS7mrBz1IfSHlw43y SrAz8uq2zPgtDlbGpejhilBGaadSr8WX5g== X-Google-Smtp-Source: ABdhPJw4WhNk6zPkGd/8qkGjNJF85BRa+D64tOslumcDZ0M7N+BvPX6k5eeSdTGOWe3LnJ4GAqLa9Q== X-Received: by 2002:a37:c07:: with SMTP id 7mr6659379qkm.312.1616109905679; Thu, 18 Mar 2021 16:25:05 -0700 (PDT) Received: from [192.168.1.37] ([181.64.231.211]) by smtp.gmail.com with ESMTPSA id i78sm3029863qke.46.2021.03.18.16.25.03 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 18 Mar 2021 16:25:05 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 18 Mar 2021 18:25:02 -0500 Subject: Re: namd-l: Lipid into sphere From: "Ropon-Palacios G." To: , Jeffrey Potoff Message-ID: <4D92F25B-4847-421C-894C-3022076D0BD7@gmail.com> Thread-Topic: namd-l: Lipid into sphere References: <6A9AFCFE-5DAF-4FA1-BCF5-565D47B4FDFE@gmail.com> <14CB4794-7C37-4CB0-BBE6-26E4F5E70F51@gmail.com> In-Reply-To: Content-type: multipart/alternative; boundary="B_3698936704_1904654132" X-CLX-Response: 1TFkXGx0YEQpMehcZGx4RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGB8eEQpDWRcYGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGHEZGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdlH1N7Ql9HUEBLcGZrTGRNSUNhWGMeYHtudVJBekscTREKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JDc3JeEQpNXBcYExwRCkxaF39pTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx 0YEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2Np WW96Tx1yR09/EQpCQBdpZXBZb0hNfm0FTBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnl DF2tlfF1vGwVYZhJnEQpZSxcTGR4TEQpwZxdtR2FrTWMZTFNpbhAbEhEKcGgXa3tkclJYH2hjc2 sQGhEKcGgXYRMFQgF/ZXNaBVkQGxoSEQpwaBdhb0FHSWhBHH9hExAaEQpwaBdgQGxpXF5oQVJce hAbGxIRCnBoF2h8bGNHR0NsWWtIEBoRCnBnF2lDblABWXNHAR5TEBkaEQpwfRdjW3pzWGl5YUZJ QhAaEQpwfRdkBR5BQnpQXGFlSRAaEQpwfxdtZh9lUgVNYB9SBRATExEKcF8XYAF9QB15fmIdc0w QGhEKcH8XYWZvWxpnZEJIHVsQGxsfEQpwXxduAW0YR0ReGmQBcBAbGRgRCnBsF3pHQGsYWXl/Hh tIEBkaEQpwQxdkekR7Zn1bTmtTbhAcGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=314 mlxscore=0 malwarescore=0 phishscore=0 adultscore=0 bulkscore=0 mlxlogscore=492 spamscore=0 lowpriorityscore=0 impostorscore=0 suspectscore=0 clxscore=172 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103180167 domainage_hfrom=9349 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3698936704_1904654132 Content-type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks so much. =20 From: on behalf of Jeffrey Potoff Reply-To: , Jeffrey Potoff Date: Thursday, March 18, 2021 at 6:13 PM To: "namd-l@ks.uiuc.edu" Subject: RE: namd-l: Lipid into sphere =20 https://urldefense.com/v3/__http://vision.ime.usp.br/*randrade/parpackmol/i= ndex.html__;fg!!DZ3fjg!qIFLgnSterIdc0L7jXfRqOV23fbhhctYscI4h3PFlk9jlF513mmh= 2IYm6M3oQ4dSYQ$=20 --B_3698936704_1904654132 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Thanks so much.

<= o:p> 

From: &= lt;owner-namd-l@ks.uiuc.edu> on behalf of Jeffrey Potoff <jpotoff@wayn= e.edu>
Reply-To: <namd-l@ks.uiuc.edu>, Jeffrey Potoff <= ;jpotoff@wayne.edu>
Date: Thursday, March 18, 2021 at 6:13 PMTo: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject:
RE: namd-l: Lipid into sphere

=

 

http://vision.ime.usp.br/~randrade/pa= rpackmol/index.html

--B_3698936704_1904654132-- From owner-namd-l@halifax.ks.uiuc.edu Sat Mar 20 05:00:21 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12KA0L8J003216; Sat, 20 Mar 2021 05:00:21 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12KA0L5M003215; Sat, 20 Mar 2021 05:00:21 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12KA0KmK003211; Sat, 20 Mar 2021 05:00:20 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12KA0Kh5003210; Sat, 20 Mar 2021 05:00:20 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12KA0Edg003201 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000fddd5105bdf4e5db" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGR4SEQpMehcaEQpZRBdrQGJJRxx5RRhYXREKWFgXZH1afnlfQEZaYFA RCnhOF2QdeR9fZF9iRxt7EQp5TBdiRwFuWklJa34fXREKQ0gXBxkcGBEKQ1kXBxMSEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbEnEbBhkfdwYYGhoGGgYaBhsaGgYZGnEbEBp3BhoGGgYaBhoGGgYac RoQGncGGhEKWV4XaG55EQpJRhdfQ19JdUJFWV5PThEKQ04XG2BFY3lORkttG39pTk8baUFic3BF REVwQkhFb3tfe1ARClhcFx8EGgQYGBwFGxoEGxsaBB8aBBseHxAbHhofGhEKXlkXckMYUmMRCk1 cFxkSHBEKTFoXaGlNa2sRCkJPF2V+XFlbW0djU2FsEQpDWhcYGhMEEh8EGBsSBB8bEQpCXhcbEQ pCRRdpWm9gGGhweXB8XxEKQk4XZB15H19kX2JHG3sRCkJMF2R9Wn55X0BGWmBQEQpCbBduZxJOW FtwRWRTGhEKQkAXYX4SeElTWV8deFARCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdlYBgSXElE SUBtYxEKWUsXHR4dGBEKcGgXY2JQGUlwbGFEY0wQGRoRCnBoF25hfB8ZfkdHeUkFEBkaEQpwaBd pfGkdaUxCXH5QfBAZGhEKcGgXYB1YQUNlGBhIAWMQGRoRCnBoF2dHRX1PfWVBax5AEBkaEQpwbB dsBVgBfX9eX0QSSBAZGhEKbX4XGhEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=348 mlxlogscore=389 suspectscore=0 adultscore=0 bulkscore=0 lowpriorityscore=0 phishscore=0 mlxscore=0 spamscore=0 priorityscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103200073 domainage_hfrom=7472 X-Spam-Score: 0 X-Spam-OrigSender: suryanar@ualberta.ca X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Suryanarayanan Chandrasekaran --000000000000fddd5105bdf4e5db Content-Type: text/plain; charset="UTF-8" Hello, I have a workstation with 2 CPU and 2 GPU. I downloaded NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA and tried to compile it with the below options, I want to use all GPU for a single CPU or both the CPU and GPU in the workstation. 1) namd2 +p18 +idlepoll stmv.namd +setcpuaffinity +isomalloc_sync 2) namd2 +idlepoll +p4 +devices 0,1 *But getting the same error* Charm++> Running on 1 hosts (2 sockets x 10 cores x 2 PUs = 40-way SMP) Charm++> cpu topology info is gathered in 0.006 seconds. Info: Built with CUDA version 10010 FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/DeviceCUDA.C, function initialize, line 135 on Pe 0 (surya): unknown error FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/DeviceCUDA.C, function initialize, line 135 on Pe 0 (surya): unknown error Thanks, Surya --000000000000fddd5105bdf4e5db Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 I have a workstation with 2 CPU and 2 GPU. I downl= oaded NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA and tried to compile = it with the below options, I want to use all GPU for a single CPU or both t= he CPU and GPU in the workstation.=C2=A0

1) n= amd2 +p18 +idlepoll stmv.namd +setcpuaffinity +isomalloc_sync
2) = namd2 +idlepoll +p4 +devices 0,1 <configfile>
But getting the same error
Charm++> Running on 1 hosts (2 sockets x 10 cores x 2 PUs =3D 40-w= ay SMP)
Charm++> cpu topology info is gathered in 0.006 seconds.
I= nfo: Built with CUDA version 10010
FATAL ERROR: CUDA error cudaGetDevice= Count(&deviceCount) in file src/DeviceCUDA.C, function initialize, line= 135
=C2=A0on Pe 0 (surya): unknown error
FATAL ERROR: CUDA error cud= aGetDeviceCount(&deviceCount) in file src/DeviceCUDA.C, function initia= lize, line 135
=C2=A0on Pe 0 (surya): unknown error

Thanks,
=
Surya
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mail-pg1-f176.google.com with SMTP id n11so7033819pgm.12 for ; Sun, 21 Mar 2021 09:19:03 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=bag58Aun79XkV51wEp1RgTdgUwmnz7LIbibMPYa0uX8=; b=IVcOj29OYXIGBHU9GB4wIRmegVCwz0qInoqwkN4bZ7g3HD7q/6viVHjQdCABx6myeB fwU+RS20GgEQyoUxJT38ko1NsbPWewAvPuMSNcEfpkF1iduzH1/u3aTbBJQtbB//AWWT XNZvvjhHWWzemo0eZtb5LoHoOsbPEUCRbKUooVXqbih8vE4d/2M6mtR00/pqQYeiqsJw z5CcC70bud/vr+s7lZEiLRixtlC5P8jWF02bQL+yq1oIz2R66xVzkAtfr8g/r8943ArR y9KyedESlIVwK3isFXdx84wBscf0WsYznt0m0yw2eaNuPSH3x7aYgz0uZLrz2x8wBE1L TcDA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=bag58Aun79XkV51wEp1RgTdgUwmnz7LIbibMPYa0uX8=; b=l71+k9M9JqEZHwj6rv4svr7f78580O0whNKxvcxOAhCX1yA6ebAjqUzu/UvZpCUTfy mD+jM54Ky53F2OyAxFySY8OxyGYJlz9zK/iqpkYW8HJGls5XLumgzdCTVDeFCm8956SQ 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LexEKeE4XY1Nja3sTWH4aX14RCnlMF2RcE3NIBRhHeENQEQpDSBcHGB8bEQpDWRcHGxwSEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRccH3EbBhsZGncGHB0GGgYaBhIcBhpxGhAadwYaBhoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF2ZAR35AeUBiaX1QSH58fBhQS1Ne cG9yG2FEHxgfZ1J7EQpYXBcfBBoEGBgcBRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXckB4S3kRCk1 cFxsdGREKTFoXaGlNa2sRCkxGF29ra2traxEKQk8XbRNgEwFhWmttQBIRCkNaFxgaEwQSHwQYGx 8EGx0cEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RC kJFF21eW1loe1kTbFpBEQpCThdjU2NrexNYfhpfXhEKQkwXehxDcwVye2McS3sRCkJsF21ScBsZ Y10TBXBsEQpCQBdsaRlaZk1MXUhgchEKQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcYEQp5Qxd pYmwdGnp7ekZuWREKWUsXExkfGBEKcGgXZH1mXX0FQlkfHRwQBxkaEQpwaBdoEkdobHxuH25rHx AHGRoRCnBoF2JJeV9Cel95E2YBEAcZGhEKcGgXbGdyS2NCRxJJYh8QBxkaEQpwaBdkaBwdQkhOE kMdExAHGRoRCnBsF21THlgTEkIFY195EAcZGhEKbX4XBxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 adultscore=0 spamscore=0 impostorscore=0 mlxlogscore=402 priorityscore=361 phishscore=0 malwarescore=0 bulkscore=0 lowpriorityscore=0 clxscore=218 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103210129 domainage_hfrom=9352 X-Spam-Score: 0 X-Spam-OrigSender: basudebadrita@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Debadrita Basu --000000000000ab093f05be0e4eb9 Content-Type: text/plain; charset="UTF-8" Hello Everyone, My protein of interest has ~850 residues (quite big) where a Magnesium ion is intrinsically bound. Also some ligands are known to bind to some specific grooves of this protein. I wanted to see the role of Magnesium on the ligand binding (ie whether it has a facilitating or inhibiting role). So, I decided to carry out the FEP calculation where I discharge the Magnesium atom to a dummy Magnesium atom, (in two different systems: ligand bound and apo) followed by thermodynamic integration. I used CGENFF to parameterize. I decided to follow the FEP algorithm implemented in NAMD, but I have a couple of questions in my mind: 1. Whether I will get a true result by using the whole protein. 2. While discharging the Magnesium atom I will end up changing the total charge of the system, is that acceptable? If not, how can it be solved? Hope, I get something to learn from your answers. Thank You. -- Debadrita Basu. Senior Research Fellow Bose Institute Kolkata, India. --000000000000ab093f05be0e4eb9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Everyone,

My protein of inte= rest has ~850 residues (quite big) where a Magnesium ion=C2=A0 is intrinsic= ally=C2=A0bound. Also some ligands are known to bind to some specific groov= es of this protein. I wanted to see the role of Magnesium on the ligand bin= ding (ie whether it has a facilitating or inhibiting role). So, I decided t= o carry out the FEP calculation where I discharge the Magnesium atom to a d= ummy Magnesium atom, (in two different systems: ligand bound and apo) follo= wed by thermodynamic integration. I used CGENFF to parameterize.
=
I decided to follow the FEP algorithm implemented in NAMD, b= ut I have a couple of questions in my mind:

1. Whe= ther I will get a true result by using the whole protein.
2. Whil= e discharging=C2=A0the Magnesium atom I will end up changing the total char= ge of the system, is that acceptable? If not, how can it be solved?

Hope, I get something to learn from your answers.

Thank You.=C2=A0

--
Debadrita Basu.

Senior Re= search Fellow
Bose Institute=C2=A0
Kolkata, India.
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boundary="0000000000003d3eaf05be11224f" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwbEQpMehcZGR4RCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHHx4YEQpDWRcHGBwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhtxHxoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XaUt9BxxyHV5FUklpRl5kbGliTnJ/QWRyRHJMQGVnREARClhcFx8EGgQYGBwF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXckB/chMRCk1cFxgaExEKTFoXfGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdtbVJNa2xbb0hsbREKQ1oXGBoTBBIfBBscHA QbEhoRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaxMaYU5fXlgYHWURCkJOF2NTY2t7E1h+Gl9eEQpCTBdpSUgaS35pRht4cxEKQmwX YR4ZeFpubGdjX2IRCkJAF2F+bFpOQk56TUtgEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXaHp6QG9waxgZZkgRCllLFxMZHxgRCnBoF21JHHxIGENiSwVCEBkaEQpwaBdkfWZdfQVCWR 8dHBAHGxIRCnBoF2BcfGtTTBprTXJmEBkaEQpwaBdkcGNoQ0geY1pFYRAZGhEKcGgXZXkZZEF6H RluRXkQGRoRCnBsF24dZnsSSxp4ElxtEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=161 mlxlogscore=952 suspectscore=0 adultscore=0 bulkscore=0 lowpriorityscore=0 phishscore=0 mlxscore=0 spamscore=0 priorityscore=334 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103210156 domainage_hfrom=9352 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --0000000000003d3eaf05be11224f Content-Type: text/plain; charset="UTF-8" 1) Using the whole protein is almost always technically more correct, but makes sampling more expensive and harder to converge (potentially unattainable on such large a system). Unless you think there are important conformational changes involved, I would consider a specialized strategy for your quantity of interest. 2) Charge changing perturbations do cause a shift in dG values due to a change in the zero of energy arising from PME. However, the shift vanishes when the periodic box is large and the mean dielectric is high (eg if the system is mostly water). I would look up the work of Rocklin, et al. on using continuum corrections, but other strategies may also work. Also, divalent ion parameters in fixed charge force fields are notoriously poor. You generally either get good structure or good energetics - rarely both. I would validate your model in someway first, bc the results are unlikely to just work out nicely on your first try. Hope that helps, BKR On Sun, Mar 21, 2021, 12:21 PM Debadrita Basu wrote: > Hello Everyone, > > My protein of interest has ~850 residues (quite big) where a Magnesium > ion is intrinsically bound. Also some ligands are known to bind to some > specific grooves of this protein. I wanted to see the role of Magnesium on > the ligand binding (ie whether it has a facilitating or inhibiting role). > So, I decided to carry out the FEP calculation where I discharge the > Magnesium atom to a dummy Magnesium atom, (in two different systems: ligand > bound and apo) followed by thermodynamic integration. I used CGENFF to > parameterize. > > I decided to follow the FEP algorithm implemented in NAMD, but I have a > couple of questions in my mind: > > 1. Whether I will get a true result by using the whole protein. > 2. While discharging the Magnesium atom I will end up changing the total > charge of the system, is that acceptable? If not, how can it be solved? > > Hope, I get something to learn from your answers. > > Thank You. > > -- > Debadrita Basu. > > Senior Research Fellow > Bose Institute > Kolkata, India. > --0000000000003d3eaf05be11224f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
1) Using the whole protein is almost always technica= lly more correct, but makes sampling more expensive and harder to converge = (potentially unattainable on such large a system). Unless you think there a= re important conformational changes involved, I would consider a specialize= d strategy for your quantity of interest.=C2=A0

=
2) Charge changing perturbations do cause a shift i= n dG values due to a change in the zero of energy arising from PME. However= , the shift vanishes when the periodic box is large and the mean dielectric= is high (eg if the system is mostly water). I would look up the work of Ro= cklin, et al. on using continuum corrections, but other strategies may also= work.=C2=A0

Also, dival= ent ion parameters in fixed charge force fields are notoriously poor. You g= enerally either get good structure or good energetics - rarely both. I woul= d validate your model in someway first, bc the results are unlikely to just= work out nicely on your first try.=C2=A0

=
Hope that helps,=C2=A0
BKR

On Sun, Mar 21, 2021, 12:21 PM Debadrita Basu <basudebadrita@gmail.com> wr= ote:
Hello Everyon= e,

My protein of interest has ~850 residues (quite = big) where a Magnesium ion=C2=A0 is intrinsically=C2=A0bound. Also some lig= ands are known to bind to some specific grooves of this protein. I wanted t= o see the role of Magnesium on the ligand binding (ie whether it has a faci= litating or inhibiting role). So, I decided to carry out the FEP calculatio= n where I discharge the Magnesium atom to a dummy Magnesium atom, (in two d= ifferent systems: ligand bound and apo) followed by thermodynamic integrati= on. I used CGENFF to parameterize.

I decided to fo= llow the FEP algorithm implemented in NAMD, but I have a couple of question= s in my mind:

1. Whether I will get a true result = by using the whole protein.
2. While discharging=C2=A0the Magnesi= um atom I will end up changing the total charge of the system, is that acce= ptable? If not, how can it be solved?

Hope, I get = something to learn from your answers.

Thank You.= =C2=A0

--
Debadrita Basu.

<= /div>
Senior Research Fellow
Bose Institute=C2=A0
K= olkata, India.
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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=LAV99E12A7LPZWsEmAygD/vDAa/YIROWLDR28zHYrX4=; b=JwGFlHYVkeF5v0x+hZ0XATyDAdb9u4PJNoYN2b5npHMK64ehlOwfrmBZ+NuhLJfDwX tvt979+LsOdGeh3NvtH2ScFPdXkFgzo+ob9vG8g2nhd5mLEyHgx6meiXPM3ISktJluAK impfFkKD1YDlIATj5/jkCw5aOYZ+vD2qPL7Jcbd5Q8nZwJ+cV9bWWD0eDoBTF/5iZCWm hLL1dY2nGAWJ7lAcG4e2yqpYhfIGHkDz9SMW7e2avXtPWx2bauUjKXRs1ipefNpnOMpj ze1qgDEKq0CQ/yTD081BQcD2ozW8gaFFWxiggvt03nKzoVxe645A/NNrAS1dJKuXGoe5 VxlA== X-Gm-Message-State: AOAM531i0zvtLQ5CYQBJVNthFOZVnZKNsdw8mRxxeahIyPo039GalZE6 DqVlItiuA71mUY1PSM/Vho835nEkFdRWnxE67QBPfg== X-Google-Smtp-Source: ABdhPJzQzjx9fx7HzamKoNZV0kam6PkOXD2df9POQy3S1rBBBx9twBxT5ApyWIEl/RMngHZQeur3C5GSLD7InHigT98= X-Received: by 2002:a2e:3611:: with SMTP id d17mr8357206lja.392.1616387159921; Sun, 21 Mar 2021 21:25:59 -0700 (PDT) MIME-Version: 1.0 References: <8D7AB8A8-4050-4D7A-AFC9-0AB20F30BD44@msu.edu> In-Reply-To: <8D7AB8A8-4050-4D7A-AFC9-0AB20F30BD44@msu.edu> From: Suryanarayanan Chandrasekaran Date: Mon, 22 Mar 2021 09:54:45 +0530 Message-ID: Subject: Re: namd-l: Compiling namd2 in 2 GPU 2 CPU workstation To: "Vermaas, Josh" , namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000007ca69c05be18763b" X-CLX-Response: 1TFkXGxgSEQpMehcaEQpZRBdrQGJJRxx5RRhYXREKWFgXZH1afnlfQEZaYFA RCnhOF2QdeR9fZF9iRxt7EQp5TBdiRwFuWklJa34fXREKQ0gXBxgfExEKQ1kXBxkaEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxoScRsbEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxt9fxJTS01tdUh4Rm1JaxgdTnNHT34eQxtYfR5kTHxwEQpYXBcfBBoEGBgcBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3JASW4aEQpNXBcYExwRCkxaF3hpTWtNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGx0fEQ pCXhcbEQpEXhcYEQpCRRdpWm9gGGhweXB8XxEKQk4XZB15H19kX2JHG3sRCkJMF2R9Wn55X0BGW mBQEQpCbBduZxJOWFtwRWRTGhEKQkAXYUd6HH8BS1pHHlMRCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcYEQp5QxdoXhJAAW57QGUeeBEKWUsXHR4dHhEKcGcXbUdha01jGUxTaW4QGRoRCnBoF3p QQ3p6UkRCR2dIEBkaEQpwaBdlRWhka0kZZ2NuExAZGhEKcGgXYB1YQUNlGBhIAWMQGRoRCnBoF2 FFRUJlbkVOHkVSEBkaEQpwaBdlRWRaG2R4b1teXxAZGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnBsF 2wFWAF9f15fRBJIEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 bulkscore=0 priorityscore=0 impostorscore=0 malwarescore=0 spamscore=0 clxscore=128 lowpriorityscore=0 suspectscore=0 mlxlogscore=999 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103220032 domainage_hfrom=7474 X-Spam-Score: 0 X-Spam-OrigSender: suryanar@ualberta.ca X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Suryanarayanan Chandrasekaran --0000000000007ca69c05be18763b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I don't think this is a driver issue, Given below is the output from nvidia-smi. In the installation manual, it is mentioned only one GPU can be used in Multicore Cuda in a single node. Probably mine is a workstation, so the problem might be identifying 2 GPU. I want to use both the two CPUs and two GPUs, in the workstation. $ nvidia-smi Mon Mar 22 09:49:28 2021 +--------------------------------------------------------------------------= ---+ | NVIDIA-SMI 455.45.01 Driver Version: 455.45.01 CUDA Version: 11.1 | |-------------------------------+----------------------+-------------------= ---+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D| | 0 Quadro RTX 5000 Off | 00000000:17:00.0 Off | Off | | 33% 37C P8 18W / 230W | 1MiB / 16125MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+-------------------= ---+ | 1 Quadro RTX 5000 Off | 00000000:73:00.0 On | Off | | 33% 40C P8 18W / 230W | 652MiB / 16117MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+-------------------= ---+ +--------------------------------------------------------------------------= ---+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D| | 0 N/A N/A 2584 G /usr/lib/xorg/Xorg 0MiB | | 0 N/A N/A 2911 G /usr/bin/gnome-shell 0MiB | | 0 N/A N/A 8657 G ...gAAAAAAAAA --shared-files 0MiB | | 0 N/A N/A 12099 G /usr/lib/firefox/firefox 0MiB | | 0 N/A N/A 12615 G /usr/lib/firefox/firefox 0MiB | | 0 N/A N/A 13032 G /usr/lib/firefox/firefox 0MiB | | 0 N/A N/A 13527 G /usr/lib/firefox/firefox 0MiB | | 0 N/A N/A 25049 G /usr/lib/firefox/firefox 0MiB | | 1 N/A N/A 2584 G /usr/lib/xorg/Xorg 484MiB | | 1 N/A N/A 2911 G /usr/bin/gnome-shell 86MiB | | 1 N/A N/A 8657 G ...gAAAAAAAAA --shared-files 19MiB | | 1 N/A N/A 12099 G /usr/lib/firefox/firefox 2MiB | | 1 N/A N/A 12615 G /usr/lib/firefox/firefox 2MiB | | 1 N/A N/A 13032 G /usr/lib/firefox/firefox 2MiB | | 1 N/A N/A 13527 G /usr/lib/firefox/firefox 2MiB | | 1 N/A N/A 25049 G /usr/lib/firefox/firefox 44MiB | +--------------------------------------------------------------------------= ---+ On Sun, Mar 21, 2021 at 4:42 AM Vermaas, Josh wrote: > What is the output of nvidia-smi? NAMD isn=E2=80=99t able to ask CUDA how= many > GPUs there are. Sometimes this is a driver issue, and sometimes this is > just a compatibility issue between your hardware and what NAMD expects. > > > > -Josh > > > > *From: * on behalf of Suryanarayanan > Chandrasekaran > *Reply-To: *"namd-l@ks.uiuc.edu" , Suryanarayanan > Chandrasekaran > *Date: *Saturday, March 20, 2021 at 6:09 AM > *To: *"namd-l@ks.uiuc.edu" > *Subject: *namd-l: Compiling namd2 in 2 GPU 2 CPU workstation > > > > Hello, > > I have a workstation with 2 CPU and 2 GPU. I downloaded > NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA and tried to compile it > with the below options, I want to use all GPU for a single CPU or both th= e > CPU and GPU in the workstation. > > > > 1) namd2 +p18 +idlepoll stmv.namd +setcpuaffinity +isomalloc_sync > > 2) namd2 +idlepoll +p4 +devices 0,1 > > *But getting the same error* > > Charm++> Running on 1 hosts (2 sockets x 10 cores x 2 PUs =3D 40-way SMP) > Charm++> cpu topology info is gathered in 0.006 seconds. > Info: Built with CUDA version 10010 > FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/Devi= ceCUDA.C, function initialize, line 135 > on Pe 0 (surya): unknown error > FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/Devi= ceCUDA.C, function initialize, line 135 > on Pe 0 (surya): unknown error > > Thanks, > > Surya > > --0000000000007ca69c05be18763b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I don't think this is a driver issue, Given below= is the output from nvidia-smi. In the installation manual, it is mentioned= only one GPU can be used in Multicore Cuda in a single node. Probably mine= is a workstation, so the problem might be identifying 2 GPU. I want to use= both the two CPUs and two GPUs, in the workstation.

$ nvidia-smi
Mon Mar 22 09:49:28 2021 =C2=A0 =C2=A0 =C2=A0 +-------------------------------------------------------------------------= ----+
| NVIDIA-SMI 455.45.01 =C2=A0 =C2=A0Driver Version: 455.45.01 =C2= =A0 =C2=A0CUDA Version: 11.1 =C2=A0 =C2=A0 |
|--------------------------= -----+----------------------+----------------------+
| GPU =C2=A0Name = =C2=A0 =C2=A0 =C2=A0 =C2=A0Persistence-M| Bus-Id =C2=A0 =C2=A0 =C2=A0 =C2= =A0Disp.A | Volatile Uncorr. ECC |
| Fan =C2=A0Temp =C2=A0Perf =C2=A0Pwr= :Usage/Cap| =C2=A0 =C2=A0 =C2=A0 =C2=A0 Memory-Usage | GPU-Util =C2=A0Compu= te M. |
| =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 | =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0| =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 MIG M. |
|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D|
| =C2=A0 0 =C2=A0Quadro R= TX 5000 =C2=A0 =C2=A0 Off =C2=A0| 00000000:17:00.0 Off | =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Off |
| 33% =C2=A0 37C =C2= =A0 =C2=A0P8 =C2=A0 =C2=A018W / 230W | =C2=A0 =C2=A0 =C2=A01MiB / 16125MiB = | =C2=A0 =C2=A0 =C2=A00% =C2=A0 =C2=A0 =C2=A0Default |
| =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 | =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0| =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0N/A |
+-------------------------------+----------------------+= ----------------------+
| =C2=A0 1 =C2=A0Quadro RTX 5000 =C2=A0 =C2=A0 O= ff =C2=A0| 00000000:73:00.0 =C2=A0On | =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0Off |
| 33% =C2=A0 40C =C2=A0 =C2=A0P8 =C2=A0= =C2=A018W / 230W | =C2=A0 =C2=A0652MiB / 16117MiB | =C2=A0 =C2=A0 =C2=A00%= =C2=A0 =C2=A0 =C2=A0Default |
| =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 | =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0| =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0N/A |
+------= -------------------------+----------------------+----------------------+=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
+-----------= ------------------------------------------------------------------+
| Pr= ocesses: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0|
| =C2=A0GPU =C2=A0 GI =C2=A0 CI =C2=A0 =C2=A0 =C2=A0 = =C2=A0PID =C2=A0 Type =C2=A0 Process name =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0GPU Memory |
| =C2=A0 =C2=A0 =C2=A0 =C2= =A0ID =C2=A0 ID =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Usage =C2=A0 =C2=A0 =C2=A0|
|= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D|
| =C2=A0 =C2=A00 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 =C2=A02584 = =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/xorg/Xorg =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00MiB |
| =C2=A0 =C2=A00 =C2=A0 N/A = =C2=A0N/A =C2=A0 =C2=A0 =C2=A02911 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/bin/gn= ome-shell =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00MiB |
= | =C2=A0 =C2=A00 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 =C2=A08657 =C2=A0 =C2= =A0 =C2=A0G =C2=A0 ...gAAAAAAAAA --shared-files =C2=A0 =C2=A0 =C2=A0 =C2=A0= 0MiB |
| =C2=A0 =C2=A00 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 12099 =C2=A0 = =C2=A0 =C2=A0G =C2=A0 /usr/lib/firefox/firefox =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A00MiB |
| =C2=A0 =C2=A00 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 = 12615 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/firefox/firefox =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A00MiB |
| =C2=A0 =C2=A00 =C2=A0 N/A =C2=A0N/A = =C2=A0 =C2=A0 13032 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/firefox/firefox = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00MiB |
| =C2=A0 =C2=A00 =C2=A0 = N/A =C2=A0N/A =C2=A0 =C2=A0 13527 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/fir= efox/firefox =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00MiB |
| =C2=A0 = =C2=A00 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 25049 =C2=A0 =C2=A0 =C2=A0G =C2= =A0 /usr/lib/firefox/firefox =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00MiB = |
| =C2=A0 =C2=A01 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 =C2=A02584 =C2=A0 = =C2=A0 =C2=A0G =C2=A0 /usr/lib/xorg/Xorg =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0484MiB |
| =C2=A0 =C2=A01 =C2=A0 N/A =C2=A0N/A =C2= =A0 =C2=A0 =C2=A02911 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/bin/gnome-shell =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 86MiB |
| =C2=A0 =C2=A01 = =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 =C2=A08657 =C2=A0 =C2=A0 =C2=A0G =C2=A0 = ..gAAAAAAAAA --shared-files =C2=A0 =C2=A0 =C2=A0 19MiB |
| =C2=A0 =C2= =A01 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 12099 =C2=A0 =C2=A0 =C2=A0G =C2=A0 = /usr/lib/firefox/firefox =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A02MiB || =C2=A0 =C2=A01 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 12615 =C2=A0 =C2=A0 = =C2=A0G =C2=A0 /usr/lib/firefox/firefox =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A02MiB |
| =C2=A0 =C2=A01 =C2=A0 N/A =C2=A0N/A =C2=A0 =C2=A0 13032 = =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/firefox/firefox =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A02MiB |
| =C2=A0 =C2=A01 =C2=A0 N/A =C2=A0N/A =C2=A0 = =C2=A0 13527 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/firefox/firefox =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A02MiB |
| =C2=A0 =C2=A01 =C2=A0 N/A =C2= =A0N/A =C2=A0 =C2=A0 25049 =C2=A0 =C2=A0 =C2=A0G =C2=A0 /usr/lib/firefox/fi= refox =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 44MiB |
+----------------------= -------------------------------------------------------+

On Sun, Mar 21,= 2021 at 4:42 AM Vermaas, Josh <verm= aasj@msu.edu> wrote:

What is the output of nvidia-smi? NAMD isn=E2=80=99t= able to ask CUDA how many GPUs there are. Sometimes this is a driver issue= , and sometimes this is just a compatibility issue between your hardware an= d what NAMD expects.

=C2=A0

-Josh

=C2=A0

From: = <owner-namd-l@ks.uiuc.edu&g= t; on behalf of Suryanarayanan Chandrasekaran <suryanar@ualberta.ca>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, Suryanarayanan Chandrasekaran= <suryanar@ual= berta.ca>
Date: Saturday, March 20, 2021 at 6:09 AM
To: "na= md-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: Compiling namd2 in 2 GPU 2 CPU workstation

=C2=A0

Hello,

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 I have a workstation with 2 CPU and 2 GPU. I downloaded NAMD_Git-2021-0= 3-03_Linux-x86_64-multicore-CUDA and tried to compile it with the below opt= ions, I want to use all GPU for a single CPU or both the CPU and GPU in the= workstation.=C2=A0

=C2=A0

1) namd2 +p18 +idlepoll stmv.namd +setcpuaffinity +i= somalloc_sync

2) namd2 +idlepoll +p4 +devices 0,1 <configfile&g= t;

But getting the same error

Charm++> Running on 1 hosts (2 s= ockets x 10 cores x 2 PUs =3D 40-way SMP)
Charm++> cpu topology info = is gathered in 0.006 seconds.
Info: Built with CUDA version 10010
FAT= AL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/Devic= eCUDA.C, function initialize, line 135
=C2=A0on Pe 0 (surya): unknown er= ror
FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file= src/DeviceCUDA.C, function initialize, line 135
=C2=A0on Pe 0 (surya): = unknown error
Thanks,
Surya<=
u>
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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=H20SPU5YBYNR7stOe3eF4qWZLziktLbCXTfRSzLDBW8=; b=IaFLVB8ETBzgwVdT8G1CvDUf2Wi/nW5vdhHr3H4zjKKL/+ITxWd3+ekBukcqDvFMIy GVlUow7bWWqdOWHelS4Ed3K48TMtVyzGRXEYxCRCm3eTNsifqjdObvrkWTryWdyAaPHb PzTnXzMETlbZQlR88ytjBXS5NzFYj3ZoxOgvtY+wBJsuwo/yBBiMBVRGEdCQwCUmn8Un YDQuJZsi6YYlwvyH3Tv1TL9Qgaz9F+OI/JbEn/UNcopjsWo/stUqyJQxYRxmrAqcDo6j WT+RQre25K0+6jjNzwtByhv7/liXzaE+/dXr1qVphAeZmDf0binKHGytzxoQLyIBWfld oVZw== X-Gm-Message-State: AOAM533QeGh4Jpv3JEb5o+wtgXWtMcncGVR+ubLmteGgn+1/EHs1U9N8 GrAvS2Pk3zNgOgElMXM7ARQcPIj+no/X1aFLaQw= X-Google-Smtp-Source: ABdhPJxUtUAf2oacSYE/ZJyrVxYpxeEJ+E0JFn1b3/0o4lGtzwOztF5pcugKIH5+lqWE0o8k12eGx6cuVdpzAfZfTA8= X-Received: by 2002:a17:90a:1f49:: with SMTP id y9mr13492494pjy.69.1616412648801; Mon, 22 Mar 2021 04:30:48 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Debadrita Basu Date: Mon, 22 Mar 2021 17:18:57 +0530 Message-ID: Subject: Re: namd-l: Some Basic queries for FEP and TI To: Brian Radak Cc: namd-l Content-Type: multipart/alternative; boundary="000000000000be06f505be1e65d4" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIfEQpMehcZHh0RCllEF25Za1IYXXweZUAZEQpYWBd6HENzBXJ7Yxx LexEKeE4XY1Nja3sTWH4aX14RCnlMF2RcE3NIBRhHeENQEQpDSBcHHhobEQpDWRcHGB0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwfcRsGGxkadwYcEwYZGkIZBhoGGxoaBhkacRsQGncGGgYHHxoGG gYHHBoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04Xax1MblpjE2R/aFxs R0RZblpMQEZ1E0B8U05+BxthUF8RClhcFx8EGgQYGBwFGxoEGxoaBB4SBBgYEBseGh8aEQpeWRd yQEN5bxEKTVwXGBoeEQpMWhd8aU1raxEKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2 sRCkJPF2R+WE9mbnNJcFtPEQpDWhcYGhMEEh8EGBscBB4SEQpCXhcbEQpESRcbEQpCXBcbEQpeT hcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF21eW1loe1kTbFpBEQpCThdj U2NrexNYfhpfXhEKQkwXehxDcwVye2McS3sRCkJsF21ScBsZY10TBXBsEQpCQBdhfmxaTkJOek1 LYBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2h6ekBvcGsYGWZIEQpZSxcTGR8ZEQ pwaBdla2gdTGZIbxhTcBAZGhEKcGgXZH1mXX0FQlkfHRwQGhEKcGgXYFx8a1NMGmtNcmYQGRoRC nBoF2V5GWRBeh0ZbkV5EBkaEQpwaBdpfXljWmMYXkJgGRAZGhEKcGwXbVMeWBMSQgVjX3kQGhEK bX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 impostorscore=0 phishscore=0 lowpriorityscore=0 mlxlogscore=999 suspectscore=0 mlxscore=0 priorityscore=347 bulkscore=0 spamscore=0 malwarescore=0 clxscore=185 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103220083 domainage_hfrom=9353 X-Spam-Score: 0 X-Spam-OrigSender: basudebadrita@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Debadrita Basu --000000000000be06f505be1e65d4 Content-Type: text/plain; charset="UTF-8" Thank you for your reply. I could understand the problems associated with such calculations. Moreover, I would like to ask if the ligand is neutral will that lessen the complications or if we do the FEP to know the effect of a structural water(which is also neutral) will that have lesser difficulties? On Mon, Mar 22, 2021 at 1:11 AM Brian Radak wrote: > 1) Using the whole protein is almost always technically more correct, but > makes sampling more expensive and harder to converge (potentially > unattainable on such large a system). Unless you think there are important > conformational changes involved, I would consider a specialized strategy > for your quantity of interest. > > 2) Charge changing perturbations do cause a shift in dG values due to a > change in the zero of energy arising from PME. However, the shift vanishes > when the periodic box is large and the mean dielectric is high (eg if the > system is mostly water). I would look up the work of Rocklin, et al. on > using continuum corrections, but other strategies may also work. > > Also, divalent ion parameters in fixed charge force fields are notoriously > poor. You generally either get good structure or good energetics - rarely > both. I would validate your model in someway first, bc the results are > unlikely to just work out nicely on your first try. > > Hope that helps, > BKR > > On Sun, Mar 21, 2021, 12:21 PM Debadrita Basu > wrote: > >> Hello Everyone, >> >> My protein of interest has ~850 residues (quite big) where a Magnesium >> ion is intrinsically bound. Also some ligands are known to bind to some >> specific grooves of this protein. I wanted to see the role of Magnesium on >> the ligand binding (ie whether it has a facilitating or inhibiting role). >> So, I decided to carry out the FEP calculation where I discharge the >> Magnesium atom to a dummy Magnesium atom, (in two different systems: ligand >> bound and apo) followed by thermodynamic integration. I used CGENFF to >> parameterize. >> >> I decided to follow the FEP algorithm implemented in NAMD, but I have a >> couple of questions in my mind: >> >> 1. Whether I will get a true result by using the whole protein. >> 2. While discharging the Magnesium atom I will end up changing the total >> charge of the system, is that acceptable? If not, how can it be solved? >> >> Hope, I get something to learn from your answers. >> >> Thank You. >> >> -- >> Debadrita Basu. >> >> Senior Research Fellow >> Bose Institute >> Kolkata, India. >> > -- Debadrita Basu. Senior Research Fellow Bose Institute Kolkata, India. --000000000000be06f505be1e65d4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you for your reply. I could understand the problems = associated=C2=A0with such calculations. Moreover, I would like to ask if th= e ligand is neutral will that lessen the complications or if we do the=C2= =A0FEP to know the effect=C2=A0of a structural water(which is also neutral)= will that have lesser difficulties?

On Mon, Mar 22, 2021 at 1:11 AM Brian R= adak <brian.r= adak@gmail.com> wrote:
1) Using the whole protein is almost a= lways technically more correct, but makes sampling more expensive and harde= r to converge (potentially unattainable on such large a system). Unless you= think there are important conformational changes involved, I would conside= r a specialized strategy for your quantity of interest.=C2=A0

2) Charge changing perturbations do c= ause a shift in dG values due to a change in the zero of energy arising fro= m PME. However, the shift vanishes when the periodic box is large and the m= ean dielectric is high (eg if the system is mostly water). I would look up = the work of Rocklin, et al. on using continuum corrections, but other strat= egies may also work.=C2=A0

Also, divalent ion parameters in fixed charge force fields are notorious= ly poor. You generally either get good structure or good energetics - rarel= y both. I would validate your model in someway first, bc the results are un= likely to just work out nicely on your first try.=C2=A0

Hope that helps,=C2=A0
BKR

<= div dir=3D"ltr" class=3D"gmail_attr">On Sun, Mar 21, 2021, 12:21 PM Debadri= ta Basu <ba= sudebadrita@gmail.com> wrote:
Hello Everyone,

My protein of interest has ~850 residues (quite big) where a Magnesium i= on=C2=A0 is intrinsically=C2=A0bound. Also some ligands are known to bind t= o some specific grooves of this protein. I wanted to see the role of Magnes= ium on the ligand binding (ie whether it has a facilitating or inhibiting r= ole). So, I decided to carry out the FEP calculation where I discharge the = Magnesium atom to a dummy Magnesium atom, (in two different systems: ligand= bound and apo) followed by thermodynamic integration. I used CGENFF to par= ameterize.

I decided to follow the FEP algorithm i= mplemented in NAMD, but I have a couple of questions in my mind:
=
1. Whether I will get a true result by using the whole prote= in.
2. While discharging=C2=A0the Magnesium atom I will end up ch= anging the total charge of the system, is that acceptable? If not, how can = it be solved?

Hope, I get something to learn from = your answers.

Thank You.=C2=A0

--
Debadrita B= asu.

Senior Research Fellow
Bose Institute=C2= =A0
Kolkata, India.


--
Debadrita Basu.

= Senior Research Fellow
Bose Institute=C2=A0
Kolkata, In= dia.
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X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 21e3413f-e6d9-407e-a509-08d8edfbb0be X-MS-Exchange-CrossTenant-originalarrivaltime: 23 Mar 2021 13:00:52.9584 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: oCkgcimwNbiBnppLpEqBQ1C7xkw8d0486fSfNKmSa7SCEexkEkY/GB2PcQVhn2hqhn8hth0IG0+FBjc846TZNQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR1201MB0149 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwTEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxgeHBEKQ1kXBx4YEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4TcRwaEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0VJXmBAeXhMUh5gG31ubx5iEmhsehJuWHoHa2VjaGJcEQpYXBcfBBoEGBgcBRsa 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definitions=main-2103230095 domainage_hfrom=12375 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_22c2fbb7ce7544901d998edcd7591b36msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable If you are running standard equilibrium MD, the only thing that is likely t= o give you markedly different performance is using NAMD 3.0a9 with CUDASOAI= ntegrate turned on, ideally with a NVLINK connection between the two Quadro= s. -Josh On 3/23/21 1:28 AM, Suryanarayanan Chandrasekaran wrote: I restarted the system, I think it worked attached are the log files of the= given below commands. ~/NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA/namd2 +p18 +idlepoll ste= p5_production4.inp +setcpuaffinity +isomalloc_sync | tee stmv1.log ~/NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA/namd2 +p18 step5_producti= on4.inp | tee stmv.log Please check once and let me know. If you have anytips to improve the calcu= lation speed, plz let me know Thanks, Surya On Mon, Mar 22, 2021 at 7:17 PM Vermaas, Josh > wrote: I=E2=80=99ve run the multicore method with up to 6 GPUs at once. 2 in princ= iple is just fine. I can confirm that the 2.14 release will run just fine, = and I=E2=80=99d start there when trying to figure out what is wrong. If 2.1= 4 is giving you the same error message, I=E2=80=99d try rebooting the works= tation, as I have seen instances where that solves weird hardware glitches.= If 2.14 works, but the git version doesn=E2=80=99t, then it=E2=80=99s a bu= g in the development version. The way I=E2=80=99d test NAMD on your hardware would be something like: namd2 +p18 stmv.namd | tee stmv.log -Josh From: Suryanarayanan Chandrasekaran > Date: Monday, March 22, 2021 at 12:26 AM To: "Vermaas, Josh" >, "namd-l@ks= .uiuc.edu" > Subject: Re: namd-l: Compiling namd2 in 2 GPU 2 CPU workstation I don't think this is a driver issue, Given below is the output from nvidia= -smi. In the installation manual, it is mentioned only one GPU can be used = in Multicore Cuda in a single node. Probably mine is a workstation, so the = problem might be identifying 2 GPU. I want to use both the two CPUs and two= GPUs, in the workstation. $ nvidia-smi Mon Mar 22 09:49:28 2021 +--------------------------------------------------------------------------= ---+ | NVIDIA-SMI 455.45.01 Driver Version: 455.45.01 CUDA Version: 11.1 = | |-------------------------------+----------------------+-------------------= ---+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. E= CC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute = M. | | | | MIG = M. | |=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D| | 0 Quadro RTX 5000 Off | 00000000:17:00.0 Off | O= ff | | 33% 37C P8 18W / 230W | 1MiB / 16125MiB | 0% Defau= lt | | | | N= /A | +-------------------------------+----------------------+-------------------= ---+ | 1 Quadro RTX 5000 Off | 00000000:73:00.0 On | O= ff | | 33% 40C P8 18W / 230W | 652MiB / 16117MiB | 0% Defau= lt | | | | N= /A | +-------------------------------+----------------------+-------------------= ---+ +--------------------------------------------------------------------------= ---+ | Processes: = | | GPU GI CI PID Type Process name GPU Memo= ry | | ID ID Usage = | |=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D| | 0 N/A N/A 2584 G /usr/lib/xorg/Xorg 0M= iB | | 0 N/A N/A 2911 G /usr/bin/gnome-shell 0M= iB | | 0 N/A N/A 8657 G ...gAAAAAAAAA --shared-files 0M= iB | | 0 N/A N/A 12099 G /usr/lib/firefox/firefox 0M= iB | | 0 N/A N/A 12615 G /usr/lib/firefox/firefox 0M= iB | | 0 N/A N/A 13032 G /usr/lib/firefox/firefox 0M= iB | | 0 N/A N/A 13527 G /usr/lib/firefox/firefox 0M= iB | | 0 N/A N/A 25049 G /usr/lib/firefox/firefox 0M= iB | | 1 N/A N/A 2584 G /usr/lib/xorg/Xorg 484M= iB | | 1 N/A N/A 2911 G /usr/bin/gnome-shell 86M= iB | | 1 N/A N/A 8657 G ...gAAAAAAAAA --shared-files 19M= iB | | 1 N/A N/A 12099 G /usr/lib/firefox/firefox 2M= iB | | 1 N/A N/A 12615 G /usr/lib/firefox/firefox 2M= iB | | 1 N/A N/A 13032 G /usr/lib/firefox/firefox 2M= iB | | 1 N/A N/A 13527 G /usr/lib/firefox/firefox 2M= iB | | 1 N/A N/A 25049 G /usr/lib/firefox/firefox 44M= iB | +--------------------------------------------------------------------------= ---+ On Sun, Mar 21, 2021 at 4:42 AM Vermaas, Josh > wrote: What is the output of nvidia-smi? NAMD isn=E2=80=99t able to ask CUDA how m= any GPUs there are. Sometimes this is a driver issue, and sometimes this is= just a compatibility issue between your hardware and what NAMD expects. -Josh From: > on behalf= of Suryanarayanan Chandrasekaran > Reply-To: "namd-l@ks.uiuc.edu" >, Suryanarayanan Chandrasekaran > Date: Saturday, March 20, 2021 at 6:09 AM To: "namd-l@ks.uiuc.edu" > Subject: namd-l: Compiling namd2 in 2 GPU 2 CPU workstation Hello, I have a workstation with 2 CPU and 2 GPU. I downloaded NAMD_Git-= 2021-03-03_Linux-x86_64-multicore-CUDA and tried to compile it with the bel= ow options, I want to use all GPU for a single CPU or both the CPU and GPU = in the workstation. 1) namd2 +p18 +idlepoll stmv.namd +setcpuaffinity +isomalloc_sync 2) namd2 +idlepoll +p4 +devices 0,1 But getting the same error Charm++> Running on 1 hosts (2 sockets x 10 cores x 2 PUs =3D 40-way SMP) Charm++> cpu topology info is gathered in 0.006 seconds. Info: Built with CUDA version 10010 FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/Device= CUDA.C, function initialize, line 135 on Pe 0 (surya): unknown error FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/Device= CUDA.C, function initialize, line 135 on Pe 0 (surya): unknown error Thanks, Surya -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!u8uwow0Q8_aauHqwgMuMa59oggiyhmBXFEWWpmVq8qlrCW7Dq-P29j2= zzLsgqJp7eA$=20 --_000_22c2fbb7ce7544901d998edcd7591b36msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <16875B83E6E7C74380C3550D7C43AA50@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable If you are running standard equilibrium MD, the only thing that is likely t= o give you markedly different performance is using NAMD 3.0a9 with CUDASOAI= ntegrate turned on, ideally with a NVLINK connection between the two Quadro= s.

-Josh

On 3/23/21 1:28 AM, Suryanarayanan Chandrase= karan wrote:
I restarted the system, I think it worked attached are the log files o= f the given below commands.

~/NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA/namd2 +p18  +id= lepoll step5_production4.inp +setcpuaffinity +isomalloc_sync | tee stmv1.lo= g
~/NAMD_Git-2021-03-03_Linux-x86_64-multicore-CUDA/namd2 +p18 step5_pro= duction4.inp | tee stmv.log

Please check once and let me know. If you have anytips to improve the = calculation speed, plz let me know

Thanks,
Surya



On Mon, Mar 22, 2021 at 7:17 PM Verma= as, Josh <v= ermaasj@msu.edu> wrote:

I=E2=80=99ve run the multicore method with up to 6 G= PUs at once. 2 in principle is just fine. I can confirm that the 2.14 relea= se will run just fine, and I=E2=80=99d start there when trying to figure ou= t what is wrong. If 2.14 is giving you the same error message, I=E2=80=99d try rebooting the workstation, as I have seen instanc= es where that solves weird hardware glitches. If 2.14 works, but the git ve= rsion doesn=E2=80=99t, then it=E2=80=99s a bug in the development version.<= /p>

 

The way I=E2=80=99d test NAMD on your hardware would= be something like:

 

namd2 +p18 stmv.namd | tee stmv.log

 

-Josh

 

From: = Suryanarayanan Chandr= asekaran <suryanar@ualberta.ca>
Date: Monday, March 22, 2021 at 12:26 AM
To: "Vermaas, Josh" <vermaasj@msu.edu>, &quo= t;namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>=
Subject: Re: namd-l: Compiling namd2 in 2 GPU 2 CPU workstation

 

I don't think this is a driver issue, Given below is= the output from nvidia-smi. In the installation manual, it is mentioned on= ly one GPU can be used in Multicore Cuda in a single node. Probably mine is= a workstation, so the problem might be identifying 2 GPU. I want to use both the two CPUs and two GPUs, in the= workstation.

 

$ nvidia-smi

Mon Mar 22 09:49:28 2021      
+--------------------------------------------------------------------------= ---+
| NVIDIA-SMI 455.45.01    Driver Version: 455.45.01    = CUDA Version: 11.1     |
|-------------------------------+----------------------+-------------------= ---+
| GPU  Name        Persistence-M| Bus-Id   &n= bsp;    Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|        = ; Memory-Usage | GPU-Util  Compute M. |
|                     &nb= sp;         |            =          |           &nb= sp;   MIG M. |
|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D|
|   0  Quadro RTX 5000     Off  | 00000000:17:00.0= Off |                  Off |<= br> | 33%   37C    P8    18W / 230W |     &n= bsp;1MiB / 16125MiB |      0%      Default |<= br> |                     &nb= sp;         |            =          |           &nb= sp;      N/A |
+-------------------------------+----------------------+-------------------= ---+
|   1  Quadro RTX 5000     Off  | 00000000:73:00.0=  On |                  O= ff |
| 33%   40C    P8    18W / 230W |    652= MiB / 16117MiB |      0%      Default |
|                     &nb= sp;         |            =          |           &nb= sp;      N/A |
+-------------------------------+----------------------+-------------------= ---+
                     = ;                     &nb= sp;                     &= nbsp;              
+--------------------------------------------------------------------------= ---+
| Processes:                  =                     &nbs= p;                     &n= bsp;    |
|  GPU   GI   CI        PID   Type =   Process name                =  GPU Memory |
|        ID   ID          = ;                     &nb= sp;                   Usage &n= bsp;    |
|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D|
|    0   N/A  N/A      2584    = ;  G   /usr/lib/xorg/Xorg           &nbs= p;      0MiB |
|    0   N/A  N/A      2911    = ;  G   /usr/bin/gnome-shell           &n= bsp;    0MiB |
|    0   N/A  N/A      8657    = ;  G   ...gAAAAAAAAA --shared-files        0M= iB |
|    0   N/A  N/A     12099     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;0MiB |
|    0   N/A  N/A     12615     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;0MiB |
|    0   N/A  N/A     13032     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;0MiB |
|    0   N/A  N/A     13527     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;0MiB |
|    0   N/A  N/A     25049     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;0MiB |
|    1   N/A  N/A      2584    = ;  G   /usr/lib/xorg/Xorg           &nbs= p;    484MiB |
|    1   N/A  N/A      2911    = ;  G   /usr/bin/gnome-shell           &n= bsp;   86MiB |
|    1   N/A  N/A      8657    = ;  G   ...gAAAAAAAAA --shared-files       19MiB |<= br> |    1   N/A  N/A     12099     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;2MiB |
|    1   N/A  N/A     12615     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;2MiB |
|    1   N/A  N/A     13032     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;2MiB |
|    1   N/A  N/A     13527     &nb= sp;G   /usr/lib/firefox/firefox           &nb= sp;2MiB |
|    1   N/A  N/A     25049     &nb= sp;G   /usr/lib/firefox/firefox           44M= iB |
+--------------------------------------------------------------------------= ---+

 

On Sun, Mar 21, 2021 at 4:42 AM Vermaas, Josh <vermaasj@msu.edu> wrote:

What is the output of nvidia-smi? NAMD isn=E2=80=99t= able to ask CUDA how many GPUs there are. Sometimes this is a driver issue= , and sometimes this is just a compatibility issue between your hardware an= d what NAMD expects.

 

-Josh

 

From: = <owner= -namd-l@ks.uiuc.edu> on behalf of Suryanarayanan Chandrasekaran <suryanar@ualberta.ca>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@= ks.uiuc.edu>, Suryanarayanan Chandrasekaran <suryanar@ual= berta.ca>
Date: Saturday, March 20, 2021 at 6:09 AM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiu= c.edu>
Subject: namd-l: Compiling namd2 in 2 GPU 2 CPU workstation

 

Hello,

        &nbs= p; I have a workstation with 2 CPU and 2 GPU. I downloaded NAMD_Git-2021-03= -03_Linux-x86_64-multicore-CUDA and tried to compile it with the below opti= ons, I want to use all GPU for a single CPU or both the CPU and GPU in the = workstation. 

 

1) namd2 +p18 +idlepoll stmv.namd +setcpuaffinity +i= somalloc_sync

2) namd2 +idlepoll +p4 +devices 0,1 <configfile&g= t;

But getting the same error

Charm++> Running on 1 hosts (2 sockets x 10 cores x 2 PUs =3D 40-way SMP)
Charm++> cpu topology info is gathered in 0.006 seconds.
Info: Built with CUDA version 10010
FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/De=
viceCUDA.C, function initialize, line 135
 on Pe 0 (surya): unknown error
FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/De=
viceCUDA.C, function initialize, line 135
 on Pe 0 (surya): unknown error
Thanks,
Surya<=
/pre>

--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
--_000_22c2fbb7ce7544901d998edcd7591b36msuedu_-- From owner-namd-l@halifax.ks.uiuc.edu Wed Mar 24 08:13:18 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12ODDItY009042; Wed, 24 Mar 2021 08:13:18 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12ODDIvS009041; Wed, 24 Mar 2021 08:13:18 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12ODDHYj009037; Wed, 24 Mar 2021 08:13:17 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12ODDHUh009036; Wed, 24 Mar 2021 08:13:17 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12ODD743009027 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 24 Mar 2021 08:13:08 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12OD84gA028433 for ; Wed, 24 Mar 2021 13:13:07 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 37da0j9c6u-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 24 Mar 2021 13:13:07 +0000 Received: from [IPv6:2a02:810c:300:6724:cde2:434e:3250:9509] ([IPv6:2a02:810c:300:6724:cde2:434e:3250:9509]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 12ODD4a0045604 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 24 Mar 2021 14:13:04 +0100 To: "namd-l@ks.uiuc.edu" From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Subject: namd-l: how to properly end NAMD replica job on slurm batch system Message-ID: <4839530d-2efe-bc2b-867b-4c69d341a6f2@physik.uni-kl.de> Date: Wed, 24 Mar 2021 14:13:04 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.8.0 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="------------5B4A1E605E49C3711C6147F2" Content-Language: de-DE X-Spam-Status: No, hits=0.176, tests=HELO_MISC_IP=0.174,HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001 X-Spam-Score: (0.176) X-Spam-Flag: NO X-CLX-Response: 1TFkXGx0eEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxkTGhEKQ1kXBxgYHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfHnEZHhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThd/Zh5Tex0ZZ25jUngee0VjHB9rTgd1GxNoYElSSE1iXhEKWFwXHwQaBBgYHAUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdyQWQTAREKTVwXGxkfEQpMWhdoaU1NTREKQk8XbF9sZl9 wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGhEKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCk JOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YGlJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2xla2Rff UFkBWd4EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaVBZBVtyWEYcWUARCnBoF2NG RgV8GnN5YlhCEBkaEQpwaBdpGE1LUG19RltfcBAZGhEKcGgXb0xtR1JYfWFiaX0QGRoRCnBoF2F Pbn1FRBpbZh5nEBkaEQpwaBdpHEt8Ymd+GkhjSBAZGhEKcGwXeh94eW94TENfcEQQGRoRCm1+Fx sRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 bulkscore=0 priorityscore=0 impostorscore=0 malwarescore=0 spamscore=0 clxscore=174 lowpriorityscore=0 suspectscore=0 mlxlogscore=999 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103240099 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------5B4A1E605E49C3711C6147F2 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear NAMD Maintainers, I work on cluster with SLURM batch system.  I am currently testing replica simulations and         experience the issue that when the replica simulation ends with an error or I cancel the job via scancel (since I am only testing...)     the node gets "closed" with the error that "*kill task failed*". (it then takes intervention by cluster admins to reopen/reboot the node but thats local policy I guess) Have you ever experienced this? Is there a way to savely end the replica runs even when an error occurs? Do I have to collect processIDs to kill the replica runs myself before the submission script (containing the call to charmrun namd2... ) ends ? Kind regards René -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------5B4A1E605E49C3711C6147F2 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Dear NAMD Maintainers,


I work on cluster with SLURM batch system.

 I am currently testing replica simulations and

        experience the issue that when the replica simulation ends with an error or I cancel the job via scancel (since I am only testing...)

    the node gets "closed" with the error that "kill task failed". (it then takes intervention by cluster admins to reopen/reboot the node but thats local policy I guess)

   

Have you ever experienced this?

Is there a way to savely end the replica runs even when an error occurs?

Do I have to collect processIDs to kill the replica runs myself before the submission script (containing the call to charmrun namd2... ) ends ?


Kind regards
René

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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([IPv6:2a02:810c:300:6724:cde2:434e:3250:9509]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 12OEvQpX112560 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Wed, 24 Mar 2021 15:57:26 +0100 Subject: Re: namd-l: how to properly end NAMD replica job on slurm batch system To: namd-l@ks.uiuc.edu, "Vermaas, Josh" References: <4839530d-2efe-bc2b-867b-4c69d341a6f2@physik.uni-kl.de> <51542953-E9CA-4893-9CD4-9C1F605270CA@msu.edu> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <2931c148-b5f3-ff07-fa22-2dafefab1e22@physik.uni-kl.de> Date: Wed, 24 Mar 2021 15:57:26 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.8.0 MIME-Version: 1.0 In-Reply-To: <51542953-E9CA-4893-9CD4-9C1F605270CA@msu.edu> Content-Type: multipart/alternative; boundary="------------4A1E39AC8E5BFE7FCA72C60F" Content-Language: de-DE X-Spam-Status: No, hits=0.175, tests=HELO_MISC_IP=0.174,HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.001 X-Spam-Score: (0.175) X-Spam-Flag: NO X-CLX-Response: 1TFkXGxIcEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxwZGBEKQ1kXBxsdGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscHHEeHxAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdwRX9OQUlgQ3NrSB0YQVBJHGdlfm4TTRl9fllYEmVcaREKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JBekwbEQpNXBceGBwRCkxaF2l4aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2xfbGZfcExLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGB oRCkJeFxsRCkReFxgRCkJFF2wdWHJFHxxHSQVuEQpCThdkGkluenp4GmR9XBEKQkwXYGAbUhkdG BpScgURCkJsF2ZrYmQYWWJtSH5sEQpCQBd6RFNhS0R4bWVdTBEKQlgXZ3Nlc0BuYWFMXWIRClpY FxsRCnlDF2BdU1ocGBlIYxJAEQpwZxdtR2FrTWMZTFNpbhAeEhEKcGgXYBtTcHpaYUBiUhoQGhE KcGgXekBoE0RoHBwcWGYQGxoSEQpwaBdvZGVTTnJMbmRDHhAaEQpwaBdtGk1meWUdeUlvWBAaEQ pwaBdiWV94c3lAUBISSxAaEQpwZxdgGUZFe05HGW1cRRAeEhEKcGcXaUNuUAFZc0cBHlMQHhIRC nBnF2NcYUV9f2dmWkdIEBoRCnBsF3ofeHlveExDX3BEEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 lowpriorityscore=0 malwarescore=0 phishscore=0 mlxlogscore=999 priorityscore=0 impostorscore=0 spamscore=0 mlxscore=0 adultscore=0 bulkscore=0 clxscore=186 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103240114 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------4A1E39AC8E5BFE7FCA72C60F Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Josh,     I use NAMD 2.14.     Though when using 2 replicas forcing a crash they both had an error/end message in the logfile     while for 4 I *had **at least one* replica logfile that has no error/end message written at the end.     Therefore I guess there is one zombie still left.     I wanted to try this now with "top -b > file.txt" in my submission script after  the line "charmrun namd2..." but need to wait until a proper node becomes available again. Kind regards René On 3/24/2021 3:40 PM, Vermaas, Josh wrote: > > Hi Rene, > > Is this 2.13 or 2.14? I seem to recall that 2.13 (or maybe it was > 2.12?) **didn’t** kill the other replicas when one replica received a > termination signal, and so you might legitimately be running into an > issue where there are zombie namd processes roaming around on slurm. > > I typically do not do anything special to clean up after a job > crashes, since it is supposed to take itself down cleanly. > > -Josh > > *From: * on behalf of René Hafner TUK > > *Reply-To: *"namd-l@ks.uiuc.edu" , René Hafner TUK > > *Date: *Wednesday, March 24, 2021 at 9:22 AM > *To: *"namd-l@ks.uiuc.edu" > *Subject: *namd-l: how to properly end NAMD replica job on slurm batch > system > > Dear NAMD Maintainers, > > I work on cluster with SLURM batch system. > >  I am currently testing replica simulations and > >         experience the issue that when the replica simulation ends > with an error or I cancel the job via scancel (since I am only testing...) > >     the node gets "closed" with the error that "*kill task failed*". > (it then takes intervention by cluster admins to reopen/reboot the > node but thats local policy I guess) > > Have you ever experienced this? > > Is there a way to savely end the replica runs even when an error occurs? > > Do I have to collect processIDs to kill the replica runs myself before > the submission script (containing the call to charmrun namd2... ) ends ? > > Kind regards > René > -- > -- > Dipl.-Phys. René Hafner > TU Kaiserslautern > Germany -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------4A1E39AC8E5BFE7FCA72C60F Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Josh,

    I use NAMD 2.14.

    Though when using 2 replicas forcing a crash they both had an error/end message in the logfile

    while for 4 I had at least one replica logfile that has no error/end message written at the end.

    Therefore I guess there is one zombie still left.

    I wanted to try this now with "top -b > file.txt" in my submission script after  the line "charmrun namd2..." but need to wait until a proper node becomes available again.

Kind regards

René

On 3/24/2021 3:40 PM, Vermaas, Josh wrote:

Hi Rene,

 

Is this 2.13 or 2.14? I seem to recall that 2.13 (or maybe it was 2.12?) *didn’t* kill the other replicas when one replica received a termination signal, and so you might legitimately be running into an issue where there are zombie namd processes roaming around on slurm.

 

I typically do not do anything special to clean up after a job crashes, since it is supposed to take itself down cleanly.

 

-Josh

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of René Hafner TUK <hamburge@physik.uni-kl.de>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, René Hafner TUK <hamburge@physik.uni-kl.de>
Date: Wednesday, March 24, 2021 at 9:22 AM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: how to properly end NAMD replica job on slurm batch system

 

Dear NAMD Maintainers,

 

I work on cluster with SLURM batch system.

 I am currently testing replica simulations and

        experience the issue that when the replica simulation ends with an error or I cancel the job via scancel (since I am only testing...)

    the node gets "closed" with the error that "kill task failed". (it then takes intervention by cluster admins to reopen/reboot the node but thats local policy I guess)

   

Have you ever experienced this?

Is there a way to savely end the replica runs even when an error occurs?

Do I have to collect processIDs to kill the replica runs myself before the submission script (containing the call to charmrun namd2... ) ends ?

 
Kind regards
René
 
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
--------------4A1E39AC8E5BFE7FCA72C60F-- From owner-namd-l@halifax.ks.uiuc.edu Wed Mar 24 12:18:05 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12OHI520019677; Wed, 24 Mar 2021 12:18:05 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12OHI5iZ019676; Wed, 24 Mar 2021 12:18:05 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12OHI4xi019672; Wed, 24 Mar 2021 12:18:04 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12OHI4FK019671; Wed, 24 Mar 2021 12:18:04 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12OHHsFQ019660 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 24 Mar 2021 12:17:55 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12OHFNjb001258 for ; Wed, 24 Mar 2021 17:17:54 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0a-00007101.pphosted.com with ESMTP id 37da2tnbx4-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 24 Mar 2021 17:17:54 +0000 Received: from [IPv6:2a02:810c:300:6724:cde2:434e:3250:9509] ([IPv6:2a02:810c:300:6724:cde2:434e:3250:9509]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 12OHHnu0194804 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Wed, 24 Mar 2021 18:17:50 +0100 Subject: Re: namd-l: how to properly end NAMD replica job on slurm batch system From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= To: namd-l@ks.uiuc.edu, "Vermaas, Josh" References: <4839530d-2efe-bc2b-867b-4c69d341a6f2@physik.uni-kl.de> <51542953-E9CA-4893-9CD4-9C1F605270CA@msu.edu> <2931c148-b5f3-ff07-fa22-2dafefab1e22@physik.uni-kl.de> Message-ID: Date: Wed, 24 Mar 2021 18:17:49 +0100 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.8.0 MIME-Version: 1.0 In-Reply-To: <2931c148-b5f3-ff07-fa22-2dafefab1e22@physik.uni-kl.de> Content-Type: multipart/alternative; boundary="------------4B9CC0DF98DBA833524E36D3" Content-Language: de-DE X-Spam-Status: No, hits=0.175, tests=HELO_MISC_IP=0.174,HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.001 X-Spam-Score: (0.175) X-Spam-Flag: NO X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp4SxdgYBtSGR0YGlJyBREKeEwXaAFEXFxeW19GfE4RCnlMF25hXE NOaFhHEn5HEQpDSBcHHBkTEQpDWRcHGx0cEQpDSRcaBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGG xwTcR4SEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCRVleT04RCkNOF1J4U2lYHkBgQHhweR5z a3hCHWFMe0ZbemtySBNmZWFyEQpYXBcfBBoEGBgcBRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXckF 4QE4RCk1cFxkZExEKTFoXeGlNTU0RCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTx dsX2xmX3BMSxxSSxEKQ1oXGxkbBBgeHAQbGBoEGBgaEQpCXhcbEQpEXhcYEQpCRRdsHVhyRR8cR 0kFbhEKQk4XZBpJbnp6eBpkfVwRCkJMF2BgG1IZHRgaUnIFEQpCbBdma2JkGFlibUh+bBEKQkAX ekRTYUtEeG1lXUwRCkJYF2dzZXNAbmFhTF1iEQpaWBcbEQp5QxdgXVNaHBgZSGMSQBEKcGcXbUd ha01jGUxTaW4QHBoRCnBoF2AbU3B6WmFAYlIaEBkaEQpwaBd6QGgTRGgcHBxYZhAbGx8RCnBoF2 4eZhleRXAcQhhQEBoRCnBoF29kZVNOckxuZEMeEBkaEQpwaBdiWV94c3lAUBISSxAZGhEKcGcXY BlGRXtORxltXEUQHBoRCnBnF2lDblABWXNHAR5TEBwaEQpwZxdtUE5pT25zcEtDGhAaEQpwZxdj XGFFfX9nZlpHSBAZGhEKcGwXeh94eW94TENfcEQQHhIRCm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 impostorscore=0 phishscore=0 lowpriorityscore=0 mlxlogscore=999 suspectscore=0 mlxscore=0 priorityscore=0 bulkscore=0 spamscore=0 malwarescore=0 clxscore=189 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103240125 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------4B9CC0DF98DBA833524E36D3 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit I was able to "end" the job properly by killing the zombies via pgrep "namd2" | xargs kill -- René On 3/24/2021 3:57 PM, René Hafner TUK wrote: > > Hi Josh, > >     I use NAMD 2.14. > >     Though when using 2 replicas forcing a crash they both had an > error/end message in the logfile > >     while for 4 I *had **at least one* replica logfile that has no > error/end message written at the end. > >     Therefore I guess there is one zombie still left. > >     I wanted to try this now with "top -b > file.txt" in my submission > script after  the line "charmrun namd2..." but need to wait until a > proper node becomes available again. > > Kind regards > > René > > On 3/24/2021 3:40 PM, Vermaas, Josh wrote: >> >> Hi Rene, >> >> Is this 2.13 or 2.14? I seem to recall that 2.13 (or maybe it was >> 2.12?) **didn’t** kill the other replicas when one replica received a >> termination signal, and so you might legitimately be running into an >> issue where there are zombie namd processes roaming around on slurm. >> >> I typically do not do anything special to clean up after a job >> crashes, since it is supposed to take itself down cleanly. >> >> -Josh >> >> *From: * on behalf of René Hafner TUK >> >> *Reply-To: *"namd-l@ks.uiuc.edu" , René Hafner >> TUK >> *Date: *Wednesday, March 24, 2021 at 9:22 AM >> *To: *"namd-l@ks.uiuc.edu" >> *Subject: *namd-l: how to properly end NAMD replica job on slurm >> batch system >> >> Dear NAMD Maintainers, >> >> I work on cluster with SLURM batch system. >> >>  I am currently testing replica simulations and >> >>         experience the issue that when the replica simulation ends >> with an error or I cancel the job via scancel (since I am only >> testing...) >> >>     the node gets "closed" with the error that "*kill task failed*". >> (it then takes intervention by cluster admins to reopen/reboot the >> node but thats local policy I guess) >> >> Have you ever experienced this? >> >> Is there a way to savely end the replica runs even when an error occurs? >> >> Do I have to collect processIDs to kill the replica runs myself >> before the submission script (containing the call to charmrun >> namd2... ) ends ? >> >> Kind regards >> René >> -- >> -- >> Dipl.-Phys. René Hafner >> TU Kaiserslautern >> Germany > -- > -- > Dipl.-Phys. René Hafner > TU Kaiserslautern > Germany -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------4B9CC0DF98DBA833524E36D3 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

I was able to "end" the job properly by killing the zombies via

pgrep "namd2" | xargs kill

--

René

On 3/24/2021 3:57 PM, René Hafner TUK wrote:

Hi Josh,

    I use NAMD 2.14.

    Though when using 2 replicas forcing a crash they both had an error/end message in the logfile

    while for 4 I had at least one replica logfile that has no error/end message written at the end.

    Therefore I guess there is one zombie still left.

    I wanted to try this now with "top -b > file.txt" in my submission script after  the line "charmrun namd2..." but need to wait until a proper node becomes available again.

Kind regards

René

On 3/24/2021 3:40 PM, Vermaas, Josh wrote:

Hi Rene,

 

Is this 2.13 or 2.14? I seem to recall that 2.13 (or maybe it was 2.12?) *didn’t* kill the other replicas when one replica received a termination signal, and so you might legitimately be running into an issue where there are zombie namd processes roaming around on slurm.

 

I typically do not do anything special to clean up after a job crashes, since it is supposed to take itself down cleanly.

 

-Josh

 

From: <owner-namd-l@ks.uiuc.edu> on behalf of René Hafner TUK <hamburge@physik.uni-kl.de>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, René Hafner TUK <hamburge@physik.uni-kl.de>
Date: Wednesday, March 24, 2021 at 9:22 AM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: how to properly end NAMD replica job on slurm batch system

 

Dear NAMD Maintainers,

 

I work on cluster with SLURM batch system.

 I am currently testing replica simulations and

        experience the issue that when the replica simulation ends with an error or I cancel the job via scancel (since I am only testing...)

    the node gets "closed" with the error that "kill task failed". (it then takes intervention by cluster admins to reopen/reboot the node but thats local policy I guess)

   

Have you ever experienced this?

Is there a way to savely end the replica runs even when an error occurs?

Do I have to collect processIDs to kill the replica runs myself before the submission script (containing the call to charmrun namd2... ) ends ?

 
Kind regards
René
 
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear NAMD experts, I am trying to run simulations with volumetric map-based variables. At the moment I am trying to bias the number of water molecules inside the pore of an ion channel following the instructions in the Reference manual for the Collective Variables Module. I built the pore occupancy map using VMD on a preliminary trajectory set sel [atomselect top "water and (z > -40) and (z < 25) and (sqrt(x*x+y*y) < 12)"] volmap occupancy $sel -allframes -combine max -o Occupancy.dx package require volutil volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx The map, visualized with VMD, looks reasonable in that all the pore region appears to be filled. Following the manual, I also created a file where all water molecules are marked in the occupancy column. Is that correct ? Maybe I had to mark only the water molecule initially inside the pore ? The file was generated with the following tcl script mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb set all [atomselect top "all"] $all set occupancy 0 set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $all writepdb mark_water.pdb I added the following commands to the main NAMD input file mGridForce yes mGridForcePotFile Cavity Occupancy_smooth.dx mGridForceFile Cavity mark_water.pdb mGridForceCol Cavity O mGridForceChargeCol Cavity B mGridForceScale Cavity 0.0 0.0 0.0 colvars on colvarsConfig ./ColvarConfig.conf Finally, I defined in file ColvarConfig.conf a collective variable that, I expected, should count the number of water molecules in the cavity. colvar { name nwaters mapTotal { mapName Cavity componentCoeff 1.0 } } harmonic { colvars nwaters centers 277 # centered around initial number of water molecules forceConstant 50000 } As you can see, I applied an harmonic bias to keep the number of water molecules in the cavity close to the initial value (277 molecules). Here comes the problem: according to the .traj file the value of collective variable nwaters is constantly equal to zero which is clearly wrong. The system was run for 5.0 ns with NAMD 2.14. During the simulation the number of water molecules inside the pore made oscillations of the order of 10% with respect to the initial value. However, I suspect that an unbiased equilibrium simulation would have done the same, so that this cannot be used as a diagnostic criterium that the simulation is doing what it was intended to do. Could you please tell me what to do ? This is the first time I run this kind of simulations so that some trivial mistake is highly possible. Many thanks for your help, Carlo Guardiani --=20 ________________________________________________________ Le informazioni=20 contenute in questo messaggio di posta elettronica sono strettamente=20 riservate e indirizzate esclusivamente al destinatario. Si prega di non=20 leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non= =20 si =C3=A8 il legittimo destinatario dello stesso. Qualora tale messaggio si= a=20 stato ricevuto per errore, si prega di restituirlo al mittente e di=20 cancellarlo permanentemente dal proprio computer. The information contained=20 in this e mail message is strictly confidential and intended for the use of= =20 the addressee only.=C2=A0 If you are not the intended recipient, please do = not=20 read, copy, forward or store it on your computer. If you have received the= =20 message in error, please forward it back to the sender and delete it=20 permanently from your computer system. --0000000000008d709a05be59cc1e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD experts,
I am trying to run simulations with = volumetric map-based
variables. At the moment I am trying to bias the n= umber
of water molecules inside the pore of an ion channel
following= the instructions in the Reference manual for
the Collective Variables = Module. I built the pore occupancy
map using VMD on a preliminary trajec= tory

set sel [atomselect top "water and (z > -40) and (z <= ; 25) and (sqrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allf= rames -combine max -o Occupancy.dx

package require volutil

vo= lutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The ma= p, visualized with VMD, looks reasonable in that all
the pore region ap= pears to be filled.

Following the manual, I also created a file wher= e all water
molecules are marked in the occupancy column. Is that corre= ct ?
Maybe I had to mark only the water molecule initially inside the pore ? The file was generated with the following tcl script

mol lo= ad pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all&qu= ot;]
$all set occupancy 0
set wat [atomselect top "water and (na= me O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb
I added the following commands to the main NAMD input file

mGridFor= ce yes
mGridForcePotFile Cavity Occupancy_smooth.dx =C2=A0 =C2=A0
mGr= idForceFile Cavity =C2=A0 =C2=A0mark_water.pdb =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
mGridForceCol Cavity O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
mGridForceChargeCol Cavity B = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
mG= ridForceScale Cavity 0.0 0.0 0.0 =C2=A0

colvars on
colvarsConfig = =C2=A0 ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.c= onf a collective
variable that, I expected, should count the number of w= ater
molecules in the cavity.

colvar {
=C2=A0 =C2=A0name nwat= ers
=C2=A0 =C2=A0mapTotal {
=C2=A0 =C2=A0 mapName Cavity
=C2=A0 = =C2=A0 componentCoeff 1.0
=C2=A0 =C2=A0}
}



harmonic {<= br>=C2=A0 colvars nwaters
=C2=A0 centers 277 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 # centered around initial number of water molecules=C2=A0 forceConstant 50000 =C2=A0 =C2=A0 =C2=A0
}

As you can se= e, I applied an harmonic bias to keep the number
of water molecules in = the cavity close to the initial value
(277 molecules). Here comes the p= roblem: according to the
.traj file the value of collective variable nw= aters is constantly
equal to zero which is clearly wrong. The system was= run for 5.0 ns
with NAMD 2.14. During the simulation the number of wat= er molecules
inside the pore made oscillations of the order of 10% with = respect
to the initial value. However, I suspect that an unbiased equil= ibrium
simulation would have done the same, so that this cannot be used = as
a diagnostic criterium that the simulation is doing what it was
= intended to do.

Could you please tell me what to do ? This is the fi= rst time I run this
kind of simulations so that some trivial mistake is= highly possible.

Many thanks for your help,

Carlo Guardiani<= br>

=C2=A0


=C2=A0 =C2=A0 =C2=A0=C2=A0

_= _______________________________________________________<= /div>Le informazioni contenute i= n questo messaggio di posta elettronica sono strettamente riservate e indir= izzate esclusivamente al destinatario. Si prega di non leggere, fare copia,= inoltrare a terzi o conservare tale messaggio se non si =C3=A8 il legittim= o destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per = errore, si prega di restituirlo al mittente e di cancellarlo permanentement= e dal proprio computer.
The information contained in this e mail message is strictly confident= ial and intended for the use of the addressee only.=C2=A0 If you are not th= e intended recipient, please do not read, copy, forward or store it on your= computer. If you have received the message in error, please forward it bac= k to the sender and delete it permanently from your computer system.=

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charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Carlo, What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weight" f= or each atom also matters. For traditional grid forces, when it was being u= sed to apply an electric field, folks would copy the atomic charges to the = beta column so that a carbon and hydrogen atom wouldn't feel the same attra= ctive force. MDFF folks will use the mass of the element. The point being, = is that your beta column can't be zero, otherwise it doesn't contribute to = the gridforce value colvars is depending on. If you just want to count wate= rs, I *think* the correct thing is to have the "noh and water" have a 1 in = the beta column. You should then see non-zero values for the colvar. -Josh On 3/25/21 6:22 AM, Carlo Guardiani wrote: Dear NAMD experts, I am trying to run simulations with volumetric map-based variables. At the moment I am trying to bias the number of water molecules inside the pore of an ion channel following the instructions in the Reference manual for the Collective Variables Module. I built the pore occupancy map using VMD on a preliminary trajectory set sel [atomselect top "water and (z > -40) and (z < 25) and (sqrt(x*x+y*y= ) < 12)"] volmap occupancy $sel -allframes -combine max -o Occupancy.dx package require volutil volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx The map, visualized with VMD, looks reasonable in that all the pore region appears to be filled. Following the manual, I also created a file where all water molecules are marked in the occupancy column. Is that correct ? Maybe I had to mark only the water molecule initially inside the pore ? The file was generated with the following tcl script mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb set all [atomselect top "all"] $all set occupancy 0 set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $all writepdb mark_water.pdb I added the following commands to the main NAMD input file mGridForce yes mGridForcePotFile Cavity Occupancy_smooth.dx mGridForceFile Cavity mark_water.pdb mGridForceCol Cavity O mGridForceChargeCol Cavity B mGridForceScale Cavity 0.0 0.0 0.0 colvars on colvarsConfig ./ColvarConfig.conf Finally, I defined in file ColvarConfig.conf a collective variable that, I expected, should count the number of water molecules in the cavity. colvar { name nwaters mapTotal { mapName Cavity componentCoeff 1.0 } } harmonic { colvars nwaters centers 277 # centered around initial number of water molec= ules forceConstant 50000 } As you can see, I applied an harmonic bias to keep the number of water molecules in the cavity close to the initial value (277 molecules). Here comes the problem: according to the .traj file the value of collective variable nwaters is constantly equal to zero which is clearly wrong. The system was run for 5.0 ns with NAMD 2.14. During the simulation the number of water molecules inside the pore made oscillations of the order of 10% with respect to the initial value. However, I suspect that an unbiased equilibrium simulation would have done the same, so that this cannot be used as a diagnostic criterium that the simulation is doing what it was intended to do. Could you please tell me what to do ? This is the first time I run this kind of simulations so that some trivial mistake is highly possible. Many thanks for your help, Carlo Guardiani ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono str= ettamente riservate e indirizzate esclusivamente al destinatario. Si prega = di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio s= e non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale messag= gio sia stato ricevuto per errore, si prega di restituirlo al mittente e di= cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential a= nd intended for the use of the addressee only. If you are not the intended= recipient, please do not read, copy, forward or store it on your computer.= If you have received the message in error, please forward it back to the s= ender and delete it permanently from your computer system. ________________________________ -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!vf1OksGrvmaNdGhfe05Ths_wW2XkImtUO-ap3ohAbsjbYDwiTZu5jMM= Dfiw4w_hyKw$=20 --_000_7d100dcff171cd09f8b9b65253e3589cmsuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <18F97E2239C9FE4E8F7E1EC36993AABA@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Hi Carlo,

What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weig= ht" for each atom also matters. For traditional grid forces, when it w= as being used to apply an electric field, folks would copy the atomic charges to the beta column so that a carbon an= d hydrogen atom wouldn't feel the same attractive force. MDFF folks will us= e the mass of the element. The point being, is that your beta column can't = be zero, otherwise it doesn't contribute to the gridforce value colvars is depending on. If you just want to count = waters, I *think* the correct thing is to have the "noh and water"= ; have a 1 in the beta column. You should then see non-zero values for the = colvar.

-Josh

On 3/25/21 6:22 AM, Carlo Guardiani wrote:
Dear NAMD experts,
I am trying to run simulations with volumetric map-based
variables. At the moment I am trying to bias the number
of water molecules inside the pore of an ion channel
following the instructions in the Reference manual for
the Collective Variables Module. I built the pore occupancy
map using VMD on a preliminary trajectory

set sel [atomselect top "water and (z > -40) and (z < 25) and (s= qrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allframes -combine max -o Occupancy.dx

package require volutil

volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The map, visualized with VMD, looks reasonable in that all
the pore region appears to be filled.

Following the manual, I also created a file where all water
molecules are marked in the occupancy column. Is that correct ?
Maybe I had to mark only the water molecule initially inside the
pore ? The file was generated with the following tcl script

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

I added the following commands to the main NAMD input file

mGridForce yes
mGridForcePotFile Cavity Occupancy_smooth.dx    
mGridForceFile Cavity    mark_water.pdb       &nbs= p;
mGridForceCol Cavity O               &nb= sp;          
mGridForceChargeCol Cavity B             &nbs= p;      
mGridForceScale Cavity 0.0 0.0 0.0  

colvars on
colvarsConfig   ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.conf a collective
variable that, I expected, should count the number of water
molecules in the cavity.

colvar {
   name nwaters
   mapTotal {
    mapName Cavity
    componentCoeff 1.0
   }
}



harmonic {
  colvars nwaters
  centers 277               # cente= red around initial number of water molecules
  forceConstant 50000      
}

As you can see, I applied an harmonic bias to keep the number
of water molecules in the cavity close to the initial value
(277 molecules). Here comes the problem: according to the
.traj file the value of collective variable nwaters is constantly
equal to zero which is clearly wrong. The system was run for 5.0 ns
with NAMD 2.14. During the simulation the number of water molecules
inside the pore made oscillations of the order of 10% with respect
to the initial value. However, I suspect that an unbiased equilibrium
simulation would have done the same, so that this cannot be used as
a diagnostic criterium that the simulation is doing what it was
intended to do.

Could you please tell me what to do ? This is the first time I run this
kind of simulations so that some trivial mistake is highly possible.

Many thanks for your help,

Carlo Guardiani


 


      

_= _______________________________________________________<= /div> Le informazioni contenute in que= sto messaggio di posta elettronica sono strettamente riservate e indirizzat= e esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale mess= aggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale= messaggio sia stato ricevuto per errore, si prega di restituirlo al mitten= te e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message = is strictly confidential and intended for the use of the addressee only.&nb= sp; If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you hav= e received the message in error, please forward it back to the sender and d= elete it permanently from your computer system.


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="000000000000b6554a05be5d9128" X-CLX-Response: 1TFkXGxIYEQpMehcZHh0RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHx0SEQpDWRceGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGHEeGxAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd6GH5PX1BuT39BZEJyTlxDXmlSel5SbWZzREAZElwbHhEKWFwXHwQaBBgYHAUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdyQUFCThEKTVwXHhkaEQpMWhd7aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2FZHHkYSAUSG0J4EQpDWhcYGhMEEh8EGBsTBB sdGhEKQl4XGxEKRF4XGBEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY 2t7E1h+Gl9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3IdbmxPWHhg EQpCbBdhX3pTGUNEGnobfhEKQkAXYRlbYUYeaURneGURCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp 5QxduQW9rengdGXhCbxEKWUsXExkfHBEKcGcXYB5FbEJma0caX2AQGRoRCnBoF2lnQh5FRl1JS0 1iEBkaEQpwaBdvfEhLSxpBTB5YaxAZGhEKcGgXentSRH1aeWtOX28QGRoRCnBoF3pwbXpeYx9rT 3tFEBkaEQpwaBdtfmJPRWVdbQVSARAZGhEKcH0XZ3gfQh5HQ114aBsQGRoRCnB9F29IcBpjZHBc UEJtEB4SEQpwfRdvTFpQS25yf0x7fBAZGhEKcH8XYk4FAXBEXmlEe2UQGxodEQpwXxd6ExtAZEl dGG5BehAZGhEKcH8XYWZvWxpnZEJIHVsQGxkaEQpwXxdjYhJQSGN4H3xCfRATEhEKcGwXZh97WF xiBUtYZB8QGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 clxscore=182 suspectscore=0 priorityscore=347 impostorscore=0 adultscore=0 mlxlogscore=999 mlxscore=0 bulkscore=0 lowpriorityscore=0 malwarescore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103250109 domainage_hfrom=9356 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000b6554a05be5d9128 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Carlo, Josh is correct. A zero beta column is the most likely explanation: if not, please let us know. When implementing the NAMD backend of the mapTotal variable (based on GridForces), I tried to keep the new functionality as consistent as possible with the use cases that Josh mentioned (custom electric fields, MDFF, etc). But that also means inheriting technicalities like this one. FYI there is a tutorial available at https://urldefense.com/v3/__https://colvars.github.io/multi-map/multi-map.h= tml__;!!DZ3fjg!qB5CRc-AwU64OMfr1bYNOpTM7vcKDjLCEAs9qFj1Im6wgSeelgHIHzs_KyZ-= pcN1cg$ . The NAMD manual doesn't have it linked, because I wrote it after NAMD 2.14 was released. It's geared toward variables with more than one map, but for a single map the syntax is otherwise almost identical, as I'm sure you noticed. You may also find the latest VMD alpha build to visualize/test the variable. (Note however that VMD doesn't have GridForces, so the way map variables are defined there is slightly different). Giacomo On Thu, Mar 25, 2021 at 10:35 AM Vermaas, Josh wrote: > Hi Carlo, > > What is in the beta column? You are using the occupancy column to > determine if the atoms should be coupled to the potential or not. But the > "weight" for each atom also matters. For traditional grid forces, when it > was being used to apply an electric field, folks would copy the atomic > charges to the beta column so that a carbon and hydrogen atom wouldn't fe= el > the same attractive force. MDFF folks will use the mass of the element. T= he > point being, is that your beta column can't be zero, otherwise it doesn't > contribute to the gridforce value colvars is depending on. If you just wa= nt > to count waters, I *think* the correct thing is to have the "noh and wate= r" > have a 1 in the beta column. You should then see non-zero values for the > colvar. > > -Josh > > On 3/25/21 6:22 AM, Carlo Guardiani wrote: > > Dear NAMD experts, > I am trying to run simulations with volumetric map-based > variables. At the moment I am trying to bias the number > of water molecules inside the pore of an ion channel > following the instructions in the Reference manual for > the Collective Variables Module. I built the pore occupancy > map using VMD on a preliminary trajectory > > set sel [atomselect top "water and (z > -40) and (z < 25) and > (sqrt(x*x+y*y) < 12)"] > > volmap occupancy $sel -allframes -combine max -o Occupancy.dx > > package require volutil > > volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx > > The map, visualized with VMD, looks reasonable in that all > the pore region appears to be filled. > > Following the manual, I also created a file where all water > molecules are marked in the occupancy column. Is that correct ? > Maybe I had to mark only the water molecule initially inside the > pore ? The file was generated with the following tcl script > > mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb > set all [atomselect top "all"] > $all set occupancy 0 > set wat [atomselect top "water and (name O)"] > $wat set occupancy 1 > $all writepdb mark_water.pdb > > I added the following commands to the main NAMD input file > > mGridForce yes > mGridForcePotFile Cavity Occupancy_smooth.dx > mGridForceFile Cavity mark_water.pdb > mGridForceCol Cavity O > mGridForceChargeCol Cavity B > mGridForceScale Cavity 0.0 0.0 0.0 > > colvars on > colvarsConfig ./ColvarConfig.conf > > Finally, I defined in file ColvarConfig.conf a collective > variable that, I expected, should count the number of water > molecules in the cavity. > > colvar { > name nwaters > mapTotal { > mapName Cavity > componentCoeff 1.0 > } > } > > > > harmonic { > colvars nwaters > centers 277 # centered around initial number of water > molecules > forceConstant 50000 > } > > As you can see, I applied an harmonic bias to keep the number > of water molecules in the cavity close to the initial value > (277 molecules). Here comes the problem: according to the > .traj file the value of collective variable nwaters is constantly > equal to zero which is clearly wrong. The system was run for 5.0 ns > with NAMD 2.14. During the simulation the number of water molecules > inside the pore made oscillations of the order of 10% with respect > to the initial value. However, I suspect that an unbiased equilibrium > simulation would have done the same, so that this cannot be used as > a diagnostic criterium that the simulation is doing what it was > intended to do. > > Could you please tell me what to do ? This is the first time I run this > kind of simulations so that some trivial mistake is highly possible. > > Many thanks for your help, > > Carlo Guardiani > > > > > > > > ________________________________________________________ > Le informazioni contenute in questo messaggio di posta elettronica sono > strettamente riservate e indirizzate esclusivamente al destinatario. Si > prega di non leggere, fare copia, inoltrare a terzi o conservare tale > messaggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualor= a tale > messaggio sia stato ricevuto per errore, si prega di restituirlo al > mittente e di cancellarlo permanentemente dal proprio computer. > The information contained in this e mail message is strictly confidential > and intended for the use of the addressee only. If you are not the > intended recipient, please do not read, copy, forward or store it on your > computer. If you have received the message in error, please forward it ba= ck > to the sender and delete it permanently from your computer system. > ------------------------------ > > > -- > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochem= isty and Molecular Biologyvermaasj@msu.eduhttps://prl.natsci.msu.edu/people= /faculty/josh-vermaas/ > > --000000000000b6554a05be5d9128 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Carlo, Josh is correct.=C2=A0 A zero beta column is the= most likely explanation: if not, please let us know.

Wh= en implementing the NAMD backend of the mapTotal variable (based on GridFor= ces), I tried to keep the new functionality as consistent as possible with = the use cases that Josh mentioned (custom electric fields, MDFF, etc).=C2= =A0 But that also means inheriting technicalities like this one.
=
FYI there is a tutorial=C2=A0available at=C2=A0https://colvars.github.io/multi-map/multi-map.html= .=C2=A0 The NAMD manual doesn't have it linked, because I wrote it = after NAMD 2.14 was released.=C2=A0 It's geared toward variables with m= ore than one map, but for a single map the syntax is otherwise almost ident= ical,=C2=A0as I'm sure you noticed.

You may al= so find the latest VMD alpha build to visualize/test the variable.=C2=A0 (N= ote however that VMD doesn't have GridForces, so the way map variables = are defined there is slightly different).

Giacomo<= /div>


On Thu, Mar 25, 2021 at 10:35 AM Vermaas, J= osh <vermaasj@msu.= edu> wrote:
Hi Carlo,

What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weig= ht" for each atom also matters. For traditional grid forces, when it w= as being used to apply an electric field, folks would copy the atomic charges to the beta column so that a carbon an= d hydrogen atom wouldn't feel the same attractive force. MDFF folks wil= l use the mass of the element. The point being, is that your beta column ca= n't be zero, otherwise it doesn't contribute to the gridforce value colvars is depending on. If you just want to count = waters, I *think* the correct thing is to have the "noh and water"= ; have a 1 in the beta column. You should then see non-zero values for the = colvar.

-Josh

On 3/25/21 6:22 AM, Carlo Guardiani wrote:
Dear NAMD experts,
I am trying to run simulations with volumetric map-based
variables. At the moment I am trying to bias the number
of water molecules inside the pore of an ion channel
following the instructions in the Reference manual for
the Collective Variables Module. I built the pore occupancy
map using VMD on a preliminary trajectory

set sel [atomselect top "water and (z > -40) and (z < 25) and (s= qrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allframes -combine max -o Occupancy.dx

package require volutil

volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The map, visualized with VMD, looks reasonable in that all
the pore region appears to be filled.

Following the manual, I also created a file where all water
molecules are marked in the occupancy column. Is that correct ?
Maybe I had to mark only the water molecule initially inside the
pore ? The file was generated with the following tcl script

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

I added the following commands to the main NAMD input file

mGridForce yes
mGridForcePotFile Cavity Occupancy_smooth.dx =C2=A0 =C2=A0
mGridForceFile Cavity =C2=A0 =C2=A0mark_water.pdb =C2=A0 =C2=A0 =C2=A0 =C2= =A0
mGridForceCol Cavity O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
mGridForceChargeCol Cavity B =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0
mGridForceScale Cavity 0.0 0.0 0.0 =C2=A0

colvars on
colvarsConfig =C2=A0 ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.conf a collective
variable that, I expected, should count the number of water
molecules in the cavity.

colvar {
=C2=A0 =C2=A0name nwaters
=C2=A0 =C2=A0mapTotal {
=C2=A0 =C2=A0 mapName Cavity
=C2=A0 =C2=A0 componentCoeff 1.0
=C2=A0 =C2=A0}
}



harmonic {
=C2=A0 colvars nwaters
=C2=A0 centers 277 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 # cente= red around initial number of water molecules
=C2=A0 forceConstant 50000 =C2=A0 =C2=A0 =C2=A0
}

As you can see, I applied an harmonic bias to keep the number
of water molecules in the cavity close to the initial value
(277 molecules). Here comes the problem: according to the
.traj file the value of collective variable nwaters is constantly
equal to zero which is clearly wrong. The system was run for 5.0 ns
with NAMD 2.14. During the simulation the number of water molecules
inside the pore made oscillations of the order of 10% with respect
to the initial value. However, I suspect that an unbiased equilibrium
simulation would have done the same, so that this cannot be used as
a diagnostic criterium that the simulation is doing what it was
intended to do.

Could you please tell me what to do ? This is the first time I run this
kind of simulations so that some trivial mistake is highly possible.

Many thanks for your help,

Carlo Guardiani


=C2=A0


=C2=A0 =C2=A0 =C2=A0=C2=A0

_= _______________________________________________________
Le informazioni contenute in que= sto messaggio di posta elettronica sono strettamente riservate e indirizzat= e esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale mess= aggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale= messaggio sia stato ricevuto per errore, si prega di restituirlo al mitten= te e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message = is strictly confidential and intended for the use of the addressee only.=C2= =A0 If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you hav= e received the message in error, please forward it back to the sender and d= elete it permanently from your computer system.


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
--000000000000b6554a05be5d9128-- From owner-namd-l@halifax.ks.uiuc.edu Thu Mar 25 11:26:21 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12PGQLUa022369; Thu, 25 Mar 2021 11:26:21 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12PGQLsp022368; Thu, 25 Mar 2021 11:26:21 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12PGQK1r022363; Thu, 25 Mar 2021 11:26:20 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12PGQKon022362; Thu, 25 Mar 2021 11:26:20 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12PGQBtV022349 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="00000000000083f7f605be5edfc0" X-CLX-Response: 1TFkXGBoaEQpMehcdGhIRCllEF29HYBkeHE0ZYFxOEQpYWBdnTEcdHnlhXHA SbBEKeE4XY1Nja3sTWH4aX14RCnlMF2FoWGhtWhpbBRkTEQpDSBcHGR8eEQpDWRcHGx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhpxGxgfEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2lIG3NgH0JHB2sbaUtTbEUcel58R2ccTwdNHWN8bV1aEQpYXBcfBBoEGBgc BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JBRh4BEQpNXBcbExkRCkxaF39pTVJrEQpFWRdoEQp MXxd6BQUFBQUFBQUFUhEKTU4XaWsRCkxGF29ra2traxEKQk8XaH1BYENafXNHQRMRCkNaFxgaEw QSHwQbGBIEHh8RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaUZ/QBpaZk5rRBwRCkJOF2NTY2t7E1h+Gl9eEQpCTBdnTEcdHnlhXHASbBEKQmwX YGxJUmhQfxhCHlkRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQpZSxcTGR8cEQpwaBdkbBt bTVIcZltwehAZGhEKcGgXYAVSXlkfeRpMHGgQGRoRCnBoF3oYRBh5T00cRn5HEBkaEQpwaBdnTh phaRoYbXNCXxAZGhEKcGgXYXtMRUcTARh4AVoQGRoRCnB9F3pGQkBfYWFfHExMEBkaEQpwfxdvR GFQEhN/GxwSfhAbGxgRCnBfF2wSaF96TlBAbEtsEBkaEQpwbBdiAX1fYVx5bEITbhAZGhEKbX4X GxEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 clxscore=200 suspectscore=0 priorityscore=708 impostorscore=0 adultscore=0 mlxlogscore=386 mlxscore=0 bulkscore=0 lowpriorityscore=0 malwarescore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103250117 domainage_hfrom=9356 X-Spam-Score: 0 X-Spam-OrigSender: soumadwipghosh@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, soumadwip ghosh --00000000000083f7f605be5edfc0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi all I have created coordinate and psf files for my system (step5_input.pdb/psf/crd). However, I would like to add one triple bond between atom# 22424 and 23768 and also obtain the updated PSF and CRD files. I tried using molfracture and topotools ion VMD but I am having difficulty perhaps due to the large size of the system. My question is there a way to get a CRD and a PSF file for the system with the above new bond, angle, improper and dihedral info? Is topotool suitable for this purpose? I have limited experience with these tools (esp toptool or psfgen) and that's why I am asking for your help. If you can provide me with some help on how to write a sample psfgen script with my system for the triple covalent bond that I am looking for that would be of tremendous help. I am not sure what my PATCH statement would be for PSFGEN to work. You may find the associated files in the attached link. The FF parameters are in the toppar directory. https://urldefense.com/v3/__https://drive.google.com/drive/folders/1z6efalq= xQsHyGrljsD07zZ6wOCtYV5mC__;!!DZ3fjg!rsVyllqX1Ad8Xhi6nizuf5uM5looeMfnMm2V4h= QoawVVgYwsDDB-FjCq9M0m_VJFHQ$=20 There are two topotool script in the link that I wrote as well but they did not get the job done. If you think Topotool should perform the job would you mind commenting on the script(s) attached for me to figure out what really went wrong? Thank you ! Soumadwip Ghosh --00000000000083f7f605be5edfc0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi= all

I have created coordinate and psf files for my= system (step5_input.pdb/psf/crd). However, I would like to add one triple = bond between atom# 22424 and 23768 and also obtain the updated PSF and CRD = files. I tried using molfracture=C2=A0and topotools ion VMD but I am having= difficulty perhaps=C2=A0 due to the large size of the system. My question = is there a way to get a CRD and a PSF file for the system with the above ne= w bond, angle, improper and dihedral info? Is topotool suitable for this pu= rpose? I have limited experience with these tools (esp toptool or psfgen) a= nd that's why I am asking for your help. If you can provide me with som= e help on how to write a sample psfgen script with my system for the triple= covalent bond that I am looking for that would be of tremendous help. I am= not sure what my PATCH statement would be for PSFGEN to work. You may find= the associated files in the=C2=A0attached link. The FF parameters are in t= he toppar directory.

There are two topo= tool=C2=A0script in the link that I wrote as well but they did not get the = job done. If you think Topotool=C2=A0should perform the job would you mind = commenting on the script(s) attached for me to figure out what really went = wrong?

Thank you !

Soumadwip Ghosh

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Thu, 25 Mar 2021 17:37:58 +0000 Date: Thu, 25 Mar 2021 17:37:54 +0000 (UTC) From: Osvalds Verners To: "namd-l@ks.uiuc.edu" Message-ID: <2089087596.180773.1616693874777@mail.yahoo.com> Subject: namd-l: potential bug while compiling the Windows version of NAMD MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_180772_747611715.1616693874776" References: <2089087596.180773.1616693874777.ref@mail.yahoo.com> X-Mailer: WebService/1.1.17936 YMailNorrin Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/89.0.4389.90 Safari/537.36 X-CLX-Shades: MLX X-CLX-Response: 1TFkXHBIRCkx6FxkfHREKWUQXYH1hb0RbX3tmcmYRClhYF255HVlDBX1wWX5 iEQp4Thd6RBwdb0VsbURDZhEKeUwXaUIeHX4cTmcdWXIRCkNIFwcZGhgRCkNZFwcbGBoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYeEnEYEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFx9dGWVaSEdhTWMbUn9HRHlmGRh/XUcZZkVtXEd+eWREEQpYXBcfBBoEGBgcBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JBRxJ5EQpNXBcYHx8RCkxaF2hpTWtrEQpMRhdva2tva2s RCkJPF2hGeUdMAUwcW3JuEQpDWhcdHgQcBBsYEwQbGB4RCkJeFxsRCkReFxgRCkJcFxsRCl5OFx sRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0VsbURDZhEKQkUXZH9zBR1me0RlSXoRCkJOF3pEH B1vRWxtRENmEQpCTBdueR1ZQwV9cFl+YhEKQmwXZ2tTYhxMX2BOAV4RCkJAF2BeU0NsEnpeU0Rg EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXb0xAZUFEfmBtQGARCllLFxMfHBkRCnB oF20SbUFAUhleU0MaEBkaEQpwaBdnE2sFGGJrTl9AeBAZGhEKcGgXehhCa2NraUFQZQEQGRoRCn BoF25Lfm1aW0NbUEIYEBkaEQpwaBdmR0ccXBkce0F9GRAZGhEKcGwXelx9bktfBU5QXVwQGRoRC m1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 malwarescore=0 priorityscore=357 mlxscore=0 spamscore=0 phishscore=0 mlxlogscore=779 adultscore=0 lowpriorityscore=0 suspectscore=0 bulkscore=0 clxscore=68 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2103250128 domainage_hfrom=9563 X-Spam-Score: 0 X-Spam-OrigSender: osvalds.verners@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Osvalds Verners ------=_Part_180772_747611715.1616693874776 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Sir/Madam, I would like to report an error which occurred while compiling the=C2=A0NAM= D_2.14_Win64-multicore version using the following command: ./build charm++=C2=A0 multicore-win64 gcc --with-production --- In file included from bind.c:11:bind.c: In function =E2=80=98cmi_hwloc_allo= c_heap=E2=80=99:/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwlo= c/include/private/private.h:282:29: warning: implicit declaration of functi= on =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99? [-Wim= plicit-function-declaration]=C2=A0 282 | #define hwloc_getpagesize() syscon= f(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~= ~/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: note: in definition of macro =E2=80=98hwloc_getpagesiz= e=E2=80=99=C2=A0 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)= =C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~/NAMD_2.14_Sourc= e/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:= 37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared (first use in this fu= nction); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99?=C2=A0 282 | #define = hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~/NAMD_2.14_Sou= rce/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:28= 2:37: note: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99=C2= =A0 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 = =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~= ~~~~/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/pr= ivate/private.h:282:37: note: each undeclared identifier is reported only o= nce for each function it appears in=C2=A0 282 | #define hwloc_getpagesize()= sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~/NAMD_2.14_Source/charm-6.10.2/= multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:37: note: in de= finition of macro =E2=80=98hwloc_getpagesize=E2=80=99=C2=A0 282 | #define h= wloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~make[2]: *** [= Makefile:721: bind.lo] Error 1make[2]: Leaving directory '/NAMD_2.14_Source= /charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'make[1]: *** [Makefile:418:= all-recursive] Error 1make[1]: Leaving directory '/NAMD_2.14_Source/charm-= 6.10.2/multicore-win64-gcc/tmp/hwloc'make: *** [Makefile:565: hwloc-target]= Error 2 --- Since I have not changed any source file, it could be considered as a poten= tial bug (did not find in the known bugs list though). Best regards, Osvalds Verners =20 ------=_Part_180772_747611715.1616693874776 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Sir/Madam,=

I would like to report a= n error which occurred while compiling the NAMD_2.14_Win64-multi= core version using the following command:

=
./build charm++  multicore-win64 gcc = --with-production

---

In = file included from bind.c:11:
bind.c: In function =E2=80=98cmi_hw= loc_alloc_heap=E2=80=99:
/NAMD_2.14_Source/charm-6.10.2/multicore= -win64-gcc/tmp/hwloc/include/private/private.h:282:29: warning: implicit de= claration of function =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98sisc= anf=E2=80=99? [-Wimplicit-function-declaration]
  282 | #def= ine hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
    &nbs= p; |                    &= nbsp;        ^~~~~~~
/NAMD_2.14_Source/charm-= 6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:29: note= : in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99
&nbs= p; 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
 = ;     |                &n= bsp;            ^~~~~~~
/NAMD_2.14_= Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h= :282:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared (first use in th= is function); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99?
 = ; 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
 =     |                &nb= sp;                    ^~= ~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tm= p/hwloc/include/private/private.h:282:37: note: in definition of macro =E2= =80=98hwloc_getpagesize=E2=80=99
  282 | #define hwloc_getpa= gesize() sysconf(_SC_PAGE_SIZE)
      |  &nbs= p;                     &n= bsp;            ^~~~~~~~~~~~~
/NAMD= _2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/pri= vate.h:282:37: note: each undeclared identifier is reported only once for e= ach function it appears in
  282 | #define hwloc_getpagesize= () sysconf(_SC_PAGE_SIZE)
      |    &nb= sp;                     &= nbsp;          ^~~~~~~~~~~~~
/NAMD_2.14_= Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h= :282:37: note: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99
  282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |            &nb= sp;                     &= nbsp;  ^~~~~~~~~~~~~
make[2]: *** [Makefile:721: bind.lo] Er= ror 1
make[2]: Leaving directory '/NAMD_2.14_Source/charm-6.10.2/= multicore-win64-gcc/tmp/hwloc/src'
make[1]: *** [Makefile:418: al= l-recursive] Error 1
make[1]: Leaving directory '/NAMD_2.14_Sourc= e/charm-6.10.2/multicore-win64-gcc/tmp/hwloc'
make: *** [Makefile= :565: hwloc-target] Error 2

---

Since I have not changed any source file, i= t could be considered as a potential bug (did not find in the known bugs li= st though).

Best regards,<= /div>

Osvalds Verners
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boundary="0000000000006a8cb005be627150" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0dEQpMehccGhEKWUQXbxNrZ0NFfhxeaFMRClhYF2UafRgaHB1SUEk TEQp4ThdpWEhpfR1jU3JdfhEKeUwXZkcbR2dDf2sZe2IRCkNIFwcYEx4RCkNZFx4aEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8dcRkcEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFx9rRlJhXnxESVlLekV5chptQEhacB9ZQUFTfnxtQhtQEQpYXBcfBBoEGBgcBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXckFaRUMRCk1cFxkTExEKTFoXeGlrTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxd6TENJc2l5AVtAexEKQ1oXGBoTBBIfBBgbGgQeHh EKQl4XGxEKREkXGBEKQlwXGxEKXk4XGxEKQksXaVhIaX0dY1NyXX4RCkJJF2lYSGl9HWNTcl1+E QpCRRdtG14ZW3xvHXwcSREKQk4XaVhIaX0dY1NyXX4RCkJMF2UafRgaHB1SUEkTEQpCbBdkR2dO fEEfeXNoXREKQkAXYRlbYUYeaURneGURCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp5QxduQW9reng dGXhCbxEKcGcXYB5FbEJma0caX2AQGRoRCnBoF2N9bml/aWJwQl9iEBkaEQpwaBdofhlLH2JTQF wdRRAZGhEKcGgXbQV9X3hEQX5iHX0QGRoRCnBoF20BbUAFWRtveE9tEBkaEQpwaBdkZ2hmS0VQe ll5YBAZGhEKcH0XZ3gfQh5HQ114aBsQGRoRCnB9F29IcBpjZHBcUEJtEBkaEQpwfRdvTFpQS25y f0x7fBAZGhEKcH8XYk4FAXBEXmlEe2UQGxsYEQpwXxd6ExtAZEldGG5BehAZGhEKcH8XYWZvWxp nZEJIHVsQGxgfEQpwXxdjYhJQSGN4H3xCfRATGREKcGwXekh9aFoZGE1ASWQQGxIRCnBMF21oZR lBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 5AlxKtVncsaPoSX0GjbpZ5skkyTVGh1z X-Proofpoint-ORIG-GUID: 5AlxKtVncsaPoSX0GjbpZ5skkyTVGh1z MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 bulkscore=0 phishscore=0 malwarescore=0 mlxlogscore=999 priorityscore=60 adultscore=0 spamscore=0 impostorscore=0 suspectscore=0 clxscore=177 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103250000 definitions=main-2103250152 X-Spam-Score: 0 X-Spam-OrigSender: carlo.guardiani@uniroma1.it X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Carlo Guardiani --0000000000006a8cb005be627150 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Josh and Giacomo, first of all, many thanks for your prompt reply. Following your advice I did the following tests, but unfortunately none of them had success. 1) Following Josh advice, I used the beta column to mark water oxygens witha label 1 while all other atoms were assigned a flag 0. mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb set all [atomselect top "all"] $all set occupancy 0 $all set beta 0 set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $wat set beta 1 $all writepdb mark_water.pdb Using this input the simulation started running with reasonable values of the collective variable nwaters, but as soon as the minimization finished the program aborted with a "Segmentation fault" error message. 2) Since Josh told me that traditionally the beta column had been used to store the charge, I also tried this approach. mol load parm7 6BBF_Ext_assembly_xleap.prmtop pdb TMD_4HKR_to_6BBF_frame_0.pdb set natm 279195 set indmax [expr $natm - 1] set all [atomselect top "all"] $all set occupancy 0 $all set beta 0 for { set ind 0 } { $ind <=3D $indmax } { incr ind } { set atm [atomselect top "index $ind"] set charge [$atm get charge] $atm set beta $charge #$atm set beta [expr abs($charge)] $atm delete puts "$ind" } set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $all writepdb mark_water.pdb As soon as the minimization finished I had a series of error messages of the kind ERROR: Constraint failure in RATTLE algorithm for atom 86370! ERROR: Constraint failure; simulation has become unstable. I tried using the standard fix for this kind of problems: I increased the number of minimization steps from 100 to 1000 and I decreased the time-step from 2 fs to 1 fs. However, also in this case after the minimization the program crashed with a "segmentation fault" message and I also noted several "nan" in the energy values. This behaviour could suggest a bad starting structure. However, I remind you that when I ran the simulations with all zeros in the beta column (which likely made the collective variable inactive) I could run for 5 ns without any problem, which suggests that the structure is not so bad. Also, I noted that when using the atom charge in the beta column the values of the collective variable nwaters are negative (but in absolute value correct) which does not make any sense since it is a number of water molecules. I suppose this behaviour is due to the fact that the charge of water oxygens is negative. I therefore ran another test writing in the beta column the absolute value of the charge $atm set beta [expr abs($charge)] This test also ended with a segmentation fault immediately after minimization but as I expected the values of the colvar returned to be positive and correct. 3) As a final test, since Josh told me that some people use the beta column to store the mass value I also tried this approach. Also in this case the job ended with a segmentation fault and lots of "nan" in the energy values. Additionally, in this case the values of the colvar were badly over-estimated being of the order of several thousands instead of a few hundreds. I really don't know what else I could try. Could you please tell me what I need to put in the beta column to constrain the number of water molecules in the pore of my ion channels ? Many thanks for the help and best wishes, Carlo Il giorno gio 25 mar 2021 alle ore 15:52 Giacomo Fiorin < giacomo.fiorin@gmail.com> ha scritto: > Hi Carlo, Josh is correct. A zero beta column is the most likely > explanation: if not, please let us know. > > When implementing the NAMD backend of the mapTotal variable (based on > GridForces), I tried to keep the new functionality as consistent as > possible with the use cases that Josh mentioned (custom electric fields, > MDFF, etc). But that also means inheriting technicalities like this one. > > FYI there is a tutorial available at > https://urldefense.com/v3/__https://colvars.github.io/multi-map/multi-map= .html__;!!DZ3fjg!s3P3t_M35V4F51gpAHVZ4PjhMQsHf_7O2lN5LSXXbHM5xmNZxb8nD_MZQx= oIdv_GHw$ . The NAMD manual > doesn't have it linked, because I wrote it after NAMD 2.14 was released. > It's geared toward variables with more than one map, but for a single map > the syntax is otherwise almost identical, as I'm sure you noticed. > > You may also find the latest VMD alpha build to visualize/test the > variable. (Note however that VMD doesn't have GridForces, so the way map > variables are defined there is slightly different). > > Giacomo > > > On Thu, Mar 25, 2021 at 10:35 AM Vermaas, Josh wrote: > >> Hi Carlo, >> >> What is in the beta column? You are using the occupancy column to >> determine if the atoms should be coupled to the potential or not. But the >> "weight" for each atom also matters. For traditional grid forces, when it >> was being used to apply an electric field, folks would copy the atomic >> charges to the beta column so that a carbon and hydrogen atom wouldn't f= eel >> the same attractive force. MDFF folks will use the mass of the element. = The >> point being, is that your beta column can't be zero, otherwise it doesn't >> contribute to the gridforce value colvars is depending on. If you just w= ant >> to count waters, I *think* the correct thing is to have the "noh and wat= er" >> have a 1 in the beta column. You should then see non-zero values for the >> colvar. >> >> -Josh >> >> On 3/25/21 6:22 AM, Carlo Guardiani wrote: >> >> Dear NAMD experts, >> I am trying to run simulations with volumetric map-based >> variables. At the moment I am trying to bias the number >> of water molecules inside the pore of an ion channel >> following the instructions in the Reference manual for >> the Collective Variables Module. I built the pore occupancy >> map using VMD on a preliminary trajectory >> >> set sel [atomselect top "water and (z > -40) and (z < 25) and >> (sqrt(x*x+y*y) < 12)"] >> >> volmap occupancy $sel -allframes -combine max -o Occupancy.dx >> >> package require volutil >> >> volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx >> >> The map, visualized with VMD, looks reasonable in that all >> the pore region appears to be filled. >> >> Following the manual, I also created a file where all water >> molecules are marked in the occupancy column. Is that correct ? >> Maybe I had to mark only the water molecule initially inside the >> pore ? The file was generated with the following tcl script >> >> mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb >> set all [atomselect top "all"] >> $all set occupancy 0 >> set wat [atomselect top "water and (name O)"] >> $wat set occupancy 1 >> $all writepdb mark_water.pdb >> >> I added the following commands to the main NAMD input file >> >> mGridForce yes >> mGridForcePotFile Cavity Occupancy_smooth.dx >> mGridForceFile Cavity mark_water.pdb >> mGridForceCol Cavity O >> mGridForceChargeCol Cavity B >> mGridForceScale Cavity 0.0 0.0 0.0 >> >> colvars on >> colvarsConfig ./ColvarConfig.conf >> >> Finally, I defined in file ColvarConfig.conf a collective >> variable that, I expected, should count the number of water >> molecules in the cavity. >> >> colvar { >> name nwaters >> mapTotal { >> mapName Cavity >> componentCoeff 1.0 >> } >> } >> >> >> >> harmonic { >> colvars nwaters >> centers 277 # centered around initial number of water >> molecules >> forceConstant 50000 >> } >> >> As you can see, I applied an harmonic bias to keep the number >> of water molecules in the cavity close to the initial value >> (277 molecules). Here comes the problem: according to the >> .traj file the value of collective variable nwaters is constantly >> equal to zero which is clearly wrong. The system was run for 5.0 ns >> with NAMD 2.14. During the simulation the number of water molecules >> inside the pore made oscillations of the order of 10% with respect >> to the initial value. However, I suspect that an unbiased equilibrium >> simulation would have done the same, so that this cannot be used as >> a diagnostic criterium that the simulation is doing what it was >> intended to do. >> >> Could you please tell me what to do ? This is the first time I run this >> kind of simulations so that some trivial mistake is highly possible. >> >> Many thanks for your help, >> >> Carlo Guardiani >> >> >> >> >> >> >> >> ________________________________________________________ >> Le informazioni contenute in questo messaggio di posta elettronica sono >> strettamente riservate e indirizzate esclusivamente al destinatario. Si >> prega di non leggere, fare copia, inoltrare a terzi o conservare tale >> messaggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualo= ra tale >> messaggio sia stato ricevuto per errore, si prega di restituirlo al >> mittente e di cancellarlo permanentemente dal proprio computer. >> The information contained in this e mail message is strictly confidential >> and intended for the use of the addressee only. If you are not the >> intended recipient, please do not read, copy, forward or store it on your >> computer. If you have received the message in error, please forward it b= ack >> to the sender and delete it permanently from your computer system. >> ------------------------------ >> >> >> -- >> Josh Vermaas >> Assistant Professor, MSU-DOE Plant Research Lab and Department of Bioche= misty and Molecular Biologyvermaasj@msu.eduhttps://prl.natsci.msu.edu/peopl= e/faculty/josh-vermaas/ >> >> --=20 ________________________________________________________ Le informazioni=20 contenute in questo messaggio di posta elettronica sono strettamente=20 riservate e indirizzate esclusivamente al destinatario. Si prega di non=20 leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non=20 si =C3=A8 il legittimo destinatario dello stesso. Qualora tale messaggio si= a=20 stato ricevuto per errore, si prega di restituirlo al mittente e di=20 cancellarlo permanentemente dal proprio computer. The information contained=20 in this e mail message is strictly confidential and intended for the use of= =20 the addressee only.=C2=A0 If you are not the intended recipient, please do = not=20 read, copy, forward or store it on your computer. If you have received the= =20 message in error, please forward it back to the sender and delete it=20 permanently from your computer system. --0000000000006a8cb005be627150 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear Josh and Giacomo,
first of all, many thanks for yo= ur prompt reply.
Following your advice I did the following tests,
bu= t unfortunately none of them had success.

1) Following Josh advice, = I used the beta column
=C2=A0 =C2=A0to mark water oxygens witha label 1 = while all
=C2=A0 =C2=A0other atoms were assigned a flag 0.

mol l= oad pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all&q= uot;]
$all set occupancy 0
$all set beta 0
set wat [atomselect top= "water and (name O)"]
$wat set occupancy 1
$wat set beta 1=
$all writepdb mark_water.pdb

Using this input the simulation sta= rted running
with reasonable values of the collective variable
nwater= s, but as soon as the minimization finished
the program aborted with a &= quot;Segmentation fault"
error message.

2) Since Josh told = me that traditionally the beta
column had been used to store the charge= , I also
tried this approach.

mol load parm7 6BBF_Ext_assembly_x= leap.prmtop pdb TMD_4HKR_to_6BBF_frame_0.pdb
set natm 279195
set indm= ax [expr $natm - 1]

set all [atomselect top "all"]
$all= set occupancy 0
$all set beta 0

for { set ind 0 } { $ind <=3D= $indmax } { incr ind } {
set atm [atomselect top "index $ind"= ]
set charge [$atm get charge]
$atm set beta $charge
#$atm set bet= a [expr abs($charge)]
$atm delete
puts "$ind"
}

s= et wat [atomselect top "water and (name O)"]
$wat set occupanc= y 1
$all writepdb mark_water.pdb

As soon as the minimization fini= shed I had a
series of error messages of the kind

ERROR: Constra= int failure in RATTLE algorithm for atom 86370!
ERROR: Constraint failur= e; simulation has become unstable.

I tried using the standard fix fo= r this kind of problems:
I increased the number of minimization steps fr= om 100 to 1000
and I decreased the time-step from 2 fs to 1 fs. However,=
also in this case after the minimization the program crashed
with a = "segmentation fault" message and I also noted several
"n= an" in the energy values. This behaviour could suggest a bad
starti= ng structure. However, I remind you that when I ran the
simulations wit= h all zeros in the beta column (which likely
made the collective variab= le inactive) I could run for 5 ns
without any problem, which suggests th= at the structure is not
so bad.

Also, I noted that when using th= e atom charge in the beta column
the values of the collective variable n= waters are negative (but
in absolute value correct) which does not make = any sense since it
is a number of water molecules. I suppose this behav= iour is due to
the fact that the charge of water oxygens is negative. I= therefore
ran another test writing in the beta column the absolute val= ue of
the charge

$atm set beta [expr abs($charge)]

This t= est also ended with a segmentation fault immediately after
minimization= but as I expected the values of the colvar returned to
be positive and = correct.

3) As a final test, since Josh told me that some people use= the
beta column to store the mass value I also tried this approach. Also in this case the job ended with a segmentation fault and lots
of = "nan" in the energy values. Additionally, in this case the values=
of the colvar were badly over-estimated being of the order of several<= br>thousands instead of a few hundreds.

I really don't know what= else I could try. Could you please tell me
what I need to put in the b= eta column to constrain the number of water
molecules in the pore of my = ion channels ?

Many thanks for the help and best wishes,

Carl= o
=C2=A0






Il giorno gio 25 mar 2021 alle ore 15:52= Giacomo Fiorin <giacomo.fio= rin@gmail.com> ha scritto:
Hi Carlo, Josh is correct.=C2=A0 A zero = beta column is the most likely explanation: if not, please let us know.
When implementing the NAMD backend of the mapTotal variable= (based on GridForces), I tried to keep the new functionality as consistent= as possible with the use cases that Josh mentioned (custom electric fields= , MDFF, etc).=C2=A0 But that also means inheriting technicalities like this= one.

FYI there is a tutorial=C2=A0available at=C2= =A0https://colvars.github.io/multi-ma= p/multi-map.html.=C2=A0 The NAMD manual doesn't have it linked, bec= ause I wrote it after NAMD 2.14 was released.=C2=A0 It's geared toward = variables with more than one map, but for a single map the syntax is otherw= ise almost identical,=C2=A0as I'm sure you noticed.

You may also find the latest VMD alpha build to visualize/test the va= riable.=C2=A0 (Note however that VMD doesn't have GridForces, so the wa= y map variables are defined there is slightly different).

Giacomo


On Thu, Mar 25, 2021 at 10:= 35 AM Vermaas, Josh <vermaasj@msu.edu> wrote:
Hi Carlo,

What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weig= ht" for each atom also matters. For traditional grid forces, when it w= as being used to apply an electric field, folks would copy the atomic charges to the beta column so that a carbon an= d hydrogen atom wouldn't feel the same attractive force. MDFF folks wil= l use the mass of the element. The point being, is that your beta column ca= n't be zero, otherwise it doesn't contribute to the gridforce value colvars is depending on. If you just want to count = waters, I *think* the correct thing is to have the "noh and water"= ; have a 1 in the beta column. You should then see non-zero values for the = colvar.

-Josh

On 3/25/21 6:22 AM, Carlo Guardiani wrote:
Dear NAMD experts,
I am trying to run simulations with volumetric map-based
variables. At the moment I am trying to bias the number
of water molecules inside the pore of an ion channel
following the instructions in the Reference manual for
the Collective Variables Module. I built the pore occupancy
map using VMD on a preliminary trajectory

set sel [atomselect top "water and (z > -40) and (z < 25) and (s= qrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allframes -combine max -o Occupancy.dx

package require volutil

volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The map, visualized with VMD, looks reasonable in that all
the pore region appears to be filled.

Following the manual, I also created a file where all water
molecules are marked in the occupancy column. Is that correct ?
Maybe I had to mark only the water molecule initially inside the
pore ? The file was generated with the following tcl script

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

I added the following commands to the main NAMD input file

mGridForce yes
mGridForcePotFile Cavity Occupancy_smooth.dx =C2=A0 =C2=A0
mGridForceFile Cavity =C2=A0 =C2=A0mark_water.pdb =C2=A0 =C2=A0 =C2=A0 =C2= =A0
mGridForceCol Cavity O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
mGridForceChargeCol Cavity B =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0
mGridForceScale Cavity 0.0 0.0 0.0 =C2=A0

colvars on
colvarsConfig =C2=A0 ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.conf a collective
variable that, I expected, should count the number of water
molecules in the cavity.

colvar {
=C2=A0 =C2=A0name nwaters
=C2=A0 =C2=A0mapTotal {
=C2=A0 =C2=A0 mapName Cavity
=C2=A0 =C2=A0 componentCoeff 1.0
=C2=A0 =C2=A0}
}



harmonic {
=C2=A0 colvars nwaters
=C2=A0 centers 277 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 # cente= red around initial number of water molecules
=C2=A0 forceConstant 50000 =C2=A0 =C2=A0 =C2=A0
}

As you can see, I applied an harmonic bias to keep the number
of water molecules in the cavity close to the initial value
(277 molecules). Here comes the problem: according to the
.traj file the value of collective variable nwaters is constantly
equal to zero which is clearly wrong. The system was run for 5.0 ns
with NAMD 2.14. During the simulation the number of water molecules
inside the pore made oscillations of the order of 10% with respect
to the initial value. However, I suspect that an unbiased equilibrium
simulation would have done the same, so that this cannot be used as
a diagnostic criterium that the simulation is doing what it was
intended to do.

Could you please tell me what to do ? This is the first time I run this
kind of simulations so that some trivial mistake is highly possible.

Many thanks for your help,

Carlo Guardiani


=C2=A0


=C2=A0 =C2=A0 =C2=A0=C2=A0

_= _______________________________________________________
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--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/

_= _______________________________________________________<= /div>Le informazioni contenute i= n questo messaggio di posta elettronica sono strettamente riservate e indir= izzate esclusivamente al destinatario. Si prega di non leggere, fare copia,= inoltrare a terzi o conservare tale messaggio se non si =C3=A8 il legittim= o destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per = errore, si prega di restituirlo al mittente e di cancellarlo permanentement= e dal proprio computer.
The information contained in this e mail message is strictly confident= ial and intended for the use of the addressee only.=C2=A0 If you are not th= e intended recipient, please do not read, copy, forward or store it on your= computer. If you have received the message in error, please forward it bac= k to the sender and delete it permanently from your computer system.=

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boundary="_000_8275f3e1a531d57cd51fb034f7140cdamsuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 57d7fcb1-9583-4171-030d-08d8efecd534 X-MS-Exchange-CrossTenant-originalarrivaltime: 26 Mar 2021 00:19:34.0461 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: B6iwLEaG3cnMzG0M8ZYSRzrahmqADt76swNUUhkKYSNxKqvSH9uwObhlYJEQ5u7fi76750uAR1lHnJw/MqYHdw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR1201MB2487 X-Proofpoint-GUID: i3Cjw4vubkMBpoipkuMS7UoQqrfnuIjg X-Proofpoint-ORIG-GUID: i3Cjw4vubkMBpoipkuMS7UoQqrfnuIjg X-CLX-Response: 1TFkXGx0bEQpMehceEhEKWUQXaXtSfmRsGVBgYWQRClhYF29hWBMaS10bQ0F lEQp4Thdob0xmAXJmZEtdEhEKeUwXYGVTYE0dTx5nGFwRCkNIFwcYHxkRCkNZFx4eEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0MZaUBdHlxfSEFnaFpFQ1pBX2d5HX9Fe1tYTERfY0BNEQpYXBcfBBoEGBgcBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3JBWRpQEQpNXBcHGB0RCkxaF3hpa01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF3oef2ZvQh9Tcmt9EQpDWhceGgQbGh0EExkEHB MRCkJeFxsRCkReFxgRCkRJFxsRCkJFF2hta2B5EktAWh59EQpCThdob0xmAXJmZEtdEhEKQkwXb 2FYExpLXRtDQWURCkJsF2F5HB8SXHtPWmlCEQpCQBdhGVthRh5pRGd4ZREKQlgXZ3Nlc0BuYWFM XWIRCk1eFxsRClpYFx4RCnlDF25Bb2t6eB0ZeEJvEQpZSxcbGBkdEhEKcGgXZV5pbVISQmQBZVo QGRoRCnBoF2BTTlhHUG9GYWASEBkaEQpwaBdofhlLH2JTQFwdRRAZGhEKcGgXZGdoZktFUHpZeW AQGRoRCnBoF3pvTmBGc1x6b3gbEBkaEQpwfRdpa0gYYk1hUmhmaBAZGhEKcH0XbWZrRRleH0VTG VwQGRoRCnB9F2t6HGBTGRhvUEVgEBkaEQpwfxdiTgUBcEReaUR7ZRAbGxIRCnBfF2B6RRIZQGQd f0tyEBkaEQpwfxduH2ddfV5AE3hkeRAbGxkRCnBfF2RjaG0efVBrTFBgEBkaEQpwbBdneBpAYhh JGn55TRAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 malwarescore=0 suspectscore=0 mlxscore=0 lowpriorityscore=0 clxscore=171 bulkscore=0 priorityscore=48 impostorscore=0 spamscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103250000 definitions=main-2103250180 domainage_hfrom=12378 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_8275f3e1a531d57cd51fb034f7140cdamsuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Carlo, Segfaults are progress! Now comes another question. What does a force const= ant of 50000 mean? Your intuition is right, that your system is likely pret= ty well behaved on its own since it didn't crash when you ran it when no bi= as was effectively applied. I suspect once you math out what you are doing = to your poor simulation (like what happens if there are 326 waters in the c= olumn instead of 327) that you'll find that your force constant is *very* h= igh. My intuition is that you can probably get away with a force constant i= n the tens of kcal/mol/cv^2. -Josh On 3/25/21 4:40 PM, Carlo Guardiani wrote: Dear Josh and Giacomo, first of all, many thanks for your prompt reply. Following your advice I did the following tests, but unfortunately none of them had success. 1) Following Josh advice, I used the beta column to mark water oxygens witha label 1 while all other atoms were assigned a flag 0. mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb set all [atomselect top "all"] $all set occupancy 0 $all set beta 0 set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $wat set beta 1 $all writepdb mark_water.pdb Using this input the simulation started running with reasonable values of the collective variable nwaters, but as soon as the minimization finished the program aborted with a "Segmentation fault" error message. 2) Since Josh told me that traditionally the beta column had been used to store the charge, I also tried this approach. mol load parm7 6BBF_Ext_assembly_xleap.prmtop pdb TMD_4HKR_to_6BBF_frame_0.= pdb set natm 279195 set indmax [expr $natm - 1] set all [atomselect top "all"] $all set occupancy 0 $all set beta 0 for { set ind 0 } { $ind <=3D $indmax } { incr ind } { set atm [atomselect top "index $ind"] set charge [$atm get charge] $atm set beta $charge #$atm set beta [expr abs($charge)] $atm delete puts "$ind" } set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $all writepdb mark_water.pdb As soon as the minimization finished I had a series of error messages of the kind ERROR: Constraint failure in RATTLE algorithm for atom 86370! ERROR: Constraint failure; simulation has become unstable. I tried using the standard fix for this kind of problems: I increased the number of minimization steps from 100 to 1000 and I decreased the time-step from 2 fs to 1 fs. However, also in this case after the minimization the program crashed with a "segmentation fault" message and I also noted several "nan" in the energy values. This behaviour could suggest a bad starting structure. However, I remind you that when I ran the simulations with all zeros in the beta column (which likely made the collective variable inactive) I could run for 5 ns without any problem, which suggests that the structure is not so bad. Also, I noted that when using the atom charge in the beta column the values of the collective variable nwaters are negative (but in absolute value correct) which does not make any sense since it is a number of water molecules. I suppose this behaviour is due to the fact that the charge of water oxygens is negative. I therefore ran another test writing in the beta column the absolute value of the charge $atm set beta [expr abs($charge)] This test also ended with a segmentation fault immediately after minimization but as I expected the values of the colvar returned to be positive and correct. 3) As a final test, since Josh told me that some people use the beta column to store the mass value I also tried this approach. Also in this case the job ended with a segmentation fault and lots of "nan" in the energy values. Additionally, in this case the values of the colvar were badly over-estimated being of the order of several thousands instead of a few hundreds. I really don't know what else I could try. Could you please tell me what I need to put in the beta column to constrain the number of water molecules in the pore of my ion channels ? Many thanks for the help and best wishes, Carlo Il giorno gio 25 mar 2021 alle ore 15:52 Giacomo Fiorin > ha scritto: Hi Carlo, Josh is correct. A zero beta column is the most likely explanati= on: if not, please let us know. When implementing the NAMD backend of the mapTotal variable (based on GridF= orces), I tried to keep the new functionality as consistent as possible wit= h the use cases that Josh mentioned (custom electric fields, MDFF, etc). B= ut that also means inheriting technicalities like this one. FYI there is a tutorial available at https://urldefense.com/v3/__https://co= lvars.github.io/multi-map/multi-map.html__;!!DZ3fjg!vpzN6tjmxs60J62CsW_mkYJ= R6NM-jPeG0J85DFZ9RllTAh6g5RfTjhsxZ9wR6_Qbpw$ . The NAMD manual does= n't have it linked, because I wrote it after NAMD 2.14 was released. It's = geared toward variables with more than one map, but for a single map the sy= ntax is otherwise almost identical, as I'm sure you noticed. You may also find the latest VMD alpha build to visualize/test the variable= . (Note however that VMD doesn't have GridForces, so the way map variables= are defined there is slightly different). Giacomo On Thu, Mar 25, 2021 at 10:35 AM Vermaas, Josh > wrote: Hi Carlo, What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weight" f= or each atom also matters. For traditional grid forces, when it was being u= sed to apply an electric field, folks would copy the atomic charges to the = beta column so that a carbon and hydrogen atom wouldn't feel the same attra= ctive force. MDFF folks will use the mass of the element. The point being, = is that your beta column can't be zero, otherwise it doesn't contribute to = the gridforce value colvars is depending on. If you just want to count wate= rs, I *think* the correct thing is to have the "noh and water" have a 1 in = the beta column. You should then see non-zero values for the colvar. -Josh On 3/25/21 6:22 AM, Carlo Guardiani wrote: Dear NAMD experts, I am trying to run simulations with volumetric map-based variables. At the moment I am trying to bias the number of water molecules inside the pore of an ion channel following the instructions in the Reference manual for the Collective Variables Module. I built the pore occupancy map using VMD on a preliminary trajectory set sel [atomselect top "water and (z > -40) and (z < 25) and (sqrt(x*x+y*y= ) < 12)"] volmap occupancy $sel -allframes -combine max -o Occupancy.dx package require volutil volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx The map, visualized with VMD, looks reasonable in that all the pore region appears to be filled. Following the manual, I also created a file where all water molecules are marked in the occupancy column. Is that correct ? Maybe I had to mark only the water molecule initially inside the pore ? The file was generated with the following tcl script mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb set all [atomselect top "all"] $all set occupancy 0 set wat [atomselect top "water and (name O)"] $wat set occupancy 1 $all writepdb mark_water.pdb I added the following commands to the main NAMD input file mGridForce yes mGridForcePotFile Cavity Occupancy_smooth.dx mGridForceFile Cavity mark_water.pdb mGridForceCol Cavity O mGridForceChargeCol Cavity B mGridForceScale Cavity 0.0 0.0 0.0 colvars on colvarsConfig ./ColvarConfig.conf Finally, I defined in file ColvarConfig.conf a collective variable that, I expected, should count the number of water molecules in the cavity. colvar { name nwaters mapTotal { mapName Cavity componentCoeff 1.0 } } harmonic { colvars nwaters centers 277 # centered around initial number of water molec= ules forceConstant 50000 } As you can see, I applied an harmonic bias to keep the number of water molecules in the cavity close to the initial value (277 molecules). Here comes the problem: according to the .traj file the value of collective variable nwaters is constantly equal to zero which is clearly wrong. The system was run for 5.0 ns with NAMD 2.14. During the simulation the number of water molecules inside the pore made oscillations of the order of 10% with respect to the initial value. However, I suspect that an unbiased equilibrium simulation would have done the same, so that this cannot be used as a diagnostic criterium that the simulation is doing what it was intended to do. Could you please tell me what to do ? This is the first time I run this kind of simulations so that some trivial mistake is highly possible. Many thanks for your help, Carlo Guardiani ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono str= ettamente riservate e indirizzate esclusivamente al destinatario. Si prega = di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio s= e non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale messag= gio sia stato ricevuto per errore, si prega di restituirlo al mittente e di= cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential a= nd intended for the use of the addressee only. If you are not the intended= recipient, please do not read, copy, forward or store it on your computer.= If you have received the message in error, please forward it back to the s= ender and delete it permanently from your computer system. ________________________________ -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!vpzN6tjmxs60J62CsW_mkYJR6NM-jPeG0J85DFZ9RllTAh6g5RfTjhs= xZ9wd8sVdsw$ ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono str= ettamente riservate e indirizzate esclusivamente al destinatario. Si prega = di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio s= e non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale messag= gio sia stato ricevuto per errore, si prega di restituirlo al mittente e di= cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential a= nd intended for the use of the addressee only. If you are not the intended= recipient, please do not read, copy, forward or store it on your computer.= If you have received the message in error, please forward it back to the s= ender and delete it permanently from your computer system. ________________________________ -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!vpzN6tjmxs60J62CsW_mkYJR6NM-jPeG0J85DFZ9RllTAh6g5RfTjhs= xZ9wd8sVdsw$=20 --_000_8275f3e1a531d57cd51fb034f7140cdamsuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <488F1311A8349B45BD4D8D1E12AC8852@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Hi Carlo,

Segfaults are progress! Now comes another question. What does a force const= ant of 50000 mean? Your intuition is right, that your system is likely pret= ty well behaved on its own since it didn't crash when you ran it when no bi= as was effectively applied. I suspect once you math out what you are doing to your poor simulation (like what ha= ppens if there are 326 waters in the column instead of 327) that you'll fin= d that your force constant is *very* high. My intuition is that you can pro= bably get away with a force constant in the tens of kcal/mol/cv^2.

-Josh

On 3/25/21 4:40 PM, Carlo Guardiani wrote:
Dear Josh and Giacomo,
first of all, many thanks for your prompt reply.
Following your advice I did the following tests,
but unfortunately none of them had success.

1) Following Josh advice, I used the beta column
   to mark water oxygens witha label 1 while all
   other atoms were assigned a flag 0.

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
$all set beta 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$wat set beta 1
$all writepdb mark_water.pdb

Using this input the simulation started running
with reasonable values of the collective variable
nwaters, but as soon as the minimization finished
the program aborted with a "Segmentation fault"
error message.

2) Since Josh told me that traditionally the beta
column had been used to store the charge, I also
tried this approach.

mol load parm7 6BBF_Ext_assembly_xleap.prmtop pdb TMD_4HKR_to_6BBF_frame_0.= pdb
set natm 279195
set indmax [expr $natm - 1]

set all [atomselect top "all"]
$all set occupancy 0
$all set beta 0

for { set ind 0 } { $ind <=3D $indmax } { incr ind } {
set atm [atomselect top "index $ind"]
set charge [$atm get charge]
$atm set beta $charge
#$atm set beta [expr abs($charge)]
$atm delete
puts "$ind"
}

set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

As soon as the minimization finished I had a
series of error messages of the kind

ERROR: Constraint failure in RATTLE algorithm for atom 86370!
ERROR: Constraint failure; simulation has become unstable.

I tried using the standard fix for this kind of problems:
I increased the number of minimization steps from 100 to 1000
and I decreased the time-step from 2 fs to 1 fs. However,
also in this case after the minimization the program crashed
with a "segmentation fault" message and I also noted several
"nan" in the energy values. This behaviour could suggest a bad
starting structure. However, I remind you that when I ran the
simulations with all zeros in the beta column (which likely
made the collective variable inactive) I could run for 5 ns
without any problem, which suggests that the structure is not
so bad.

Also, I noted that when using the atom charge in the beta column
the values of the collective variable nwaters are negative (but
in absolute value correct) which does not make any sense since it
is a number of water molecules. I suppose this behaviour is due to
the fact that the charge of water oxygens is negative. I therefore
ran another test writing in the beta column the absolute value of
the charge

$atm set beta [expr abs($charge)]

This test also ended with a segmentation fault immediately after
minimization but as I expected the values of the colvar returned to
be positive and correct.

3) As a final test, since Josh told me that some people use the
beta column to store the mass value I also tried this approach.
Also in this case the job ended with a segmentation fault and lots
of "nan" in the energy values. Additionally, in this case the val= ues
of the colvar were badly over-estimated being of the order of several
thousands instead of a few hundreds.

I really don't know what else I could try. Could you please tell me
what I need to put in the beta column to constrain the number of water
molecules in the pore of my ion channels ?

Many thanks for the help and best wishes,

Carlo
 






Il giorno gio 25 mar 2021 alle ore 15= :52 Giacomo Fiorin <giacomo.fiorin@gmail.com> ha scritto:
Hi Carlo, Josh is correct.  A zero beta column is the= most likely explanation: if not, please let us know.

When implementing the NAMD backend of the mapTotal variable (based on = GridForces), I tried to keep the new functionality as consistent as possibl= e with the use cases that Josh mentioned (custom electric fields, MDFF, etc= ).  But that also means inheriting technicalities like this one.

FYI there is a tutorial available at https://colvars.github.io/multi-map/m= ulti-map.html.  The NAMD manual doesn't have it linked, because I wrote it after NAMD 2.14= was released.  It's geared toward variables with more than one map, b= ut for a single map the syntax is otherwise almost identical, as I'm s= ure you noticed.

You may also find the latest VMD alpha build to visualize/test the var= iable.  (Note however that VMD doesn't have GridForces, so the way map= variables are defined there is slightly different).

Giacomo


On Thu, Mar 25, 2021 at 10:35 AM Verm= aas, Josh <vermaasj@msu.edu> wrote:
Hi Carlo,

What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weig= ht" for each atom also matters. For traditional grid forces, when it w= as being used to apply an electric field, folks would copy the atomic charges to the beta column so that a carbon an= d hydrogen atom wouldn't feel the same attractive force. MDFF folks will us= e the mass of the element. The point being, is that your beta column can't = be zero, otherwise it doesn't contribute to the gridforce value colvars is depending on. If you just want to count = waters, I *think* the correct thing is to have the "noh and water"= ; have a 1 in the beta column. You should then see non-zero values for the = colvar.

-Josh

On 3/25/21 6:22 AM, Carlo Guardiani wrote:
Dear NAMD experts,
I am trying to run simulations with volumetric map-based
variables. At the moment I am trying to bias the number
of water molecules inside the pore of an ion channel
following the instructions in the Reference manual for
the Collective Variables Module. I built the pore occupancy
map using VMD on a preliminary trajectory

set sel [atomselect top "water and (z > -40) and (z < 25) and (s= qrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allframes -combine max -o Occupancy.dx

package require volutil

volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The map, visualized with VMD, looks reasonable in that all
the pore region appears to be filled.

Following the manual, I also created a file where all water
molecules are marked in the occupancy column. Is that correct ?
Maybe I had to mark only the water molecule initially inside the
pore ? The file was generated with the following tcl script

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

I added the following commands to the main NAMD input file

mGridForce yes
mGridForcePotFile Cavity Occupancy_smooth.dx    
mGridForceFile Cavity    mark_water.pdb       &nbs= p;
mGridForceCol Cavity O               &nb= sp;          
mGridForceChargeCol Cavity B             &nbs= p;      
mGridForceScale Cavity 0.0 0.0 0.0  

colvars on
colvarsConfig   ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.conf a collective
variable that, I expected, should count the number of water
molecules in the cavity.

colvar {
   name nwaters
   mapTotal {
    mapName Cavity
    componentCoeff 1.0
   }
}



harmonic {
  colvars nwaters
  centers 277               # cente= red around initial number of water molecules
  forceConstant 50000      
}

As you can see, I applied an harmonic bias to keep the number
of water molecules in the cavity close to the initial value
(277 molecules). Here comes the problem: according to the
.traj file the value of collective variable nwaters is constantly
equal to zero which is clearly wrong. The system was run for 5.0 ns
with NAMD 2.14. During the simulation the number of water molecules
inside the pore made oscillations of the order of 10% with respect
to the initial value. However, I suspect that an unbiased equilibrium
simulation would have done the same, so that this cannot be used as
a diagnostic criterium that the simulation is doing what it was
intended to do.

Could you please tell me what to do ? This is the first time I run this
kind of simulations so that some trivial mistake is highly possible.

Many thanks for your help,

Carlo Guardiani


 


      

_= _______________________________________________________
Le informazioni contenute in que= sto messaggio di posta elettronica sono strettamente riservate e indirizzat= e esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale mess= aggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale= messaggio sia stato ricevuto per errore, si prega di restituirlo al mitten= te e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message = is strictly confidential and intended for the use of the addressee only.&nb= sp; If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you hav= e received the message in error, please forward it back to the sender and d= elete it permanently from your computer system.


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https:/=
/prl.natsci.msu.edu/people/faculty/josh-vermaas/

_= _______________________________________________________<= /div> Le informazioni contenute in que= sto messaggio di posta elettronica sono strettamente riservate e indirizzat= e esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale mess= aggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale= messaggio sia stato ricevuto per errore, si prega di restituirlo al mitten= te e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message = is strictly confidential and intended for the use of the addressee only.&nb= sp; If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you hav= e received the message in error, please forward it back to the sender and d= elete it permanently from your computer system.


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="000000000000b41d6705be66424e" X-Proofpoint-GUID: MWD8CECE8QAxqTfmK9eFvTHALaAf9koR X-Proofpoint-ORIG-GUID: MWD8CECE8QAxqTfmK9eFvTHALaAf9koR X-CLX-Response: 1TFkXGxwfEQpMehcZHh4RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHxsfEQpDWRceHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseH3EYHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdnfW4SaW9pbxJ7a1JbfkxHYRNPbFx+YmtmS2tME0FFeBEKWFwXHwQaBBgYHAUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdyQV5FXxEKTVwXGRMfEQpMWhd4aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2FZHHkYSAUSG0J4EQpDWhcYGhMEEh8EGBsTBB sdEhEKQl4XGxEKREkXGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3IdbmxPWHhgEQpCbBdh X3pTGUNEGnobfhEKQkAXYRlbYUYeaURneGURCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp5QxduQW9 rengdGXhCbxEKWUsXExkfHREKcGcXYB5FbEJma0caX2AQGRoRCnBoF2ZOfWVvT2RQQVpFEBkaEQ pwaBdlXmltUhJCZAFlWhAcGhEKcGgXZllpfBtpe1NoXmAQGRoRCnBoF2VSEk5+SEUTaX9aEBkaE QpwaBd6b05gRnNcem94GxAZGhEKcH0Xb0xaUEtucn9Me3wQGRoRCnB9F25tTGFhGXhsG0t8EBwa EQpwfRdvSHAaY2RwXFBCbRAcGhEKcH8XYk4FAXBEXmlEe2UQGxscEQpwXxd6ExtAZEldGG5BehA ZGhEKcH8XYWZvWxpnZEJIHVsQGxgcEQpwXxdjYhJQSGN4H3xCfRAbGxoRCnBsF2Yfe1hcYgVLWG QfEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 malwarescore=0 suspectscore=0 mlxscore=0 lowpriorityscore=0 clxscore=165 bulkscore=0 priorityscore=344 impostorscore=0 spamscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103250000 definitions=main-2103260004 domainage_hfrom=9357 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000b41d6705be66424e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Carlo, I would stick with ones on both the occupancy and beta columns for counting the water molecules. The other two options are likely not meaningful for your application. As for the cause of the segfault, I suspect (but haven't verified yet) that the grid interpolation functions may crap out when one of your coordinates is NaN, as you are likely to get with a very large force. Keep the restraint off until you have figured out the correct scale of values for the CV. One thing not mentioned yet. What is the range of values for the map? Does it have values between 0 and 1? If not, you can either normalize the map with volutil, or use a componentCoeff to rescale it after the fact (your preference). I mentioned already using the Colvars Dashboard iin the latest VMD alpha build, which will help you troubleshoot any inconsistencies, especially when you use just ones for O and B. If you do that, the VMD version of the variable is this: colvar { name nwaters mapTotal { mapID 0 atoms { atomsFile mark_water.pdb atomsCol O } componentCoeff 1.0 } } With that configuration loaded, you should get on the Dashboard display more or less the same number that you'd get in NAMD (grid interpolation in VMD is different). A nice feature is that when you also include your harmonic restraint, you can type this at the command line: cv getenergy If you have a bad restraint, that will show you a crazy energy value *before* you go running a simulation with it... ;-) Giacomo On Thu, Mar 25, 2021 at 8:19 PM Vermaas, Josh wrote: > Hi Carlo, > > Segfaults are progress! Now comes another question. What does a force > constant of 50000 mean? Your intuition is right, that your system is like= ly > pretty well behaved on its own since it didn't crash when you ran it when > no bias was effectively applied. I suspect once you math out what you are > doing to your poor simulation (like what happens if there are 326 waters = in > the column instead of 327) that you'll find that your force constant is > *very* high. My intuition is that you can probably get away with a force > constant in the tens of kcal/mol/cv^2. > > -Josh > > On 3/25/21 4:40 PM, Carlo Guardiani wrote: > > Dear Josh and Giacomo, > first of all, many thanks for your prompt reply. > Following your advice I did the following tests, > but unfortunately none of them had success. > > 1) Following Josh advice, I used the beta column > to mark water oxygens witha label 1 while all > other atoms were assigned a flag 0. > > mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb > set all [atomselect top "all"] > $all set occupancy 0 > $all set beta 0 > set wat [atomselect top "water and (name O)"] > $wat set occupancy 1 > $wat set beta 1 > $all writepdb mark_water.pdb > > Using this input the simulation started running > with reasonable values of the collective variable > nwaters, but as soon as the minimization finished > the program aborted with a "Segmentation fault" > error message. > > 2) Since Josh told me that traditionally the beta > column had been used to store the charge, I also > tried this approach. > > mol load parm7 6BBF_Ext_assembly_xleap.prmtop pdb > TMD_4HKR_to_6BBF_frame_0.pdb > set natm 279195 > set indmax [expr $natm - 1] > > set all [atomselect top "all"] > $all set occupancy 0 > $all set beta 0 > > for { set ind 0 } { $ind <=3D $indmax } { incr ind } { > set atm [atomselect top "index $ind"] > set charge [$atm get charge] > $atm set beta $charge > #$atm set beta [expr abs($charge)] > $atm delete > puts "$ind" > } > > set wat [atomselect top "water and (name O)"] > $wat set occupancy 1 > $all writepdb mark_water.pdb > > As soon as the minimization finished I had a > series of error messages of the kind > > ERROR: Constraint failure in RATTLE algorithm for atom 86370! > ERROR: Constraint failure; simulation has become unstable. > > I tried using the standard fix for this kind of problems: > I increased the number of minimization steps from 100 to 1000 > and I decreased the time-step from 2 fs to 1 fs. However, > also in this case after the minimization the program crashed > with a "segmentation fault" message and I also noted several > "nan" in the energy values. This behaviour could suggest a bad > starting structure. However, I remind you that when I ran the > simulations with all zeros in the beta column (which likely > made the collective variable inactive) I could run for 5 ns > without any problem, which suggests that the structure is not > so bad. > > Also, I noted that when using the atom charge in the beta column > the values of the collective variable nwaters are negative (but > in absolute value correct) which does not make any sense since it > is a number of water molecules. I suppose this behaviour is due to > the fact that the charge of water oxygens is negative. I therefore > ran another test writing in the beta column the absolute value of > the charge > > $atm set beta [expr abs($charge)] > > This test also ended with a segmentation fault immediately after > minimization but as I expected the values of the colvar returned to > be positive and correct. > > 3) As a final test, since Josh told me that some people use the > beta column to store the mass value I also tried this approach. > Also in this case the job ended with a segmentation fault and lots > of "nan" in the energy values. Additionally, in this case the values > of the colvar were badly over-estimated being of the order of several > thousands instead of a few hundreds. > > I really don't know what else I could try. Could you please tell me > what I need to put in the beta column to constrain the number of water > molecules in the pore of my ion channels ? > > Many thanks for the help and best wishes, > > Carlo > > > > > > > > Il giorno gio 25 mar 2021 alle ore 15:52 Giacomo Fiorin < > giacomo.fiorin@gmail.com> ha scritto: > >> Hi Carlo, Josh is correct. A zero beta column is the most likely >> explanation: if not, please let us know. >> >> When implementing the NAMD backend of the mapTotal variable (based on >> GridForces), I tried to keep the new functionality as consistent as >> possible with the use cases that Josh mentioned (custom electric fields, >> MDFF, etc). But that also means inheriting technicalities like this one. >> >> FYI there is a tutorial available at >> https://urldefense.com/v3/__https://colvars.github.io/multi-map/multi-ma= p.html__;!!DZ3fjg!qd7GE6GLlSbSJlprRkl0e9b13CGy_Bi7_M84vYKLEpDyGJnoSnajP0XP9= Rc3dhb3hw$=20 >> . >> The NAMD manual doesn't have it linked, because I wrote it after NAMD 2.= 14 >> was released. It's geared toward variables with more than one map, but = for >> a single map the syntax is otherwise almost identical, as I'm sure you >> noticed. >> >> You may also find the latest VMD alpha build to visualize/test the >> variable. (Note however that VMD doesn't have GridForces, so the way map >> variables are defined there is slightly different). >> >> Giacomo >> >> >> On Thu, Mar 25, 2021 at 10:35 AM Vermaas, Josh wrote: >> >>> Hi Carlo, >>> >>> What is in the beta column? You are using the occupancy column to >>> determine if the atoms should be coupled to the potential or not. But t= he >>> "weight" for each atom also matters. For traditional grid forces, when = it >>> was being used to apply an electric field, folks would copy the atomic >>> charges to the beta column so that a carbon and hydrogen atom wouldn't = feel >>> the same attractive force. MDFF folks will use the mass of the element.= The >>> point being, is that your beta column can't be zero, otherwise it doesn= 't >>> contribute to the gridforce value colvars is depending on. If you just = want >>> to count waters, I *think* the correct thing is to have the "noh and wa= ter" >>> have a 1 in the beta column. You should then see non-zero values for the >>> colvar. >>> >>> -Josh >>> >>> On 3/25/21 6:22 AM, Carlo Guardiani wrote: >>> >>> Dear NAMD experts, >>> I am trying to run simulations with volumetric map-based >>> variables. At the moment I am trying to bias the number >>> of water molecules inside the pore of an ion channel >>> following the instructions in the Reference manual for >>> the Collective Variables Module. I built the pore occupancy >>> map using VMD on a preliminary trajectory >>> >>> set sel [atomselect top "water and (z > -40) and (z < 25) and >>> (sqrt(x*x+y*y) < 12)"] >>> >>> volmap occupancy $sel -allframes -combine max -o Occupancy.dx >>> >>> package require volutil >>> >>> volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx >>> >>> The map, visualized with VMD, looks reasonable in that all >>> the pore region appears to be filled. >>> >>> Following the manual, I also created a file where all water >>> molecules are marked in the occupancy column. Is that correct ? >>> Maybe I had to mark only the water molecule initially inside the >>> pore ? The file was generated with the following tcl script >>> >>> mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb >>> set all [atomselect top "all"] >>> $all set occupancy 0 >>> set wat [atomselect top "water and (name O)"] >>> $wat set occupancy 1 >>> $all writepdb mark_water.pdb >>> >>> I added the following commands to the main NAMD input file >>> >>> mGridForce yes >>> mGridForcePotFile Cavity Occupancy_smooth.dx >>> mGridForceFile Cavity mark_water.pdb >>> mGridForceCol Cavity O >>> mGridForceChargeCol Cavity B >>> mGridForceScale Cavity 0.0 0.0 0.0 >>> >>> colvars on >>> colvarsConfig ./ColvarConfig.conf >>> >>> Finally, I defined in file ColvarConfig.conf a collective >>> variable that, I expected, should count the number of water >>> molecules in the cavity. >>> >>> colvar { >>> name nwaters >>> mapTotal { >>> mapName Cavity >>> componentCoeff 1.0 >>> } >>> } >>> >>> >>> >>> harmonic { >>> colvars nwaters >>> centers 277 # centered around initial number of water >>> molecules >>> forceConstant 50000 >>> } >>> >>> As you can see, I applied an harmonic bias to keep the number >>> of water molecules in the cavity close to the initial value >>> (277 molecules). Here comes the problem: according to the >>> .traj file the value of collective variable nwaters is constantly >>> equal to zero which is clearly wrong. The system was run for 5.0 ns >>> with NAMD 2.14. During the simulation the number of water molecules >>> inside the pore made oscillations of the order of 10% with respect >>> to the initial value. However, I suspect that an unbiased equilibrium >>> simulation would have done the same, so that this cannot be used as >>> a diagnostic criterium that the simulation is doing what it was >>> intended to do. >>> >>> Could you please tell me what to do ? This is the first time I run this >>> kind of simulations so that some trivial mistake is highly possible. >>> >>> Many thanks for your help, >>> >>> Carlo Guardiani >>> >>> >>> >>> >>> >>> >>> >>> ________________________________________________________ >>> Le informazioni contenute in questo messaggio di posta elettronica sono >>> strettamente riservate e indirizzate esclusivamente al destinatario. Si >>> prega di non leggere, fare copia, inoltrare a terzi o conservare tale >>> messaggio se non si =C3=A8 il legittimo destinatario dello stesso. Qual= ora tale >>> messaggio sia stato ricevuto per errore, si prega di restituirlo al >>> mittente e di cancellarlo permanentemente dal proprio computer. >>> The information contained in this e mail message is strictly >>> confidential and intended for the use of the addressee only. If you are >>> not the intended recipient, please do not read, copy, forward or store = it >>> on your computer. If you have received the message in error, please for= ward >>> it back to the sender and delete it permanently from your computer syst= em. >>> ------------------------------ >>> >>> >>> -- >>> Josh Vermaas >>> Assistant Professor, MSU-DOE Plant Research Lab and Department of Bioch= emisty and Molecular Biologyvermaasj@msu.eduhttps://prl.natsci.msu.edu/peop= le/faculty/josh-vermaas/ >>> >>> > ________________________________________________________ > Le informazioni contenute in questo messaggio di posta elettronica sono > strettamente riservate e indirizzate esclusivamente al destinatario. Si > prega di non leggere, fare copia, inoltrare a terzi o conservare tale > messaggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualor= a tale > messaggio sia stato ricevuto per errore, si prega di restituirlo al > mittente e di cancellarlo permanentemente dal proprio computer. > The information contained in this e mail message is strictly confidential > and intended for the use of the addressee only. If you are not the > intended recipient, please do not read, copy, forward or store it on your > computer. If you have received the message in error, please forward it ba= ck > to the sender and delete it permanently from your computer system. > ------------------------------ > > > -- > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochem= isty and Molecular Biologyvermaasj@msu.eduhttps://prl.natsci.msu.edu/people= /faculty/josh-vermaas/ > > --000000000000b41d6705be66424e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Carlo, I would stick=C2=A0with ones on both the occupan= cy and beta columns for counting=C2=A0the water molecules.=C2=A0 The other= =C2=A0two options are likely not meaningful for your application.
=

As for the cause of the segfault, I suspect (but = haven't verified yet) that the grid interpolation functions may crap ou= t when one of your coordinates is NaN, as you are likely to get with a very= large force.=C2=A0 Keep the restraint off until you have figured out the c= orrect scale of values for the CV.

One thing not m= entioned yet.=C2=A0 What is the range of values for the map?=C2=A0 Does it = have values between 0 and 1?=C2=A0 If not, you can either normalize the map= with volutil, or use a componentCoeff to rescale it after the fact (your p= reference).

I mentioned already u= sing the Colvars Dashboard iin the latest VMD alpha build, which will help = you troubleshoot any inconsistencies, especially when you use just ones for= O and B.=C2=A0 If you do that, the VMD version of the variable is this:

colvar {
=C2=A0 =C2=A0na= me nwaters
=C2=A0 =C2=A0mapTotal {
=C2=A0 =C2=A0 mapID 0
=C2=A0 =C2= =A0 atoms {=C2=A0
=C2=A0 =C2=A0 =C2=A0 atomsFile=C2=A0mark_water.pdb
=C2=A0 =C2=A0 =C2=A0 atomsCo= l O
=C2=A0 =C2=A0 }
=C2=A0 = =C2=A0 componentCoeff 1.0
=C2=A0 =C2=A0}
<= span style=3D"color:rgb(0,0,0)">}

With that configuration loaded, you should get on the= Dashboard display more or less the same number that you'd get in NAMD = (grid interpolation in VMD is different).

A nice f= eature is that when you also include your harmonic restraint, you can type = this at the command line:
cv getenergy
If you have a ba= d restraint, that will show you a crazy energy value before you go r= unning a simulation with it... ;-)

Giacomo


On Thu, Mar 25, 2021 at 8:19 PM Vermaas, Josh <vermaasj@msu.edu> wrote:
Hi Carlo,

Segfaults are progress! Now comes another question. What does a force const= ant of 50000 mean? Your intuition is right, that your system is likely pret= ty well behaved on its own since it didn't crash when you ran it when n= o bias was effectively applied. I suspect once you math out what you are doing to your poor simulation (like what ha= ppens if there are 326 waters in the column instead of 327) that you'll= find that your force constant is *very* high. My intuition is that you can= probably get away with a force constant in the tens of kcal/mol/cv^2.

-Josh

On 3/25/21 4:40 PM, Carlo Guardiani wrote:
Dear Josh and Giacomo,
first of all, many thanks for your prompt reply.
Following your advice I did the following tests,
but unfortunately none of them had success.

1) Following Josh advice, I used the beta column
=C2=A0 =C2=A0to mark water oxygens witha label 1 while all
=C2=A0 =C2=A0other atoms were assigned a flag 0.

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
$all set beta 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$wat set beta 1
$all writepdb mark_water.pdb

Using this input the simulation started running
with reasonable values of the collective variable
nwaters, but as soon as the minimization finished
the program aborted with a "Segmentation fault"
error message.

2) Since Josh told me that traditionally the beta
column had been used to store the charge, I also
tried this approach.

mol load parm7 6BBF_Ext_assembly_xleap.prmtop pdb TMD_4HKR_to_6BBF_frame_0.= pdb
set natm 279195
set indmax [expr $natm - 1]

set all [atomselect top "all"]
$all set occupancy 0
$all set beta 0

for { set ind 0 } { $ind <=3D $indmax } { incr ind } {
set atm [atomselect top "index $ind"]
set charge [$atm get charge]
$atm set beta $charge
#$atm set beta [expr abs($charge)]
$atm delete
puts "$ind"
}

set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

As soon as the minimization finished I had a
series of error messages of the kind

ERROR: Constraint failure in RATTLE algorithm for atom 86370!
ERROR: Constraint failure; simulation has become unstable.

I tried using the standard fix for this kind of problems:
I increased the number of minimization steps from 100 to 1000
and I decreased the time-step from 2 fs to 1 fs. However,
also in this case after the minimization the program crashed
with a "segmentation fault" message and I also noted several
"nan" in the energy values. This behaviour could suggest a bad
starting structure. However, I remind you that when I ran the
simulations with all zeros in the beta column (which likely
made the collective variable inactive) I could run for 5 ns
without any problem, which suggests that the structure is not
so bad.

Also, I noted that when using the atom charge in the beta column
the values of the collective variable nwaters are negative (but
in absolute value correct) which does not make any sense since it
is a number of water molecules. I suppose this behaviour is due to
the fact that the charge of water oxygens is negative. I therefore
ran another test writing in the beta column the absolute value of
the charge

$atm set beta [expr abs($charge)]

This test also ended with a segmentation fault immediately after
minimization but as I expected the values of the colvar returned to
be positive and correct.

3) As a final test, since Josh told me that some people use the
beta column to store the mass value I also tried this approach.
Also in this case the job ended with a segmentation fault and lots
of "nan" in the energy values. Additionally, in this case the val= ues
of the colvar were badly over-estimated being of the order of several
thousands instead of a few hundreds.

I really don't know what else I could try. Could you please tell me
what I need to put in the beta column to constrain the number of water
molecules in the pore of my ion channels ?

Many thanks for the help and best wishes,

Carlo
=C2=A0






Il giorno gio 25 mar 2021 alle ore 15= :52 Giacomo Fiorin <giacomo.fiorin@gmail.com> ha scritto:
Hi Carlo, Josh is correct.=C2=A0 A zero beta column is the= most likely explanation: if not, please let us know.

When implementing the NAMD backend of the mapTotal variable (based on = GridForces), I tried to keep the new functionality as consistent as possibl= e with the use cases that Josh mentioned (custom electric fields, MDFF, etc= ).=C2=A0 But that also means inheriting technicalities like this one.

FYI there is a tutorial=C2=A0available at=C2=A0https://colvars.github.io/multi-map/multi-map.html.=C2=A0 The NAMD manual doesn't have it linked, because I wrote it after NAMD = 2.14 was released.=C2=A0 It's geared toward variables with more than on= e map, but for a single map the syntax is otherwise almost identical,=C2=A0= as I'm sure you noticed.

You may also find the latest VMD alpha build to visualize/test the var= iable.=C2=A0 (Note however that VMD doesn't have GridForces, so the way= map variables are defined there is slightly different).

Giacomo


On Thu, Mar 25, 2021 at 10:35 AM Verm= aas, Josh <vermaas= j@msu.edu> wrote:
Hi Carlo,

What is in the beta column? You are using the occupancy column to determine= if the atoms should be coupled to the potential or not. But the "weig= ht" for each atom also matters. For traditional grid forces, when it w= as being used to apply an electric field, folks would copy the atomic charges to the beta column so that a carbon an= d hydrogen atom wouldn't feel the same attractive force. MDFF folks wil= l use the mass of the element. The point being, is that your beta column ca= n't be zero, otherwise it doesn't contribute to the gridforce value colvars is depending on. If you just want to count = waters, I *think* the correct thing is to have the "noh and water"= ; have a 1 in the beta column. You should then see non-zero values for the = colvar.

-Josh

On 3/25/21 6:22 AM, Carlo Guardiani wrote:
Dear NAMD experts,
I am trying to run simulations with volumetric map-based
variables. At the moment I am trying to bias the number
of water molecules inside the pore of an ion channel
following the instructions in the Reference manual for
the Collective Variables Module. I built the pore occupancy
map using VMD on a preliminary trajectory

set sel [atomselect top "water and (z > -40) and (z < 25) and (s= qrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allframes -combine max -o Occupancy.dx

package require volutil

volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The map, visualized with VMD, looks reasonable in that all
the pore region appears to be filled.

Following the manual, I also created a file where all water
molecules are marked in the occupancy column. Is that correct ?
Maybe I had to mark only the water molecule initially inside the
pore ? The file was generated with the following tcl script

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

I added the following commands to the main NAMD input file

mGridForce yes
mGridForcePotFile Cavity Occupancy_smooth.dx =C2=A0 =C2=A0
mGridForceFile Cavity =C2=A0 =C2=A0mark_water.pdb =C2=A0 =C2=A0 =C2=A0 =C2= =A0
mGridForceCol Cavity O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
mGridForceChargeCol Cavity B =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0
mGridForceScale Cavity 0.0 0.0 0.0 =C2=A0

colvars on
colvarsConfig =C2=A0 ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.conf a collective
variable that, I expected, should count the number of water
molecules in the cavity.

colvar {
=C2=A0 =C2=A0name nwaters
=C2=A0 =C2=A0mapTotal {
=C2=A0 =C2=A0 mapName Cavity
=C2=A0 =C2=A0 componentCoeff 1.0
=C2=A0 =C2=A0}
}



harmonic {
=C2=A0 colvars nwaters
=C2=A0 centers 277 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 # cente= red around initial number of water molecules
=C2=A0 forceConstant 50000 =C2=A0 =C2=A0 =C2=A0
}

As you can see, I applied an harmonic bias to keep the number
of water molecules in the cavity close to the initial value
(277 molecules). Here comes the problem: according to the
.traj file the value of collective variable nwaters is constantly
equal to zero which is clearly wrong. The system was run for 5.0 ns
with NAMD 2.14. During the simulation the number of water molecules
inside the pore made oscillations of the order of 10% with respect
to the initial value. However, I suspect that an unbiased equilibrium
simulation would have done the same, so that this cannot be used as
a diagnostic criterium that the simulation is doing what it was
intended to do.

Could you please tell me what to do ? This is the first time I run this
kind of simulations so that some trivial mistake is highly possible.

Many thanks for your help,

Carlo Guardiani


=C2=A0


=C2=A0 =C2=A0 =C2=A0=C2=A0

_= _______________________________________________________
Le informazioni contenute in que= sto messaggio di posta elettronica sono strettamente riservate e indirizzat= e esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale mess= aggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale= messaggio sia stato ricevuto per errore, si prega di restituirlo al mitten= te e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message = is strictly confidential and intended for the use of the addressee only.=C2= =A0 If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you hav= e received the message in error, please forward it back to the sender and d= elete it permanently from your computer system.


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/

_= _______________________________________________________
Le informazioni contenute in que= sto messaggio di posta elettronica sono strettamente riservate e indirizzat= e esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale mess= aggio se non si =C3=A8 il legittimo destinatario dello stesso. Qualora tale= messaggio sia stato ricevuto per errore, si prega di restituirlo al mitten= te e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message = is strictly confidential and intended for the use of the addressee only.=C2= =A0 If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you hav= e received the message in error, please forward it back to the sender and d= elete it permanently from your computer system.


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
--000000000000b41d6705be66424e-- From owner-namd-l@halifax.ks.uiuc.edu Mon Mar 29 18:37:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12TNbHxx028334; Mon, 29 Mar 2021 18:37:17 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12TNbHBU028333; Mon, 29 Mar 2021 18:37:17 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12TNbGXS028329; Mon, 29 Mar 2021 18:37:16 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12TNbG9v028328; Mon, 29 Mar 2021 18:37:16 -0500 (CDT) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12TNbDbX028319 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 29 Mar 2021 18:37:13 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_A2CA22D0-7555-4795-937F-7FC7ABFEC1F3" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: potential bug while compiling the Windows version of NAMD Date: Mon, 29 Mar 2021 18:37:07 -0500 References: <2089087596.180773.1616693874777.ref@mail.yahoo.com> <2089087596.180773.1616693874777@mail.yahoo.com> To: NAMD list , Osvalds Verners In-Reply-To: <2089087596.180773.1616693874777@mail.yahoo.com> Message-Id: <69A27ECB-6F2C-44B8-BC82-2562245A79FB@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_A2CA22D0-7555-4795-937F-7FC7ABFEC1F3 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Osvalds, What version of gcc are you using? Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 25, 2021, at 12:37 PM, Osvalds Verners = wrote: >=20 > Dear Sir/Madam, >=20 > I would like to report an error which occurred while compiling the = NAMD_2.14_Win64-multicore version using the following command: >=20 > ./build charm++ multicore-win64 gcc --with-production >=20 > --- >=20 > In file included from bind.c:11: > bind.c: In function =E2=80=98cmi_hwloc_alloc_heap=E2=80=99: > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: warning: implicit declaration of function = =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99? = [-Wimplicit-function-declaration] > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99 > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared = (first use in this function); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99= ? > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99 > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: note: each undeclared identifier is reported only = once for each function it appears in > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99 > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > make[2]: *** [Makefile:721: bind.lo] Error 1 > make[2]: Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src' > make[1]: *** [Makefile:418: all-recursive] Error 1 > make[1]: Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc' > make: *** [Makefile:565: hwloc-target] Error 2 >=20 > --- >=20 > Since I have not changed any source file, it could be considered as a = potential bug (did not find in the known bugs list though). >=20 > Best regards, >=20 > Osvalds Verners --Apple-Mail=_A2CA22D0-7555-4795-937F-7FC7ABFEC1F3 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Osvalds,

What = version of gcc are you using?

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Mar 25, 2021, at 12:37 PM, Osvalds Verners <osvalds.verners@REMOVE_yahoo.com> wrote:

=
Dear Sir/Madam,

I would like to report an = error which occurred while compiling the NAMD_2.14_Win64-multicore version using the following = command:

./build = charm++  multicore-win64 gcc --with-production

---

In file included from = bind.c:11:
bind.c: In function = =E2=80=98cmi_hwloc_alloc_heap=E2=80=99:
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:29: warning: implicit declaration of = function =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99= ? [-Wimplicit-function-declaration]
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                   =  ^~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:29: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                   =  ^~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 = undeclared (first use in this function); did you mean = =E2=80=98USN_PAGE_SIZE=E2=80=99?
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                     =        ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                     =        ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: note: each undeclared identifier is = reported only once for each function it appears in
  282 | #define hwloc_getpagesize() = sysconf(_SC_PAGE_SIZE)
      |  =                     =               =  ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                     =        ^~~~~~~~~~~~~
make[2]: = *** [Makefile:721: bind.lo] Error 1
make[2]: = Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'
make[1]: *** [Makefile:418: all-recursive] Error = 1
make[1]: Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc'
make: *** [Makefile:565: hwloc-target] Error 2

---

Since I have = not changed any source file, it could be considered as a potential bug = (did not find in the known bugs list though).

Best = regards,

Osvalds Verners

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boundary="0000000000009d33db05bebdd35e" X-Proofpoint-GUID: djVFhgiCMqdtiF9hKgZX7Ui2nRvibqLg X-Proofpoint-ORIG-GUID: djVFhgiCMqdtiF9hKgZX7Ui2nRvibqLg X-CLX-Response: 1TFkXGxofEQpMehcZHxoRCllEF2daeXhSQW1aeERaEQpYWBdjc2ZjEhNwTXw eTBEKeE4XY1Nja3sTWH4aX14RCnlMF2lhGGFZHGZfU1xEEQpDSBcHGR0bEQpDWRcHGxocEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGEh9xHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdOQHxsQk1DaWdbTl5DbBNCYU1wch1/QxhEeFxDSFtmTREKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3JHYE5kEQpNXBcYHx4RCkxaF29pTWtrEQpMRhdva2tra2s RCkJPF2h9QWBDWn1zR0ETEQpDWhcYGhMEEh8EGxgSBB4bEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2lGYk1bbx5zHVMeEQpCThdjU2NrexNYf hpfXhEKQkwXY3NmYxITcE18HkwRCkJsF3pvWFxuZXhFbB9ZEQpCQBdueEN6T1IbaENlQxEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnlDF2lzekJ+cnhoQnlFEQpZSxcTGRwbEQpwaBdvUBN SfnxPTXBzRBAZGhEKcGgXZ2BOYnNNW1pQSXMQGRoRCnBoF2x6clBYRGxlQnxdEBkaEQpwaBdrXB x9H0NwaUNmUxAZGhEKcGgXem0Sa2VhTmlPZ2cQGRoRCnB9F2JLYGNkYl1FX19wEBkaEQpwfRdrT kFsU1kZGHBAaxAZGhEKcH0Xbx95c3lvZUZ4YEgQGRoRCnB9F24aARxleGJSbhlQEBkaEQpwfxdt U0hiYktITRpGXxAbGhoRCnBfF2hMaEdNTmtTXE1NEBkaEQpwfxdlHhtpRVJ8YGVeYhAbGRoRCnB fF2RgZXtgf0YfWk4aEBkaEQpwfxd6GltbcBhnWVhrZRAbGBIRCnBfF21lGW1/bkBtWkJDEBsZHx EKcH8Xb0RhUBITfxscEn4QEhwRCnBfF2x5RFpHb1BZSV9DEBkaEQpwbBdpeUIbRmNlbV9SYxAZG hEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 phishscore=0 suspectscore=0 spamscore=0 priorityscore=350 mlxlogscore=999 mlxscore=0 clxscore=105 adultscore=0 lowpriorityscore=0 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103250000 definitions=main-2103300066 domainage_hfrom=9361 X-Spam-Score: 0 X-Spam-OrigSender: raghavbioinfo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, raghav singh --0000000000009d33db05bebdd35e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear NAMD-Users, I am writing to you all regarding results from Accelerated MD simulations via NAMD/2.13. I have a protein(Bovine Beta-casein, 224 aa long), I have generated it's 3D model using LOMETS, as there is next to zero 3D data available in PDB regarding the protein as well as no suitable homologs were found using BLAST search against PDB database. On the generated model, I have run 1ms of cMD and aMD simulations(RMSD, PCA and structural information attached). Upon looking at the results, it appears that in aMD simulations, the protein escapes the starting energy minima and in full 1ms aMD never revisits the initial conformational space. Though cMD shows that structural fold is stable in the entirety of the 1ms simulation time. In my understanding upon smoothening of energy barriers between different minimas, there should be revisiting/ diffusive events present in the trajectory!! I have followed the Amber Accelerated MD tutorial, as well as the following publications to calculate the aMD parameters for my simulation system. *1- https://urldefense.com/v3/__http://ambermd.org/tutorials/advanced/tutor= ial22/__;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXo= Mw5vWsqRg$=20 * *2- Hu et al : Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods (https://urldefense.com/v3/__https://peerj.com/articles/9241/__;!!DZ3fjg!oT= RxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXoMxu5rhvwg$ )* *3- Gedeon et al : Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter (https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4= 518716/__;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JX= oMyzHwrjXQ$=20 )* Given that the protein is highly disordered and has a very small percentage of secondary structure attached to it. Is this behaviour normal ?? or Am I doing something wrong with my simulation set up?? Most of the structural transitions during the MD are also attached to the disordered regions of the protein. Please find the RMSD, RG, PCA and probability histograms and conformational transition over the course of simulation. https://urldefense.com/v3/__https://drive.google.com/file/d/1RNsfG84uj08T5a= eJbPRwGiQQZfY6BYU4/view?usp=3Dsharing__;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhct= bxm-1msfErThnElf2fpbLduFEkE5JXoMwRn3oLsw$=20 I would greatly appreciate your help and support to understand if necessary rectify the problem in my simulations. Thanking you all for your help and support in advance. Best, Raghav --0000000000009d33db05bebdd35e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear NAMD-Users,
I am writing to you a= ll regarding results from Accelerated MD simulations via NAMD/2.13.
I have a protein(Bovine Beta-casein, 224 aa long), I have generated it's= =20 3D model using LOMETS, as there is next to zero 3D data available in PDB regarding the protein as well as no suitable homologs were found using=20 BLAST search against PDB database.

On the=20 generated model, I have run 1ms of cMD and aMD simulations(RMSD, PCA and structural information attached). Upon looking at the results, it=20 appears that in aMD simulations, the protein escapes the starting energy minima and in full 1ms aMD never revisits the initial conformational=20 space. Though cMD shows that structural fold is stable in the entirety=20 of the 1ms simulation time. In my understanding upon smoothening of=20 energy barriers between different minimas, there should be revisiting/=20 diffusive events present in the trajectory!!

I have followed the Amber Accelerated MD tutorial, as well as the=20 following publications to calculate the aMD parameters for my simulation system.

=20=20=20=20 =20=20

2- Hu et al : Revealing th= e selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple comp= utational methods (https://peerj.com/articles/9241/= )
3- Gedeon et al : Accelerated molecular dynamics and protein=20 conformational change: a theoretical and practical guide using a=20 membrane embedded model neurotransmitter transporter (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518716/)



I would greatly appr= eciate your help and support to understand if necessary rectify the problem= in my simulations.

Thanking you all for your help= and support in advance.

Best,
Ragh= av
--0000000000009d33db05bebdd35e-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 30 13:36:22 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12UIaMqD012069; Tue, 30 Mar 2021 13:36:22 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12UIaLsu012068; Tue, 30 Mar 2021 13:36:21 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12UIaLw9012064; Tue, 30 Mar 2021 13:36:21 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12UIaLXE012063; Tue, 30 Mar 2021 13:36:21 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12UIaBN9012055 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 30 Mar 2021 13:36:11 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 12UISsNe007267 for ; Tue, 30 Mar 2021 18:36:11 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=norman.geist@uni-greifswald.de Received: from mailgate2.uni-greifswald.de (mailgate2.uni-greifswald.de [141.53.10.23]) by mx0b-00007101.pphosted.com with ESMTP id 37khhep59q-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 30 Mar 2021 18:36:10 +0000 Received: from localhost (localhost [127.0.0.1]) by mailgate2.uni-greifswald.de (Postfix) with ESMTP id 81DB910309A0; Tue, 30 Mar 2021 20:36:08 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at Received: from smtp1.rz.uni-greifswald.de ([141.53.10.101]) (using TLS with cipher TLS_AES_256_GCM_SHA384) by localhost (mailgate2.uni-greifswald.de [141.53.10.23]) (amavisd-new, port 10026) with ESMTPS id UmnX0Ynr3wWd; Tue, 30 Mar 2021 20:36:08 +0200 (CEST) Received: from groupware.uni-greifswald.de (groupware1.rz.uni-greifswald.de [141.53.10.24]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp1.rz.uni-greifswald.de (Postfix) with ESMTPSA id E64C910309A0; Tue, 30 Mar 2021 20:36:07 +0200 (CEST) Message-ID: Date: Tue, 30 Mar 2021 20:36:07 +0200 Subject: namd-l: Re: Infrared spectrum prediction From: "Geist, Norman" To: NAMD list , Raman Preet Singh Content-Type: multipart/alternative; boundary="_=_swift_v4_1617129367_da9c0a5cce1e05a54b22aeb1ce88c0bd_=_" References: In-Reply-To: X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0TEQpMehcaEQpZRBdmSHx+GkhzekJ7XBEKWFgXaV1YRRlJeUFrZU8 RCnhOF2Qab28bYhx6aXNEEQp5TBdreUJBWUtnRUx/UxEKQ0gXBx4SGBEKQ1kXHx8RCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHxNxGRIQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XHVJvG3VLHX8aTH5FRV9bTVwSfGxNGWdMXV1MYx5PUHsRClhcFx8EGgQYGBwFGxoE GxsaBB8aBBseGxAbHhofGhEKXlkXckd4exgRCk1cFxgbHBEKTFoXfGlrTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGlrEQpCTxdsWkBHe2JBZHtISREKQ1oXGx4bBB8ZBBsaBBgZEQpCXh cbEQpEXhcYEQpCRRdobWRnbmdaBUcFHhEKQk4XZBpvbxtiHHppc0QRCkJMF2ldWEUZSXlBa2VPE QpCbBdkU2MZEmV4SGRlcBEKQkAXa3pbekJce2tAe04RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpa WBcSEQp5QxdpQ31sGxocQnwTQhEKcGcXaUNuUAFZc0cBHlMQGRoRCnBoF2QfUn19GGx4HGFMEBk aEQpwaBdpGmhSc05gfH9lbBAZGhEKcGgXa20ZbnlEXkNMcGwQGRoRCnBoF2FAfEYBZx9IbGdOEB kaEQpwaBdiWEhFT2FoYW1AbxAZGhEKcH0XZWMFTW1GTBhCWWkQGRoRCnB9F2tsGWhYXkNAGAViE BkaEQpwfRdgThJLbVseRwFLWhAZGhEKcH0XbUBIbUtYWh4TW0UQHRsRCnB9F2cSW2BEXE9hckJj EBkaEQpwfxdmRB0ZSFNgS01zYhAZGhEKcF8XY1NFSH1iGxloT0QQGRoRCnB/F2Fmb1saZ2RCSB1 bEBsYExEKcF8XY2ISUEhjeB98Qn0QGxoYEQpwXxdvXRJsUE1+QGRjaxAZGhEKcF8Xaxh+bWgYUl 18QGIQGxgfEQpwfxdvG0ISRUxvGEZZHxAbGhoRCnBfF20dZFtCfXNEEh4BEBISEQpwbBdlYExuE 09OQURiHRAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: 7xE1_a7U0fToouqgv8VFg3MfwwfI4ezQ X-Proofpoint-ORIG-GUID: 7xE1_a7U0fToouqgv8VFg3MfwwfI4ezQ MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 bulkscore=0 mlxlogscore=999 clxscore=179 impostorscore=0 phishscore=0 spamscore=0 lowpriorityscore=0 mlxscore=0 suspectscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103250000 definitions=main-2103300134 X-Spam-Score: 0 X-Spam-OrigSender: norman.geist@uni-greifswald.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Geist, Norman" --_=_swift_v4_1617129367_da9c0a5cce1e05a54b22aeb1ce88c0bd_=_ Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Fot this purpose you'd rather refer to QM based calculations. Find a good tutorial behind below link: https://urldefense.com/v3/__http://www.travis-analyzer.de/files/travis_ir_r= aman.pdf__;!!DZ3fjg!shD_LRxBkThJByHDlMssfMeuItny_Use7pEerr7Eon_BwbVtUPgCIDz= X1pzsOG7urg$=20 Bests Norman Geist Am Freitag, den 12-02-2021 um 11:34 schrieb Raman Preet Singh: Dear All, I posted this earlier but received no directions. Reposting the same in case someone who might help me missed it. Thanks in advance. RPS Get Outlook for Android [1] ------------------------- From: Raman Preet Singh Sent: Monday, January 18, 2021 11:51:23 PM To: NAMD list=20 Subject: Infrared spectrum prediction =C2=A0 Dear All, =20 I have come across some papers where MD has been=C2=A0 used to predict IR spectrum of proteins. Is it possible to predict IR spectrum of small organic molecules from NAMD simulations? Can changes in IR spectra due to interactions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, scripts, etc. would be highly appreciated. =20 Thanks in advance. =20 Regards, Raman =20 =20 Links: ------ [1] https://urldefense.com/v3/__https://aka.ms/ghei36__;!!DZ3fjg!s7x-r3noyN8OZQ= liu4Ygo-KOeWXgXVFjdIIVlu7Ctp-0BkICtEJ4cr7rk4j5N4xT0Q$ --_=_swift_v4_1617129367_da9c0a5cce1e05a54b22aeb1ce88c0bd_=_ Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Fot this purpose you'd rather refer to QM based calculations. Find a = good tutorial behind below link:

http://www= .travis-analyzer.de/files/travis_ir_raman.pdf

Bests
Norman Geist

Am Freitag, = den 12-02-2021 um 11:34 schrieb Raman Preet Singh:
Dear All,

I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it.

Thanks in advance.

RPS


From: Raman Preet Singh
Sent: Monday, January 18, 2021 11:51:23 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Infrared spectrum prediction
 
Dear All,

I have come across some papers where MD has been  used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


--_=_swift_v4_1617129367_da9c0a5cce1e05a54b22aeb1ce88c0bd_=_-- From owner-namd-l@halifax.ks.uiuc.edu Tue Mar 30 13:43:28 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12UIhSHL013324; Tue, 30 Mar 2021 13:43:28 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12UIhSXJ013323; Tue, 30 Mar 2021 13:43:28 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12UIhRXx013314; Tue, 30 Mar 2021 13:43:27 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12UIhRJr013313; Tue, 30 Mar 2021 13:43:27 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12UIhIAF013292 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000000dd29405bec55f96" X-Proofpoint-GUID: _H2FqKS881fF636_FfqGA31Y3nXgm9kB X-Proofpoint-ORIG-GUID: _H2FqKS881fF636_FfqGA31Y3nXgm9kB X-CLX-Response: 1TFkXGx8SEQpMehcZHx4RCllEF2VpGh9+Q3lIclp5EQpYWBdoZB5JXgF+H30 FaREKeE4XY1Nja3sTWH4aX14RCnlMF2hucB9JcmZke21YEQpDSBcHGRgZEQpDWRccGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsZEnEYGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd1YhhsW2F5EhIbTGwcGRx1bExbbWsZG3MZRHJNRxNBaBEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JHeHJNEQpNXBcYGB4RCkxaF3xpTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYmdbH1AZU2B7HBMRCkNaFxgaEwQSHwQYGxoEGx 0fEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF3pyXlt/WXNOfkxdEQpCThdjU2NrexNYfhpfXhEKQkwXaGQeSV4Bfh99BWkRCkJsF2hN emd6Z0xpbVpPEQpCQBd6Q38eQxh/Rn94XBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnl DF2ZSYGBdGmdFbHJsEQpZSxcTGRwbEQpwZxdpQ25QAVlzRwEeUxAZGhEKcGgXZEV+ZHpeW1preW MQGRoRCnBoF3pMekFHaR9cQGV4EBkaEQpwaBdoRx9JT3lEcnBDQxAZGhEKcGgXYl4eRkQTGBNLb BIQGRoRCnBoF2J/Z1xOfgVwY1wZEBkaEQpwfRdrbBloWF5DQBgFYhAZGhEKcH8XYWZvWxpnZEJI HVsQGxgcEQpwXxdjYhJQSGN4H3xCfRATGxEKcGwXYmZJbWVeX3x+eFIQGRoRCm1+FxsRClhNF0s RIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 phishscore=0 suspectscore=0 spamscore=0 priorityscore=354 mlxlogscore=678 mlxscore=0 clxscore=158 adultscore=0 lowpriorityscore=0 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103250000 definitions=main-2103300134 domainage_hfrom=9361 X-Spam-Score: 0 X-Spam-OrigSender: mb.ucdelcaribe@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maria Bykhovskaia --0000000000000dd29405bec55f96 Content-Type: text/plain; charset="UTF-8" NAMD only gives you MD trajectories. To derive IR spectra from the trajectories, you have to use other tools such as normal mode analysis. Most of the groups use custom-made software for this, as far as I know On Fri, Feb 12, 2021 at 4:36 AM Raman Preet Singh < ramanpreetsingh@hotmail.com> wrote: > Dear All, > > I posted this earlier but received no directions. Reposting the same in > case someone who might help me missed it. > > Thanks in advance. > > RPS > > Get Outlook for Android > > > ------------------------------ > *From:* Raman Preet Singh > *Sent:* Monday, January 18, 2021 11:51:23 PM > *To:* NAMD list > *Subject:* Infrared spectrum prediction > > Dear All, > > I have come across some papers where MD has been used to predict IR > spectrum of proteins. Is it possible to predict IR spectrum of small > organic molecules from NAMD simulations? Can changes in IR spectra due to > interactions between two molecules (H-bonding, pi-pi interactions, etc ) be > also predicted? Any papers, tutorials, scripts, etc. would be highly > appreciated. > > Thanks in advance. > > Regards, > Raman > > > --0000000000000dd29405bec55f96 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
NAMD only gives you MD trajectories. To derive IR spectra = from the trajectories, you have to use other tools such as normal mode anal= ysis. Most of the groups use custom-made software for this, as far as I kno= w

On Fri, Feb 12, 2021 at 4:36 AM Raman Preet Singh <ramanpreetsingh@hotmail.com> wrote:
Dear All,=

I posted this earlier but received no directions. Reposting the same in cas= e someone who might help me missed it.

Thanks in advance.

RPS


From= : Raman Preet Singh
Sent: Monday, January 18, 2021 11:51:23 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: Infrared spectrum prediction
=C2=A0
Dear All,

I have come across some papers where MD has been=C2=A0 used to predict IR s= pectrum of proteins. Is it possible to predict IR spectrum of small organic= molecules from NAMD simulations? Can changes in IR spectra due to interact= ions between two molecules (H-bonding, pi-pi interactions, etc ) be also predicted? Any papers, tutorials, script= s, etc. would be highly appreciated.

Thanks in advance.

Regards,
Raman


--0000000000000dd29405bec55f96-- From owner-namd-l@halifax.ks.uiuc.edu Wed Mar 31 14:53:08 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12VJr8of003022; Wed, 31 Mar 2021 14:53:08 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12VJr8wN003021; Wed, 31 Mar 2021 14:53:08 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12VJr72u003017; Wed, 31 Mar 2021 14:53:07 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 12VJr7wA003016; Wed, 31 Mar 2021 14:53:07 -0500 (CDT) Received: from wirelessprv-10-194-17-142.near.illinois.edu ([10.194.17.142]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 12VJr4GH003009 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Wed, 31 Mar 2021 14:53:04 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_ACAA37FF-6A70-4526-8938-CAE1DDF75918" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: potential bug while compiling the Windows version of NAMD Date: Wed, 31 Mar 2021 14:53:04 -0500 References: <2089087596.180773.1616693874777.ref@mail.yahoo.com> <2089087596.180773.1616693874777@mail.yahoo.com> To: NAMD list , Osvalds Verners In-Reply-To: <2089087596.180773.1616693874777@mail.yahoo.com> Message-Id: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_ACAA37FF-6A70-4526-8938-CAE1DDF75918 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Osvalds, I emailed the Charm++ developers about your issue. Their response: This is an issue in hwloc, which for some reason here is trying to use = the POSIX sysconf function. This is likely due to a misconfiguration in = the build environment or something like that, hwloc's configure should = pick the right thing to use here. To note, sysconf should be usable with = Cygwin on Windows, but not with native Windows or MinGW builds. Hope this helps, Dave > On Mar 25, 2021, at 12:37 PM, Osvalds Verners = wrote: >=20 > Dear Sir/Madam, >=20 > I would like to report an error which occurred while compiling the = NAMD_2.14_Win64-multicore version using the following command: >=20 > ./build charm++ multicore-win64 gcc --with-production >=20 > --- >=20 > In file included from bind.c:11: > bind.c: In function =E2=80=98cmi_hwloc_alloc_heap=E2=80=99: > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: warning: implicit declaration of function = =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99? = [-Wimplicit-function-declaration] > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99 > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared = (first use in this function); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99= ? > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99 > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: note: each undeclared identifier is reported only = once for each function it appears in > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > = /NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99 > 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE) > | ^~~~~~~~~~~~~ > make[2]: *** [Makefile:721: bind.lo] Error 1 > make[2]: Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src' > make[1]: *** [Makefile:418: all-recursive] Error 1 > make[1]: Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc' > make: *** [Makefile:565: hwloc-target] Error 2 >=20 > --- >=20 > Since I have not changed any source file, it could be considered as a = potential bug (did not find in the known bugs list though). >=20 > Best regards, >=20 > Osvalds Verners --Apple-Mail=_ACAA37FF-6A70-4526-8938-CAE1DDF75918 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Osvalds,

I emailed = the Charm++ developers about your issue. Their response:

This is an issue in = hwloc, which for some reason here is trying to use the POSIX sysconf = function. This is likely due to a misconfiguration in the build = environment or something like that, hwloc's configure should pick the = right thing to use here. To note, sysconf should be usable with Cygwin = on Windows, but not with native Windows or MinGW builds.

Hope this = helps,
Dave


On Mar 25, 2021, at 12:37 PM, Osvalds Verners <osvalds.verners@REMOVE_yahoo.com> wrote:

=
Dear Sir/Madam,

I would like to report an = error which occurred while compiling the NAMD_2.14_Win64-multicore version using the following = command:

./build = charm++  multicore-win64 gcc --with-production

---

In file included from = bind.c:11:
bind.c: In function = =E2=80=98cmi_hwloc_alloc_heap=E2=80=99:
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:29: warning: implicit declaration of = function =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99= ? [-Wimplicit-function-declaration]
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                   =  ^~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:29: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                   =  ^~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 = undeclared (first use in this function); did you mean = =E2=80=98USN_PAGE_SIZE=E2=80=99?
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                     =        ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                     =        ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: note: each undeclared identifier is = reported only once for each function it appears in
  282 | #define hwloc_getpagesize() = sysconf(_SC_PAGE_SIZE)
      |  =                     =               =  ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/in= clude/private/private.h:282:37: note: in definition of macro = =E2=80=98hwloc_getpagesize=E2=80=99
  282 | = #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |          =                     =        ^~~~~~~~~~~~~
make[2]: = *** [Makefile:721: bind.lo] Error 1
make[2]: = Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'
make[1]: *** [Makefile:418: all-recursive] Error = 1
make[1]: Leaving directory = '/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc'
make: *** [Makefile:565: hwloc-target] Error 2

---

Since I have = not changed any source file, it could be considered as a potential bug = (did not find in the known bugs list though).

Best = regards,

Osvalds Verners

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X-OriginatorOrg: depaul.edu X-MS-Exchange-CrossTenant-OriginalArrivalTime: 01 Apr 2021 16:18:53.6508 (UTC) X-MS-Exchange-CrossTenant-Network-Message-Id: e55ec43e-176e-4953-ab86-08d8f529d7e6 X-MS-Exchange-CrossTenant-Id: 750d3a3f-1f46-4da2-8a64-7605e75ea2f9 X-MS-Exchange-CrossTenant-OriginalAttributedTenantConnectingIp: TenantId=750d3a3f-1f46-4da2-8a64-7605e75ea2f9;Ip=[140.192.190.48];Helo=[outlook.depaul.edu] X-MS-Exchange-CrossTenant-AuthSource: MW2NAM10FT022.eop-nam10.prod.protection.outlook.com X-MS-Exchange-CrossTenant-AuthAs: Anonymous X-MS-Exchange-CrossTenant-FromEntityHeader: HybridOnPrem X-MS-Exchange-Transport-CrossTenantHeadersStamped: BY5PR16MB3301 X-Proofpoint-ORIG-GUID: ElzjAQ3B1S_QOEQx0K0bh4DgWroI3Z72 X-CLX-Response: 1TFkXGxkfEQpMehceEhEKWUQXbHhPTUxAaUVGBUsRClhYF2NOa399YRNBEwF AEQp4ThdmfRJ4RF5QaRJvHBEKeUwXY2NYbEMfSQFBHVIRCkNIFwcSHREKQ1kXBxseExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsbH3EbGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdvRlBAa3sZaBt5dXtlb3tSGmEaSEIebk19WEVjGXAdGBEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JHH0lmEQpNXBcYGBkRCkxaF2hpTWtrEQpMRhdvb2tra2t rEQpCTxd6XnNBEk8baRxGcxEKQ1oXHhoEGxodBBgZHQQcGBEKQl4XGxEKRF4XGBEKQlwXGxEKXk 4XGxEKQksXZn0SeEReUGkSbxwRCkJJF2Z9EnhEXlBpEm8cEQpCRRdof3MfSUMbG1JHcBEKQk4XZ n0SeEReUGkSbxwRCkJMF2NOa399YRNBEwFAEQpCbBdrRGxHE1t5U2wcZxEKQkAXYmFpE1xtSR58 SWkRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdhcnpIWG1DfBNtYhEKWUsXGxgcGRo RCnBoF2FhZHtGbnNCSV0fEBkaEQpwaBdoRAFYbUddZ3xiRxAZGhEKcGgXY01HE2lfSHBCaG8QGR oRCnBoF2ZIGQVoQB1zc1gaEBkaEQpwaBdpAU1pGmllTG5LYhAZGhEKcGwXbmN5Y1NaQmt6W08QG RoRCnBDF25pAV1jXW5NZXxyEBsbEhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-GUID: ElzjAQ3B1S_QOEQx0K0bh4DgWroI3Z72 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=135 suspectscore=0 impostorscore=0 mlxscore=0 spamscore=0 adultscore=0 bulkscore=0 malwarescore=0 mlxlogscore=718 phishscore=0 lowpriorityscore=0 priorityscore=48 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103310000 definitions=main-2104010106 domainage_hfrom=12630 X-Spam-Score: 0 X-Spam-OrigSender: CGOEDDE@depaul.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by halifax.ks.uiuc.edu id 131GIwB0017529 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Goedde, Chris" Hi all, I’m thinking of upgrading the GPU in the linux box I use for namd to take advantage of namd 3.0. Given the constraints of my current hardware, I’m trying to choose between a 10 GB GeForce RTX 3080 and a 48 GB A6000. The A6000 is about $4k more than the 3080, and I’m wondering if it’s worth it. My systems are generally relatively small, let’s say 10k to 25k atoms. I’m wondering how much difference I might expect between these two cards on systems of this size and if the difference in price can be justified. Thanks for any insight. Chris Goedde Department of Physics DePaul University From owner-namd-l@halifax.ks.uiuc.edu Thu Apr 1 12:52:44 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 131Hqi20020823; Thu, 1 Apr 2021 12:52:44 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 131Hqi7m020822; Thu, 1 Apr 2021 12:52:44 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 131HqhQc020818; Thu, 1 Apr 2021 12:52:43 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 131HqhNF020817; Thu, 1 Apr 2021 12:52:43 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 131HqWBs020810 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="utf-8" Content-ID: <8259A673EA7A0D48B7D74840DB81E8BF@namprd12.prod.outlook.com> X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 05210da8-713a-4b88-d6f8-08d8f536ebc1 X-MS-Exchange-CrossTenant-originalarrivaltime: 01 Apr 2021 17:52:30.4873 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: OatOsaPYNspaUihI2nTzc0/n69ao29NdVgWF+oC4a0Dscw1mBPxID3MdO8XDnW3G7Qk7hGWBCXdINPmJdMzZoQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR1201MB0214 X-Proofpoint-ORIG-GUID: 0EJE9vOq9d9g3aOvupemdsG34aA-aBnf X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBkeEQpMehcZGhEKWUQXaXtSfmRsGVBgYWQRClhYF29hWBMaS10bQ0F lEQp4Thdob0xmAXJmZEtdEhEKeUwXYGVTYE0dTx5nGFwRCkNIFwcbHBkRCkNZFxoRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYYGx5xGxkcEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxpvYG8TXGVbE04TTRlLZVxfWk9HTlltGR5LawdLaERMEQpYXBcfBBoEGBgcBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3JHHFAdEQpNXBcYHBoRCkxaF2l4aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxd6Hn9mb0IfU3JrfREKQ1oXHhoEGxodBBgYGQ QSExEKQl4XGxEKRF4XGREKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCTBdvYVgTG ktdG0NBZREKQmwXYXkcHxJce09aaUIRCkJAF3ocRH9pchJCSEd6EQpCWBdnc2VzQG5hYUxdYhEK TV4XGxEKWlgXGREKeUMXa20aYRNCRHpPZEkRCllLFxsYGRIeEQpwaBdue29kR2Z+ZAFQcBAaEQp waBdmXGtGQVltXXh4RBAaEQpwaBdmSBkFaEAdc3NYGhAeEhEKcGgXaQFNaRppZUxuS2IQHhIRCn BoF2VGZUVJZGxDaWN/EBoRCnB9F2t6HGBTGRhvUEVgEBkaEQpwfxduH2ddfV5AE3hkeRAbGhMRC nBfF2RjaG0efVBrTFBgEBkaEQpwbBdneBpAYhhJGn55TRAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: 0EJE9vOq9d9g3aOvupemdsG34aA-aBnf MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=30 malwarescore=0 mlxscore=0 clxscore=234 suspectscore=0 lowpriorityscore=0 adultscore=0 mlxlogscore=999 bulkscore=0 phishscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2103310000 definitions=main-2104010115 domainage_hfrom=12384 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 131HqXBr020811 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Hi Chris, The price is unlikely to be justified for the desktop/workstation/ad-hoc computing you are describing. The big benefit for the A6000 or other cards in what used to be called the quadro line are that they have gobs of memory. So while my older 8GB GTX 980 card will sometimes throw out of memory exceptions if I try rendering too big of a structure, the RTX 8000 in lab with its 48GB of RAM will render multi-million atom structures just fine. In terms of CUDA performance, I believe that they are pretty comparable for NAMD3 performance on smaller systems, although I've never had hardware in hand to try. They both basically use the same chip, the GA102. I think the real trick will be getting your hand on either card though, as there have been relatively widespread shortages for consumer GPU hardware. -Josh On 4/1/21 12:18 PM, Goedde, Chris wrote: > Hi all, > > I’m thinking of upgrading the GPU in the linux box I use for namd to take advantage of namd 3.0. Given the constraints of my current hardware, I’m trying to choose between a 10 GB GeForce RTX 3080 and a 48 GB A6000. The A6000 is about $4k more than the 3080, and I’m wondering if it’s worth it. > > My systems are generally relatively small, let’s say 10k to 25k atoms. I’m wondering how much difference I might expect between these two cards on systems of this size and if the difference in price can be justified. > > Thanks for any insight. > > Chris Goedde > Department of Physics > DePaul University > > -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tfqRDHfuVb04CMjidGFwAtVj7yfwSNpjirTopBEQgS7hznWnOaylHbR2nNgkAldSxA$ From owner-namd-l@halifax.ks.uiuc.edu Mon Apr 5 10:55:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 135FtenC012586; Mon, 5 Apr 2021 10:55:40 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 135FtdtA012584; Mon, 5 Apr 2021 10:55:39 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 135Ftcmh012577; 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boundary="_000_DM6PR08MB53389F04DDCAD22E9B4BBFF4E5779DM6PR08MB5338namp_" MIME-Version: 1.0 X-OriginatorOrg: ndsu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: DM6PR08MB5338.namprd08.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 7fc6be1e-9dde-4957-544e-08d8f84b3148 X-MS-Exchange-CrossTenant-originalarrivaltime: 05 Apr 2021 15:55:08.9184 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: ec37a091-b9a6-47e5-98d0-903d4a419203 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: SM5poVTHHJBfmu9UrzH6QjtDY8dqnPr/Q7HZ49QK0oAKxetDdj/QlPjdxaN87OIzq5+146VJtk+cYxutiOsHYw75PzXj+YFjrrcUnZAuZtw= X-MS-Exchange-Transport-CrossTenantHeadersStamped: DM6PR08MB5849 X-Proofpoint-ORIG-GUID: Kg4otBGgZgVbl6uIVM1OflIIlHBOMepy X-Proofpoint-GUID: Kg4otBGgZgVbl6uIVM1OflIIlHBOMepy X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIbEQpMehcaEQpZRBd6YgFHWx5PfGh4AREKWFgXel5uT0BaGUtTT0I RCnhOF2sdXRlIckJoZnAcEQp5TBdhYBp4E31ZchxrbBEKQ0gXBxMdEQpDWRcHGBEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhscG3EeGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZX k9OEQpDThdhTR5FXmhtTXBNfEhGHF9jfGcbZUxGY2NGYmhlZ09aUxEKWFwXHwQaBBgYHAUbGgQb GhoEHhIEGxMQGx4aHxoRCl5ZF3JFZE9jEQpNXBcZGxEKTFoXaGlrTU0RCkxGF29va2tra2sRCkJ PF3pec0ESTxtpHEZzEQpDWhceGgQbGh0EExgEEx8RCkJeFxsRCkRYFxkRCkRJFx4RCkJcFxsRCl 5OFxsRCkJLF2sdXRlIckJoZnAcEQpCSRdrHV0ZSHJCaGZwHBEKQkUXZgUSAUhBfF1QQ1ARCkJOF 2sdXRlIckJoZnAcEQpCTBd6Xm5PQFoZS1NPQhEKQmwXbV9pc15sGh9rcHARCkJAF24eaR96YVlL ZXoSEQpNXhcbEQpaWBcZEQp5QxduZk5yH1NbGxhEWxEKWUsXHRIcEhEKcGgXY2FZfUVFHXhCTU8 QGRoRCnBoF2VLBWsaHRxnS2FuEBkaEQpwaBdkR0xnE2VtHEROSRAZGhEKcGgXYFNrXHxaeWYBW1 wQHRoRCnBoF2wcYHheTXxHXF5SEBkaEQpwbBdnE2djGUNTTnBjZxAZGhEKcEwXaUQTbX8FbBpHW XwQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 adultscore=0 mlxlogscore=757 impostorscore=0 mlxscore=0 suspectscore=0 lowpriorityscore=0 clxscore=181 phishscore=0 malwarescore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104030000 definitions=main-2104050107 domainage_hfrom=7868 X-Spam-Score: 0 X-Spam-OrigSender: hmnasrullah.faisal@ndsu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Faisal, H M Nasrullah" --_000_DM6PR08MB53389F04DDCAD22E9B4BBFF4E5779DM6PR08MB5338namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Dr. John Stone, Hope you are doing well. I am just wondering whether we can simulate Ultra-= violet light application on atomic structure in NAMD? If yes, are there any= resources available regarding it. I am kind of stuck here. Best Regards H M Nasrullah Faisal Ph.D. Candidate/Materials and Nanotechnology North Dakota State University --_000_DM6PR08MB53389F04DDCAD22E9B4BBFF4E5779DM6PR08MB5338namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Dr. John Stone,

Hope you are doing well. I am just wondering whether we can simulate Ultra-= violet light application on atomic structure in NAMD? If yes, are there any= resources available regarding it. I am kind of stuck here.


Best Regards
H M Nasrullah Faisal
Ph.D. Candidate/Materials and Nanotechnology
North Dakota State University
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Tue, 6 Apr 2021 04:11:15 +0000 Date: Tue, 6 Apr 2021 04:11:10 +0000 (UTC) From: Osvalds Verners To: NAMD list , David Hardy Message-ID: <1039957203.2438503.1617682270596@mail.yahoo.com> In-Reply-To: <69A27ECB-6F2C-44B8-BC82-2562245A79FB@ks.uiuc.edu> References: <2089087596.180773.1616693874777.ref@mail.yahoo.com> <2089087596.180773.1616693874777@mail.yahoo.com> <69A27ECB-6F2C-44B8-BC82-2562245A79FB@ks.uiuc.edu> Subject: Re: namd-l: potential bug while compiling the Windows version of NAMD MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_2438502_230761419.1617682270593" X-Mailer: WebService/1.1.17936 YMailNorrin Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/89.0.4389.90 Safari/537.36 Edg/89.0.774.63 X-Proofpoint-GUID: ovibYKjgUw6Df_n4dZUZoF4_ncfs5BQk X-CLX-Response: 1TFkXExoRCkx6FxkZEhEKWUQXYH1hb0RbX3tmcmYRClhYF255HVlDBX1wWX5 iEQp4Thd6RBwdb0VsbURDZhEKeUwXaUIeHX4cTmcdWXIRCkNIFwceGhsRCkNZFxsRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYdGnEeEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCRVleT 04RCkNOF0VcQ0hzYUBNf10cbkx1RB5OcH9wRWwedURJTFkfaHtBEQpYXBcfBBoEGBgcBRsaBBsa GgQeEgQYGBAbHhofGhEKXlkXckVzegURCk1cFxgYExEKTFoXeGtra2sRCkVZF29rEQpMXxd6BQU FBQUFBQUFbxEKTEYXb2trYmtrEQpCTxdmeGYfaVlsYX5daxEKQ1oXHR4EHAQbGBMEHhoRCkJeFx sRCkReFxgRCkJcFxsRCl5OFxsRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0VsbURDZhEKQkUXZ H9zBR1me0RlSXoRCkJOF3pEHB1vRWxtRENmEQpCTBdueR1ZQwV9cFl+YhEKQmwXZ2tTYhxMX2BO AV4RCkJAF2RgEh9SGxhrYEBNEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUMXa0xyQBg FUFJMU10RCllLFxMfHR8RCnBnF2tNTXxOTF96Rx5NEBkaEQpwaBdrcmVBRW0fZ097fxAZGhEKcG gXaxIZZlp6RENYbRgQGRoRCnBoF2R6XmxAY2RGZkISEBkaEQpwaBdiGnhrX18FcF5PBRAZGhEKc GgXZxNaYV9aGRNHZh0QGRoRCnBnF25tXhpZZBhnYnByEBkaEQpwfRdubklHWmtJaU5PWxAZGhEK cGcXbBwFGkEFXXtgRVkQGRoRCnB/F2VYchgdSRheRml8EBsaGhEKcF8XZnBIXEB5AUEeTxIQGRo RCnBsF3pcfW5LXwVOUF1cEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: ovibYKjgUw6Df_n4dZUZoF4_ncfs5BQk X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=804 spamscore=0 priorityscore=338 adultscore=0 suspectscore=0 bulkscore=0 mlxscore=0 lowpriorityscore=0 malwarescore=0 impostorscore=0 clxscore=90 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104030000 definitions=main-2104060024 domainage_hfrom=9575 X-Spam-Score: 0 X-Spam-OrigSender: osvalds.verners@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Osvalds Verners ------=_Part_2438502_230761419.1617682270593 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello David, thank you for getting back and apologies for a delayed response. I am using= gcc version=C2=A010.2.0. Best regards, Osvalds Verners On Tuesday, March 30, 2021, 03:26:36 AM GMT+3, David Hardy wrote: =20 =20 Hi Osvalds, What version of gcc are you using? Best regards,Dave --David J. Hardy, Ph.D.Beckman InstituteUniversity of Illinois at Urbana-Ch= ampaign405 N. Mathews Ave., Urbana, IL 61801dhardy@ks.uiuc.edu, http://www.= ks.uiuc.edu/~dhardy/ On Mar 25, 2021, at 12:37 PM, Osvalds Verners wrote: Dear Sir/Madam, I would like to report an error which occurred while compiling the=C2=A0NAM= D_2.14_Win64-multicore version using the following command: ./build charm++=C2=A0 multicore-win64 gcc --with-production --- In file included from bind.c:11:bind.c: In function =E2=80=98cmi_hwloc_allo= c_heap=E2=80=99:/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwlo= c/include/private/private.h:282:29: warning: implicit declaration of functi= on =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99? [-Wim= plicit-function-declaration]=C2=A0 282 | #define hwloc_getpagesize() syscon= f(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~= ~/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: note: in definition of macro =E2=80=98hwloc_getpagesiz= e=E2=80=99=C2=A0 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)= =C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~/NAMD_2.14_Sourc= e/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:= 37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared (first use in this fu= nction); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99?=C2=A0 282 | #define = hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~/NAMD_2.14_Sou= rce/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:28= 2:37: note: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99=C2= =A0 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 = =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~= ~~~~/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/pr= ivate/private.h:282:37: note: each undeclared identifier is reported only o= nce for each function it appears in=C2=A0 282 | #define hwloc_getpagesize()= sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~/NAMD_2.14_Source/charm-6.10.2/= multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:37: note: in de= finition of macro =E2=80=98hwloc_getpagesize=E2=80=99=C2=A0 282 | #define h= wloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~make[2]: *** [= Makefile:721: bind.lo] Error 1make[2]: Leaving directory '/NAMD_2.14_Source= /charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'make[1]: *** [Makefile:418:= all-recursive] Error 1make[1]: Leaving directory '/NAMD_2.14_Source/charm-= 6.10.2/multicore-win64-gcc/tmp/hwloc'make: *** [Makefile:565: hwloc-target]= Error 2 --- Since I have not changed any source file, it could be considered as a poten= tial bug (did not find in the known bugs list though). Best regards, Osvalds Verners =20 =20 ------=_Part_2438502_230761419.1617682270593 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello David,

thank you for getting back and apologies for a delayed response. I am = using gcc version 10.2.0.

= Best regards,

Osvalds Ver= ners

=20
=20
On Tuesday, March 30, 2021, 03:26:36 AM GMT+3, David Ha= rdy <dhardy@ks.uiuc.edu> wrote:


Hi Osvalds,

What version of gcc are you using?

Best regards,
Dave

<= div class=3D"yiv4862334918">
--
David = J. Hardy, Ph.D.
B= eckman Institute
= University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801
=

On Mar 25, 2021, at 12:37 P= M, Osvalds Verners <osva= lds.verners@REMOVE_yahoo.com> wrote:

Dear Sir/Madam,

I would like to report an e= rror which occurred while compiling the = NAMD_2.14_Win64-multicore version using the following command:
=

./build charm++  multicore-win6= 4 gcc --with-production

---

In file included from bind.c:11:
bind.c: In function =E2=80=98cmi_hwloc_alloc_heap=E2=80= =99:
/NAMD_2.14_Source/charm-6.10.2/multi= core-win64-gcc/tmp/hwloc/include/private/private.h:282:29: warning: implici= t declaration of function =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98= siscanf=E2=80=99? [-Wimplicit-function-declaration]
  282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)<= /div>
      |     = ;                     &nb= sp;  ^~~~~~~
/NAMD_2.14_Source/charm= -6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:29: not= e: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99
  282 | #define hwloc_getpagesize() sysconf(_SC_P= AGE_SIZE)
      |  &n= bsp;                     =      ^~~~~~~
/NAMD_2.14_So= urce/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:2= 82:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared (first use in this= function); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99?
  282 | #define hwloc_getpagesize() sysconf(_SC_PAG= E_SIZE)
      |  &nbs= p;                     &n= bsp;            ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/h= wloc/include/private/private.h:282:37: note: in definition of macro =E2=80= =98hwloc_getpagesize=E2=80=99
  282 = | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |           =                     &nbs= p;    ^~~~~~~~~~~~~
/NAMD_2.14_= Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h= :282:37: note: each undeclared identifier is reported only once for each fu= nction it appears in
  282 | #define= hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |              &= nbsp;                    =  ^~~~~~~~~~~~~
/NAMD_2.14_Source/ch= arm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:37: = note: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99
  282 | #define hwloc_getpagesize() sysconf(_S= C_PAGE_SIZE)
      | =                     &nbs= p;              ^~~~~~~~~~~~~
make[2]: *** [Makefile:721: bind.lo] Error 1
<= div class=3D"yiv4862334918">make[2]: Leaving directory '/NAMD_2.14_Source/c= harm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'
make[1]: *** [Makefile:418: all-recursive] Error 1
make[1]: Leaving directory '/NAMD_2.14_Source/charm-6.10.2/= multicore-win64-gcc/tmp/hwloc'
make: *** = [Makefile:565: hwloc-target] Error 2

---

=
Since I have not changed any sourc= e file, it could be considered as a potential bug (did not find in the know= n bugs list though).

Best regards,

Osvalds Verners

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Tue, 6 Apr 2021 04:18:17 +0000 Date: Tue, 6 Apr 2021 04:18:16 +0000 (UTC) From: Osvalds Verners To: NAMD list , David Hardy Message-ID: <1551461533.2437105.1617682696834@mail.yahoo.com> In-Reply-To: <1039957203.2438503.1617682270596@mail.yahoo.com> References: <2089087596.180773.1616693874777.ref@mail.yahoo.com> <2089087596.180773.1616693874777@mail.yahoo.com> <69A27ECB-6F2C-44B8-BC82-2562245A79FB@ks.uiuc.edu> <1039957203.2438503.1617682270596@mail.yahoo.com> Subject: Re: namd-l: potential bug while compiling the Windows version of NAMD MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_2437104_990380783.1617682696831" X-Mailer: WebService/1.1.17936 YMailNorrin Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/89.0.4389.90 Safari/537.36 Edg/89.0.774.63 X-CLX-Shades: MLX X-Proofpoint-GUID: tPadsTsVk5vMlDNXSg6_YQk8Nqlkofhy X-CLX-Response: 1TFkXGx4cEQpMehcYEhwRCllEF2B9YW9EW197ZnJmEQpYWBdueR1ZQwV9cFl +YhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lCHh1+HE5nHVlyEQpDSBcHHh8ZEQpDWRcbEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxgccRsdEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF156S05Zfll8QR9cZ0ZuZHJ5TRx1c3tBEmRbRkFFTEJTEQpYXBcfBBoEGBgcBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXckVzfUQRCk1cFxgSExEKTFoXaXhpa2trEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZnhmH2lZbGF+XWsRCkNaFx0eBBwEGxkfBB4aEQ pCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRC kJFF2R/cwUdZntEZUl6EQpCThd6RBwdb0VsbURDZhEKQkwXbnkdWUMFfXBZfmIRCkJsF2drU2Ic TF9gTgFeEQpCQBdkYBIfUhsYa2BATREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnlDF2t MckAYBVBSTFNdEQpZSxcTHx0fEQpwZxdrTU18TkxfekceTRAeEhEKcGgXZF5vRUJ4bn8cfWwQGh EKcGgXa3JlQUVtH2dPe38QHhIRCnBoF2R6XmxAY2RGZkISEBwaEQpwaBdoTVseaWRBekVDUBAaE QpwaBdiGnhrX18FcF5PBRAeEhEKcGcXbm1eGllkGGdicHIQHhIRCnB9F25uSUdaa0lpTk9bEB4S EQpwZxdoUnlAcFlNXhNoZxAaEQpwfxdlWHIYHUkYXkZpfBAbGx8RCnBfF2ZwSFxAeQFBHk8SEB4 SEQpwbBd6XH1uS18FTlBdXBAeEhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: tPadsTsVk5vMlDNXSg6_YQk8Nqlkofhy X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 priorityscore=286 mlxlogscore=792 impostorscore=0 adultscore=0 mlxscore=0 phishscore=0 lowpriorityscore=0 clxscore=146 bulkscore=0 suspectscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104030000 definitions=main-2104060026 domainage_hfrom=9575 X-Spam-Score: 0 X-Spam-OrigSender: osvalds.verners@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Osvalds Verners ------=_Part_2437104_990380783.1617682696831 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable PS: the gcc in this case is accessed through Cygwin terminal.=C2=A0 On Tuesday, April 6, 2021, 07:11:10 AM GMT+3, Osvalds Verners wrote: =20 =20 Hello David, thank you for getting back and apologies for a delayed response. I am using= gcc version=C2=A010.2.0. Best regards, Osvalds Verners On Tuesday, March 30, 2021, 03:26:36 AM GMT+3, David Hardy wrote: =20 =20 Hi Osvalds, What version of gcc are you using? Best regards,Dave --David J. Hardy, Ph.D.Beckman InstituteUniversity of Illinois at Urbana-Ch= ampaign405 N. Mathews Ave., Urbana, IL 61801dhardy@ks.uiuc.edu, http://www.= ks.uiuc.edu/~dhardy/ On Mar 25, 2021, at 12:37 PM, Osvalds Verners wrote: Dear Sir/Madam, I would like to report an error which occurred while compiling the=C2=A0NAM= D_2.14_Win64-multicore version using the following command: ./build charm++=C2=A0 multicore-win64 gcc --with-production --- In file included from bind.c:11:bind.c: In function =E2=80=98cmi_hwloc_allo= c_heap=E2=80=99:/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwlo= c/include/private/private.h:282:29: warning: implicit declaration of functi= on =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98siscanf=E2=80=99? [-Wim= plicit-function-declaration]=C2=A0 282 | #define hwloc_getpagesize() syscon= f(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~= ~/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/priva= te/private.h:282:29: note: in definition of macro =E2=80=98hwloc_getpagesiz= e=E2=80=99=C2=A0 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)= =C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~/NAMD_2.14_Sourc= e/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:= 37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared (first use in this fu= nction); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99?=C2=A0 282 | #define = hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~/NAMD_2.14_Sou= rce/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:28= 2:37: note: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99=C2= =A0 282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 = =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~= ~~~~/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/pr= ivate/private.h:282:37: note: each undeclared identifier is reported only o= nce for each function it appears in=C2=A0 282 | #define hwloc_getpagesize()= sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~/NAMD_2.14_Source/charm-6.10.2/= multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:37: note: in de= finition of macro =E2=80=98hwloc_getpagesize=E2=80=99=C2=A0 282 | #define h= wloc_getpagesize() sysconf(_SC_PAGE_SIZE)=C2=A0 =C2=A0 =C2=A0 |=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~~~~~~~~~~make[2]: *** [= Makefile:721: bind.lo] Error 1make[2]: Leaving directory '/NAMD_2.14_Source= /charm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'make[1]: *** [Makefile:418:= all-recursive] Error 1make[1]: Leaving directory '/NAMD_2.14_Source/charm-= 6.10.2/multicore-win64-gcc/tmp/hwloc'make: *** [Makefile:565: hwloc-target]= Error 2 --- Since I have not changed any source file, it could be considered as a poten= tial bug (did not find in the known bugs list though). Best regards, Osvalds Verners =20 =20 ------=_Part_2437104_990380783.1617682696831 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
PS: the gcc in this case is = accessed through Cygwin terminal. 

=20
=20
On Tuesday, April 6, 2021, 07:11:10 AM GMT+3, Osvalds V= erners <osvalds.verners@yahoo.com> wrote:


Hello David,

thank you for getting back and apologies for a d= elayed response. I am using gcc version 10.2.0.

B= est regards,

<= /div>
Osvalds Verners

=20
=20
On Tuesday, March 30, 2021, 03:26:36 AM GMT+3, David Ha= rdy <dhardy@ks.uiuc.edu> wrote:


Hi Osvalds,

What version of gcc are you using?

Best regards,
Dave

<= div class=3D"yiv7817777777">
--
David = J. Hardy, Ph.D.
B= eckman Institute
= University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801
=

On Mar 25, 2021, at 12:37 P= M, Osvalds Verners <osva= lds.verners@REMOVE_yahoo.com> wrote:

Dear Sir/Madam,

I would like to report an e= rror which occurred while compiling the = NAMD_2.14_Win64-multicore version using the following command:
=

./build charm++  multicore-win6= 4 gcc --with-production

---

In file included from bind.c:11:
bind.c: In function =E2=80=98cmi_hwloc_alloc_heap=E2=80= =99:
/NAMD_2.14_Source/charm-6.10.2/multi= core-win64-gcc/tmp/hwloc/include/private/private.h:282:29: warning: implici= t declaration of function =E2=80=98sysconf=E2=80=99; did you mean =E2=80=98= siscanf=E2=80=99? [-Wimplicit-function-declaration]
  282 | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)<= /div>
      |     = ;                     &nb= sp;  ^~~~~~~
/NAMD_2.14_Source/charm= -6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:29: not= e: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99
  282 | #define hwloc_getpagesize() sysconf(_SC_P= AGE_SIZE)
      |  &n= bsp;                     =      ^~~~~~~
/NAMD_2.14_So= urce/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:2= 82:37: error: =E2=80=98_SC_PAGE_SIZE=E2=80=99 undeclared (first use in this= function); did you mean =E2=80=98USN_PAGE_SIZE=E2=80=99?
  282 | #define hwloc_getpagesize() sysconf(_SC_PAG= E_SIZE)
      |  &nbs= p;                     &n= bsp;            ^~~~~~~~~~~~~
/NAMD_2.14_Source/charm-6.10.2/multicore-win64-gcc/tmp/h= wloc/include/private/private.h:282:37: note: in definition of macro =E2=80= =98hwloc_getpagesize=E2=80=99
  282 = | #define hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |           =                     &nbs= p;    ^~~~~~~~~~~~~
/NAMD_2.14_= Source/charm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h= :282:37: note: each undeclared identifier is reported only once for each fu= nction it appears in
  282 | #define= hwloc_getpagesize() sysconf(_SC_PAGE_SIZE)
      |              &= nbsp;                    =  ^~~~~~~~~~~~~
/NAMD_2.14_Source/ch= arm-6.10.2/multicore-win64-gcc/tmp/hwloc/include/private/private.h:282:37: = note: in definition of macro =E2=80=98hwloc_getpagesize=E2=80=99
  282 | #define hwloc_getpagesize() sysconf(_S= C_PAGE_SIZE)
      | =                     &nbs= p;              ^~~~~~~~~~~~~
make[2]: *** [Makefile:721: bind.lo] Error 1
<= div class=3D"yiv7817777777">make[2]: Leaving directory '/NAMD_2.14_Source/c= harm-6.10.2/multicore-win64-gcc/tmp/hwloc/src'
make[1]: *** [Makefile:418: all-recursive] Error 1
make[1]: Leaving directory '/NAMD_2.14_Source/charm-6.10.2/= multicore-win64-gcc/tmp/hwloc'
make: *** = [Makefile:565: hwloc-target] Error 2

---

=
Since I have not changed any sourc= e file, it could be considered as a potential bug (did not find in the know= n bugs list though).

Best regards,

Osvalds Verners

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boundary="_000_SG2PR04MB3898F8E8299990069FBD673EE1769SG2PR04MB3898apcp_" MIME-Version: 1.0 X-OriginatorOrg: research.iiit.ac.in X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SG2PR04MB3898.apcprd04.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 1a5bf3ed-f31a-4b75-04f7-08d8f8f62b21 X-MS-Exchange-CrossTenant-originalarrivaltime: 06 Apr 2021 12:19:04.1083 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 031a3bbc-cf7c-4e2b-96ec-867555540a1c X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: w9Cd6/3AmGpDthluIKzIy9pWYM4X2yEKB3i2tThqLOCvTKyUdzun7S+U8AOSiKqGTYm6Bd+JwDh1/s/ur+Ay9KK2/le1cDsP8hEq8tNJj4fZcuQ6yttIQGwtXoox3Wyv X-MS-Exchange-Transport-CrossTenantHeadersStamped: SG2PR04MB3223 X-Proofpoint-GUID: oqh5CtNG9PEvH30rJwjLo0jd18HPdxMC X-Proofpoint-ORIG-GUID: oqh5CtNG9PEvH30rJwjLo0jd18HPdxMC X-CLX-Response: 1TFkXGRwZEQpMehcaEQpZRBdsZm5FH2dQbB1ccxEKWFgXZR0BeEQbH3lNeE8 RCnhOF2FrEx1nfX4BQl1kEQp5TBdgE0VsWXNEAXhrHREKQ0gXBxkYGxEKQ1kXBx8YEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbEnEbBhkcdwYbHBoGEh9CGgYaBhsaGgYacRoQGncGGgYaBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdFW0IfaV5kbRN6b1xiGRpYYF1A ZkUaQE4bEmJ6TlJnaREKWFwXHwQaBBgYHAUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdyRUxwTxE KTVwXGB0TEQpMWhdoaU1raxEKTEYXb29ra2traxEKQk8XZk0YZH1YSBxbTG4RCkNaFx4aBBsaHQ QbGRgEHhkRCkJeFxsRCkReFxgRCkJcFxsRCkJLF2gfAXJeZW5oGEhmEQpCSRdhaxMdZ31+AUJdZ BEKQkUXaFt8XWB7TnJ4b1sRCkJOF2FrEx1nfX4BQl1kEQpCTBdlHQF4RBsfeU14TxEKQmwXb2Rp Q2VNGGVoGmkRCkJAF25lUHhCUl0ZTgVeEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxgRCnl DF2VQXnNhHAFGZmRLEQpZSxccGxgSEQpwaBdiekJbBQEBGxNEZhASGBEKcGgXY315engBYUFZZA EQBxkaEQpwaBdoXUZoZ0hTYVlYGxAHGRoRCnBoF2VPZG1rH1pfb1BzEAcZGhEKcGgXaXgeWmZEe mVHW28QBxkaEQpwbBdpa25hQm8eGmkabxAHGRoRCm1+FwcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 priorityscore=0 mlxlogscore=999 bulkscore=0 phishscore=0 spamscore=0 clxscore=363 impostorscore=0 malwarescore=0 mlxscore=0 suspectscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104030000 definitions=main-2104060085 domainage_hfrom=6128 X-Spam-Score: 0 X-Spam-OrigSender: shivansh.seth@research.iiit.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Shivansh Seth --_000_SG2PR04MB3898F8E8299990069FBD673EE1769SG2PR04MB3898apcp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I have been trying to run a simulation with 80 ABFs on different colvars (s= ide chain dihedrals). The 7ns simulation ran without any errors but the fin= al *.pmf, *.count, *.grad files were empty (0 bytes). All other files (colv= ar.state, restart, dcd) were non-empty and the simulation can be restarted = without any errors. I tried reducing the number of ABFs (and colvars) to 20= and the final files were non-empty in this case. However, on the fourth re= start, the files are again empty. I'm using the CUDA accelerated version of NAMD 2.13 with 2 GeForce RTX 208= 0 Ti and 20 CPU cores. The run command is as follows: namd2 +p20 +idlepoll +devices $CUDA_VISIBLE_DEVICES d1-4.conf > d1-4.log I have been stuck on this for a while now and any help would be much apprec= iated. Thank you Shivansh Seth --_000_SG2PR04MB3898F8E8299990069FBD673EE1769SG2PR04MB3898apcp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear All,

I have been trying to run a simulation with 80 ABFs on different colvars (s= ide chain dihedrals). The 7ns simulation ran without any errors but the fin= al *.pmf, *.count, *.grad files were empty (0 bytes). All other files (colv= ar.state, restart, dcd) were non-empty and the simulation can be restarted without any errors. I tried reducing t= he number of ABFs (and colvars) to 20 and the final files were non-empty in= this case. However, on the fourth restart, the files are again empty. = ;
I'm using the CUDA accelerated version of NAMD 2.13 with 2  GeForce RTX 2080 Ti and 20 CPU cores. The run command is as fol= lows:
namd2 +p20 +idlepoll +devices $CUDA_VISIBLE_DEVICES d1-4.conf > d1-4.log=

I have been stuck on this for a while now and any help would be much apprec= iated.

Thank you
Shivansh Seth
--_000_SG2PR04MB3898F8E8299990069FBD673EE1769SG2PR04MB3898apcp_-- From owner-namd-l@halifax.ks.uiuc.edu Tue Apr 6 09:07:56 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 136E7uC0007426; Tue, 6 Apr 2021 09:07:56 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 136E7uVL007425; Tue, 6 Apr 2021 09:07:56 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 136E7tvn007421; Tue, 6 Apr 2021 09:07:55 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 136E7teo007420; Tue, 6 Apr 2021 09:07:55 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 136E7mlL007413 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 6 Apr 2021 09:07:49 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 136DvRmd022712 for ; Tue, 6 Apr 2021 14:07:48 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=yasser.almeida-hernandez@uni-due.de Received: from mailoutzim.uni-due.de (mailoutzim.uni-due.de [134.91.56.37]) by mx0a-00007101.pphosted.com with ESMTP id 37rqrwh5e4-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 06 Apr 2021 14:07:48 +0000 Received: from EX5.win.uni-due.de (ns1-owa.uni-duisburg-essen.de [132.252.183.35]) by mailoutzim.uni-due.de (8.14.7/8.14.7) with ESMTP id 136E7j5H001605 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Tue, 6 Apr 2021 16:07:45 +0200 Received: from EX3.win.uni-due.de (134.91.18.65) by EX5.win.uni-due.de (132.252.183.50) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.2242.4; Tue, 6 Apr 2021 16:07:44 +0200 Received: from EX3.win.uni-due.de ([134.91.18.65]) by EX3.win.uni-due.de ([134.91.18.65]) with mapi id 15.01.2242.004; Tue, 6 Apr 2021 16:07:44 +0200 From: =?iso-8859-1?Q?Almeida-Hern=E1ndez=2C_Yasser=2C_Dr=2E?= To: "namd-l@ks.uiuc.edu" Subject: namd-l: Spherical restraints Thread-Topic: Spherical restraints Thread-Index: AQHXKu27y0PNj0vcJ0ab7qb8Va6J0A== Date: Tue, 6 Apr 2021 14:07:44 +0000 Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [132.252.183.35] Content-Type: multipart/alternative; boundary="_000_d76a76c373464151aaa716dede1765c4uniduede_" MIME-Version: 1.0 X-Virus-Scanned: Clam Anti Virus - http://www.clamav.net X-Spam-Scanned: SpamAssassin: 3.004000 - http://www.spamassassin.org X-Scanned-By: MIMEDefang 2.84 X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBduS39HeRJcWF5AQxEKWFgXaHxGZ05ucAFZWVI RCnhOF298QmxwTUJneFxZEQp5TBdvRHljckNZflxafBEKQ0gXBxgSGxEKQ1kXBxseExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseGXEfGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdNU09pfH0cQx8TexxHU29Sb0tYW3NMW3pOGn5BTkZkThEKWFwXHwQaBBgYHAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JFTQV6EQpNXBcbGBkRCkxaF3xpTU1NEQpFWRd7axEKTF8 XegUFBQUFBQUFBUMRCkxGF2lrEQpCTxd6Ql1SbGAbGllsbREKQ1oXGxkeBBMbBB8cBBkdEQpCXh cbEQpEXhcYEQpCRRdhRBsSZU57bBhYGBEKQk4Xb3xCbHBNQmd4XFkRCkJMF2h8RmdObnABWVlSE QpCbBdsRmtcfHNjUxp5aBEKQkAXZn1heAFAUlIeZ3gRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpa WBcbEQp5QxdjWV0fS3tbRWZ5GxEKcGcXbkB5HXtiHX1BemwQGRoRCnBoF20TWwFhXF9hRmhiEBk aEQpwaBdlf0tuelocG0NDHxAZGhEKcGgXbGBBUGx9UGhCSW0QGRoRCnBoF2VeRXpJUEtGWWtbEB kaEQpwaBdsWhJoR3l5XE9tRRAZGhEKcGwXbmFcbXhCaxoBAQEQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: gyeCVW6i59Q6myExEarqYfqPd0TkdlNd X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: gyeCVW6i59Q6myExEarqYfqPd0TkdlNd X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 priorityscore=0 bulkscore=0 phishscore=0 malwarescore=0 mlxlogscore=650 impostorscore=0 clxscore=163 spamscore=0 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104030000 definitions=main-2104060098 X-Spam-Score: 0 X-Spam-OrigSender: yasser.almeida-hernandez@uni-due.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?iso-8859-1?Q?Almeida-Hern=E1ndez=2C_Yasser=2C_Dr=2E?= --_000_d76a76c373464151aaa716dede1765c4uniduede_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I want to spherically restrain a ligand around a Cu2+ cation with harmonic = walls. For this, I am using the colvars module as: # Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ set config " colvars on colvar { name LIG_sphere distance { group1 {atomNumbers 704} # Cu2+ cation group2 {atomNumbersRange 707-734} # Ligand } } harmonicWalls { name LIG_sphere colvars HL outputEnergy on lowerWalls 0 upperWalls 15 forceConstant 1000 } " .. but it doesn't work. The ligand tumbles all around. Am I missing something? Any help will be appreciated. Best, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universit=E4tsstr. 2, 45117 Essen Email: yasser.almeida-hernandez@uni-due.de Phone: +49 201 183 2457 --_000_d76a76c373464151aaa716dede1765c4uniduede_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello,


I want to spherically restrain a ligand around a Cu2+ cation with ha= rmonic walls. For this, I am using the colvars module as:


# Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ set config "

colvars on

colvar {
  name LIG_sphere
  distance {
    group1 {atomNumbers 704}       =      # Cu2+ cation
    group2 {atomNumbersRange 707-734}    # Li= gand
  }
}

harmonicWalls {
    name LIG_sphere
    colvars HL
    outputEnergy on
    lowerWalls 0
    upperWalls 15
    forceConstant 1000
}
"


... but it doesn't work. The ligand tumbles all around.


Am I missing something? Any help will be appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=E4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" target=3D"_blank" = rel=3D"noopener noreferrer" id=3D"LPNoLP">&nb= sp;yasser.almeida-hernandez@uni-due.de

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charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Yasser, there are a few things to check, but the first one would be to make sure that you actually loaded that configuration. There will be a (fairly verbose) set of messages printed when you do. What you did there is setting a string variable "config" to contain the configuration text, which can be used in a Tcl script but you actually need to load it afterwards, e.g.: cv config ${config} On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < yasser.almeida-hernandez@uni-due.de> wrote: > Hello, > > > I want to spherically restrain a ligand around a Cu2+ cation with harmoni= c > walls. For this, I am using the colvars module as: > > > # Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ > set config " > > colvars on > > colvar { > name LIG_sphere > distance { > group1 {atomNumbers 704} # Cu2+ cation > group2 {atomNumbersRange 707-734} # Ligand > } > } > > harmonicWalls { > name LIG_sphere > colvars HL > outputEnergy on > lowerWalls 0 > upperWalls 15 > forceConstant 1000 > } > " > > > ... but it doesn't work. The ligand tumbles all around. > > > Am I missing something? Any help will be appreciated. > > > Best, > > Yasser > > > -- > Dr. Yasser Almeida-Hernandez > Postdoctoral Researcher > Computational Biochemistry group > T01 R03 D45 > Faculty of Biology > University of Duisburg-Essen > Universit=C3=A4tsstr. 2, 45117 Essen > Email: yasser.almeida-hernandez@uni-due.de > <%20yasser.almeida-hernandez@uni-due.de> > Phone: +49 201 183 2457 <+49%20201%20183%202457> > > --00000000000091f28c05bf4f2c21 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Yasser, there are a few things to check, but the fir= st one would be to make sure that you actually loaded that configuration.= =C2=A0 There will be a (fairly verbose) set of messages printed when you do= .

What you did there is setting a string variable "= config" to contain the configuration=C2=A0text, which can be used in a= Tcl script but you actually need to load it afterwards, e.g.:
cv config ${config}


<= br>
On Tue,= Apr 6, 2021 at 10:09 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-d= ue.de> wrote:

Hello,


I want to spherically restrain a ligand around a Cu2+ cation with harmon= ic walls. For this, I am using the colvars module as:


# Restraint the ligand in a sphere of r=3D15 AA around the Cu2+
set config "

colvars on

colvar {
=C2=A0 name LIG_sphere
=C2=A0 distance {
=C2=A0=C2=A0=C2=A0 group1 {atomNumbers 704} =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 =C2=A0# Cu2+ cation
=C2=A0=C2=A0=C2=A0 group2 {atomNumbersRange 707-734}=C2=A0=C2=A0 =C2=A0# Li= gand
=C2=A0 }
}

harmonicWalls {
=C2=A0=C2=A0 =C2=A0name LIG_sphere
=C2=A0=C2=A0 =C2=A0colvars HL
=C2=A0=C2=A0 =C2=A0outputEnergy on
=C2=A0=C2=A0 =C2=A0lowerWalls 0
=C2=A0=C2=A0 =C2=A0upperWalls 15
=C2=A0=C2=A0 =C2=A0forceConstant 1000
}
"


... but it doesn't work. The ligand tumbles all around.


Am I missing something? Any help will be appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=C3=A4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" rel=3D"noopener no= referrer" id=3D"gmail-m_3903892217099760008LPNoLP" target=3D"_blank">=C2=A0yasser.almeida-hernandez@uni-due.de
Phone:=C2=A0+49 201 183 2457=C2=A0

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Yes, that was the problem. The setting looks now like: set config " colvar { name LIG_sphere distance { group1 {atomNumbers 704} # Cu2+ cation group2 {atomNumbersRange 707-734} # Ligand } } harmonicWalls { colvars LIG_sphere outputEnergy on lowerWalls 0 upperWalls 15 forceConstant 1000 } " colvars on cv config ${config} Now, if I run it in my laptop it works well, but if I run it in a cluster w= ith GPU (namd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > $INP= .log), it writes -nan values: TIMING: 89000 CPU: 686.545, 0.0172745/step Wall: 737.674, 0.0173574/step,= 4.39239 hours remaining, 672.355469 MB of memory in use. ENERGY: 89000 nan 888064.2004 nan nan= nan 0.0000 0.0000 0.0000 = nan nan nan nan -nan = nan nan nan nan nan= nan Any thoughts? Best ________________________________ From: Giacomo Fiorin Sent: Tuesday, April 6, 2021 5:06:58 PM To: NAMD list; Almeida-Hern=E1ndez, Yasser, Dr. Subject: Re: namd-l: Spherical restraints Hello Yasser, there are a few things to check, but the first one would be t= o make sure that you actually loaded that configuration. There will be a (= fairly verbose) set of messages printed when you do. What you did there is setting a string variable "config" to contain the con= figuration text, which can be used in a Tcl script but you actually need to= load it afterwards, e.g.: cv config ${config} On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hern=E1ndez, Yasser, Dr. > wro= te: Hello, I want to spherically restrain a ligand around a Cu2+ cation with harmonic = walls. For this, I am using the colvars module as: # Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ set config " colvars on colvar { name LIG_sphere distance { group1 {atomNumbers 704} # Cu2+ cation group2 {atomNumbersRange 707-734} # Ligand } } harmonicWalls { name LIG_sphere colvars HL outputEnergy on lowerWalls 0 upperWalls 15 forceConstant 1000 } " .. but it doesn't work. The ligand tumbles all around. Am I missing something? Any help will be appreciated. Best, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universit=E4tsstr. 2, 45117 Essen Email: yasser.almeida-hernandez@uni-due.de Phone: +49 201 183 2457 --_000_4f376f98c7974d2c85d6ffa847289f12uniduede_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi Giacomo,


Thank you for your reply. Yes, that was the problem.


The setting looks now like:


set c= onfig "

colvar {
  nam= e LIG_sphere
  dis= tance {
 &nbs= p;  group1 {atomNumbers 704}         &nb= sp;   # Cu2+ cation
 &nbs= p;  group2 {atomNumbersRange 707-734}    # Ligand
  }
}
harmonicWa= lls {
 &nbs= p;  colvars LIG_sphere
 &nbs= p;  outputEnergy on
 &nbs= p;  lowerWalls 0
 &nbs= p;  upperWalls 15
 &nbs= p;  forceConstant 1000
} "

colvars on=
cv config = ${config}


Now, if I run it in my laptop it works well, but if I run it in a cluste= r with GPU (TIMIN= G: 89000  CPU: 686.545, 0.0172745/step  Wall: 737.674, 0.0173574/= step, 4.39239 hours remaining, 672.355469 MB of memory in use.
ENERGY:&nb= sp;  89000          =   nan    888064.2004      = ;      nan      &nbs= p;     nan       &nb= sp;         nan   &n= bsp;     0.0000      &nbs= p;  0.0000         0.0000 = ;           nan &nbs= p;            &= nbsp;  nan          =   nan           = ; nan           -nan            nan=             &nb= sp;    nan        &n= bsp;   nan         &= nbsp;  nan          =   nan           = ; nan


Any thoughts?

Best


From: Giacomo Fiorin <gi= acomo.fiorin@gmail.com>
Sent: Tuesday, April 6, 2021 5:06:58 PM
To: NAMD list; Almeida-Hern=E1ndez, Yasser, Dr.
Subject: Re: namd-l: Spherical restraints
 
Hello Yasser, there are a few things to check, but the fir= st one would be to make sure that you actually loaded that configuration.&n= bsp; There will be a (fairly verbose) set of messages printed when you do.

What you did there is setting a string variable "config" to = contain the configuration text, which can be used in a Tcl script but = you actually need to load it afterwards, e.g.:

cv config ${config}



On Tue, Apr 6, 2021 at 10:09 AM Almei= da-Hern=E1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-due.de> wrote:

Hello,


I want to spherically restrain a ligand around a Cu2+ cation with ha= rmonic walls. For this, I am using the colvars module as:


# Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ set config "

colvars on

colvar {
  name LIG_sphere
  distance {
    group1 {atomNumbers 704}       =      # Cu2+ cation
    group2 {atomNumbersRange 707-734}    # Li= gand
  }
}

harmonicWalls {
    name LIG_sphere
    colvars HL
    outputEnergy on
    lowerWalls 0
    upperWalls 15
    forceConstant 1000
}
"


... but it doesn't work. The ligand tumbles all around.


Am I missing something? Any help will be appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=E4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" rel=3D"noopener no= referrer" id=3D"gmail-m_3903892217099760008LPNoLP" target=3D"_blank"> yasser.almeida-hernandez@uni-due.de
Phone: +49 201 183 2457 

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charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Yasser, which NAMD version and build are you running on the GPU? Colvars doesn't make use of the GPU, but only of CPU code. So the only way that the CPU and GPU versions may differ is if the forces applied by Colvars are exceedingly large, and the GPU NAMD build can't deal with them correctly. Is the initial configuration compatible with the restraint? You can add outputEnergy to the restraint, or (if that's the only custom force in your workflow) look at the MISC column of the NAMD output. Giacomo On Tue, Apr 6, 2021 at 11:50 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < yasser.almeida-hernandez@uni-due.de> wrote: > Hi Giacomo, > > > Thank you for your reply. Yes, that was the problem. > > > The setting looks now like: > > > set config " > > colvar { > name LIG_sphere > distance { > group1 {atomNumbers 704} # Cu2+ cation > group2 {atomNumbersRange 707-734} # Ligand > } > } > > harmonicWalls { > colvars LIG_sphere > outputEnergy on > lowerWalls 0 > upperWalls 15 > forceConstant 1000 > } > " > > colvars on > cv config ${config} > > > Now, if I run it in my laptop it works well, but if I run it in a cluster > with GPU (namd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > > $INP.log), it writes -nan values: > > > TIMING: 89000 CPU: 686.545, 0.0172745/step Wall: 737.674, > 0.0173574/step, 4.39239 hours remaining, 672.355469 MB of memory in use. > ENERGY: 89000 nan 888064.2004 nan > nan nan 0.0000 0.0000 > 0.0000 nan nan nan > nan -nan nan nan > nan nan nan nan > > Any thoughts? > > Best > > ------------------------------ > *From:* Giacomo Fiorin > *Sent:* Tuesday, April 6, 2021 5:06:58 PM > *To:* NAMD list; Almeida-Hern=C3=A1ndez, Yasser, Dr. > *Subject:* Re: namd-l: Spherical restraints > > Hello Yasser, there are a few things to check, but the first one would be > to make sure that you actually loaded that configuration. There will be = a > (fairly verbose) set of messages printed when you do. > > What you did there is setting a string variable "config" to contain the > configuration text, which can be used in a Tcl script but you actually ne= ed > to load it afterwards, e.g.: > > cv config ${config} > > > > On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < > yasser.almeida-hernandez@uni-due.de> wrote: > >> Hello, >> >> >> I want to spherically restrain a ligand around a Cu2+ cation with >> harmonic walls. For this, I am using the colvars module as: >> >> >> # Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ >> set config " >> >> colvars on >> >> colvar { >> name LIG_sphere >> distance { >> group1 {atomNumbers 704} # Cu2+ cation >> group2 {atomNumbersRange 707-734} # Ligand >> } >> } >> >> harmonicWalls { >> name LIG_sphere >> colvars HL >> outputEnergy on >> lowerWalls 0 >> upperWalls 15 >> forceConstant 1000 >> } >> " >> >> >> ... but it doesn't work. The ligand tumbles all around. >> >> >> Am I missing something? Any help will be appreciated. >> >> >> Best, >> >> Yasser >> >> >> -- >> Dr. Yasser Almeida-Hernandez >> Postdoctoral Researcher >> Computational Biochemistry group >> T01 R03 D45 >> Faculty of Biology >> University of Duisburg-Essen >> Universit=C3=A4tsstr. 2, 45117 Essen >> Email: yasser.almeida-hernandez@uni-due.de >> <%20yasser.almeida-hernandez@uni-due.de> >> Phone: +49 201 183 2457 <+49%20201%20183%202457> >> >> --000000000000aa018a05bf50274d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi=C2=A0Yasser, which NAMD version and build are you runni= ng on the GPU?=C2=A0 Colvars doesn't make use of the GPU, but only of C= PU code.=C2=A0 So the only way that the CPU and GPU versions may differ is = if the forces applied by Colvars are exceedingly large, and the GPU NAMD bu= ild can't deal with them correctly.

Is the initial c= onfiguration compatible with the restraint?=C2=A0 You can add outputEnergy = to the restraint, or (if that's the only custom force in your workflow)= look at the MISC column of the NAMD output.

Giaco= mo

On Tue, Apr 6, 2021 at 11:50 AM Almeida-Hern=C3=A1ndez, Yasser, Dr.= <yasser.almeida-= hernandez@uni-due.de> wrote:

Hi Giacomo,


Thank you for your reply. Yes, that was the problem.


The setting looks now like:


set conf= ig "

colvar {
=C2=A0 name L= IG_sphere
=C2=A0 distan= ce {
=C2=A0=C2=A0= =C2=A0 group1 {atomNumbers 704} =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2= =A0=C2=A0=C2=A0 # Cu2+ cation
=C2=A0=C2=A0= =C2=A0 group2 {atomNumbersRange 707-734}=C2=A0=C2=A0 =C2=A0# Ligand<= br> =C2=A0 }
}

harmonicWalls= {
=C2=A0=C2=A0= =C2=A0 colvars LIG_sphere
=C2=A0=C2=A0 = =C2=A0outputEnergy on
=C2=A0=C2=A0 = =C2=A0lowerWalls 0
=C2=A0=C2=A0 = =C2=A0upperWalls 15
=C2=A0=C2=A0 = =C2=A0forceConstant 1000
}
"=

colvars on
cv config ${c= onfig}


Now, if I run it in my laptop it works well, but if I run it in a cluste= r with GPU (n= amd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > $INP.log), it writes -nan values:


TIMING: = 89000=C2=A0 CPU: 686.545, 0.0172745/step=C2=A0 Wall: 737.674, 0.0173574/ste= p, 4.39239 hours remaining, 672.355469 MB of memory in use.
ENERGY:=C2=A0= =C2=A0 89000=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 nan=C2=A0=C2=A0=C2=A0 888064.2004=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0000=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 0.0000=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00= 00=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 -nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 nan

Any thoughts?

Best


Fro= m: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Sent: Tuesday, April 6, 2021 5:06:58 PM
To: NAMD list; Almeida-Hern=C3=A1ndez, Yasser, Dr.
Subject: Re: namd-l: Spherical restraints
=C2=A0
Hello Yasser, there are a few things to check, but the fir= st one would be to make sure that you actually loaded that configuration.= =C2=A0 There will be a (fairly verbose) set of messages printed when you do= --000000000000aa018a05bf50274d-- From owner-namd-l@halifax.ks.uiuc.edu Tue Apr 6 13:12:57 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 136ICv58018741; Tue, 6 Apr 2021 13:12:57 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 136ICvhk018740; Tue, 6 Apr 2021 13:12:57 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 136ICv45018734; Tue, 6 Apr 2021 13:12:57 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 136ICu6v018733; Tue, 6 Apr 2021 13:12:56 -0500 (CDT) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 136ICsdG018724 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 6 Apr 2021 13:12:55 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_43F5271C-1021-4B5C-A6DD-25488F92AF23" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: namd-l: NAMD web/email outage today Tuesday 4/6 Message-Id: <36860DB8-892E-417C-AC96-DCBCEC536FFC@ks.uiuc.edu> Date: Tue, 6 Apr 2021 13:12:49 -0500 To: NAMD list X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_43F5271C-1021-4B5C-A6DD-25488F92AF23 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi Subscribers, Our building will have a total power outage that will affect the = delivery of NAMD-L emails, the NAMD web site, and other services until = sometime tomorrow Wednesday 4/7. The disruption in NAMD related services will begin in a few hours around = 5pm CDT (22:00 UTC), and we expect the outage to last until sometime = after 00:00 CDT (05:00 UTC) on Wednesday 4/7. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ --Apple-Mail=_43F5271C-1021-4B5C-A6DD-25488F92AF23 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
Hi Subscribers,

Our = building will have a total power outage that will affect the delivery of = NAMD-L emails, the NAMD web site, and other services until sometime = tomorrow Wednesday 4/7.

The disruption in NAMD related services will begin in a few = hours around 5pm CDT (22:00 UTC), and we expect the outage to last until = sometime after 00:00 CDT (05:00 UTC) on Wednesday 4/7.

Best regards,
Dave

=
--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

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boundary="000000000000de503f05bf52074d" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: UWohZ-3Xh3Pvj1-ojmq_YOKERK9OWRO1 X-CLX-Response: 1TFkXGxIbEQpMehcZGR4RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGRsTEQpDWRcHExgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBtxHhoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xf31FQnAHGXJCGXpcQBsHRUBHW3VzZWFveGETZX14ZRsRClhcFx8EGgQYGBwF GxoEGxsaBB8aBBseHxAbHhofGhEKXlkXckVBGAURCk1cFx8YGREKTFoXaXhpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGx0fEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9YeGARCkJs F2FfelMZQ0Qaeht+EQpCQBdgHX4ZT1J/E1hCXxEKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2M eQ3puRUlDbnBbEQpZSxcTGRwSEQpwZxdsSHJiYlseeUxLaBAeEhEKcGgXbUBAX0tvXR1vcFkQGh EKcGgXYngZRnNIAUJAEmIQGhEKcGgXZGcaYHp7c155YH4QGhEKcGgXZnpiflhoZU0dZWQQGhEKc GgXYmFvG0sYZ25tBWwQGhEKcGcXbkB5HXtiHX1BemwQHRoRCnBsF2Yfe1hcYgVLWGQfEB4SEQpw TBdtaGUZQVJ9exhFUhAaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: UWohZ-3Xh3Pvj1-ojmq_YOKERK9OWRO1 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=999 lowpriorityscore=0 phishscore=0 suspectscore=0 spamscore=0 adultscore=0 impostorscore=0 priorityscore=334 bulkscore=0 clxscore=181 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104060126 domainage_hfrom=9368 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000de503f05bf52074d Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Yasser, I can only speak for the logfile that you sent, but in that one the MISC energy is quite high, about 14,000 kcal/mol. (Note that with outputEnergy the energy of that restraint specifically would be written to the colvars.traj file, which will make it easier to confirm). Please do confirm that the initial configuration is really okay, and then check again against a run with a CPU-only build on the cluster to make sure. The restraint forces coming from Colvars will be identical: but how NAMD will deal with them differs between the CPU and GPU builds. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY *MISC* KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 235.1373 489.4649 479.7107 11.5964 -55823.9645 5575.4001 0.0000 *14283.9594* 9260.6370 -25488.0588 299.9977 -34748.6957 -25419.1273 299.9977 49231.0264 49231.6119 166940.3348 49231.0264 49231.6119 If the initial configuration is fine and that "MISC" value is something else and unrelated, then I would try to run a test with the colvar and its restraint defined but with "forceConstant 0", or something very small. Giacomo On Tue, Apr 6, 2021 at 1:28 PM Almeida-Hern=C3=A1ndez, Yasser, Dr. < yasser.almeida-hernandez@uni-due.de> wrote: > Hi Giacomo, > > > I was using NAMD_2.13_Linux-x86_64-multicore-CUDA for GPU, > NAMD_2.14b2_Linux-x86_64-multicore for CPU, and a restraining force of > 1000 kcal/mol. > > > The initial configuration (the one I am running in CPU in my laptop) is > fine a running. I tried now with NAMD_2.14b2_Linux-x86_64-multicore-CUDA > in my cluster and the same happened with the -nan values (with > outputEnergy =3D on). The MISC column in the output is 0.0000. So, no NAM= D > CUDA version for colvars. > > > Then, I tweaked the configuration file a bit (after son errors), used > NAMD_2.14b2_Linux-x86_64-multicore in my cluster (the same in my > laptop), the run starts but stops after one step, with a segfault error. > Attached are conf file, the log, and the slurm.out file. > > > Yasser > ------------------------------ > *From:* Giacomo Fiorin > *Sent:* Tuesday, April 6, 2021 6:17:11 PM > *To:* Almeida-Hern=C3=A1ndez, Yasser, Dr. > *Cc:* NAMD list > *Subject:* Re: namd-l: Spherical restraints > > Hi Yasser, which NAMD version and build are you running on the GPU? > Colvars doesn't make use of the GPU, but only of CPU code. So the only w= ay > that the CPU and GPU versions may differ is if the forces applied by > Colvars are exceedingly large, and the GPU NAMD build can't deal with the= m > correctly. > > Is the initial configuration compatible with the restraint? You can add > outputEnergy to the restraint, or (if that's the only custom force in you= r > workflow) look at the MISC column of the NAMD output. > > Giacomo > > On Tue, Apr 6, 2021 at 11:50 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < > yasser.almeida-hernandez@uni-due.de> wrote: > >> Hi Giacomo, >> >> >> Thank you for your reply. Yes, that was the problem. >> >> >> The setting looks now like: >> >> >> set config " >> >> colvar { >> name LIG_sphere >> distance { >> group1 {atomNumbers 704} # Cu2+ cation >> group2 {atomNumbersRange 707-734} # Ligand >> } >> } >> >> harmonicWalls { >> colvars LIG_sphere >> outputEnergy on >> lowerWalls 0 >> upperWalls 15 >> forceConstant 1000 >> } >> " >> >> colvars on >> cv config ${config} >> >> >> Now, if I run it in my laptop it works well, but if I run it in a cluste= r >> with GPU (namd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > >> $INP.log), it writes -nan values: >> >> >> TIMING: 89000 CPU: 686.545, 0.0172745/step Wall: 737.674, >> 0.0173574/step, 4.39239 hours remaining, 672.355469 MB of memory in use. >> ENERGY: 89000 nan 888064.2004 nan >> nan nan 0.0000 0.0000 >> 0.0000 nan nan nan >> nan -nan nan nan >> nan nan nan nan >> >> Any thoughts? >> >> Best >> >> ------------------------------ >> *From:* Giacomo Fiorin >> *Sent:* Tuesday, April 6, 2021 5:06:58 PM >> *To:* NAMD list; Almeida-Hern=C3=A1ndez, Yasser, Dr. >> *Subject:* Re: namd-l: Spherical restraints >> >> Hello Yasser, there are a few things to check, but the first one would b= e >> to make sure that you actually loaded that configuration. There will be= a >> (fairly verbose) set of messages printed when you do. >> >> What you did there is setting a string variable "config" to contain the >> configuration text, which can be used in a Tcl script but you actually n= eed >> to load it afterwards, e.g.: >> >> cv config ${config} >> >> >> >> On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < >> yasser.almeida-hernandez@uni-due.de> wrote: >> >>> Hello, >>> >>> >>> I want to spherically restrain a ligand around a Cu2+ cation with >>> harmonic walls. For this, I am using the colvars module as: >>> >>> >>> # Restraint the ligand in a sphere of r=3D15 AA around the Cu2+ >>> set config " >>> >>> colvars on >>> >>> colvar { >>> name LIG_sphere >>> distance { >>> group1 {atomNumbers 704} # Cu2+ cation >>> group2 {atomNumbersRange 707-734} # Ligand >>> } >>> } >>> >>> harmonicWalls { >>> name LIG_sphere >>> colvars HL >>> outputEnergy on >>> lowerWalls 0 >>> upperWalls 15 >>> forceConstant 1000 >>> } >>> " >>> >>> >>> ... but it doesn't work. The ligand tumbles all around. >>> >>> >>> Am I missing something? Any help will be appreciated. >>> >>> >>> Best, >>> >>> Yasser >>> >>> >>> -- >>> Dr. Yasser Almeida-Hernandez >>> Postdoctoral Researcher >>> Computational Biochemistry group >>> T01 R03 D45 >>> Faculty of Biology >>> University of Duisburg-Essen >>> Universit=C3=A4tsstr. 2, 45117 Essen >>> Email: yasser.almeida-hernandez@uni-due.de >>> <%20yasser.almeida-hernandez@uni-due.de> >>> Phone: +49 201 183 2457 <+49%20201%20183%202457> >>> >>> --000000000000de503f05bf52074d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Yasser, I can only speak for the logfile that you sent,= but in that one the MISC energy is quite high, about 14,000 kcal/mol.=C2= =A0 (Note that with outputEnergy the energy of that restraint specifically = would be written to the colvars.traj file, which will make it easier to con= firm).

Please do confirm that the initial configuration = is really okay, and then check again against a run with a CPU-only build on= the cluster to make sure.=C2=A0 The restraint forces coming from Colvars w= ill be identical: but how NAMD will deal with them differs between the CPU = and GPU builds.

ETITL= E: =C2=A0 =C2=A0 =C2=A0TS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 BOND =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0ANGLE =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0DIHED = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0IMPRP =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 ELECT =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0VDW =C2=A0 =C2= =A0 =C2=A0 BOUNDARY =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 MISC =C2=A0 = =C2=A0 =C2=A0 =C2=A0KINETIC =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 TOTAL =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 TEMP =C2=A0 =C2=A0 =C2=A0POTEN= TIAL =C2=A0 =C2=A0 =C2=A0 =C2=A0 TOTAL3 =C2=A0 =C2=A0 =C2=A0 =C2=A0TEMPAVG = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0PRESSURE =C2=A0 =C2=A0 =C2=A0GPRES= SURE =C2=A0 =C2=A0 =C2=A0 =C2=A0 VOLUME =C2=A0 =C2=A0 =C2=A0 PRESSAVG =C2= =A0 =C2=A0 =C2=A0GPRESSAVG

ENERGY: =C2=A0 =C2=A0 =C2=A0 0 =C2=A0 =C2= =A0 =C2=A0 235.1373 =C2=A0 =C2=A0 =C2=A0 489.4649 =C2=A0 =C2=A0 =C2=A0 479.= 7107 =C2=A0 =C2=A0 =C2=A0 =C2=A011.5964 =C2=A0 =C2=A0 =C2=A0 =C2=A0 -55823.= 9645 =C2=A0 =C2=A0 =C2=A05575.4001 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2= =A0 =C2=A0 14283.9594 =C2=A0 =C2=A0 =C2=A09260.6370 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 -25488.0588 =C2=A0 =C2=A0 =C2=A0 299.9977 =C2=A0 =C2=A0-34748= .6957 =C2=A0 =C2=A0-25419.1273 =C2=A0 =C2=A0 =C2=A0 299.9977 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A049231.0264 =C2=A0 =C2=A0 49231.6119 =C2=A0 =C2=A0166940= .3348 =C2=A0 =C2=A0 49231.0264 =C2=A0 =C2=A0 49231.6119

If the initial configuration is fine and that "MISC= " value is something else and unrelated, then I would try to run a tes= t with the colvar and its restraint defined but with "forceConstant 0&= quot;,=C2=A0or something very small.

Gi= acomo

On Tue, Apr 6, 2021 at 1:28 PM Almeida-Hern=C3=A1ndez, Ya= sser, Dr. <yasser.almeida-hernandez@uni-due.de> wrote:

Hi Giacomo,


I was using NAMD_2.13_Linux-x86_64-multicore-CUDA for GPU, N= AMD_2.14b2_Linux-x86_64-multicore for CPU, and a=C2=A0r= estraining force of 1000 kcal/mol.


The initial configuration (the one I am running in CPU in my laptop) is = fine a running. I tried now with NAMD_2.14b2_Linux-x86_64-multicore-CUDA in my clus= ter and the same happened with the -nan values (with outputEnergy= =C2=A0=3D on). The MISC column in the output is 0.0000. So, no NAMD CUDA version for colvars.


Then, I tweaked the configuration file a bit (after son errors), u= sed NAMD_2.14b2_Linux-x86_64-multicore in my cluster (the s= ame in my laptop),=C2=A0the run starts but stops after one step, with a seg= fault error. Attached are conf file, the log, and the slurm.out file.


Yasser


From: Giacomo Fiorin <giacomo.fiorin@gmail.com> Sent: Tuesday, April 6, 2021 6:17:11 PM
To: Almeida-Hern=C3=A1ndez, Yasser, Dr.
Cc: NAMD list
Subject: Re: namd-l: Spherical restraints
=C2=A0
Hi=C2=A0Yasser, which NAMD version and build are you runni= ng on the GPU?=C2=A0 Colvars doesn't make use of the GPU, but only of C= PU code.=C2=A0 So the only way that the CPU and GPU versions may differ is = if the forces applied by Colvars are exceedingly large, and the GPU NAMD build can't deal with them correctly.

Is the initial configuration compatible with the restraint?=C2=A0 You = can add outputEnergy to the restraint, or (if that's the only custom fo= rce in your workflow) look at the MISC column of the NAMD output.

Giacomo

On Tue, Apr 6, 2021 at 11:50 AM Almei= da-Hern=C3=A1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-due.de>= ; wrote:

Hi Giacomo,


Thank you for your reply. Yes, that was the problem.


The setting looks now like:


set conf= ig "

colvar {
=C2=A0 name L= IG_sphere
=C2=A0 distan= ce {
=C2=A0=C2=A0= =C2=A0 group1 {atomNumbers 704} =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2= =A0=C2=A0=C2=A0 # Cu2+ cation
=C2=A0=C2=A0= =C2=A0 group2 {atomNumbersRange 707-734}=C2=A0=C2=A0 =C2=A0# Ligand<= br> =C2=A0 }
}

harmonicWalls= {
=C2=A0=C2=A0= =C2=A0 colvars LIG_sphere
=C2=A0=C2=A0 = =C2=A0outputEnergy on
=C2=A0=C2=A0 = =C2=A0lowerWalls 0
=C2=A0=C2=A0 = =C2=A0upperWalls 15
=C2=A0=C2=A0 = =C2=A0forceConstant 1000
}
"=

colvars on
cv config ${c= onfig}


Now, if I run it in my laptop it works well, but if I run it in a cluste= r with GPU (n= amd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > $INP.log), it writes -nan values:


TIMING: = 89000=C2=A0 CPU: 686.545, 0.0172745/step=C2=A0 Wall: 737.674, 0.0173574/ste= p, 4.39239 hours remaining, 672.355469 MB of memory in use.
ENERGY:=C2=A0= =C2=A0 89000=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 nan=C2=A0=C2=A0=C2=A0 888064.2004=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0000=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 0.0000=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00= 00=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 -nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 nan= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 nan=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 nan

Any thoughts?

Best


From: Giacomo Fiori= n <giacomo= .fiorin@gmail.com>
Sent: Tuesday, April 6, 2021 5:06:58 PM
To: NAMD list; Almeida-Hern=C3=A1ndez, Yasser, Dr.
Subject: Re: namd-l: Spherical restraints
=C2=A0
Hello Yasser, there are a few things to check, but the fir= st one would be to make sure that you actually loaded that configuration.= =C2=A0 There will be a (fairly verbose) set of messages printed when you do= --000000000000de503f05bf52074d-- From owner-namd-l@halifax.ks.uiuc.edu Fri Apr 9 06:21:32 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 139BLWnj004073; Fri, 9 Apr 2021 06:21:32 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 139BLWaE004072; Fri, 9 Apr 2021 06:21:32 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 139BLVBj004068; Fri, 9 Apr 2021 06:21:31 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 139BLVeL004067; 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Fri, 9 Apr 2021 13:21:17 +0200 From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Subject: Re: namd-l: An running issue in eABF-replica calculations To: namd-l@ks.uiuc.edu, =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= References: <61971be9-e361-61a4-6c79-270b9047f83a@physik.uni-kl.de> Message-ID: <99f82191-ca74-586f-09c0-c32d11fd90af@physik.uni-kl.de> Date: Fri, 9 Apr 2021 13:20:59 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.9.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------5F7B22DA2426A78E1E409958" Content-Language: de-DE X-Spam-Status: No, hits=0.185, tests=HELO_MISC_IP=0.173,HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.001,T_REMOTE_IMAGE=0.01,URI_DOTEDU=0.001 X-Spam-Score: (0.185) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: TYe1hN6v_rTiDfUcfZY_dLbbB3bR6fP1 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxISEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBx8YExEKQ1kXBxsfEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwScR4dEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF35zTxtCZBxcdVh+Q25Mf0lMcHN1TmZISGgZSHgcTHobEQpYXBcfBBoEGBgdBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JaThtnEQpNXBcbHR0RCkxaF3xpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2RBEmkSZ1kcGnpOEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXHBEKeUMXZxJhWRpoHUJeZWMRCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdleGNBbwFQYR1 8TBAZGhEKcGgXbBtAGGdCE3pEQBwQGRoRCnBoF3prYQUcW2dieHAZEBkaEQpwaBdrUHxFYWBucF lFTxAZGhEKcGgXa2ZsfUVlY2tzWhsQGRoRCnB9F2tOU0ROGlxQGH9kEBkaEQpwZxdjXFBhG1Jta BxhaRAZGhEKcGcXbkB6fXtuZWdESBsQGRoRCnB9F29TZ31DQ0sZUB5mEBkaEQpwfRdkSRtdEhhS T2ByGRAZGhEKcGcXYUtpemFCeUAeS30QGRoRCnB9F2BveGBDHB15RWgbEBkaEQpwfxdjWGxIW0c aex1zGxAbGxoRCnBfF29lSW0YXGtLQRgbEBkaEQpwfxdhZm9bGmdkQkgdWxAbGx0RCnBfF2NiEl BIY3gffEJ9EBITEQpwfxdlWHIYHUkYXkZpfBASEhEKcF8XZl8SeENmW3prBVoQGRoRCnBsF3ofe HlveExDX3BEEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: TYe1hN6v_rTiDfUcfZY_dLbbB3bR6fP1 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 malwarescore=0 bulkscore=0 mlxlogscore=999 spamscore=0 mlxscore=0 impostorscore=0 priorityscore=0 adultscore=0 suspectscore=0 clxscore=188 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104090083 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------5F7B22DA2426A78E1E409958 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable On 3/17/2021 2:52 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote: > On Tue, 9 Mar 2021 at 00:26, Ren=C3=A9 Hafner TUK=20 > > wrote: > > Thanks a lot J=C3=A9r=C3=B4me! > > To understand this correctly: > > * This means that when using MW-ABF the walkers are > benefitting from each other (as gradient counts are > shared, well reflected in the files) > > Yes. > > * but in case of MW-eABF sharing of eABF data is not (and > was never?) shared (as it was not reflected in the files > before and therefore also not internally?!) or do/did the > walkers still benefit from each other? > > MW-eABF is not that different from ABF, it's just that the ABF=20 > quantities (mainly the biasing force itself) pertain to the extended=20 > coordinate. Those are shared exactly as in standard mwABF, because=20 > they are represented the same way in the implementation. > The data for the *unbiased free energy estimators* is a separate=20 > question: it is not shared in the current state of the code, and in a=20 > sense it does not need to be shared during the simulation, as these=20 > estimators are really a matter of post-processing. Anything that is=20 > done on the fly is just for convenience. 1. Does that mean that the output of multiple replicas simulations=20 (using shared (e)ABF) MUST be merged in order for results to be valid since for a single replica the "actually" applied biasing force does is=20 different from the corresponding content of the (zcount/zgrad) output=20 files produced by this walker? 2. What is actually printed to the outputname.grad/count file (named the=20 same way as in plain abf output) when using eABF, this is the=20 gradient/counts of the fictious particle, correct? > > =C2=A0=C2=A0=C2=A0 * Then latest literature would be a bit mi= sleading > when stating usage of MW-eABF. > > Is there something else than the QM/MM tutorial that=C2=A0mentions it? =C2=A0It is stated in the paper about WtM-eABF Method (Taming Rugged Free= =20 Energy Landscapes Using an Average Force=20 https://urldefense.com/v3/__http://dx.doi.org/10.1021/acs.accounts.9b00473_= _;!!DZ3fjg!pkIvIjJO9NBIUsI0DIFDIqoEmOIR-ot_UY-KI0AJeqikGqC7TOCwTJ2CJzClaXl3= 9A$ ) > On 3/8/2021 11:41 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote: >> Dear Hua Hao and Ren=C3=A9, >> >> I was not aware of that use of eABF in multiple-walker form in >> the tutorial. That is not a documented/supported feature, and >> there is a little work to properly combine the data. >> Anyway, I have just pushed a commit that partly reverts the >> previous one. What remains is that ABF files are written after >> sharing, so the plain ABF data should be the same for all replicas. >> >> Best regards, >> J=C3=A9r=C3=B4me >> >> On Mon, 1 Mar 2021 at 16:28, hua hao > > wrote: >> >> Thanks,Abhishek. >> >> I try to do it,=C2=A0but the problem=C2=A0is still present. >> >> Abhishek Acharya > >=E4=BA=8E2021=E5=B9=B43=E6=9C= =881=E6=97=A5 >> =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5=86=99=E9=81=93=EF=BC= =9A >> >> Hi, >> >> Maybe you can try something like this. >> mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout >> output_eABF/%d/job00.log >> >> Abhi >> >> >> Virus-free. https://urldefense.com/v3/__http://www.avast.co= m__;!!DZ3fjg!pkIvIjJO9NBIUsI0DIFDIqoEmOIR-ot_UY-KI0AJeqikGqC7TOCwTJ2CJzA4nM= YwsQ$=20 >> >> >> >> >> On Mon, Jan 4, 2021 at 6:02 PM hua hao >> > wrote: >> >> Hi NAMD developers and users, >> >> I am learning Tutorial_QMMM_String_eABF recently, >> which was introduced to be an advanced tutorial for >> QMMM in NAMD page >> (http://www.ks.uiuc.edu/Research/qmmm/ >> ). >> >> When running the eABF job by "mpirun -n 28 namd2 >> +replicas 14 eABF.tcl +stdout >> output_eABF/%1d/job00.%1d.log", it is strange that >> some necessary files with the suffix .grad, .count, >> .pmf, .zcount, and .zgrad were only present in the >> first=C2=A0replica (i..e 0), but not in other=C2=A0repli= cas >> (i.e. 1-13).=C2=A0NAMD-2.14 and=C2=A0NAMD-Gib-2020-12-07= =C2=A0were >> used to perform the above calculations, and these >> packages were both complied using openmpi-3.1.4 build >> on Intel-icc. We also tried the pre-compiled >> Linux-x86_64-netlrts and=C2=A0Linux-x86_64-verbs, the >> error was still present. >> >> Normally, these files should appear in each=C2=A0replica. >> >> Could you help me with this issue? Thank you very much. >> >> *Hua Hao* >> > --=20 > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------5F7B22DA2426A78E1E409958 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable


On 3/17/2021 2:52 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote:

On Tue, 9 Mar 2021 at 00:26, Ren=C3=A9 Hafner TUK = <hamburge@physik.uni-kl.de> wrote:

Thanks a lot J=C3=A9r=C3=B4me!

To understand this correctly:

* This means that when using MW-ABF the walkers are benefitting from each other (as gradient counts are shared, well reflected in the files)

Yes.=C2=A0

* but in case of MW-eABF sharing of eABF data is not (and was never?) shared (as it was not reflected in the files before and therefore also not internally?!) or do/did the walkers still benefit from each other?

MW-eABF is not that different from ABF, it's just that the ABF quantities (mainly the biasing force itself) pertain to the extended coordinate. Those are shared exactly as in standard mwABF, because they are represented the same way in the implementation.
The data for the *unbiased free energy estimators* is a separate question: it is not shared in the current state of the code, and in a sense it does not need to be shared during the simulation, as these estimators are really a matter of post-processing. Anything that is done on the fly is just for convenience.


1. Does that mean that the output of multiple replicas simulations (using shared (e)ABF) MUST be merged in order for results to be valid

since for a single replica the "actually" applied biasing force does is different from the corresponding content of the (zcount/zgrad) output files produced by this walker?


2. What is actually printed to the outputname.grad/count file (named the same way as in plain abf output) when using eABF, this is the gradient/counts of the fictious particle, correct?



=C2=A0=C2=A0=C2=A0 * Then latest literature would be a= bit misleading when stating usage of MW-eABF.

Is there something else than the QM/MM tutorial that=C2=A0mentions it?

=C2=A0It is stated in the paper about WtM-e= ABF Method (Taming Rugged Free Energy Landscapes Using an Average Force http://dx.doi.org/10.1021/acs.accounts.9b0= 0473 )







=C2=A0
On 3/8/2021 11:41 PM, J=C3=A9r=C3=B4me H=C3=A9nin wrote:=
Dear Hua Hao and Ren=C3=A9,

I was not aware of that use of eABF in multiple-walker form in the tutorial. That is not a documented/supported feature, and there is a little work to properly combine the data.
Anyway, I have just pushed a commit that partly reverts the previous one. What remains is that ABF files are written after sharing, so the plain ABF data should be the same for all replicas.

Best regards,
J=C3=A9r=C3=B4me

On Mon, 1 Mar 2021 at 16:28, hua hao <haohua0116@gmail.com> wrote:
Thanks, Abhishek.
I try to do it,=C2=A0but the problem=C2=A0is still present.=C2=A0

Abhishek Acharya <= abhi117acharya@gmail.com>=E4=BA=8E2021=E5=B9=B43=E6=9C=881=E6=97=A5 =E5=91=A8=E4=B8=80=E4=B8=8A=E5=8D=888:50=E5= =86=99=E9=81=93=EF=BC=9A
Hi,

Maybe you can try something like this.
mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%d/job00.log

Abhi

3D""= Virus-free. www.avas= t.com

On Mon, Jan 4, 2021 at 6:02 PM hua hao <haohua0116@gma= il.com> wrote:
Hi NAMD developers and users,

I am learning Tutorial_QMMM_Str= ing_eABF recently, which was introduced to be an advanced tutorial for QMMM in NAMD page (http://www.ks.uiuc.edu/Research/= qmmm/).

When running the eABF job by "mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout output_eABF/%1d/j= ob00.%1d.log", it is strange that some necessary files with the suffix .grad, .count, .pmf, .zcount, and .zgrad were only present in the first=C2=A0replica (i..e 0), but not in other=C2=A0replic= as (i.e. 1-13).=C2=A0NAMD-= 2.14 and=C2=A0NAMD-Gib-2020-12-07=C2=A0were used to perform the above calculatio= ns, and these packages were both complied using openmpi-3.1.4 build on Intel-icc. We also tried the pre-compiled Linux-x86_64-netl= rts and=C2=A0Linux-x86_64-verbs, the error was still present.

Normally, these files should appear in each=C2=A0replica= .

Could you help me with this issue? Thank you very much.

= Hua Hao

--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--------------5F7B22DA2426A78E1E409958-- From owner-namd-l@halifax.ks.uiuc.edu Mon Apr 12 05:33:32 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13CAXW8L012185; Mon, 12 Apr 2021 05:33:32 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13CAXWcf012184; Mon, 12 Apr 2021 05:33:32 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13CAXV6i012180; Mon, 12 Apr 2021 05:33:31 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13CAXVel012179; Mon, 12 Apr 2021 05:33:31 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13CAXI81012171 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 12 Apr 2021 05:33:19 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13CARxCq031271 for ; Mon, 12 Apr 2021 10:33:18 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 37u409y4hx-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 12 Apr 2021 10:33:18 +0000 Received: from [IPv6:2a02:810c:300:6724:9c1d:fde0:b6e6:d446] ([IPv6:2a02:810c:300:6724:9c1d:fde0:b6e6:d446]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 13CAX8bF045100 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 12 Apr 2021 12:33:15 +0200 Subject: Re: namd-l: Hydrogen Mass Repartitioning To: namd-l@ks.uiuc.edu, "Gumbart, JC" References: <06BB7A88-A529-458F-B1A2-E3E4FF819F9B@physics.gatech.edu> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <2858dd33-fd4a-7a45-d296-6d2bce8601e2@physik.uni-kl.de> Date: Mon, 12 Apr 2021 12:33:10 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.9.0 In-Reply-To: <06BB7A88-A529-458F-B1A2-E3E4FF819F9B@physics.gatech.edu> Content-Type: multipart/alternative; boundary="------------02EE33A42FACD6BA05D4D9C1" Content-Language: de-DE X-Spam-Status: No, hits=1.493, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,HTML_OBFUSCATE_05_10=0.001,NICE_REPLY_A=-0.001,URI_DOTEDU=1.491 X-Spam-Score: * (1.493) X-Spam-Flag: NO X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: oYvnjLiyFGrVMkEXGt9QvSMgrf3XLYqs X-Proofpoint-GUID: oYvnjLiyFGrVMkEXGt9QvSMgrf3XLYqs X-CLX-Response: 1TFkXGxwfEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsSHxEKQ1kXBxsdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4fcR8fEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0VzXERAZkNTbG1YfGdBb3JtXhN7XHlnTVhMGXJmc1tZEQpYXBcfBBoEGBgdBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3JbSUtgEQpNXBcZGhMRCkxaF3xpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2hGG14aeBoSZGFgEQpCWBdnc2VzQG5hYUxdYhEKWlgX EhEKeUMXYhlyTUF6Tlp8RmcRCnBnF3pNTUhJfWdzExppEBkaEQpwaBdkcHh9HEtZZVx+WhAZGhE KcGgXZF14eXNnRmAbWwEQGRoRCnBoF2IZex9MXV5YBXpbEBsaGBEKcGgXYRxkGGFQcmFaWUIQGR oRCnBoF2RLY19+RkZcbR5YEBkaEQpwfRducF1SAUBQG35aYBAZGhEKcH0XZX9TbW1ffW9kR0YQG RoRCnB9F2lbXUFgHURhWWceEB8TEQpwZxdkehIFaHpIAXl5exAZGhEKcGcXZGRnfm9zfHtCG1MQ GRoRCnBnF2lDblABWXNHAR5TEBkaEQpwZxdseWtHX3tkXmJpYBAZGhEKcH8XehpbW3AYZ1lYa2U QGxsTEQpwXxd6YEJrBWMceEhfZBAbGRsRCnB/F2UZeWZeR2kbZE9zEB0SEQpwXxdpHkdpbGBIAW Z4TBAZGhEKcH8XYkZrQRIaBQVLZ0UQEhIRCnBfF20dfHMeTmsSGnNhEB8fEQpwbBd6H3h5b3hMQ 19wRBAZGhEKbX4XGhEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 spamscore=0 mlxscore=0 suspectscore=0 priorityscore=0 adultscore=0 phishscore=0 mlxlogscore=999 clxscore=165 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104120069 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------02EE33A42FACD6BA05D4D9C1 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: Quoted-printable Dear Mr. Gumbart, =A0=A0=A0 why is it that with HMR we increase/repartition the mass of/to=20 hydrogens but then keeping all of them fixed using rigidBonds (according=20 to example NAMD configfile in SI of your paper mentioned below)? =A0=A0 =A0=A0 Couldn't we have increase ts to 4fs in the first place when = we=20 keep all hydrogens fixed anyway? Kind regards Ren=E9 Hafner On 12/4/2020 4:57 AM, Gumbart, JC wrote: > Also, have a look at https://urldefense.com/v3/__https://pubmed.ncbi.nlm.= nih.gov/31265271/__;!!DZ3fjg!u8OlYz6NSYuOtTS1YGhu2-uD3HiVYubDh85Fof-mYvFDUz= vIZv2MoYO_68s6tKby0g$=20=20 > and the supplemental files=20 > for examples. > > Best, > JC > >> On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff=20 >> > wrote: >> >> Ask the suitable person whose details are visible in the=20 >> webpagenamd-l: Re: Hydrogen Mass Repartitioning in NAMD (uiuc.edu)=20 >> >> Sent fromMail for=20 >> Windows 10 >> *From:*McGuire, Kelly >> *Sent:*04 December 2020 08:38 >> *To:*namd-l@ks.uiuc.edu >> *Subject:*namd-l: Hydrogen Mass Repartitioning >> Does anyone have a tutorial on how to implement hydrogen mass=20 >> repartitioning in NAMD? I have never used this method before. Thanks! >> >> /Dr. Kelly L. McGuire/ >> >> /PhD=A0Biophysics/ >> >> /Department of Physiology and Developmental Biology/ >> >> /Brigham Young University/ >> >> /LSB 3050/ >> >> /Provo, UT 84602/ >> > --=20 -- Dipl.-Phys. Ren=E9 Hafner TU Kaiserslautern Germany --------------02EE33A42FACD6BA05D4D9C1 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: Quoted-printable

Dear Mr. Gumbart,

=A0=A0=A0 why is it that with HMR we increase/repartition the mass of/to hydrogens but then keeping all of them fixed using rigidBonds (according to example NAMD configfile in SI of your paper mentioned below)?

=A0=A0 =A0=A0 Couldn't we have increase ts to 4fs in the first place= when we keep all hydrogens fixed anyway?

Kind regards

Ren=E9 Hafner

On 12/4/2020 4:57 AM, Gumbart, JC wrote:
Also, have a look at=A0https://pubmed.ncbi.nlm.nih.gov/31265271/=A0 and the supplemental files for examples.

Best,
JC

On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff <ms7.umar185@gmail.com> wrote:

=A0
Sent from=A0= Mail=A0for Windows 1= 0
=A0
From:=A0McGuire, Kelly
Sent:=A004 December 2020 08:38
To:= =A0namd-l@ks.uiuc.edu
Subject:=A0namd-= l: Hydrogen Mass Repartitioning
=A0
Does anyone have a tutorial on how to implement hydrogen mass repartitioning in NAMD? I have never used this method before. Thanks!
=A0

Dr. Kelly L. McGuire=

PhD=A0Biophysics=

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602<= /p>


--=20
--
Dipl.-Phys. Ren=E9 Hafner
TU Kaiserslautern
Germany
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boundary="000000000000e465f205bfc526d2" X-Proofpoint-GUID: YQIS5hSPnHRkG1eJWP-aK8hMyMIsVqkn X-Proofpoint-ORIG-GUID: YQIS5hSPnHRkG1eJWP-aK8hMyMIsVqkn X-CLX-Response: 1TFkXGx0dEQpMehcZHBoRCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGRsZEQpDWRcHGx0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHx1xGRwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xc3tjeR9CeXpEYnhBbRtPYH16B0thEkJnU2djWXxbQUQRClhcFx8EGgQYGB0F GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyW05BWBEKTVwXGBsYEQpMWhd8aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB 8ZEQpCXhcbEQpEXhcYEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja 3sTWH4aX14RCkJFF2BgSxlmRGNeXlB4EQpCThdjU2NrexNYfhpfXhEKQkwXelhrTGNlXVsFRHAR CkJsF2Z4bn4YZGVBElh/EQpCQBdoRhteGngaEmRhYBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClp YFx0RCnlDF2IZck1Bek5afEZnEQpZSxcTGR0eEQpwZxdgGUZFe05HGW1cRRAeEhEKcGgXbGNJeW xJSGB6W1IQGRoRCnBoF3pwGmFgRntQeU5DEBkaEQpwaBdjbFtrRGRlAWxETxAZGhEKcGgXY1xna QEZTVlNbBgQGRoRCnBoF2FnQVNoH0xaaGNLEBkaEQpwfRdgGEUbAUgaExp5UhAcGhEKcH0XbnBd UgFAUBt+WmAQGRoRCnB9F2BCXWFpYnsSfmRYEB4SEQpwZxd6TU1ISX1ncxMaaRAeEhEKcH0XZX9 TbW1ffW9kR0YQHhIRCnB9F2xJGkRLQ0hmGFwFEB4SEQpwZxdkehIFaHpIAXl5exAeEhEKcGcXZG Rnfm9zfHtCG1MQHhIRCnBnF2lDblABWXNHAR5TEB4SEQpwfxdoel9iHn5bBWRSGxAcGhEKcF8XY BMZZktObE5FU3sQHBoRCnB/F3oaW1twGGdZWGtlEBsbEhEKcF8XemBCawVjHHhIX2QQGxgTEQpw fxdhZm9bGmdkQkgdWxAbGBoRCnBfF2NiElBIY3gffEJ9EBIdEQpwfxdlGXlmXkdpG2RPcxAbGh4 RCnBfF2keR2lsYEgBZnhMEB4SEQpwbBdgaUdnaVJff194TBAeEhEKcEwXbWhlGUFSfXsYRVIQGR oRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 spamscore=0 lowpriorityscore=0 suspectscore=0 priorityscore=360 mlxlogscore=994 impostorscore=0 phishscore=0 bulkscore=0 clxscore=177 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104120080 domainage_hfrom=9374 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --000000000000e465f205bfc526d2 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable While keeping bonds with hydrogen atoms rigid, eliminates the need to represent the high frequency motions of those bonds, it does not slow down the rotation of the hydrogen atoms around their heavier bond partners. Axel. -- Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://go= o.gl/1wk0__;!!DZ3fjg!o9KbzmsK-IhYkBZmqCx3ieRid6lFDkr-s7pZYzOzsJzAViX-GiVSNk= 0l86cHx9T76w$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste, Italy On Mon, Apr 12, 2021, 06:35 Ren=C3=A9 Hafner TUK wrote: > Dear Mr. Gumbart, > > why is it that with HMR we increase/repartition the mass of/to > hydrogens but then keeping all of them fixed using rigidBonds (according = to > example NAMD configfile in SI of your paper mentioned below)? > > Couldn't we have increase ts to 4fs in the first place when we keep > all hydrogens fixed anyway? > > Kind regards > > Ren=C3=A9 Hafner > On 12/4/2020 4:57 AM, Gumbart, JC wrote: > > Also, have a look at https://urldefense.com/v3/__https://pubmed.ncbi.nlm.= nih.gov/31265271/__;!!DZ3fjg!o9KbzmsK-IhYkBZmqCx3ieRid6lFDkr-s7pZYzOzsJzAVi= X-GiVSNk0l86d7wVJNfw$=20 > > and the supplemental files for examples. > > Best, > JC > > On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff > wrote: > > Ask the suitable person whose details are visible in the webpage namd-l: > Re: Hydrogen Mass Repartitioning in NAMD (uiuc.edu) > > > Sent from Mail > > for Windows 10 > > *From: *McGuire, Kelly > *Sent: *04 December 2020 08:38 > *To: *namd-l@ks.uiuc.edu > *Subject: *namd-l: Hydrogen Mass Repartitioning > > Does anyone have a tutorial on how to implement hydrogen mass > repartitioning in NAMD? I have never used this method before. Thanks! > > > *Dr. Kelly L. McGuire* > > *PhD Biophysics* > > *Department of Physiology and Developmental Biology* > > *Brigham Young University* > > *LSB 3050* > > *Provo, UT 84602* > > > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --000000000000e465f205bfc526d2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
While keeping bonds with hydrogen atoms rigid, eliminates= the need to represent the high frequency motions of those bonds, it does n= ot slow down the rotation of the hydrogen atoms around their heavier bond p= artners.=C2=A0

Axel.=C2=A0
--
Dr. Axel Kohlmeyer akohlmey@g= mail.com http://goo.gl/1wk0
College of Science & Technology, Temple Univ= ersity, Philadelphia PA, USA
International Centre for Theoretical Physic= s, Trieste, Italy

On Mon, Apr 12, 2021, 06:35 Ren=C3=A9 Hafner TUK <= ;hamburge@physik.uni-kl.de= > wrote:
=20=20 =20=20=20=20 =20=20

Dear Mr. Gumbart,

=C2=A0=C2=A0=C2=A0 why is it that with HMR we increase/repartition t= he mass of/to hydrogens but then keeping all of them fixed using rigidBonds (according to example NAMD configfile in SI of your paper mentioned below)?

=C2=A0=C2=A0 =C2=A0=C2=A0 Couldn't we have increase ts to 4fs in= the first place when we keep all hydrogens fixed anyway?

Kind regards

Ren=C3=A9 Hafner

On 12/4/2020 4:57 AM, Gumbart, JC wrote:
=20=20=20=20=20=20 Also, have a look at=C2=A0https://pubmed.ncbi.nlm.nih.gov/31265271/=C2=A0 and the supplemental files for examples.

Best,
JC

On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff <ms7.umar185@gmail.com> wrote:

Ask the suitable person whose details are visible in the webpage=C2=A0namd-l: Re: Hydrogen Mass Repartitioning in NAMD (uiuc.edu)
=C2=A0
Sent from=C2=A0Ma= il=C2=A0for Windows 10
=C2=A0
From:=C2=A0McGuire, Kelly
Sent:=C2=A004 December 2020 08:38
To:=C2=A0namd-l@ks.uiuc.edu
Subject:=C2=A0namd-l: Hydrogen Mass Repartitioning
=C2=A0
Does anyone have a tutorial on how to implement hydrogen mass repartitioning in NAMD? I have never used this method before. Thanks!
=C2=A0

Dr. Kelly L. M= cGuire

PhD=C2=A0Bioph= ysics

Department of = Physiology and Developmental Biology

Brigham Young = University

LSB 3050

Provo, UT 8460= 2


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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boundary="_000_2CBD3041599245299978E4CAC9C2F23Fphysicsgatechedu_" X-OriginatorOrg: physics.gatech.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BN7PR07MB4481.namprd07.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 267a3b79-6010-4730-d9c4-08d8fdaaa875 X-MS-Exchange-CrossTenant-originalarrivaltime: 12 Apr 2021 12:01:08.5158 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 482198bb-ae7b-4b25-8b7a-6d7f32faa083 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: Ktom7ebe6xzcCbQN5/XA/JArBZlug2zygEhG6vZPPJG9ChrH+ry2oli4aqJuavc957vox/WgIEYeaBca1AC6UA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BN8PR07MB6387 X-Proofpoint-GUID: ld6JRRbVJFew95NbfJfcbu_E7F7W9FzD X-Proofpoint-ORIG-GUID: ld6JRRbVJFew95NbfJfcbu_E7F7W9FzD X-CLX-Response: 1TFkXGBgSEQpMehcaEQpZRBdie05gWEVmQ09tTREKWFgXZhlwY2FScgFYG3A RCnhOF2hpBUkaRWhhHWVvEQp5TBdnbmRSR2NCG25rehEKQ0gXBxgeHxEKQ1kXBxsdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGBoScRgeGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdGThxgeHhIfGBsT10TH2RITGBMSUhfdW8dbB19E2xQbhEKWFwXHwQaBBgYHQUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JbTllDEQpNXBcfGhMRCkxaF3xpa01rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29va2tsa2sRCkJPF3oef2ZvQh9Tcmt9EQpDWhceGgQbGh0EExkEGx sTEQpCXhcbEQpESRcYEQpCXBcbEQpCSxdoE09QEnxjAX5zRxEKQkkXaGkFSRpFaGEdZW8RCkJFF 29tfGJOc29NfU99EQpCThdoaQVJGkVoYR1lbxEKQkwXZhlwY2FScgFYG3ARCkJsF2xNQUVATltv WUtyEQpCQBdoRhteGngaEmRhYBEKQlgXZ3Nlc0BuYWFMXWIRClpYFx8RCnlDF2IZck1Bek5afEZ nEQpwZxdgGUZFe05HGW1cRRAaEQpwaBdtRRhOUh5QW2dJUhAZGhEKcGgXYmx6WEFyGURQfF8QGR oRCnBoF25Fa0NzAWJOX3hzEBkaEQpwaBdgWhJYQk9GBURzeBAZGhEKcGgXa2RmfEFtQU4TZE4QG RoRCnB9F2AYRRsBSBoTGnlSEBwaEQpwfRdmbBNvGQVmQ3odRxAZGhEKcGcXek1NSEl9Z3MTGmkQ GhEKcH0XZX9TbW1ffW9kR0YQGhEKcH0XbEkaREtDSGYYXAUQGhEKcGcXZHoSBWh6SAF5eXsQGhE KcGcXaUNuUAFZc0cBHlMQGhEKcH0XYEJdYWliexJ+ZFgQGhEKcH8XaHpfYh5+WwVkUhsQHxwRCn BfF2ATGWZLTmxORVN7EBwaEQpwfxd6GltbcBhnWVhrZRAbGx8RCnBfF2lnaxpSbWBwbX0aEBsZG hEKcH8XZRl5Zl5HaRtkT3MQHxgRCnBfF2keR2lsYEgBZnhMEBoRCnB/F2Fmb1saZ2RCSB1bEBsb HBEKcF8XY2ISUEhjeB98Qn0QExsRCnBsF21ZaxhZfQEfHX1ZEBkaEQpwTBdtaGUZQVJ9exhFUhA ZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 spamscore=0 lowpriorityscore=0 suspectscore=0 priorityscore=0 mlxlogscore=999 impostorscore=0 phishscore=0 bulkscore=0 clxscore=228 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104120082 X-Spam-Score: 0 X-Spam-OrigSender: gumbart@physics.gatech.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Gumbart, JC" --_000_2CBD3041599245299978E4CAC9C2F23Fphysicsgatechedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Indeed - see this paper, particularly Table 1: Feenstra KA; Hess B; Berendsen HJC Improving efficiency of large time-scale= molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem 1= 999, 20, 786=E2=80=93798. Best, JC On Apr 12, 2021, at 7:52 AM, Axel Kohlmeyer > wrote: While keeping bonds with hydrogen atoms rigid, eliminates the need to repre= sent the high frequency motions of those bonds, it does not slow down the r= otation of the hydrogen atoms around their heavier bond partners. Axel. -- Dr. Axel Kohlmeyer akohlmey@gmail.com https://ur= ldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vUkIugtBr4wiDY787KF_QZm1nAp= Bk90ujXA_kvmhMb5RSs0sXXpuIaLWOdICQANsWA$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste, Italy On Mon, Apr 12, 2021, 06:35 Ren=C3=A9 Hafner TUK > wrote: Dear Mr. Gumbart, why is it that with HMR we increase/repartition the mass of/to hydrogen= s but then keeping all of them fixed using rigidBonds (according to example= NAMD configfile in SI of your paper mentioned below)? Couldn't we have increase ts to 4fs in the first place when we keep a= ll hydrogens fixed anyway? Kind regards Ren=C3=A9 Hafner On 12/4/2020 4:57 AM, Gumbart, JC wrote: Also, have a look at https://urldefense.com/v3/__https://pubmed.ncbi.nlm.ni= h.gov/31265271/__;!!DZ3fjg!vUkIugtBr4wiDY787KF_QZm1nApBk90ujXA_kvmhMb5RSs0s= XXpuIaLWOdKXL4lKGQ$ and the supplemental files for examples. Best, JC On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff > wrote: Ask the suitable person whose details are visible in the webpage namd-l: Re= : Hydrogen Mass Repartitioning in NAMD (uiuc.edu) Sent from Mail for Windows 10 From: McGuire, Kelly Sent: 04 December 2020 08:38 To: namd-l@ks.uiuc.edu Subject: namd-l: Hydrogen Mass Repartitioning Does anyone have a tutorial on how to implement hydrogen mass repartitionin= g in NAMD? I have never used this method before. Thanks! Dr. Kelly L. McGuire PhD Biophysics Department of Physiology and Developmental Biology Brigham Young University LSB 3050 Provo, UT 84602 -- -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --_000_2CBD3041599245299978E4CAC9C2F23Fphysicsgatechedu_ Content-Type: text/html; charset="utf-8" Content-ID: <747FC3EA50BE2647873508D5345BABCD@namprd07.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Indeed - see this paper, particularly Table 1:

Feenstra KA; Hess B; Berendsen HJC Improving efficienc= y of large time-scale molecular dynamics simulations of hydrogen-rich syste= ms. J. Comput. Chem 1999, 20, 786=E2=80=93798. 
Best,
JC

On Apr 12, 2021, at 7:52 AM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:
While keeping bonds with hydrogen atoms rigid,= eliminates the need to represent the high frequency motions of those bonds= , it does not slow down the rotation of the hydrogen atoms around their hea= vier bond partners. 

Axel. 
--
Dr. Axel Kohlmeyer akohlme= y@gmail.com h= ttp://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, US= A
International Centre for Theoretical Physics, Trieste, Italy

On Mon, Apr 12, 2021, 06:35 Ren=C3=A9= Hafner TUK <ham= burge@physik.uni-kl.de> wrote:

Dear Mr. Gumbart,

    why is it that with HMR we increase/repart= ition the mass of/to hydrogens but then keeping all of them fixed using rig= idBonds (according to example NAMD configfile in SI of your paper mentioned= below)?

      Couldn't we have increase ts to 4fs= in the first place when we keep all hydrogens fixed anyway?

Kind regards

Ren=C3=A9 Hafner

On 12/4/2020 4:57 AM, Gumbart, JC wrote:
Also, have a look at https://pubmed.ncbi.nlm.nih.= gov/31265271/  and the supplemental files for examples.

Best,
JC

On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff <ms7.umar185@gmail.com> wrote:

Ask the suitable person whose detai= ls are visible in the webpage namd-l: Re: Hydrogen Mass Repartitioning in NAMD (uiuc.edu)
 
Sent from Mail for Windows 10
 
From: McGuire, Kelly
Sent: 04 December 2020 08:38=
To: namd-l@ks.uiuc.edu
Subject: namd-l: Hydrogen Ma= ss Repartitioning
 
Does anyone have a tutori= al on how to implement hydrogen mass repartitioning in NAMD? I have never u= sed this method before. Thanks!<= /div>
 <= u class=3D"">

Dr. K= elly L. McGuire

PhD&n= bsp;Biophysics

Depar= tment of Physiology and Developmental Biology

Brigh= am Young University

LSB 3= 050<= u class=3D"">

Provo= , UT 84602


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany

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Mon, 12 Apr 2021 07:37:42 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13CCSrL9018119 for ; Mon, 12 Apr 2021 12:37:41 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0a-00007101.pphosted.com with ESMTP id 37u2h0rgb2-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 12 Apr 2021 12:37:41 +0000 Received: from [IPv6:2a02:810c:300:6724:9c1d:fde0:b6e6:d446] ([IPv6:2a02:810c:300:6724:9c1d:fde0:b6e6:d446]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 13CCbbZA146439 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 12 Apr 2021 14:37:37 +0200 Subject: Re: namd-l: Hydrogen Mass Repartitioning To: namd-l@ks.uiuc.edu, "Gumbart, JC" References: <06BB7A88-A529-458F-B1A2-E3E4FF819F9B@physics.gatech.edu> <2858dd33-fd4a-7a45-d296-6d2bce8601e2@physik.uni-kl.de> <2CBD3041-5992-4529-9978-E4CAC9C2F23F@physics.gatech.edu> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <15e592c4-00f3-913a-f4d5-375405a2f21f@physik.uni-kl.de> Date: Mon, 12 Apr 2021 14:37:38 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.9.0 In-Reply-To: <2CBD3041-5992-4529-9978-E4CAC9C2F23F@physics.gatech.edu> Content-Type: multipart/alternative; boundary="------------9DF039C7B9B816663DC1B0CE" Content-Language: de-DE X-Spam-Status: No, hits=1.592, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,HTTPS_HTTP_MISMATCH=0.1,NICE_REPLY_A=-0.001,URI_DOTEDU=1.491 X-Spam-Score: * (1.592) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: jEm5oEWaMNvy7xOw3nMzHvFjMa2rcQfM X-Proofpoint-GUID: jEm5oEWaMNvy7xOw3nMzHvFjMa2rcQfM X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0ZEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxgdGREKQ1kXBxsdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ZcRkZEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0BvRx9Fb31LZ2RcUx1SZV0ZRGdQYlxsQGdLGFhJe0xnEQpYXBcfBBoEGBgdBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXcltPZV0RCk1cFwcSGREKTFoXaXhpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2hGG14aeBoSZGFgEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXExEKeUMXYhlyTUF6Tlp8RmcRCnBnF2RnW2ZlXkFNbn9ZEB4SEQpwaBd6ZlhlSHB9fR9 8RhAaEQpwaBdjewFubmxCcEFYehAaEQpwaBduRWtDcwFiTl94cxAeEhEKcGgXbl0baEtzcnJmGk 0QGhEKcGgXYRlmWXxgbmB4HFIQGhEKcH0XYBhFGwFIGhMaeVIQHBoRCnB9F21CRV96aGRoWm97E B4SEQpwZxdgGUZFe05HGW1cRRAcGhEKcH0XbnBdUgFAUBt+WmAQGhEKcH0XYEJdYWliexJ+ZFgQ HRoRCnBnF3pNTUhJfWdzExppEB0aEQpwfRdlf1NtbV99b2RHRhAdGhEKcH0XbEkaREtDSGYYXAU QHRoRCnBnF2R6EgVoekgBeXl7EB0aEQpwZxdkZGd+b3N8e0IbUxAeEhEKcGcXaUNuUAFZc0cBHl MQHRoRCnBnF2AcBR1OGEZFXhtpEBoRCnB9F3ppQVBCZFxwHBt/EB4SEQpwfxdoel9iHn5bBWRSG xAfExEKcF8XYBMZZktObE5FU3sQHRoRCnB/F21EX0ZFbX1IeRluEBsZHBEKcF8Xa0ZLE3loaW58 E3gQGxoaEQpwfxd6GltbcBhnWVhrZRAbGB8RCnBfF3pgQmsFYxx4SF9kEBsZHxEKcH8XYWZvWxp nZEJIHVsQGxgdEQpwXxdjYhJQSGN4H3xCfRATHBEKcH8XZRl5Zl5HaRtkT3MQGxsfEQpwXxdpHk dpbGBIAWZ4TBAdGhEKcGwXeh94eW94TENfcEQQHhIRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 adultscore=0 mlxscore=0 clxscore=173 lowpriorityscore=0 phishscore=0 impostorscore=0 priorityscore=0 malwarescore=0 spamscore=0 suspectscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104120085 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------9DF039C7B9B816663DC1B0CE Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable I see, now to slow down the rotation of hydrogen atoms about heavy bond=20 partners, they need to be made havier. Got it, thanks a lot to both of you! On 4/12/2021 2:01 PM, Gumbart, JC wrote: > Indeed - see this paper, particularly Table 1: > > Feenstra KA; Hess B; Berendsen HJC=C2=A0Improving efficiency of large=20 > time-scale molecular dynamics simulations of hydrogen-rich=20 > systems.=C2=A0J.=C2=A0Comput. Chem=C2=A01999,=C2=A020, 786=E2=80=93798. > > Best, > JC > >> On Apr 12, 2021, at 7:52 AM, Axel Kohlmeyer > > wrote: >> >> While keeping bonds with hydrogen atoms rigid, eliminates the need to=20 >> represent the high frequency motions of those bonds, it does not slow=20 >> down the rotation of the hydrogen atoms around their heavier bond=20 >> partners. >> >> Axel. >> -- >> Dr. Axel Kohlmeyer akohlmey@gmail.com =20 >> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vnvupqEoTR2qTp= 7hmP3ir2pLfJNKYFvbkGXUqHeW-3GSeIQRe9Udvv-BGYtCugxmpg$=20=20 >> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste, Italy >> >> On Mon, Apr 12, 2021, 06:35 Ren=C3=A9 Hafner TUK=20 >> > wrote: >> >> Dear Mr. Gumbart, >> >> =C2=A0=C2=A0=C2=A0 why is it that with HMR we increase/repartition t= he mass >> of/to hydrogens but then keeping all of them fixed using >> rigidBonds (according to example NAMD configfile in SI of your >> paper mentioned below)? >> >> =C2=A0=C2=A0 =C2=A0=C2=A0 Couldn't we have increase ts to 4fs in the= first place when >> we keep all hydrogens fixed anyway? >> >> Kind regards >> >> Ren=C3=A9 Hafner >> >> On 12/4/2020 4:57 AM, Gumbart, JC wrote: >>> Also, have a look at https://urldefense.com/v3/__https://pubmed.ncb= i.nlm.nih.gov/31265271/__;!!DZ3fjg!vnvupqEoTR2qTp7hmP3ir2pLfJNKYFvbkGXUqHeW= -3GSeIQRe9Udvv-BGYv617EZUw$=20 >>> >>> and the supplemental files for examples. >>> >>> Best, >>> JC >>> >>>> On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff >>>> > wrote: >>>> >>>> Ask the suitable person whose details are visible in the >>>> webpagenamd-l: Re: Hydrogen Mass Repartitioning in NAMD >>>> (uiuc.edu) >>>> >>>> Sent fromMail >>>> for >>>> Windows 10 >>>> *From:*McGuire, Kelly >>>> *Sent:*04 December 2020 08:38 >>>> *To:*namd-l@ks.uiuc.edu >>>> *Subject:*namd-l: Hydrogen Mass Repartitioning >>>> Does anyone have a tutorial on how to implement hydrogen mass >>>> repartitioning in NAMD? I have never used this method before. >>>> Thanks! >>>> >>>> /Dr. Kelly L. McGuire/ >>>> >>>> /PhD=C2=A0Biophysics/ >>>> >>>> /Department of Physiology and Developmental Biology/ >>>> >>>> /Brigham Young University/ >>>> >>>> /LSB 3050/ >>>> >>>> /Provo, UT 84602/ >>>> >>> >> --=20 >> -- >> Dipl.-Phys. Ren=C3=A9 Hafner >> TU Kaiserslautern >> Germany >> > --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------9DF039C7B9B816663DC1B0CE Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

I see, now to slow down the rotation of hydrogen atoms about heavy bond partners, they need to be made havier.

Got it, thanks a lot to both of you!

On 4/12/2021 2:01 PM, Gumbart, JC wrote:
Indeed - see this paper, particularly Table 1:

Feenstra KA; Hess B; Berendsen HJC Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem 1999, 20, 786–798. 

Best,
JC

On Apr 12, 2021, at 7:52 AM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:

While keeping bonds with hydrogen atoms rigid, eliminates the need to represent the high frequency motions of those bonds, it does not slow down the rotation of the hydrogen atoms around their heavier bond partners. 

Axel. 
--
Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy

On Mon, Apr 12, 2021, 06:35 René Hafner TUK <hamburge@physik.uni-kl.de> wrote:

Dear Mr. Gumbart,

    why is it that with HMR we increase/repartition the mass of/to hydrogens but then keeping all of them fixed using rigidBonds (according to example NAMD configfile in SI of your paper mentioned below)?

      Couldn't we have increase ts to 4fs in the first place when we keep all hydrogens fixed anyway?

Kind regards

René Hafner

On 12/4/2020 4:57 AM, Gumbart, JC wrote:
Also, have a look at https://pubmed.ncbi.nlm.nih.gov/31265271/  and the supplemental files for examples.

Best,
JC

On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff <ms7.umar185@gmail.com> wrote:

Ask the suitable person whose details are visible in the webpage namd-l: Re: Hydrogen Mass Repartitioning in NAMD (uiuc.edu)
 
Sent from Mail for Windows 10
 
From: McGuire, Kelly
Sent: 04 December 2020 08:38
To: namd-l@ks.uiuc.edu
Subject: namd-l: Hydrogen Mass Repartitioning
 
Does anyone have a tutorial on how to implement hydrogen mass repartitioning in NAMD? I have never used this method before. Thanks!
 

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Ren=C3=A9,=20 >> MW-eABF is not that different from ABF, it's just that the ABF quantities >> (mainly the biasing force itself) pertain to the extended coordinate. Th= ose are >> shared exactly as in standard mwABF, because they are represented the sa= me way >> in the implementation. >> The data for the *unbiased free energy estimators* is a separate questio= n: it is >> not shared in the current state of the code, and in a sense it does not = need to >> be shared during the simulation, as these estimators are really a matter= of >> post-processing. Anything that is done on the fly is just for convenienc= e. > 1. Does that mean that the output of multiple replicas simulations (using= shared > (e)ABF) MUST be merged in order for results to be valid > since for a single replica the "actually" applied biasing force does is > different from the corresponding content of the (zcount/zgrad) output fil= es > produced by this walker? The zcount/zgrad data for each walker is still valid for the given replica.= As the simulation converges they should converge to the same final values = across replicas, even without sharing.=20 > 2. What is actually printed to the outputname.grad/count file (named the = same > way as in plain abf output) when using eABF, this is the gradient/counts = of the > fictious particle, correct? That is correct.=20 >>>>> * Then latest literature would be a bit misleading when stating usage= of >>>>> MW-eABF. >> Is there something else than the QM/MM tutorial that mentions it? > It is stated in the paper about WtM-eABF Method ( Taming Rugged Free Ener= gy > Landscapes Using an Average Force [ > https://urldefense.com/v3/__http://dx.doi.org/10.1021/acs.accounts.9b0047= 3__;!!DZ3fjg!pkIvIjJO9NBIUsI0DIFDIqoEmOIR-ot_UY-KI0AJeqikGqC7TOCwTJ2CJzClaX= l39A$ > | https://urldefense.com/v3/__http://dx.doi.org/10.1021/acs.accounts.9b00= 473__;!!DZ3fjg!uPMvYCFbbdXOyaMgjQOMbuuCd681Djcttd8uytDXrz09dJFFUsowi6-jGHVG= 9H8jxg$ ] ) Ah, indeed.=20 J=C3=A9r=C3=B4me=20 --=_6fd2e882-5afc-4188-beac-15d0a82fec15 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Ren= =C3=A9,

=
MW-eABF is not that different from ABF, it's just that the ABF quantities (mainly the biasing force itself) pertain to the extended coordinate. Those are shared exactly as in standard mwABF, because they are represented the same way in the implementation.
The data for the *unbiased free energy estimators* is a separate question: it is not shared in the current state of the code, and in a sense it does not need to be shared during the simulation, as these estimators are really a matter of post-processing. Anything that is done on the fly is just for convenience.


1. Does that mean that the output of multiple replicas simulations (using shared (e)ABF) MUST be merged in order for results to be valid

since for a single replica the "actually" applied biasing force does is different from the corresponding content of the (zcount/zgrad) output files produced by this walker?

The zcount/zgrad data for each = walker is still valid for the given replica. As the simulation converges th= ey should converge to the same final values across replicas, even without s= haring.

2. What is actually printed to the outputname.grad/count file (named the same way as in plain abf output) when using eABF, this is the gradient/counts of the fictious particle, correct?

That is cor= rect.

  &nbs= p; * Then latest literature would be a bit misleading when stating usage of MW-eABF.

Is there something else than the QM/MM tutorial that mentions it?

 It is stated in the paper about WtM-e= ABF Method (= Taming Rugged Free Energy Landscapes Using an Average Forcehttp://dx.doi.org/10= .1021/acs.accounts.9b00473 )


Ah, indeed.
=
J=C3=A9r=C3=B4me
--=_6fd2e882-5afc-4188-beac-15d0a82fec15-- From owner-namd-l@halifax.ks.uiuc.edu Mon Apr 12 10:58:46 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13CFwjpb027076; Mon, 12 Apr 2021 10:58:45 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13CFwjmE027075; Mon, 12 Apr 2021 10:58:45 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13CFwjTh027071; Mon, 12 Apr 2021 10:58:45 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13CFwich027070; Mon, 12 Apr 2021 10:58:44 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13CFwVow027060 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 12 Apr 2021 10:58:31 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13CFr9c3013905 for ; Mon, 12 Apr 2021 15:58:31 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=kbyler@polarisqb.com; dkim=pass header.s=google header.d=polarisqb.com Received: from mail-qk1-f176.google.com (mail-qk1-f176.google.com [209.85.222.176]) by mx0b-00007101.pphosted.com with ESMTP id 37u2utjq9y-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 12 Apr 2021 15:58:30 +0000 Received: by mail-qk1-f176.google.com with SMTP id 130so285559qkm.4 for ; Mon, 12 Apr 2021 08:58:30 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=polarisqb.com; s=google; h=mime-version:from:date:message-id:subject:to; bh=30MgKdC0mH89f/AdLY9wyoc3m6g5dQsf3VRwwoxNLQA=; b=mmgYOiNyK9sqV18VntO3imKWAREmiJ/BlNiaCyFWVzliBBI8tNGh//BxUhKt77Ie28 Zsmshe3PC7FnHYR2yvd+VeXQ5ukoMWN+ZautHo5MEj+RM9rgKDoUcxlY+3wL+TOgQqfN zH9S0ewu/8KOYJPJQcCNoO1G7YwxvMSSkcTBo= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=30MgKdC0mH89f/AdLY9wyoc3m6g5dQsf3VRwwoxNLQA=; b=MWLLMQzMSNDs2TtzKF4sgiwiXIOIa/VZFWq5qJr29zG0Zs7fT2geC90syuPpCfx63J SsYRoSdxzty3/Bq6CKn55gVtkP+QtrP2nGKt/JAKCTvjXgBNxbA+7jJ333HGpfr3w02f AMv1jebi+kmU5NKMJrPgwZOP21WO+Ji9sTu0fzHT/qbfF7t18hXMWitl9I1jswYAQYr9 27LpmOWohMxWHhvG6aJkNFBDqxG1V3lSy2YPC2QdTMGLaMV5bZ/1rBQiRGCp38T6YT2L 5ZxuQ3C/bz8UuPn8xsGr5ng0+SIQSYQbgbyElmzRUYIcT6DwkmO/kCFNcXnVBDX9/Zfn /xkA== X-Gm-Message-State: AOAM531+Vz2w8PC8qS/7C82zAtaGjPs4iZwmihWNwu5o9/bjRdvjrZje v6pZ276Oog3NECdVr9AovmdAvSxUqSA01FoEvPGOoIHuty073zUiC5g= X-Google-Smtp-Source: ABdhPJwX//RWkYBUPYlQPAlrrnf4iTfSVhVSFvsBvC0Azx4dr4vm7oN+Gbl7Mdn9oTq+co1JkWwyGb1OoTsF7A2Nnfc= X-Received: by 2002:a25:850b:: with SMTP id w11mr39038322ybk.518.1618243109839; Mon, 12 Apr 2021 08:58:29 -0700 (PDT) MIME-Version: 1.0 From: Kendall Byler Date: Mon, 12 Apr 2021 10:58:19 -0500 Message-ID: Subject: namd-l: A question about PME correction term in QM/MM To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000b8f73f05bfc895b3" X-CLX-Response: 1TFkXGRkSEQpMehcaEQpZRBd6YR5STGxIUmwFZBEKWFgXZllIAV8FQnNoH20 RCnhOF2tBT3NsGlNpZ0toEQp5TBdkZBNHY09YG0weQhEKQ0gXBxkfGhEKQ1kXBxgeGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGB1xGAYYHXcGGxIbBhoGGgYbGhoGGRpxGxAadwYaBhoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF0xpcwdzYk1GX1kHUENdTGkHSR9u UlsSaGkeUx9QaFNwEQpYXBcfBBoEGBgdBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JbQmZpEQp NXBcYGx0RCkxaF2loaU1vaxEKTEYXb2tra2trEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBB gYGAQbHRwRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2tBT3NsGlNpZ0toEQpCSRdrQU9zbBpTaWdLa BEKQkUXaWJQRnNiRHNQY2kRCkJOF2tBT3NsGlNpZ0toEQpCTBdmWUgBXwVCc2gfbREKQmwXa2da QXNBZHBhTm4RCkJAF2NBXAFcE39ybVptEQpCWBdnc2VzQG5hYUxdYhEKWlgXGxEKeUMXZlNaZkE fRh9yf1kRCnBoF2NtclNSX0cTUG9cEBoRCnBoF2VraVAZaHNeGFNiEBoRCnBoF25IZkxzcn5cZx ljEBoRCnBoF2lgRVNNXEtgAR5tEBoRCnBoF218aGZoQ29pY2xrEBoRCnBsF2xAfEBOb09zWGBiE AcZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: fCY-YHglus-ziwfC-c5Dxq8BC4y5zByZ X-Proofpoint-ORIG-GUID: fCY-YHglus-ziwfC-c5Dxq8BC4y5zByZ X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 bulkscore=0 mlxscore=0 phishscore=0 clxscore=338 mlxlogscore=811 impostorscore=0 adultscore=0 spamscore=0 malwarescore=0 priorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104120102 X-Spam-Score: 0 X-Spam-OrigSender: kbyler@polarisqb.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kendall Byler --000000000000b8f73f05bfc895b3 Content-Type: text/plain; charset="UTF-8" Hi there! I'm checking to see if I am understand correctly what's happening in PME during QM/MM from *NAMD goes quantum: An integrative suite for QM/MM simulations*, wherein it states, " The forces and energy derived from PME interactions between QM atoms, and between QM atoms and the surrounding point charges are re-calculated within the QM module and subtracted from the direct electrostatic calculations, to avoid double counting these contributions." Is this the PMECORRENERGY term and is it correcting for counting the self energy twice? Thanks in advance, Ken Byler --000000000000b8f73f05bfc895b3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi there!
=C2=A0 =C2=A0 =C2=A0I'm checking to see = if I am understand=C2=A0correctly what's happening in PME during QM/MM = from NAMD goes quantum: An integrative suite for QM/MM simulations, = wherein it states, "=C2=A0The forces and energy derived from PME inter= actions between QM atoms, and between QM atoms and the surrounding point ch= arges are re-calculated within the QM module and subtracted from the direct= electrostatic calculations, to avoid double counting these contributions.&= quot; Is this the PMECORRENERGY term and is it correcting for counting the = self energy twice?

Thanks in advance,
Ke= n Byler
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boundary="00000000000063897d05bfd63744" X-Proofpoint-GUID: HKn-OgLdTfeaytglt_CWe6PPPBzt_PVA X-CLX-Response: 1TFkXGxkfEQpMehcZHhwRCllEF2ltSV5uekVpZBhAEQpYWBd6ell9RkVfGx1 dHBEKeE4XY1Nja3sTWH4aX14RCnlMF2NfHU5/Z04ebmdvEQpDSBcHGx4ZEQpDWRcHHBoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGx9xGxkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYmFEB2VNZk5+TE9LU15NRl51aX1PHHp6emhQXnV6fGsRClhcFx8EGgQYGB0F GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyW1xOGBEKTVwXGBMRCkxaF2xpTWtrEQpMRhdva2tra2s RCkJPF2hYXlBJBRJce2R7EQpDWhcYGhMEEh8EGBgbBB4fEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF25gcmRoW0x6b2AFEQpCThdjU2NrexNYf hpfXhEKQkwXenpZfUZFXxsdXRwRCkJsF2lcY1hPbmFnSVATEQpCQBduT1tETUJiBXN9YBEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2UaZWUeHRpvHFJjEQpZSxcTGR0fEQpwaBdsX2t vHRJJTG8BUBAZGhEKcGgXZBhrSXtvcxxHE30QGRoRCnBoF298U1J5a2Z9bE9PEBkaEQpwbBdoGR toH2JlRkhOQBAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: HKn-OgLdTfeaytglt_CWe6PPPBzt_PVA X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 impostorscore=0 adultscore=0 spamscore=0 priorityscore=346 suspectscore=0 bulkscore=0 mlxlogscore=412 lowpriorityscore=0 malwarescore=0 phishscore=0 clxscore=135 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104130055 domainage_hfrom=9375 X-Spam-Score: 0 X-Spam-OrigSender: jingliang2015@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, jing liang --00000000000063897d05bfd63744 Content-Type: text/plain; charset="UTF-8" Hi, is it possible to visualize the molecular orbitals from a QM/MM simulation (using NAMD + Gaussian) in VMD? Thanks in advance --00000000000063897d05bfd63744 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

is it possible to visualize the mol= ecular orbitals from a QM/MM simulation (using=C2=A0
NAMD=C2=A0+ = Gaussian) in VMD?

Thanks in advance
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To: KS UIUC Message-ID: <0FF813A0-32FF-43F9-B7FF-B7F800318BDE@gmail.com> Thread-Topic: Multi-node-gpu NAMD Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3701251327_597649877" X-Proofpoint-GUID: 3NsHuQ5XO2Xj7yQQ6hq02DPixe4-xoGv X-CLX-Response: 1TFkXGx0YEQpMehcZGRIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGxkeEQpDWRcHGx0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxhxGRgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XGWRZYl97H3JlGHJAHVN7exxCWxoYbnpDUk8eB1JFbVwRClhcFx8EGgQYGB0F GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyWGROXhEKTVwXGBoSEQpMWhdsaWtNaxEKTEYXb2tra2t rEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGAQbHRMRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E 1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXY2lZb3pPHXJHT38RCkJAF2MdWntFYWd9WWlTEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXehNOR1htAR94b2URCllLFxMZHRwRCnBoF2B wGm1GS29vUk8YEBkaEQpwaBdraGN9ZGBbeEROehAZGhEKcGgXbVx8S2JDaWgbGUAQGRoRCnBoF2 RyTwVwfmBofGRZEBkaEQpwaBdiXURQH1lcQmQSGRAZGhEKcGwXekdAaxhZeX8eG0gQGRoRCnBMF 2d+UH1Na1BPT0ZiEBkaEQpwQxdhYGVhHR96Uh4SchAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 3NsHuQ5XO2Xj7yQQ6hq02DPixe4-xoGv X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 bulkscore=0 spamscore=0 mlxlogscore=586 phishscore=0 adultscore=0 priorityscore=338 suspectscore=0 malwarescore=0 clxscore=172 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104140118 domainage_hfrom=9376 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3701251327_597649877 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear user,=20 =20 I=E2=80=99m try run NAMD on 4 node each with 2 GPU Tesla K80=20 =20 My PBS file=20 =20 #PBS -N test_nand_GPU #PBS -l nodes=3Dn004+n005+n006:ppn=3D28:gpus=3D2 =20 =20 cd $PBS_O_WORKDIR =20 /opt/shared/NAMD_2.13-multinode-gpu/charmrun=C2=A0 /opt/shared/NAMD_2.13-multin= ode-gpu/namd2 +idlepoll +p 12 +devices 0=C2=A0 ++ppn 4=C2=A0 run_fixed/md_run.namd |= tee md2.log =20 When set =E2=80=9C+devices 0,1=E2=80=9D not run, only run when set to 0 . =20 How can correct it?=20 =20 Help me.=20 =20 Geo.=20 =20 =20 --B_3701251327_597649877 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear user,

I=E2=80=99m try run NAMD on= 4 node each with 2 GPU Tesla K80

<= span style=3D'font-size:11.0pt;font-family:"Calibri Light",sans-serif'>&n= bsp;

My PBS file

 

#PBS -N test_nand_GP= U

#PBS -l nodes=3Dn004+n005+n006:p= pn=3D28:gpus=3D2

 

 

cd $PBS_O_WORKDIR

&n= bsp;

/opt/shared/NAMD_2.13-multinode-= gpu/charmrun=C2=A0 /opt/shared/NAMD_2.13-multinode-gpu/namd2 +idlepoll +p 12 +de= vices 0=C2=A0 ++ppn 4=C2=A0 run_fixed/md_run.namd | tee md2.log

When set =E2=80=9C+devices 0,1=E2=80=9D not run, only run when set to 0 .

 

How can correct it?

 

Help me.

 

Geo.

 

 

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Content-Type: multipart/alternative; boundary="00000000000023c3c105bff4d920" X-Proofpoint-ORIG-GUID: vBXZwatr735iWRiREbS8vWB3rtd7mQmz X-Proofpoint-GUID: vBXZwatr735iWRiREbS8vWB3rtd7mQmz X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0dEQpMehcZGB0RCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGB8cEQpDWRceHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfHXEdGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdcaHJwXUteWB0ZH0N9eEN4b0h5Elx9aBlYXk4dR3tHUBEKWFwXHwQaBBgYHQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdyWHpGTREKTVwXGBMSEQpMWhd8aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2t8WVBYGWleGGZaEQpDWhcYGhMEEh8EGBoSBB sdGBEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdgYEsZZkRjXl5QeBEKQk4XY1Nja3sTWH4aX14RCkJMF3pYa0xjZV1bBURwEQpCbBdm eG5+GGRlQRJYfxEKQkAXZGZOT2ZiTHBNclsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp 5QxduHlNoQGMcXUBNQBEKWUsXExkdHBEKcGgXYUdbHRhZSRscE38QGRoRCnBoF24bUE5mBU1lel plEBkaEQpwaBdlaFB7fHhwQ09ecBAZGhEKcGgXb2FycnpFTnwdY1IQGRoRCnBoF29gR2ZoZUBra RNcEBkaEQpwfRdgGEUbAUgaExp5UhAcGhEKcH8XaHpfYh5+WwVkUhsQGxoYEQpwXxdgExlmS05s TkVTexAcGhEKcGwXYGlHZ2lSX39feEwQHhIRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRd LESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 adultscore=0 impostorscore=0 priorityscore=327 mlxlogscore=469 lowpriorityscore=0 phishscore=0 mlxscore=0 spamscore=0 bulkscore=0 clxscore=177 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104140133 domainage_hfrom=9376 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --00000000000023c3c105bff4d920 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable n004+n005+n006 would be 3 nodes not 4. axel. On Wed, Apr 14, 2021 at 2:24 PM Ropon-Palacios G. wrote: > Dear user, > > > > I=E2=80=99m try run NAMD on 4 node each with 2 GPU Tesla K80 > > > > My PBS file > > > > #PBS -N test_nand_GPU > > #PBS -l nodes=3Dn004+n005+n006:ppn=3D28:gpus=3D2 > > > > > > cd $PBS_O_WORKDIR > > > > /opt/shared/NAMD_2.13-multinode-gpu/charmrun > /opt/shared/NAMD_2.13-multinode-gpu/namd2 +idlepoll +p 12 +devices 0 ++p= pn > 4 run_fixed/md_run.namd | tee md2.log > > > > When set =E2=80=9C+devices 0,1=E2=80=9D not run, only run when set to 0 . > > > > How can correct it? > > > > Help me. > > > > Geo. > > > > > --=20 Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!uHBiqpz2dukYWF-FoQUTWxEZ5i9wMU8PEuhkpL_WqkzPYwXo3Gsk= TToKR0Ckc30neg$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. --00000000000023c3c105bff4d920 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
n004+n005+n006 would be 3 nodes not 4.
=

axel= .

On Wed, Apr 14, 2021 at 2:24 PM Ropon-Palacios G. <biodano.geo@gmail.com> wrote:

Dear user,

=C2=A0

I= =E2=80=99m try run NAMD on 4 node each with 2 GPU Tesla K80 <= /span>

=C2=A0

My PBS file

=C2=A0

#PBS -N test_nand_GPU

= #PBS -l nodes=3Dn004+n005+n006:ppn=3D28:gpus=3D2

=C2=A0

=C2=A0

cd $PBS_O_WORKDIR

=C2=A0

=

/opt/shared/NAMD_2.13-multinode-gpu/c= harmrun=C2=A0 /opt/shared/NAMD_2.13-multinode-gpu/namd2 +idlepoll +p 12 +de= vices 0=C2=A0 ++ppn 4=C2=A0 run_fixed/md_run.namd | tee md2.log

=C2=A0

When set =E2=80=9C+devices 0= ,1=E2=80=9D not run, only run when set to 0 .

=C2=A0

How can correct it?

=C2=A0

Help me.

=C2=A0

Geo.

=C2=A0

=C2=A0



--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://= goo.gl/1wk0
College of Science & Technology, Temple University, = Philadelphia PA, USA
International Centre for Theoretical Physics, Tries= te. Italy.
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boundary="_000_SG2PR04MB389854F16FBB8746A026B50DE14D9SG2PR04MB3898apcp_" MIME-Version: 1.0 X-OriginatorOrg: research.iiit.ac.in X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SG2PR04MB3898.apcprd04.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 1bc29f9c-bc5f-4ff4-d95e-08d8ffc31e28 X-MS-Exchange-CrossTenant-originalarrivaltime: 15 Apr 2021 04:01:16.1954 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 031a3bbc-cf7c-4e2b-96ec-867555540a1c X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: kqRxyL67AlJ6qjcgnewHG/qvE+QlWBuDd6TGlEqvbEMiFYA42JCvbK1spm8qy5lAkS7LQYBdltZR37yTdpzQOkxsAUHmfCO61BkJpAlcuxnGVUa9qkb3fH5BOkW4QqMd X-MS-Exchange-Transport-CrossTenantHeadersStamped: SG2PR04MB3271 X-CLX-Response: 1TFkXHxoSEQpMehcaEQpZRBdsZm5FH2dQbB1ccxEKWFgXZR0BeEQbH3lNeE8 RCnhOF2FrEx1nfX4BQl1kEQp5TBdgE0VsWXNEAXhrHREKQ0gXBx4YExEKQ1kXBx0eEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbHBlxHwYcH3cGGx4fBhoGGgYbGhoGGxoacRMQGncGGgYaBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdOXl9jS3lPSBseTBlwE35eTl9m e3xnRUsYQ0FQXkxvchEKWFwXHwQaBBgYHQUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3JYfBJcEQp NXBcYGhMRCkxaF2hpa2trEQpMRhdvb2tra2trEQpCTxdmTRhkfVhIHFtMbhEKQ1oXHhoEGxodBB sZGAQdHxEKQl4XGxEKQlwXGxEKQksXaB8Bcl5lbmgYSGYRCkJJF2FrEx1nfX4BQl1kEQpCRRdoW 3xdYHtOcnhvWxEKQk4XYWsTHWd9fgFCXWQRCkJMF2UdAXhEGx95TXhPEQpCbBdvZGlDZU0YZWga aREKQkAXYFkcY39BcB5vfHIRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdkXEFcTm1 vYHgBExEKWUsXHBsZHREKcGgXbU9oZmBJfFNoXV8QGRoRCnBoF25SbH1dTG97Ylh9EBkaEQpwaB dpXQVCc2xvH2RgTBAZGhEKcGgXbUdvWk8Bcn4fU3IQGRoRCnBoF2VPZG1rH1pfb1BzEBkaEQpwb Bdpa25hQm8eGmkabxAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: dtuIaSeb14f3Z9TtduLQVMoa2ikztfEX X-CLX-Shades: MLX X-Proofpoint-GUID: dtuIaSeb14f3Z9TtduLQVMoa2ikztfEX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=999 impostorscore=0 clxscore=508 bulkscore=0 phishscore=0 spamscore=0 priorityscore=0 suspectscore=0 lowpriorityscore=0 malwarescore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104150025 domainage_hfrom=6137 X-Spam-Score: 0 X-Spam-OrigSender: shivansh.seth@research.iiit.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Shivansh Seth --_000_SG2PR04MB389854F16FBB8746A026B50DE14D9SG2PR04MB3898apcp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear All, I have been trying to run a simulation with 80 ABFs on different colvars (s= ide chain dihedrals). The 7ns simulation ran without any errors but the fin= al *.pmf, *.count, *.grad files were empty (0 bytes). All other files (colv= ar.state, restart, dcd) were non-empty and the simulation can be restarted = without any errors. I tried reducing the number of ABFs (and colvars) to 20= and the final files were non-empty in this case. However, on the fourth re= start, the files are again empty. I'm using the CUDA accelerated version of NAMD 2.13 with 2 GeForce RTX 2080= Ti and 20 CPU cores. The run command is as follows: namd2 +p20 +idlepoll +devices $CUDA_VISIBLE_DEVICES d1-4.conf > d1-4.log One possible workaround we found was to use just 1 thread but that slows do= wn the simulation significantly. I have been stuck on this for a while now and any help would be much apprec= iated. Thank you Shivansh Seth --_000_SG2PR04MB389854F16FBB8746A026B50DE14D9SG2PR04MB3898apcp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Dear All,

I have been trying to run a simulation with 80 ABFs on different colvars (s= ide chain dihedrals). The 7ns simulation ran without any errors but the fin= al *.pmf, *.count, *.grad files were empty (0 bytes). All other files (colv= ar.state, restart, dcd) were non-empty and the simulation can be restarted without any errors. I tried reducing t= he number of ABFs (and colvars) to 20 and the final files were non-empty in= this case. However, on the fourth restart, the files are again empty. = ;
I'm using the CUDA accelerated version of NAMD 2.13 with 2 GeForce RTX 2080= Ti and 20 CPU cores. The run command is as follows:
namd2 +p20 +idlepoll +devices $CUDA_VISIBLE_DEVICES d1-4.conf > d1-4.log=

One possible workaround we found was to use just 1 thread but that slows do= wn the simulation significantly.

I have been stuck on this for a while now and any help would be much apprec= iated.

Thank you
Shivansh Seth
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boundary="000000000000417fa905c0136bfc" X-CLX-Shades: MLX X-Proofpoint-GUID: MKT6YdyiXFC4nqOuz9wuAzCMeRsHmEE6 X-CLX-Response: 1TFkXGxobEQpMehcZGR0RCllEF2RjZFtTHXkbQm5SEQpYWBdjRUEbTnlQX2R bfhEKeE4XY1Nja3sTWH4aX14RCnlMF2JjXU5YZXhwQUJnEQpDSBcHGRgeEQpDWRcHGxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxgacRsGGRN3Bh0YBhoGGgYTBhpxGhAadwYaBhoGGgYaBhoGGnEaE Bp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF2dhfhxzTlNDcmxpHkRbZV9QE11fa1Bp Z094WWJHb28cEQpYXBcfBBoEGBgdBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JYXFpsEQpNXBc bEhEKTFoXaGlNa2sRCkxGF29ra2traxEKQk8XYhlCZxxFc2NbQWARCkNaFxgaEwQSHwQYGx0EHh 0RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXb WVTenxHbmhPUm0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdjRUEbTnlQX2RbfhEKQmwXYhloEkhQQF0d HB4RCkJAF2JOaRwYcElaREkSEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFx4RCnlDF29HYk5 FTmtiYFgSEQpZSxcTGR0SEQpwZxdmWh9aHxt/H1NsbxAHGRoRCnBoF2Ndf0VSWmdreh5BEAcZGh EKcGgXa3pHHlgfUkJZRVIQBxkaEQpwaBdoeF9NW0R6b3JvehAHGRoRCnBoF29BSxlQGHxue31HE AcZGhEKcGgXZVNib24cWHNhE1kQBxkaEQpwfRdvc3B4fWBZSG94fRAHGRoRCnB/F2hAfRtSX2ZI XlNsEBsbGREKcF8XYRNbZEJnH0BYe1sQGxsbEQpwbBdsQRpfTlpOR0sBZxAHGRoRCm1+FwcbEQp YTRdLESA= X-Proofpoint-ORIG-GUID: MKT6YdyiXFC4nqOuz9wuAzCMeRsHmEE6 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 spamscore=0 lowpriorityscore=0 phishscore=0 clxscore=101 mlxlogscore=824 suspectscore=0 adultscore=0 mlxscore=0 bulkscore=0 malwarescore=0 priorityscore=337 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104160070 domainage_hfrom=9378 X-Spam-Score: 0 X-Spam-OrigSender: ybruizblanco@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Yasser Bruno Ruiz Blanco --000000000000417fa905c0136bfc Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear all, I am trying to set up NAMD in a small dedicated cluster (20 nodes with AMD EPYC 7402 processors) connected via Ethernet 1Gbps (no high-performance network such as Infiniband or Omni path). I have tried to run directly the prebuild version: "NAMD_2.14_Linux-x86_64-netlrts". However, it produces errors related to lack of authorization for accessing the nodes I then tried to compile the code using MPI libraries but the jobs hang without output. I would be grateful to receive advice about the use of the prebuild version in a cluster with the characteristics mentioned above. Or, some additional guidelines for the compilation. Also, could you comment on the expected scaling in such a cluster? Kind regards. Stay healthy, Yasser --=20 ___ Dr. Yasser B. Ruiz-Blanco Postdoctoral Researcher Computational Biochemistry Faculty of Biology University of Duisburg-Essen email: yasser.ruizblanco@uni-due.de ORCID: https://urldefense.com/v3/__https://orcid.org/0000-0001-5400-4427__;= !!DZ3fjg!qeZG3pIPQIzDAKjiWsgBDNDPmDIyTLnaYkRHQqB4Pc2lK8ckoL2ePB0ajQ6mlWqdkA= $=20 --000000000000417fa905c0136bfc Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear all,

I am trying to set up NAMD in= a small=20 dedicated cluster (20 nodes with AMD EPYC 7402 processors) connected via Et= hernet 1Gbps (no high-performance=C2=A0network such as Infiniband or Omni p= ath).

I have tried to run directly the prebuild ve= rsion: "NAMD_2.14_Linux-x86_64-netlrts". However, it produces err= ors related to lack of authorization for accessing the nodes

=
I then tried to compile the code using MPI libraries but the job= s hang without output.

I would be grateful to rece= ive advice about the use of the prebuild version in a cluster with the char= acteristics mentioned above. Or, some additional guidelines for the compila= tion.

Also, could you comment on the expected scal= ing in such a cluster?=C2=A0

Kind regards. Stay he= althy,
Yasser

--
___
Dr. Yasser B. Ruiz-Blanco
Pos= tdoctoral Researcher
Computational Biochemistry
Faculty of Biology
University of Duisburg-Essen
email: yasser.ruizblanco@u= ni-due.de
<= /div>
--000000000000417fa905c0136bfc-- From owner-namd-l@halifax.ks.uiuc.edu Fri Apr 16 13:52:26 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13GIqQig014450; Fri, 16 Apr 2021 13:52:26 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13GIqQbp014449; Fri, 16 Apr 2021 13:52:26 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13GIqPiq014445; Fri, 16 Apr 2021 13:52:25 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13GIqPpJ014444; Fri, 16 Apr 2021 13:52:25 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13GIqFSv014437 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 16 Apr 2021 13:52:16 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13GIaZo0024589 for ; Fri, 16 Apr 2021 18:52:15 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qk1-f174.google.com (mail-qk1-f174.google.com [209.85.222.174]) by mx0b-00007101.pphosted.com with ESMTP id 37ybpvba5p-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 16 Apr 2021 18:52:15 +0000 Received: by mail-qk1-f174.google.com with SMTP id q136so8979891qka.7 for ; Fri, 16 Apr 2021 11:52:15 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=epONviGT1WMU7n01sJi6y92UhC0vMsMDurAa3cCN2Aw=; b=Mu/Vxo+bMkn8CmYSz3BxcsjQ1Ec7Wt49GDNf2Ay5ahHM38SCxpgJB9vkPHI9chHUiu cevwe2cRLtot8cwfjP9iaAOlkRNaJ8uOn7wLCgTuiXGo6O/LaK0QCY7xsKwSdyjjWS0f OKxQo5aLGPXT2pL9A61urqH1hDkgosNQCBWu0atzQMTrYKptZ1DjGdkEK017Mq8Pqyjj u7R9JC8HwTCUOougKaARBoYQjr5rwYWqBqpYVtcEcQXSVwb2N92QjoIrV+23dZoDTwfG CQa2lTzzCiElYHLP586vkf0snjcbFEPTA7W9EIDa00dKfC/wi9kFJpL/7P/hFQU5su/X A5mw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=epONviGT1WMU7n01sJi6y92UhC0vMsMDurAa3cCN2Aw=; b=DwLsY6M/usYBvHDMoIf+HXQ1HJ+N4R6Doo1lfyG+n/mrRdpu9rMYLdCqQZkukm7jS9 SOqNPBXNDgeAVyMYNKw4xK3yUZl69hE19YbFDxxVf7xXxARGhKZ3ejPZ/RYQ8IaTo/dT SG3QTNet4eosEnKdVBFzeuCKh1B9M4IUmkd0axliokIF9uJQ4lEnMwmSudZV4h0KgFhf 2VaPmHiMjTfWp37iAZ0DG7vIz1t8fmQDakfDt7qkwwVyBjdZUmn2CV/xFvLUUD/ufQ34 79FxdPlJG2I0jtrOZr7KNIKY3gryuxJiVMIWbsy/e4YcBUtfEcNOBXva4R3MWxhCTMGy Fatw== X-Gm-Message-State: AOAM532TTXyM0CTe5G9yQPQsbGXWekdpVJdOADQhAC9jEL5oHcRcINrw Mb8zwerVsKUcFt5N3Wy+hGxc/2t55EQ/XQ== X-Google-Smtp-Source: ABdhPJxlcPzmOupAbBIMXWuj/C65LV1C8DxJF922aXTMTAaLuzudXHDalAdOt3UFdz7em+M/q4WFIg== X-Received: by 2002:a05:620a:1592:: with SMTP id d18mr637239qkk.329.1618599134665; Fri, 16 Apr 2021 11:52:14 -0700 (PDT) Received: from [192.168.1.36] ([190.43.78.169]) by smtp.gmail.com with ESMTPSA id i21sm4314478qtr.94.2021.04.16.11.52.12 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Fri, 16 Apr 2021 11:52:14 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 16 Apr 2021 13:52:11 -0500 Subject: namd-l: Center trajectory with box dodecahedron From: "Ropon-Palacios G." To: KS UIUC Message-ID: <99CEC756-B759-47F6-B2DD-436CD88EC996@gmail.com> Thread-Topic: Center trajectory with box dodecahedron Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3701425933_1264825447" X-CLX-Shades: MLX X-Proofpoint-GUID: YiZOCBKPiRM9NOpcFfhXOFO-XiiM6vhv X-CLX-Response: 1TFkXGx0bEQpMehcZHx4RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGBwcEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3NDcGVpaGF6Q3hnE2RlWklsTEJyZWxlB3JDQ2ccXEJcEQpYXBcfBBoEGBgd BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JYHmwcEQpNXBcbHRwRCkxaF2xpa01rEQpMRhdva2t ra2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBBsdHhEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja 3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXelN7Q1tFQ2xhW3gR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdkRBhrUGlCaWFtRBEKWUsXExkdEhEKcGg Xen1EXBgeAR1laWQQGRoRCnBoF2daZ0RmEmhJTUZ5EBkaEQpwaBd6Wm1Ge1IefkJuWBAZGhEKcG gXaB1ie2gaBRIdZE4QGRoRCnBoF28dfhpCWUJYSx1vEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKc EwXZ35QfU1rUE9PRmIQGRoRCnBDF2FGZWEdHGtka00cEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: YiZOCBKPiRM9NOpcFfhXOFO-XiiM6vhv X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 bulkscore=0 suspectscore=0 mlxlogscore=588 spamscore=0 malwarescore=0 clxscore=171 mlxscore=0 priorityscore=354 adultscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104160131 domainage_hfrom=9378 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3701425933_1264825447 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear users, I am using MDanalysis to convert the DCD traj to XTC and the PDB to GRO then I use these to center the trajectory with gromacs command: "gmx trjconv -s prod.gro -f prod.xtc -o prod_center.xtc -center -pbc mol - ur compact ", when I load in VMD the GRO with the new heading, it throws me an error in bonds out of range, and when I load it with the original PSF and the XTC it does not give me this error. I would like to know if I can use the original PSF with the XTC centered to start doing analysis (type RMSD, RMSF, SASA, etc.) Best, Geo --B_3701425933_1264825447 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear users,

 =

I am using MDanalysis to convert= the DCD traj to XTC and the PDB to GRO then I use these to center the traje= ctory with gromacs command: "gmx trjconv -s pro= d.gro -f prod.xtc -o prod_center.xtc -center -pbc mol - ur compact ", when I load in VMD the GRO with the new heading, it throws me an error= in bonds out of range, and when I load it with the original PSF and the XTC= it does not give me this error. I would like to know if I can use the origi= nal PSF with the XTC centered to start doing analysis (type RMSD, RMSF, SASA= , etc.)

<= span style=3D'font-size:11.0pt;font-family:"Calibri Light",sans-serif'>&n= bsp;

Best,

 

Geo

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boundary="_000_BMXPR01MB32690C99529BD25E3A4EA9B3BE4B9BMXPR01MB3269INDP_" MIME-Version: 1.0 X-OriginatorOrg: iitg.ac.in X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BMXPR01MB3269.INDPRD01.PROD.OUTLOOK.COM X-MS-Exchange-CrossTenant-Network-Message-Id: 5e45b5d7-b016-409f-5dd6-08d901727262 X-MS-Exchange-CrossTenant-originalarrivaltime: 17 Apr 2021 07:28:50.5505 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 850aa78d-94e1-4bc6-9cf3-8c11b530701c X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: tGE+cPY6R8VTXH+mfcOAMGAQ62snSCVGfv3FybdaDVTWdb4xHp0maSTjZYYArYLQeELquEWDLgqzi6QNhOAB3Q== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BMXPR01MB3141 X-CLX-Response: 1TFkXGxIeEQpMehcaEQpZRBdpf0xlTWVnb256GREKWFgXb2MSUGkFZGViR1A RCnhOF25Tbh9OEmhjG1kBEQp5TBdhHRNdQxNTfW5EGhEKQ0gXBxkSHREKQ1kXBxsSGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscHnEeGRAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdmb3pdSG1vYgdccH1yB0FzW3pdS29gaVJiYxlQdUceeBEKWFwXHwQaBBgYHQUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JZbmZ8EQpNXBcHHxsRCkxaF3hpTU1rEQpFWRdvEQpMXxd 6BQUFBQUFBQUFQxEKTEYXb2tra2traxEKQk8XaUVwGwFzWHhPG0gRCkNaFx4aBBsaHQQbGRIEGx sbEQpCXhcbEQpEXhcYEQpCRRdmG1JcY0USQRoaZhEKQk4XblNuH04SaGMbWQERCkJMF29jElBpB WRlYkdQEQpCbBdvf25kf0ZtTFpmYxEKQkAXbhl+eXxdTklwe2kRCkJYF2dzZXNAbmFhTF1iEQpN XhcbEQpaWBcbEQp5QxdnQ3pARFgbTxhEZBEKWUsXHB4ZExEKcGgXaH9Sb0ZzUEVAG3IQGRoRCnB oF2F/HBhmX3JkYl9kEBkaEQpwaBdgYHgFYXgaaWJ8SRAZGhEKcGgXaBljAWZ7U3pARG8QGRoRCn BoF25feElMWXMYRGUSEBkaEQpwbBdiHFlacgFmT29MXxAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: LEPwbGEH-vZWX-kYqPwaEJCxHI3z_m4R X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: LEPwbGEH-vZWX-kYqPwaEJCxHI3z_m4R X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=808 suspectscore=0 adultscore=0 mlxscore=0 malwarescore=0 spamscore=0 bulkscore=0 clxscore=184 lowpriorityscore=0 impostorscore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104170049 domainage_hfrom=6439 X-Spam-Score: 0 X-Spam-OrigSender: t.shivam@iitg.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, SHIVAM TIWARI --_000_BMXPR01MB32690C99529BD25E3A4EA9B3BE4B9BMXPR01MB3269INDP_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I want to simulate reverse osmosis process on a box of water and ions acros= s a membrane, for which, I am applying a transmembrane pressure on the wate= r box through a graphene sheet (as a piston). I am using tclforces to achie= ve this, the script I am using is as follows: tclForces on tclForcesScript { set linaccel1 {0.0 0.0 -0.0006449914635} set linaccel2 {0.0 0.0 0.0006449914635} set watIdList1 {} set watIdList2 {} for {set i 1} {$i <=3D 5520} {incr i} { lappend watIdList1 $i addatom $i } for {set i 229378} {$i <=3D 234897} {incr i} { lappend watIdList2 $i addatom $i } But the problem with this is that the graphene sheet behaves as a graphene = sheet and not as a rigid piston, that is, the graphene sheet gets deformed = (curled up) as soon as the pressure is applied. Although, the water does ge= t pushed, but I suspect that the pressure applied in this case is much less= er than the desired, since most of the force applied on the graphene sheet = must be getting wasted on the deformation of the graphene sheet. So how can= I achieve a rigid graphene piston? regards shivam --_000_BMXPR01MB32690C99529BD25E3A4EA9B3BE4B9BMXPR01MB3269INDP_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
I want to simulate reverse osmosis process on a box of water and ions acros= s a membrane, for which, I am applying a transmembrane pressure on the wate= r box through a graphene sheet (as a piston). I am using tclforces to achie= ve this, the script I am using is as follows:

tclForces on

tclForcesScript {
  set linaccel1 {0.0 0.0 -0.0006449914635}
  set linaccel2 {0.0 0.0 0.0006449914635}


  set watIdList1 {}
  set watIdList2 {}



  for {set i 1} {$i <=3D 5520} {incr i} {
    lappend watIdList1 $i
    addatom $i
  }
  for {set i 229378} {$i <=3D 234897} {incr i} {
    lappend watIdList2 $i
    addatom $i
  }

But the problem with this is that the graphene sheet behaves as a graphene = sheet and not as a rigid piston, that is, the graphene sheet gets deformed = (curled up) as soon as the pressure is applied. Although, the water does ge= t pushed, but I suspect that the pressure applied in this case is much lesser than the desired, since most = of the force applied on the graphene sheet must be getting wasted on the de= formation of the graphene sheet. So how can I achieve a rigid graphene pist= on?

regards
shivam
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boundary="000000000000c6aa2805c0450721" X-Proofpoint-GUID: durdM5zo9_5180L8d-LT_OY62I8ZYtHP X-Proofpoint-ORIG-GUID: durdM5zo9_5180L8d-LT_OY62I8ZYtHP X-CLX-Response: 1TFkXGxIYEQpMehcZGBMRCllEF2hBb0V/U2YSa2tCEQpYWBdlAU1/ZX1MYRN mHREKeE4XY1Nja3sTWH4aX14RCnlMF3pGWl0eaHp8AWdfEQpDSBcHGB8eEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwYcR4bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF05fWE5nH1BFE3UfGxIaZhJOB2Z+dWVzHBhjEnBzXmJ6EQpYXBcfBBoEGBgd BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXcllAW0kRCk1cFxgYGhEKTFoXaGlrTWsRCkxGF29ra2t raxEKQk8XbhxnHVlyZ2ZeSHIRCkNaFxgaEwQSHwQYGhIEHhkRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXbQVBZ0J+ZGFyaEkRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdlAU1/ZX1MYRNmHREKQmwXaUVbQXJFYUlNbkERCkJAF29hXUYfZVNvc2VkEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaHhvSUUcb21eZW8RCllLFxMZEhoRCnBoF2N QUEcTRBxDGkNpEBkaEQpwaBdnUEN5H1scaEZteRAZGhEKcGgXa21LfGcfSHhMYxMQGRoRCnBoF2 1OY1JmYh4Ye3pIEBkaEQpwaBdkWXBBGlt8HFhCZRAZGhEKcGwXaX5EGAV/G1lkSRsQGRoRCnBMF 21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 lowpriorityscore=0 malwarescore=0 impostorscore=0 bulkscore=0 phishscore=0 adultscore=0 mlxscore=0 mlxlogscore=918 priorityscore=329 clxscore=182 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104180146 domainage_hfrom=9380 X-Spam-Score: 0 X-Spam-OrigSender: ecroitoru1@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ethan Croitoru --000000000000c6aa2805c0450721 Content-Type: text/plain; charset="UTF-8" Hello, I am calculating the free energy of binding between a helical dimer following the protein ligand binding tutorial. When I run the simulations to calculate the contribution of separation I set the upperboundary to 40A, and I run this for 40ns (split into 2 20ns runs). At the beginning of the second run the dimer reached the 40A and very quickly snapped back together to about 13A (their starting distance). It took about 23 ns to pull apart the dimer, but it snapped back within 5ns. I was wondering what was occurring here because I thought the upperboundary parameter did not affect dynamics and only affected the bins for ABF calculations. Any insights would be appreciated. Thank you, Ethan Croitoru --000000000000c6aa2805c0450721 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,

I am calculating the free energy= of binding between a helical dimer following the protein ligand binding tu= torial. When I run the simulations to calculate the contribution of separat= ion I set the upperboundary=C2=A0to 40A, and I run this for 40ns (split int= o 2 20ns runs). At the beginning of the second run the dimer reached the 40= A and very quickly snapped back together to about 13A (their starting dista= nce). It took about 23 ns to=C2=A0pull apart the=C2=A0dimer, but it=C2=A0sn= apped back within 5ns. I was wondering what was occurring=C2=A0here because= I thought the upperboundary=C2=A0parameter did not affect dynamics and onl= y affected the bins for ABF calculations. Any insights=C2=A0would be apprec= iated.

Thank you,
Ethan Croitoru
--000000000000c6aa2805c0450721-- From owner-namd-l@halifax.ks.uiuc.edu Mon Apr 19 05:04:21 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JA4LvH017782; Mon, 19 Apr 2021 05:04:21 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13JA4LjN017781; Mon, 19 Apr 2021 05:04:21 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JA4Kis017777; Mon, 19 Apr 2021 05:04:20 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13JA4KNw017776; Mon, 19 Apr 2021 05:04:20 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JA4B0u017769 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 19 Apr 2021 05:04:12 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13J9xrqf008436 for ; Mon, 19 Apr 2021 10:04:11 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=stefano.guglielmo@unito.it; dkim=pass header.s=google header.d=unito.it Received: from mail-lf1-f50.google.com (mail-lf1-f50.google.com [209.85.167.50]) by mx0b-00007101.pphosted.com with ESMTP id 3810s8a7n3-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 19 Apr 2021 10:04:11 +0000 Received: by mail-lf1-f50.google.com with SMTP id i10so19120496lfe.11 for ; Mon, 19 Apr 2021 03:04:11 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=unito.it; s=google; h=mime-version:from:date:message-id:subject:to; bh=kDs+7l0VfkvYCxZj509dNqQ4tluOOYyCQ38Ys1JKmpY=; b=Ub9hRtzfkPPT9XzJaSdRQTSuX32dqVNAHhxMzectvo8NkOEJzPHqQokCvbDhLY8ivd 0m/Wvxh/0vOfxIWrjdd3q6mT8XVGlAPBQI3vwcB5GKI1vrIhwBq4jdISIm7J16KzI7hl c4iqYKgmInCJF/q4fEMIMxRTZvepXaFIV+Kvs= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=kDs+7l0VfkvYCxZj509dNqQ4tluOOYyCQ38Ys1JKmpY=; b=F60uu4xWWvehha5jFedFDYzIGVOKcR2NAnvvaEzbW5W8Snpn1wj5VHfM1POmKetaKF G9el33ZtvN76lcsTfIwoudnlUb1O+Zr49kBlLDEaEtw28yegfzTELJaRhXdocisw9Mn5 LMXOrI+72ZWzS9egIZ5y2WrcsUzmhh3vktJ5lTnzZnYtcswKeHYUz3vJcigodBavFMRU XGpyQzBpPQml+9zF+K/knXTizdSSapgGV5iJV1QDT7uF0zGN8EHD3/932GULjSrVjPyP oXyuw8LyMp3U4Ao3S1vUoSTgL2H9ME1bamtWNEyXkA/aRmNbe58dk0gnhxVhGegZmvwp NDjQ== X-Gm-Message-State: AOAM531JFc4TjXnn7BbhuUkgPsWLtHM7bVpqzjIaZNdXsWltPTCLLvSC UBzThWka88UQ6XWs0+BeWe+KuCmjJERPRAnldmdBixU/FOpIFg== X-Google-Smtp-Source: ABdhPJzRpV3YCEzXd8NRrGZDzTHhC6dZfyMMm5Lnb4RCHMwsyVoA6wY0fWC0v3ujl5dcRGxZATyCXF9GuPmYxQ4uUTM= X-Received: by 2002:a19:6b11:: with SMTP id d17mr11465987lfa.382.1618826649371; Mon, 19 Apr 2021 03:04:09 -0700 (PDT) MIME-Version: 1.0 From: Stefano Guglielmo Date: Mon, 19 Apr 2021 12:03:58 +0200 Message-ID: Subject: namd-l: gpu performance To: NAMD list Content-Type: multipart/alternative; boundary="000000000000639c1a05c05073f5" X-Proofpoint-ORIG-GUID: XbWIxyA93XPfWYkxXC_GZf65sAaskDXx X-CLX-Response: 1TFkXGxwbEQpMehcaEQpZRBdoYxJpa19AYh15HxEKWFgXYGhPckVfeVJfG1k RCnhOF21/aEtAQWRgZFBrEQp5TBdnfnNzZ2UFH0hfaREKQ0gXGxgRCkNZFwcdGREKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhseG3EfGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZX k9OEQpDThdySH1jUlNrExlyekx9c0FScml1bXBMHB9Za0tZQW5yUhEKWFwXHwQaBBgYHQUbGgQb GxoEHxoEGx4YEBseGh8aEQpeWRdyWVxFGBEKTVwXGB8bEQpMWhdoaWtNaxEKTEYXb2tra2trEQp CTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQQfGhEKQl4XGxEKQlwXGxEKXk4XGxEKQksXbX 9oS0BBZGBkUGsRCkJJF21/aEtAQWRgZFBrEQpCRRdpTXpiHnNcHmJDUhEKQk4XbX9oS0BBZGBkU GsRCkJMF2BoT3JFX3lSXxtZEQpCbBd6exlJa0JSHk1yUBEKQkAXZUBHen16SGF4ewURCkJYF2dz ZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdsBR0eTmdrG0FIbREKcGgXbHkTaR9bYxNHbEIQGRo RCnBoF2ATb14Yb3BwXk5aEBkaEQpwaBdmQ2cFSG9/ZW55aBAZGhEKcGgXZhlbW0Rhe2hHQVgQGR oRCnBoF2luWRkfTVBPHB8aEBkaEQpwbBdocBtISGFla1xHBRAZGhEKcEwXbWhlGUFSfXsYRVIQG RoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: XbWIxyA93XPfWYkxXC_GZf65sAaskDXx X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 malwarescore=0 mlxscore=0 suspectscore=0 lowpriorityscore=0 mlxlogscore=747 bulkscore=0 clxscore=161 impostorscore=0 phishscore=0 spamscore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104190068 X-Spam-Score: 0 X-Spam-OrigSender: stefano.guglielmo@unito.it X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Stefano Guglielmo --000000000000639c1a05c05073f5 Content-Type: text/plain; charset="UTF-8" Dear all, I am trying to upgrade a workstation with a new gpu. The workstation is equipped with a dual core Intel Xeon Gold 5218R Processor, 27.5M Cache, 2.10 GHz 20 Cores and 192 GB of ram. Due to difficulties to get hands on Nvidia rtx 3090 (and 3080 as well), I am considering to turn to quadro rtx6000. Are there any benchmarks for this card, or does anyone have experience on that, with the most recent versions of NAMD? Thanks in advance Stefano -- Stefano GUGLIELMO PhD Associate Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178 --000000000000639c1a05c05073f5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear all, I am trying to upgrade a workstation with a new = gpu. The workstation is equipped with a dual core Intel Xeon Gold 5218R Pro= cessor, 27.5M Cache, 2.10 GHz 20 Cores and 192 GB of ram.
Due to difficu= lties to get hands on Nvidia =C2=A0rtx 3090 (and 3080 as well), I am consid= ering to turn to quadro rtx6000. Are there any benchmarks for this card, or= does anyone have experience on that, with the most recent versions of NAMD= ?
Thanks in advance
Stefano

--
Stefano GUGLIELMO P= hD
Associate Professor of Medicinal Chemistry
Department = of Drug Science and Technology
Via P. Giuria 9
10125 Turi= n, ITALY
ph. +39 (0)11 6707178

--000000000000639c1a05c05073f5-- From owner-namd-l@halifax.ks.uiuc.edu Mon Apr 19 08:33:29 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JDXTY4021432; Mon, 19 Apr 2021 08:33:29 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13JDXTG0021431; Mon, 19 Apr 2021 08:33:29 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JDXSwl021427; Mon, 19 Apr 2021 08:33:28 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13JDXS5j021426; Mon, 19 Apr 2021 08:33:28 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JDXJBH021419 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Mon, 19 Apr 2021 13:33:17 +0000 Received: from CY4PR12MB1351.namprd12.prod.outlook.com ([fe80::e424:4cee:a0a1:c34f]) by CY4PR12MB1351.namprd12.prod.outlook.com ([fe80::e424:4cee:a0a1:c34f%11]) with mapi id 15.20.4042.024; Mon, 19 Apr 2021 13:33:17 +0000 From: "Vermaas, Josh" To: "namd-l@ks.uiuc.edu" , Stefano Guglielmo Subject: Re: namd-l: gpu performance Thread-Topic: namd-l: gpu performance Thread-Index: AQHXNQSTeFkYJsXB7Ei0QZDzN62Zhaq71xOA Date: Mon, 19 Apr 2021 13:33:17 +0000 Message-ID: <9fdf0f0e-e756-c9d0-494a-3b654909a1d7@msu.edu> References: In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: user-agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.9.1 authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=msu.edu; x-originating-ip: [52.144.34.248] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: c6793d62-9580-4ce5-fb5e-08d90337b117 x-ms-traffictypediagnostic: CY4PR12MB1717: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:8273; 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boundary="_000_9fdf0f0ee756c9d0494a3b654909a1d7msuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: c6793d62-9580-4ce5-fb5e-08d90337b117 X-MS-Exchange-CrossTenant-originalarrivaltime: 19 Apr 2021 13:33:17.7819 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: vgVTELg0/FQnBn9qLstkzhsbJtIHXBZmzlcLJKOLc7mmvrDQKcWMcLYLfUvMc0WFNZ9zlG0Mxbn6skpGNVju2A== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR12MB1717 X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: Ao0j7KErH_c7Mdx6BFDPF53sxEL4eyBU X-CLX-Response: 1TFkXGBsYEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxsbGBEKQ1kXBx4SEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxMYcRscHBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdrRRpAHWFvWGJ1SR1nTlIcaGxuemwfGVlSb2YeT1NofxEKWFwXHwQaBBgYHQUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3JZU1kcEQpNXBccGBkRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF3pec0ESTxtpHEZzEQpDWhceGgQbGh0EGBkcBB wTEQpCXhcbEQpEXhcZEQpCRRdobWtgeRJLQFoefREKQk4XaG9MZgFyZmRLXRIRCkJMF29hWBMaS 10bQ0FlEQpCbBdheRwfElx7T1ppQhEKQkAXYGV/ZkBTGXBbGUkRCkJYF2dzZXNAbmFhTF1iEQpa WBcZEQp5QxdiQUhBfH17WmATfhEKWUsXGxgeGhgRCnBnF3p+XUVkRxpObk9cEBkaEQpwaBdjaUk ecgVFGFJkeBAZGhEKcGgXZHN/WnNTYmNwTlsQGRoRCnBoF2l4WW8SbBl5TWlIEBkaEQpwaBdmT0 VPZHlQR0t5WhAZGhEKcGgXaW5ZGR9NUE8cHxoQHBoRCnB9F2t6HGBTGRhvUEVgEBkaEQpwfxduH 2ddfV5AE3hkeRAbGhkRCnBfF2RjaG0efVBrTFBgEBkaEQpwbBdneBpAYhhJGn55TRAZGhEKbX4X GhEKWE0XSxEg X-Proofpoint-GUID: Ao0j7KErH_c7Mdx6BFDPF53sxEL4eyBU MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 suspectscore=0 mlxlogscore=999 lowpriorityscore=0 mlxscore=0 adultscore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=212 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104190092 domainage_hfrom=12402 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_9fdf0f0ee756c9d0494a3b654909a1d7msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable >From my albeit limited understanding, a RTX 6000 is roughly the equivalent = of a RTX2080-TI in terms of performance. The RTX 6000 has features NAMD doe= sn't really benefit from (double precision arithmetic, large amounts of RAM= ), so usually the price delta vs a "gaming" card makes them worse in terms = of price/performance at MSRP for NAMD. For the price of one RTX 6000 (~$450= 0), I basically got a complete system with an RTX 3090 preinstalled from a = system integrator ($5000 per workstation). It may be cheaper/faster to spec= a new pre-built system with 2 GPUs, and once it arrives, yank one out to u= pgrade your existing workstation. -Josh On 4/19/21 6:03 AM, Stefano Guglielmo wrote: Dear all, I am trying to upgrade a workstation with a new gpu. The workstat= ion is equipped with a dual core Intel Xeon Gold 5218R Processor, 27.5M Cac= he, 2.10 GHz 20 Cores and 192 GB of ram. Due to difficulties to get hands on Nvidia rtx 3090 (and 3080 as well), I = am considering to turn to quadro rtx6000. Are there any benchmarks for this= card, or does anyone have experience on that, with the most recent version= s of NAMD? Thanks in advance Stefano -- Stefano GUGLIELMO PhD Associate Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178 -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!r6N97z2-aPgzdUcYw7mdLvta15e-qcTVxUlj_yAiyB2Q3n0zhfztVFP= GvtzxZOBm1g$=20 --_000_9fdf0f0ee756c9d0494a3b654909a1d7msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <191BC5ACE8166643AE84F58D08B01F3B@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable >From my albeit limited understanding, a RTX 6000 is roughly the equivalent = of a RTX2080-TI in terms of performance. The RTX 6000 has features NAMD doe= sn't really benefit from (double precision arithmetic, large amounts of RAM= ), so usually the price delta vs a "gaming" card makes them worse in terms of price/performance a= t MSRP for NAMD. For the price of one RTX 6000 (~$4500), I basically got a = complete system with an RTX 3090 preinstalled from a system integrator ($50= 00 per workstation). It may be cheaper/faster to spec a new pre-built system with 2 GPUs, and once it arrives, yank one = out to upgrade your existing workstation.

-Josh

On 4/19/21 6:03 AM, Stefano Guglielmo wrote:=
Dear all, I am trying to upgrade a workstation with a new = gpu. The workstation is equipped with a dual core Intel Xeon Gold 5218R Pro= cessor, 27.5M Cache, 2.10 GHz 20 Cores and 192 GB of ram.
Due to difficulties to get hands on Nvidia  rtx 3090 (and 3080 as well= ), I am considering to turn to quadro rtx6000. Are there any benchmarks for= this card, or does anyone have experience on that, with the most recent ve= rsions of NAMD?
Thanks in advance
Stefano

--
Stefano GUGLIELMO PhD
Associate Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178


--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
--_000_9fdf0f0ee756c9d0494a3b654909a1d7msuedu_-- From owner-namd-l@halifax.ks.uiuc.edu Mon Apr 19 11:05:53 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JG5rfU024663; Mon, 19 Apr 2021 11:05:53 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13JG5qTI024662; Mon, 19 Apr 2021 11:05:52 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JG5qH5024658; Mon, 19 Apr 2021 11:05:52 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13JG5qS6024657; Mon, 19 Apr 2021 11:05:52 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13JG5jqb024650 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 19 Apr 2021 11:05:46 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13JG4f95004211 for ; Mon, 19 Apr 2021 16:05:45 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0b-00007101.pphosted.com with ESMTP id 381adsahb5-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 19 Apr 2021 16:05:45 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 59B0E1E4301B; Mon, 19 Apr 2021 18:05:43 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id y-uM6DzfHnzJ; Mon, 19 Apr 2021 18:05:36 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id BD45F1E43083; Mon, 19 Apr 2021 18:05:35 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id aLrIIV8441cX; Mon, 19 Apr 2021 18:05:35 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id DBF0D1E4306E; Mon, 19 Apr 2021 18:05:33 +0200 (CEST) Date: Mon, 19 Apr 2021 18:04:49 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , Ethan Croitoru Message-ID: <2044835454.7871026.1618848277862.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: Re: namd-l: Free Energy Calculations on Helical Dimer: Separation Run Snaps Back MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_773b2f2d-4a57-4463-93fe-7cdff463f743" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_3928 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_3928) Thread-Topic: namd-l: Free Energy Calculations on Helical Dimer: Separation Run Snaps Back Thread-Index: kSXA7quO5ij1ykxbHV7dX/eGd0NYvg== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: ExrqdKIU-i2sqmhjqcvz7DcwdJ7kk8ug X-CLX-Response: 1TFkXGxIZEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxkcGxEKQ1kXHBEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhscGXEeGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1QkVZX k9OEQpDThdvUlhbTmFjfwdDGFlbR0JAW0lcUB1uSV1OYB1BQRJfTREKWFwXHwQaBBgYHQUbGgQb GhoEHhIEGxMQGx4aHxoRCl5ZF3JZGh0aEQpNXBcbHRgRCkxaF3hta01rEQpFWRdvaxEKTF8XegU FBQUFBQUFBW8RCkxGF2xraxEKQk8XaEBFSBgYfGtbehkRCkNaFxsTGQQeEwQYGR4EGBgbEQpCXh cbEQpEXhcYEQpCRRdkWFxcTX5SSRtlSREKQk4XZU9+EkNpZlkcAWkRCkJMF3oSZ2lgWXlGQU9lE QpCbBdhEhJPT0xNf08eBREKQkAXYHJJfUgbSBhQeEsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpa WBcYEQp5QxdvGUtkGx5mTlBLEhEKcGcXZWxhXFgfQ2VMfR4QGRoRCnBoF2Aaa3J6cH9ScGVeEBM fEQpwaBdkfmZuU2ldcnIcGhAZGhEKcGgXbFxoW1J/GW5tS18QGRoRCnBoF21PRRgSHE95fGJ+EB kaEQpwaBdmRnwde3hlW2AbBRAZGhEKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17GEVSE BkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: ExrqdKIU-i2sqmhjqcvz7DcwdJ7kk8ug X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 suspectscore=0 mlxlogscore=999 lowpriorityscore=0 mlxscore=0 adultscore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=183 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104190109 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_773b2f2d-4a57-4463-93fe-7cdff463f743 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Ethan,=20 Fluctuations are always possible in ABF calculations (that's the point of A= BF, really). 5 ns is not an unreasonable timescale for that to happen. Unle= ss you see something else that looks pathological, I would not worry about = that.=20 Best,=20 J=C3=A9r=C3=B4me=20 ----- On Apr 18, 2021, at 10:26 PM, Ethan Croitoru w= rote:=20 > Hello, > I am calculating the free energy of binding between a helical dimer follo= wing > the protein ligand binding tutorial. When I run the simulations to calcul= ate > the contribution of separation I set the upperboundary to 40A, and I run = this > for 40ns (split into 2 20ns runs). At the beginning of the second run the= dimer > reached the 40A and very quickly snapped back together to about 13A (thei= r > starting distance). It took about 23 ns to pull apart the dimer, but it s= napped > back within 5ns. I was wondering what was occurring here because I though= t the > upperboundary parameter did not affect dynamics and only affected the bin= s for > ABF calculations. Any insights would be appreciated. > Thank you, > Ethan Croitoru --=_773b2f2d-4a57-4463-93fe-7cdff463f743 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Ethan,

Fluctuations are always possible in ABF calculations (that's t= he point of ABF, really). 5 ns is not an unreasonable timescale for that to= happen. Unless you see something else that looks pathological, I would not= worry about that.

Best,
J=C3=A9r=C3=B4me

----- On Apr 18, 2021, at 10:26 PM, Ethan Croitoru <= ecroitoru1@gmail.com> wrote:
Hello,
I am calculating the free energy of binding betwe= en a helical dimer following the protein ligand binding tutorial. When I ru= n the simulations to calculate the contribution of separation I set the upp= erboundary to 40A, and I run this for 40ns (split into 2 20ns runs). A= t the beginning of the second run the dimer reached the 40A and very quickl= y snapped back together to about 13A (their starting distance). It took abo= ut 23 ns to pull apart the dimer, but it snapped back within= 5ns. I was wondering what was occurring here because I thought the up= perboundary parameter did not affect dynamics and only affected the bi= ns for ABF calculations. Any insights would be appreciated.

<= div>Thank you,
Ethan Croitoru

<= /div> --=_773b2f2d-4a57-4463-93fe-7cdff463f743-- From owner-namd-l@halifax.ks.uiuc.edu Tue Apr 20 01:39:49 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13K6dnI0005225; Tue, 20 Apr 2021 01:39:49 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13K6dnPQ005224; Tue, 20 Apr 2021 01:39:49 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13K6dmVt005220; Tue, 20 Apr 2021 01:39:48 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13K6dmam005219; Tue, 20 Apr 2021 01:39:48 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13K6ddmV005211 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000b1736505c061b5b4" X-CLX-Shades: MLX X-Proofpoint-GUID: FsHhoOE470Qf1OdrwNIa8DO7d_DFzXz- X-CLX-Response: 1TFkXGxgcEQpMehcZHhwRCllEF2ZbAUJEbk8cW09oEQpYWBdmHxN7GV8bWkV vWBEKeE4XY1Nja3sTWH4aX14RCnlMF2hGWEhJcEZLQAFBEQpDSBcHGBsfEQpDWRcHHhkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwZcRsGGxgfdwYTGgYaBhoGGBkGGnEaEBp3BhoGBx8aBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdsWWJCRWVvHh0ae0wbZU5YXWRj SxJuZR1OdW5sUHJQBxEKWFwXHwQaBBgYHQUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3JeaFxsEQp NXBceHBEKTFoXbGlNa2sRCkxGF29ra2traxEKQk8XZX5cWVtbR2NTYWwRCkNaFxgaEwQSHwQYGx IEHxoRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQ kUXbH9BUkNuYxNkUB4RCkJOF2NTY2t7E1h+Gl9eEQpCTBdmHxN7GV8bWkVvWBEKQmwXYxJOWkFf TGxaHBoRCkJAF2NaG0NlfRhPXmNlEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxgRCnlDF2Z cZ21gYUtyXmRYEQpZSxcTGRIYEQpwaBduYkttQVoYE0lfTBAHGRoRCnBoF2BbS1wcXQFGe2xmEA cZGhEKcGgXbF9cck5pXF9JeGcQBxkaEQpwaBdnWGUdW34TW2ZvZxAHGRoRCnBoF2dJYR19RnNDc FhZEAcZGhEKcGwXbXoZe0ZsUm1NZGYQBxkaEQptfhcHGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: FsHhoOE470Qf1OdrwNIa8DO7d_DFzXz- X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 spamscore=0 malwarescore=0 adultscore=0 mlxscore=0 mlxlogscore=326 priorityscore=346 suspectscore=0 phishscore=0 lowpriorityscore=0 impostorscore=0 clxscore=126 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104200051 domainage_hfrom=9382 X-Spam-Score: 0 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --000000000000b1736505c061b5b4 Content-Type: text/plain; charset="UTF-8" Hi, I have done well tempered metadynamics for a system consisting of a molecule insertion into a bilayer using the colvars module. I am interested in doing an error analysis for obtained free energy preferably using colvars. Any help would be most appreciated. Thanks in advance -- Diship Srivastava JRF Department of Chemistry IIT(ISM) - Dhanbad India --000000000000b1736505c061b5b4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
I have done well tempered metadynamics for a syste= m consisting of a molecule insertion into a bilayer using the colvars modul= e. I am interested=C2=A0in doing an error analysis for obtained free energy= preferably=C2=A0using colvars.=C2=A0
Any help would be most appr= eciated.

Thanks in advance


--
Diship Srivastava= =C2=A0
JRF=C2=A0
Department of Chemistry
IIT(ISM) -= Dhanbad
India
--000000000000b1736505c061b5b4-- From owner-namd-l@halifax.ks.uiuc.edu Tue Apr 20 02:35:57 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13K7ZvUs010407; Tue, 20 Apr 2021 02:35:57 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13K7Zu0R010406; Tue, 20 Apr 2021 02:35:56 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13K7ZubS010402; Tue, 20 Apr 2021 02:35:56 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13K7ZuoJ010401; Tue, 20 Apr 2021 02:35:56 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13K7ZevF010378 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="00000000000016462a05c0627eed" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 6269fbVjf0AxMx4DtazIeWxg_GV2jS5b X-CLX-Response: 1TFkXGx0cEQpMehcZHxwRCllEF2JuE0NyXkBOE3NEEQpYWBdkXklSeh9YS25 EHhEKeE4XY1Nja3sTWH4aX14RCnlMF3p5RVtfXEV+UmlkEQpDSBcHGB4dEQpDWRcHGx0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxxxGR8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XHBgcE0xIfEBMGmtSZ1Iebl5LUGNPfVJNdW18GEB5H0gRClhcFx8EGgQYGB0F GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyXmlARxEKTVwXHBIRCkxaF3hpa01rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbXpuRH9LfR9+e0QRCkNaFxgaEwQSHwQbHBsEHh IRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXbnp4WmZsYEIFH2YRCkJOF2NTY2t7E1h+Gl9eEQpCTBdkXklSeh9YS25EHhEKQmwXenoe c2ZeEk5JWV8RCkJAF2F6HVlAS0VASHxcEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUM XYwVkGUJdbmNyWWkRCllLFxMZEhgRCnBoF25DXn8FW3oSe2BaEBkaEQpwaBdmbm15e1ATX29ZEx AZGhEKcGgXaU9HRWd6SVtTGXsQGRoRCnBoF2BiHmYbRhh+Z0VcEBkaEQpwaBdmE2NffxNnehNpA RAZGhEKcH0XZUBHZkVdRV9aS3kQGRoRCnB/F2tFUnlsGlB9QXwSEBkaEQpwXxd6RmJYGn1iXkVN cxAZGhEKcGwXYBxdHhpJTX0fQFsQGRoRCnBMF2YaXhJOZE1DeGRYEBkaEQptfhcbEQpYTRdLESA = X-Proofpoint-GUID: 6269fbVjf0AxMx4DtazIeWxg_GV2jS5b MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 mlxscore=0 mlxlogscore=733 clxscore=176 priorityscore=356 malwarescore=0 adultscore=0 phishscore=0 spamscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104200058 domainage_hfrom=9382 X-Spam-Score: 0 X-Spam-OrigSender: miro.astore@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Miro Astore --00000000000016462a05c0627eed Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Diship, you should be able to use the code/techniques in this tutorial. Good luck. https://urldefense.com/v3/__https://www.plumed.org/doc-v2.5/user-doc/html/t= rieste-4.html__;!!DZ3fjg!sp8OPR83ZO7SNR9X9YYdw-9CIV1DXCkkqKUva3mWJ5o6ou3SWv= onbwVzjmecWx3n9w$=20 On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava < dishipsrivastava@gmail.com> wrote: > Hi, > I have done well tempered metadynamics for a system consisting of a > molecule insertion into a bilayer using the colvars module. I am > interested in doing an error analysis for obtained free energy > preferably using colvars. > Any help would be most appreciated. > > Thanks in advance > > > > -- > Diship Srivastava > JRF > Department of Chemistry > IIT(ISM) - Dhanbad > India > --=20 Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney --00000000000016462a05c0627eed Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Diship, you should be able to use the code/techniq= ues in this tutorial. Good luck.


On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava <dishipsrivastava@gmail.com> w= rote:
Hi,
I have done well tempered metadynamics for a system consis= ting of a molecule insertion into a bilayer using the colvars module. I am = interested=C2=A0in doing an error analysis for obtained free energy prefera= bly=C2=A0using colvars.=C2=A0
Any help would be most appreciated.=

Thanks in advance



--
Diship Sri= vastava=C2=A0
JRF=C2=A0
Department of Chemistry
IIT= (ISM) - Dhanbad
India


--
Miro A. Astore =C2=A0 (he/him)
PhD Candidate | Computati= onal Biophysics
Office 434 A28 School of Physics
University of Sydney=
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Organization: Wroclaw University of Technology Message-id: <4de7df68-be69-9a93-33f6-ce847e4084db@pwr.edu.pl> Date: Wed, 21 Apr 2021 13:01:05 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 Content-language: en-US X-Proofpoint-GUID: ueXUqNmPgT4KZn7zd5QSCx7Pvl6blLdc X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBdtbHwZfXNCc31PbREKWFgXYEZFTEB+RGN7Znw RCnhOF21zZGBIE054GxJoEQp5TBdhHVNeHwVOa1keaREKQ0gXBx4YHBEKQ1kXBxsZEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseGXEYHBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdpW3Vne05sTF9oc0BnT19rGGZZc0RfZUgHGWtzcFkSchEKWFwXHwQaBBgYHQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdyXktZfBEKTVwXGRscEQpMWhdpTU1NEQpCTxdvRUVkaGA TbB1/SxEKQ1oXGx8cBBsdBBsTGQQbGRMRCkJeFxsRCkReFxgRCkJFF2QYZGNZE2ZtYkgBEQpCTh dtc2RgSBNOeBsSaBEKQkwXYEZFTEB+RGN7ZnwRCkJsF2NZTUJpekgcHm56EQpCQBdmGV5oYkZje kJYXBEKQlgXZ3Nlc0BuYWFMXWIRClpYFxsRCnlDF2BwSFxOUxpvXBIBEQpZSxcfExwTEQpwaBdm RQVle355XX1YUhAZGhEKcGgXYmRwbHxBWkVQeBIQGRoRCnBoF2BSfFgTGUhLfEhrEBkaEQpwaBd sb0xZfmBJY29hBRAZGhEKcGgXaE4aa2ZSXQVtbhIQGRoRCnBrF2l/Um9oAUFpW2gdEBkaEQpwSx dkGmlLHHJ8YBp5QxAZGhEKcGsXek9SSV1EXXJjaV4QGRoRCnBsF2VYR3p4RmxPTUBeEBkaEQpwQ xdme1NzG0l7ckBcARAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: Cq_MQdFfuBYjMeuA2LsYnuOb-3AYZs8X X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 malwarescore=0 mlxscore=0 mlxlogscore=999 clxscore=163 bulkscore=0 priorityscore=0 suspectscore=0 adultscore=0 lowpriorityscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=2 engine=8.12.0-2104060000 definitions=main-2104210085 domainage_hfrom=5969 X-Spam-Score: 0 X-Spam-OrigSender: pawel.kedzierski@pwr.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Pawel Kedzierski This is a multi-part message in MIME format. --Boundary_(ID_UBjdVqD1qkY/JSsBzz2neg) Content-type: multipart/alternative; boundary="Boundary_(ID_qFMpYURTWcw35pliEIeYhg)" --Boundary_(ID_qFMpYURTWcw35pliEIeYhg) Content-type: text/plain; charset=utf-8; format=flowed Content-transfer-encoding: 8BIT Dear NAMD wizards, The warning from the subject is a topic of many questions appearing on this list, but I haven't found a single answer which would explain its exact meaning and the conditions which trigger it. The usual answers are that it signs some steric or topology problems and such reasons lead to a quick crash due to divergence of movement integrations. But it does not apply to my case. In a case I am playing with - a sheet of graphene - NAMD produces immense numbers of these warnings, which seem to be false. The dynamics of the system is stable, no crash, setting cutoff and pairlist well above the system size does not help. These messages are just annoying filling 90% of the log size. I want to use this graphene example as exercise for my students, and this flood of warnings not only makes it look unprofessional, but what troubles me more is that I am unable to explain it. Specifically: * what exactly is "excluded globally" and what are the numbers reported? * are there any other conditions apart from cutoff, pairlistdist and steric problems, which I can change to silence this warning? The first number reported in the warnings changes regularly but the difference between them is rather huge, from 2340 vs 4593 when they first appear during minimization to for example 3759 vs 4593 at the end of dynamics. From my current experience, the combination of graphene and CHARMM forcefield is not optimal. I already learned that due to L-J interactions between bound carbons (in-plane) I was getting huge excess of VDW energy; this was mostly corrected with setting the 1-4 L-J parameters to 0, but possibly all in-plane L-J interactions should be discarded. Basically I use a copy of the parameters for standard CA type (which is also duplicated for CGenFF multi-ring ligands) and it provides all necessary parameters, I only changed the 1-4 part. Note that this type uses regular dihedrals instead of impropers to stiffen the ring plane, so I have generated the PSF with all planar dihedrals but without impropers. I will be grateful for any insight. With regards, Paweł Kędzierski P.S. Summary of the system for which I reported the numbers above. Note there are no hydrogens so "114 hydrogen groups" is confusing. Here I fixed atoms on the edge of the sheet but without fixing the flood of warnings is still there, only the numbers change. Info: STRUCTURE SUMMARY: Info: 603 ATOMS Info: 867 BONDS Info: 1659 ANGLES Info: 3186 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 114 FIXED ATOMS Info: 1467 DEGREES OF FREEDOM Info: 603 HYDROGEN GROUPS Info: 1 ATOMS IN LARGEST HYDROGEN GROUP Info: 603 MIGRATION GROUPS Info: 1 ATOMS IN LARGEST MIGRATION GROUP Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED Info: TOTAL MASS = 7242.63 amu Info: TOTAL CHARGE = 0 e --Boundary_(ID_qFMpYURTWcw35pliEIeYhg) Content-type: text/html; charset=utf-8 Content-transfer-encoding: 8BIT

Dear NAMD wizards,

The warning from the subject is a topic of many questions appearing on this list, but I haven't found a single answer which would explain its exact meaning and the conditions which trigger it. The usual answers are that it signs some steric or topology problems and such reasons lead to a quick crash due to divergence of movement integrations. But it does not apply to my case.

In a case I am playing with - a sheet of graphene - NAMD produces immense numbers of these warnings, which seem to be false. The dynamics of the system is stable, no crash, setting cutoff and pairlist well above the system size does not help. These messages are just annoying filling 90% of the log size.

I want to use this graphene example as exercise for my students, and this flood of warnings not only makes it look unprofessional, but what troubles me more is that I am unable to explain it. Specifically:

  • what exactly is "excluded globally" and what are the numbers reported?
  • are there any other conditions apart from cutoff, pairlistdist and steric problems, which I can change to silence this warning?

The first number reported in the warnings changes regularly but the difference between them is rather huge, from 2340 vs 4593 when they first appear during minimization to for example 3759 vs 4593 at the end of dynamics.

From my current experience, the combination of graphene and CHARMM forcefield is not optimal. I already learned that due to L-J interactions between bound carbons (in-plane) I was getting huge excess of VDW energy; this was mostly corrected with setting the 1-4 L-J parameters to 0, but possibly all in-plane L-J interactions should be discarded. Basically I use a copy of the parameters for standard CA type (which is also duplicated for CGenFF multi-ring ligands) and it provides all necessary parameters, I only changed the 1-4 part. Note that this type uses regular dihedrals instead of impropers to stiffen the ring plane, so I have generated the PSF with all planar dihedrals but without impropers.

I will be grateful for any insight.

With regards,

Paweł Kędzierski

P.S. Summary of the system for which I reported the numbers above. Note there are no hydrogens so "114 hydrogen groups" is confusing. Here I fixed atoms on the edge of the sheet but without fixing the flood of warnings is still there, only the numbers change.

Info: STRUCTURE SUMMARY:
Info: 603 ATOMS
Info: 867 BONDS
Info: 1659 ANGLES
Info: 3186 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 114 FIXED ATOMS
Info: 1467 DEGREES OF FREEDOM
Info: 603 HYDROGEN GROUPS
Info: 1 ATOMS IN LARGEST HYDROGEN GROUP
Info: 603 MIGRATION GROUPS
Info: 1 ATOMS IN LARGEST MIGRATION GROUP
Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 7242.63 amu
Info: TOTAL CHARGE = 0 e

--Boundary_(ID_qFMpYURTWcw35pliEIeYhg)-- --Boundary_(ID_UBjdVqD1qkY/JSsBzz2neg) Content-type: text/x-vcard; CHARSET=US-ASCII; name=pawel_kedzierski.vcf Content-transfer-encoding: 7BIT Content-disposition: attachment; filename=pawel_kedzierski.vcf begin:vcard fn;quoted-printable:Pawe=C5=82 K=C4=99dzierski n;quoted-printable;quoted-printable:K=C4=99dzierski;Pawe=C5=82 org;quoted-printable:Wroc=C5=82aw University of Technology, Faculty of Chemistry;Advanced Materials Engineering and Modelling Group adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:Wyb. Wyspia=C5=84skiego 27;;Politechnika Wroc=C5=82awska, Wydzia=C5=82 Chemiczny;Wroc=C5=82aw;dolno=C5=9Bl=C4=85skie;50-370;Poland email;internet:Pawel.Kedzierski@pwr.edu.pl tel;work:+48 71 3203200 tel;fax:+48 71 3203364 version:2.1 end:vcard --Boundary_(ID_UBjdVqD1qkY/JSsBzz2neg)-- From owner-namd-l@halifax.ks.uiuc.edu Wed Apr 21 15:31:54 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13LKVsL1010667; Wed, 21 Apr 2021 15:31:54 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13LKVsN0010666; Wed, 21 Apr 2021 15:31:54 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13LKVrL3010662; Wed, 21 Apr 2021 15:31:53 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13LKVrOb010661; Wed, 21 Apr 2021 15:31:53 -0500 (CDT) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13LKVnQ4010653 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Wed, 21 Apr 2021 15:31:50 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_D73F6EBE-A835-4C1F-837E-983C5318A8EC" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Meaning of the warning: Low global exclusion count! Date: Wed, 21 Apr 2021 15:31:44 -0500 References: <4de7df68-be69-9a93-33f6-ce847e4084db@pwr.edu.pl> To: namd-l@ks.uiuc.edu, Pawel Kedzierski In-Reply-To: <4de7df68-be69-9a93-33f6-ce847e4084db@pwr.edu.pl> Message-Id: <0C396555-F668-419F-BE2D-26AC0596CB30@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_D73F6EBE-A835-4C1F-837E-983C5318A8EC Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Pawel, NAMD calculates certain checksums to make sure that, due to its parallel = decomposition, no terms are accidentally dropped during force = evaluation. The =E2=80=9Cglobal exclusion=E2=80=9D checksum counts the = total number of non-bonded exclusions evaluated, where the exclusion = policy is set in the config file (usually =E2=80=9Cexclude scaled1-4=E2=80= =9D for CHARMM FF). Before the simulation begins, NAMD counts the total = number of non-bonded exclusions that it should be evaluating when = computing the force. It will then report when an undercount occurs. The = numbers reported are the checksum vs. the number of exclusions that = should have been evaluated. Since this does not end your simulation, = this must be occurring for you during minimization. If this were to = occur during dynamics, NAMD would terminate with an error. So why would this be occurring? Well, in order for an exclusion to be = calculated, the pair of atoms being excluded must be in an adjacent pair = of patches. It sounds like your graphene sheet has carbons spaced far = enough away, that you have exclusions due to a covalently bonded chain = of 3 or perhaps 4 carbon atoms that extend beyond an entire patch. To = avoid these messages, one thing you might try doing is artificially = increasing the patch size by setting =E2=80=9Cmargin=E2=80=9D to a = nonzero value large enough to pad the patches so that these 3-chains or = 4-chains of carbon atoms are kept in adjacent patches. As to the =E2=80=9Chydrogen group=E2=80=9D designation, NAMD, for = performance reasons, keeps each hydrogen atom together with its heavy = parent atoms, and refers to the resulting clusters as =E2=80=9Chydrogen = groups.=E2=80=9D In your case, every carbon atom would be its own = hydrogen group (and migration group). Since this has important meaning = for biomolecules, we report aspects of these clusters, such as the = =E2=80=9C114 hydrogen groups with all atoms fixed=E2=80=9D message. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Apr 21, 2021, at 6:01 AM, Pawel Kedzierski = wrote: >=20 > Dear NAMD wizards, >=20 > The warning from the subject is a topic of many questions appearing on = this list, but I haven't found a single answer which would explain its = exact meaning and the conditions which trigger it. The usual answers are = that it signs some steric or topology problems and such reasons lead to = a quick crash due to divergence of movement integrations. But it does = not apply to my case. >=20 > In a case I am playing with - a sheet of graphene - NAMD produces = immense numbers of these warnings, which seem to be false. The dynamics = of the system is stable, no crash, setting cutoff and pairlist well = above the system size does not help. These messages are just annoying = filling 90% of the log size. >=20 > I want to use this graphene example as exercise for my students, and = this flood of warnings not only makes it look unprofessional, but what = troubles me more is that I am unable to explain it. Specifically: >=20 > what exactly is "excluded globally" and what are the numbers reported? > are there any other conditions apart from cutoff, pairlistdist and = steric problems, which I can change to silence this warning? > The first number reported in the warnings changes regularly but the = difference between them is rather huge, from 2340 vs 4593 when they = first appear during minimization to for example 3759 vs 4593 at the end = of dynamics. >=20 > =46rom my current experience, the combination of graphene and CHARMM = forcefield is not optimal. I already learned that due to L-J = interactions between bound carbons (in-plane) I was getting huge excess = of VDW energy; this was mostly corrected with setting the 1-4 L-J = parameters to 0, but possibly all in-plane L-J interactions should be = discarded. Basically I use a copy of the parameters for standard CA type = (which is also duplicated for CGenFF multi-ring ligands) and it provides = all necessary parameters, I only changed the 1-4 part. Note that this = type uses regular dihedrals instead of impropers to stiffen the ring = plane, so I have generated the PSF with all planar dihedrals but without = impropers. >=20 > I will be grateful for any insight. >=20 > With regards, >=20 > Pawe=C5=82 K=C4=99dzierski >=20 > P.S. Summary of the system for which I reported the numbers above. = Note there are no hydrogens so "114 hydrogen groups" is confusing. Here = I fixed atoms on the edge of the sheet but without fixing the flood of = warnings is still there, only the numbers change. >=20 > Info: STRUCTURE SUMMARY: > Info: 603 ATOMS > Info: 867 BONDS > Info: 1659 ANGLES > Info: 3186 DIHEDRALS > Info: 0 IMPROPERS > Info: 0 CROSSTERMS > Info: 0 EXCLUSIONS > Info: 114 FIXED ATOMS > Info: 1467 DEGREES OF FREEDOM > Info: 603 HYDROGEN GROUPS > Info: 1 ATOMS IN LARGEST HYDROGEN GROUP > Info: 603 MIGRATION GROUPS > Info: 1 ATOMS IN LARGEST MIGRATION GROUP > Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED > Info: TOTAL MASS =3D 7242.63 amu > Info: TOTAL CHARGE =3D 0 e >=20 >=20 > --Apple-Mail=_D73F6EBE-A835-4C1F-837E-983C5318A8EC Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Pawel,

NAMD = calculates certain checksums to make sure that, due to its parallel = decomposition, no terms are accidentally dropped during force = evaluation. The =E2=80=9Cglobal exclusion=E2=80=9D checksum counts the = total number of non-bonded exclusions evaluated, where the exclusion = policy is set in the config file (usually =E2=80=9Cexclude scaled1-4=E2=80= =9D for CHARMM FF). Before the simulation begins, NAMD counts the total = number of non-bonded exclusions that it should be evaluating when = computing the force. It will then report when an undercount occurs. The = numbers reported are the checksum vs. the number of exclusions that = should have been evaluated. Since this does not end your simulation, = this must be occurring for you during minimization. If this were to = occur during dynamics, NAMD would terminate with an error.

So why would this be = occurring? Well, in order for an exclusion to be calculated, the pair of = atoms being excluded must be in an adjacent pair of patches. It sounds = like your graphene sheet has carbons spaced far enough away, that you = have exclusions due to a covalently bonded chain of 3 or perhaps 4 = carbon atoms that extend beyond an entire patch. To avoid these = messages, one thing you might try doing is artificially increasing the = patch size by setting =E2=80=9Cmargin=E2=80=9D to a nonzero value large = enough to pad the patches so that these 3-chains or 4-chains of carbon = atoms are kept in adjacent patches.

As to the =E2=80=9Chydrogen group=E2=80=9D= designation, NAMD, for performance reasons, keeps each hydrogen atom = together with its heavy parent atoms, and refers to the resulting = clusters as =E2=80=9Chydrogen groups.=E2=80=9D In your case, every = carbon atom would be its own hydrogen group (and migration group). Since = this has important meaning for biomolecules, we report aspects of these = clusters, such as the =E2=80=9C114 hydrogen groups with all atoms = fixed=E2=80=9D message.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Apr 21, 2021, at 6:01 AM, Pawel Kedzierski <pawel.kedzierski@pwr.edu.pl> wrote:

=20 =20

Dear NAMD wizards,

The = warning from the subject is a topic of many questions appearing on this list, but I haven't found a single answer which would explain its exact meaning and the conditions which trigger it. The usual answers are that it signs some steric or topology problems and such reasons lead to a quick crash due to divergence of movement integrations. But it does not apply to my case.

In a case I am playing with - a sheet of graphene = - NAMD produces immense numbers of these warnings, which seem to be false. The dynamics of the system is stable, no crash, setting cutoff and pairlist well above the system size does not help. These messages are just annoying filling 90% of the log size.

I = want to use this graphene example as exercise for my students, and this flood of warnings not only makes it look unprofessional, but what troubles me more is that I am unable to explain it. Specifically:

  • what exactly is "excluded globally" and what are = the numbers reported?
  • are there any other conditions apart from cutoff, = pairlistdist and steric problems, which I can change to silence this = warning?

The first number reported in the warnings changes = regularly but the difference between them is rather huge, from 2340 vs 4593 when they first appear during minimization to for example 3759 vs 4593 at the end of dynamics.

=46rom my current experience, the combination of = graphene and CHARMM forcefield is not optimal. I already learned that due to L-J interactions between bound carbons (in-plane) I was getting huge excess of VDW energy; this was mostly corrected with setting the 1-4 L-J parameters to 0, but possibly all in-plane L-J interactions should be discarded. Basically I use a copy of the parameters for standard CA type (which is also duplicated for CGenFF multi-ring ligands) and it provides all necessary parameters, I only changed the 1-4 part. Note that this type uses regular dihedrals instead of impropers to stiffen the ring plane, so I have generated the PSF with all planar dihedrals but without impropers.

I will be grateful for any = insight.

With regards,

Pawe=C5=82 = K=C4=99dzierski

P.S. Summary of the system for which I = reported the numbers above. Note there are no hydrogens so "114 hydrogen groups" is confusing. Here I fixed atoms on the edge of the sheet but without fixing the flood of warnings is still there, only the numbers change.

Info: STRUCTURE SUMMARY:
Info: 603 ATOMS
Info: 867 BONDS
Info: 1659 ANGLES
Info: 3186 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 114 FIXED ATOMS
Info: 1467 DEGREES OF FREEDOM
Info: 603 HYDROGEN GROUPS
Info: 1 ATOMS IN LARGEST HYDROGEN GROUP
Info: 603 MIGRATION GROUPS
Info: 1 ATOMS IN LARGEST MIGRATION GROUP
Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS =3D 7242.63 amu
Info: TOTAL CHARGE =3D 0 e

<pa= wel_kedzierski.vcf>

= --Apple-Mail=_D73F6EBE-A835-4C1F-837E-983C5318A8EC-- From owner-namd-l@halifax.ks.uiuc.edu Thu Apr 22 08:22:43 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13MDMhtZ023672; Thu, 22 Apr 2021 08:22:43 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13MDMh6r023671; Thu, 22 Apr 2021 08:22:43 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13MDMgcf023667; Thu, 22 Apr 2021 08:22:42 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13MDMgxg023666; Thu, 22 Apr 2021 08:22:42 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13MDMWqC023656 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT); Thu, 22 Apr 2021 08:22:33 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13MDI2Ib020391; Thu, 22 Apr 2021 13:22:32 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=pawel.kedzierski@pwr.edu.pl Received: from pps.reinject (localhost [127.0.0.1]) by mx0a-00007101.pphosted.com with ESMTP id 382myyeag8-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Thu, 22 Apr 2021 13:22:32 +0000 Received: from pps.reinject (m0166255.ppops.net [127.0.0.1]) by pps.reinject (8.16.0.43/8.16.0.43) with SMTP id 13MD5Tgx014567; Thu, 22 Apr 2021 13:22:31 GMT Received: from z-mta1.wcss.wroc.pl (z-mta1.wcss.wroc.pl [156.17.193.139]) by mx0a-00007101.pphosted.com with ESMTP id 382myyea11-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT); Thu, 22 Apr 2021 13:21:11 +0000 MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_booBYBRwedUZhrz6/n8/SQ)" Received: from [192.168.1.13] ([87.99.50.180]) by z-mta1.wcss.wroc.pl (Oracle Communications Messaging Server 8.0.1.1.0 64bit (built Jun 15 2016)) with ESMTPPSA id <0QRY00LQ3VR86V90@z-mta1.wcss.wroc.pl>; Thu, 22 Apr 2021 15:21:09 +0200 (CEST) X-PMX-Spam: Gauge=IIIIIIII, Probability=8%, Report=' HTML_NO_HTTP 0.1, RCVD_FROM_IP_DATE 0.1, BODYTEXTH_SIZE_3000_MORE 0, BODY_SIZE_10000_PLUS 0, FROM_EDU_TLD 0, IN_REP_TO 0, LEGITIMATE_SIGNS 0, MSG_THREAD 0, NO_URI_HTTPS 0, RDNS_GENERIC_POOLED 0, RDNS_SUSP 0, RDNS_SUSP_GENERIC 0, REFERENCES 0, SENDER_NO_AUTH 0, URI_WITH_PATH_ONLY 0, __ANY_URI 0, __ATTACHMENT_NOT_IMG 0, __BAT_BOUNDARY 0, __BITCOIN_ADDRESS_OBFU 0, __BODY_TEXT_X4 0, __BOUNCE_CHALLENGE_SUBJ 0, __BOUNCE_NDR_SUBJ_EXEMPT 0, __CP_URI_IN_BODY 0, __CT 0, __CTYPE_HAS_BOUNDARY 0, __CTYPE_MULTIPART 0, __CTYPE_MULTIPART_MIXED 0, __DQ_NEG_HEUR 0, __DQ_NEG_IP 0, __FORWARDED_MSG 0, __HAS_ATTACHMENT 0, __HAS_ATTACHMENT1 0, __HAS_FROM 0, __HAS_HTML 0, __HAS_MSGID 0, __HAS_REFERENCES 0, __HTML_BAD_END 0, __HTML_TAG_DIV 0, __IN_REP_TO 0, __MIME_HTML 0, __MIME_TEXT_H 0, __MIME_TEXT_H1 0, __MIME_TEXT_H2 0, __MIME_TEXT_P 0, __MIME_TEXT_P1 0, __MIME_TEXT_P2 0, __MIME_VERSION 0, __MOZILLA_USER_AGENT 0, __MULTIPLE_RCPTS_TO_X2 0, __PHISH_SPEAR_SUBJ_ALERT X-PMX-Version: 6.4.9.2830568, Antispam-Engine: 2.7.2.2107409, Antispam-Data: 2021.4.22.131516, AntiVirus-Engine: 5.82.0, AntiVirus-Data: 2021.4.22.5820000 Subject: Re: namd-l: Meaning of the warning: Low global exclusion count! To: David Hardy , namd-l@ks.uiuc.edu References: <4de7df68-be69-9a93-33f6-ce847e4084db@pwr.edu.pl> <0C396555-F668-419F-BE2D-26AC0596CB30@ks.uiuc.edu> From: Pawel Kedzierski Organization: Wroclaw University of Technology Message-id: <5b2a7943-f58a-de28-0589-dc6deb7585a5@pwr.edu.pl> Date: Thu, 22 Apr 2021 15:21:08 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 In-reply-to: <0C396555-F668-419F-BE2D-26AC0596CB30@ks.uiuc.edu> Content-language: en-US X-CLX-Response: 1TFkXGxIdEQpMehcaEQpZRBdtbHwZfXNCc31PbREKWFgXYEZFTEB+RGN7Znw RCnhOF21zZGBIE054GxJoEQp5TBdhHVNeHwVOa1keaREKQ0gXBxsSGBEKQ1kXGhEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhscHXEeHBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1QkVZX k9OEQpDThdtex1uXXxoXH57GE5zWx1uExNISXpfdWNhZnxneRJ4QBEKWFwXHwQaBBgYEgUbGgQb GhoEHhIEGBkQGx4aHxoRCl5ZF3JeUhpQEQpNXBcbHR0RCkxaF3hra01NEQpFWRdvaxEKTF8XegU FBQUFBQUFBW8RCkxGF2JraxEKQk8Xb0VFZGhgE2wdf0sRCkNaFxsfHAQbHQQbExkEGxkTEQpCXh cbEQpEWBcYEQpEXhcYEQpCRRdkGGRjWRNmbWJIAREKQk4XbXNkYEgTTngbEmgRCkJMF2BGRUxAf kRje2Z8EQpCbBdjWU1CaXpIHB5uehEKQkAXb11ocxwTQE1+GxwRCk1eFxsRClpYFxgRCnlDF2cd a2YdcExbbWFdEQpZSxcfEx0aEQpwZxdrTU18TkxfekceTRAZGhEKcGgXemgYWHBQAWR9WlwQGRo RCnBoF2F5ElNtR0NcH2JAEBkaEQpwaBdhBXJwUBoaTWZwZxAZGhEKcGgXbR98AWVzRx55RxIQGR oRCnBoF2cbGWljX2V+cx8ZEBkaEQpwfRdubklHWmtJaU5PWxAZGhEKcGcXaVBgBWFjR2J5ZAEQG RoRCnBnF2ZZEx1sGnpme2hsEBkaEQpwfxdlWHIYHUkYXkZpfBAbGBoRCnBfF2ZwSFxAeQFBHk8S EBkaEQpwbBdlWEd6eEZsT01AXhAZGhEKcEwXYEUbcm9OSU5oflkQGRoRCnBDF2Z7U3MbSXtyQFw BEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: DOXVns7P8Tdw1fQtYQJIjSz40LO17Ocf X-Proofpoint-ORIG-GUID: GQ7DwVBvTQ2dYq7D99bcPu_IKLVMS8Rj X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 malwarescore=0 adultscore=0 suspectscore=0 priorityscore=0 lowpriorityscore=0 mlxlogscore=999 impostorscore=0 spamscore=0 phishscore=0 clxscore=187 classifier=spam adjust=0 reason=mlx scancount=2 engine=8.12.0-2104060000 definitions=main-2104220109 domainage_hfrom=5970 X-Spam-Score: 0 X-Spam-OrigSender: pawel.kedzierski@pwr.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Pawel Kedzierski This is a multi-part message in MIME format. --Boundary_(ID_booBYBRwedUZhrz6/n8/SQ) Content-type: multipart/alternative; boundary="Boundary_(ID_t5FM8llxelluh2kCPnvreg)" --Boundary_(ID_t5FM8llxelluh2kCPnvreg) Content-type: text/plain; charset=utf-8; format=flowed Content-transfer-encoding: 8BIT Dear David, Thank you for detailed explanation. Increasing the margin to e.g. 3.0, which is more than ring diameter, didn't help. After several more tests I think, I am triggering a bug in this global exclusion checksum calculation. My grafene was generated idealized with all Z coordinates exactly 0.0, and that was the source of the problem. When I started calculations using coordinates from final MD frame of previous job, so they were slightly distorted, NOT EVEN A SINGLE WARNING appeared. On the other hand, when I start from ideally flat sheet aligned to XY plane, I am getting this warning at virtually every step. The checksum have not to be calculated from scratch, only updated, and some initial mistake is never corrected later; apparently such update occurs once per cycle (20 steps in my case). The warnings are issued both during minimization and dynamics but namd continues anyway, I run tests for 100ps with no problem. I also checked whether the problem is triggered due to zero Z thickness of the entire system; but adding a sodium ion like 5A above the graphene did not help. So my workaround now is to generate the graphene coordinates with minimal random distortion (-0.05 to +0.05A range) out of the XY plane and voila, no more warnings :-D. Thank you, Paweł W dniu 21.04.2021 o 22:31, David Hardy pisze: > Hi Pawel, > > NAMD calculates certain checksums to make sure that, due to its > parallel decomposition, no terms are accidentally dropped during force > evaluation. The “global exclusion†checksum counts the total number of > non-bonded exclusions evaluated, where the exclusion policy is set in > the config file (usually “exclude scaled1-4†for CHARMM FF). Before > the simulation begins, NAMD counts the total number of non-bonded > exclusions that it should be evaluating when computing the force. It > will then report when an undercount occurs. The numbers reported are > the checksum vs. the number of exclusions that should have been > evaluated. Since this does not end your simulation, this must be > occurring for you during minimization. If this were to occur during > dynamics, NAMD would terminate with an error. > > So why would this be occurring? Well, in order for an exclusion to be > calculated, the pair of atoms being excluded must be in an adjacent > pair of patches. It sounds like your graphene sheet has carbons spaced > far enough away, that you have exclusions due to a covalently bonded > chain of 3 or perhaps 4 carbon atoms that extend beyond an entire > patch. To avoid these messages, one thing you might try doing is > artificially increasing the patch size by setting “margin†to a > nonzero value large enough to pad the patches so that these 3-chains > or 4-chains of carbon atoms are kept in adjacent patches. > > As to the “hydrogen group†designation, NAMD, for performance reasons, > keeps each hydrogen atom together with its heavy parent atoms, and > refers to the resulting clusters as “hydrogen groups.†In your case, > every carbon atom would be its own hydrogen group (and migration > group). Since this has important meaning for biomolecules, we report > aspects of these clusters, such as the “114 hydrogen groups with all > atoms fixed†message. > > Best regards, > Dave > > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu , > http://www.ks.uiuc.edu/~dhardy/ > >> On Apr 21, 2021, at 6:01 AM, Pawel Kedzierski >> > wrote: >> >> Dear NAMD wizards, >> >> The warning from the subject is a topic of many questions appearing >> on this list, but I haven't found a single answer which would explain >> its exact meaning and the conditions which trigger it. The usual >> answers are that it signs some steric or topology problems and such >> reasons lead to a quick crash due to divergence of movement >> integrations. But it does not apply to my case. >> >> In a case I am playing with - a sheet of graphene - NAMD produces >> immense numbers of these warnings, which seem to be false. The >> dynamics of the system is stable, no crash, setting cutoff and >> pairlist well above the system size does not help. These messages are >> just annoying filling 90% of the log size. >> >> I want to use this graphene example as exercise for my students, and >> this flood of warnings not only makes it look unprofessional, but >> what troubles me more is that I am unable to explain it. Specifically: >> >> * what exactly is "excluded globally" and what are the numbers >> reported? >> * are there any other conditions apart from cutoff, pairlistdist >> and steric problems, which I can change to silence this warning? >> >> The first number reported in the warnings changes regularly but the >> difference between them is rather huge, from 2340 vs 4593 when they >> first appear during minimization to for example 3759 vs 4593 at the >> end of dynamics. >> >> From my current experience, the combination of graphene and CHARMM >> forcefield is not optimal. I already learned that due to L-J >> interactions between bound carbons (in-plane) I was getting huge >> excess of VDW energy; this was mostly corrected with setting the 1-4 >> L-J parameters to 0, but possibly all in-plane L-J interactions >> should be discarded. Basically I use a copy of the parameters for >> standard CA type (which is also duplicated for CGenFF multi-ring >> ligands) and it provides all necessary parameters, I only changed the >> 1-4 part. Note that this type uses regular dihedrals instead of >> impropers to stiffen the ring plane, so I have generated the PSF with >> all planar dihedrals but without impropers. >> >> I will be grateful for any insight. >> >> With regards, >> >> Paweł Kędzierski >> >> P.S. Summary of the system for which I reported the numbers above. >> Note there are no hydrogens so "114 hydrogen groups" is confusing. >> Here I fixed atoms on the edge of the sheet but without fixing the >> flood of warnings is still there, only the numbers change. >> >> Info: STRUCTURE SUMMARY: >> Info: 603 ATOMS >> Info: 867 BONDS >> Info: 1659 ANGLES >> Info: 3186 DIHEDRALS >> Info: 0 IMPROPERS >> Info: 0 CROSSTERMS >> Info: 0 EXCLUSIONS >> Info: 114 FIXED ATOMS >> Info: 1467 DEGREES OF FREEDOM >> Info: 603 HYDROGEN GROUPS >> Info: 1 ATOMS IN LARGEST HYDROGEN GROUP >> Info: 603 MIGRATION GROUPS >> Info: 1 ATOMS IN LARGEST MIGRATION GROUP >> Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED >> Info: TOTAL MASS = 7242.63 amu >> Info: TOTAL CHARGE = 0 e >> --Boundary_(ID_t5FM8llxelluh2kCPnvreg) Content-type: text/html; charset=utf-8 Content-transfer-encoding: 8BIT
Dear David,

Thank you for detailed explanation.
Increasing the margin to e.g. 3.0, which is more than ring diameter, didn't help.
After several more tests I think, I am triggering a bug in this global exclusion checksum calculation.

My grafene was generated idealized with all Z coordinates exactly 0.0, and that was the source of the problem.

When I started calculations using coordinates from final MD frame of previous job, so they were slightly distorted, NOT EVEN A SINGLE WARNING appeared. On the other hand, when I start from ideally flat sheet aligned to XY plane, I am getting this warning at virtually every step. The checksum have not to be calculated from scratch, only updated, and some initial mistake is never corrected later; apparently such update occurs once per cycle (20 steps in my case).
The warnings are issued both during minimization and dynamics but namd continues anyway, I run tests for 100ps with no problem.

I also checked whether the problem is triggered due to zero Z thickness of the entire system; but adding a sodium ion like 5A above the graphene did not help.

So my workaround now is to generate the graphene coordinates with minimal random distortion (-0.05 to +0.05A range) out of the XY plane and voila, no more warnings :-D.

Thank you,
Paweł

W dniu 21.04.2021 o 22:31, David Hardy pisze:
Hi Pawel,

NAMD calculates certain checksums to make sure that, due to its parallel decomposition, no terms are accidentally dropped during force evaluation. The “global exclusion†checksum counts the total number of non-bonded exclusions evaluated, where the exclusion policy is set in the config file (usually “exclude scaled1-4†for CHARMM FF). Before the simulation begins, NAMD counts the total number of non-bonded exclusions that it should be evaluating when computing the force. It will then report when an undercount occurs. The numbers reported are the checksum vs. the number of exclusions that should have been evaluated. Since this does not end your simulation, this must be occurring for you during minimization. If this were to occur during dynamics, NAMD would terminate with an error.

So why would this be occurring? Well, in order for an exclusion to be calculated, the pair of atoms being excluded must be in an adjacent pair of patches. It sounds like your graphene sheet has carbons spaced far enough away, that you have exclusions due to a covalently bonded chain of 3 or perhaps 4 carbon atoms that extend beyond an entire patch. To avoid these messages, one thing you might try doing is artificially increasing the patch size by setting “margin†to a nonzero value large enough to pad the patches so that these 3-chains or 4-chains of carbon atoms are kept in adjacent patches.

As to the “hydrogen group†designation, NAMD, for performance reasons, keeps each hydrogen atom together with its heavy parent atoms, and refers to the resulting clusters as “hydrogen groups.†In your case, every carbon atom would be its own hydrogen group (and migration group). Since this has important meaning for biomolecules, we report aspects of these clusters, such as the “114 hydrogen groups with all atoms fixed†message.

Best regards,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801

On Apr 21, 2021, at 6:01 AM, Pawel Kedzierski <pawel.kedzierski@pwr.edu.pl> wrote:

Dear NAMD wizards,

The warning from the subject is a topic of many questions appearing on this list, but I haven't found a single answer which would explain its exact meaning and the conditions which trigger it. The usual answers are that it signs some steric or topology problems and such reasons lead to a quick crash due to divergence of movement integrations. But it does not apply to my case.

In a case I am playing with - a sheet of graphene - NAMD produces immense numbers of these warnings, which seem to be false. The dynamics of the system is stable, no crash, setting cutoff and pairlist well above the system size does not help. These messages are just annoying filling 90% of the log size.

I want to use this graphene example as exercise for my students, and this flood of warnings not only makes it look unprofessional, but what troubles me more is that I am unable to explain it. Specifically:

  • what exactly is "excluded globally" and what are the numbers reported?
  • are there any other conditions apart from cutoff, pairlistdist and steric problems, which I can change to silence this warning?

The first number reported in the warnings changes regularly but the difference between them is rather huge, from 2340 vs 4593 when they first appear during minimization to for example 3759 vs 4593 at the end of dynamics.

From my current experience, the combination of graphene and CHARMM forcefield is not optimal. I already learned that due to L-J interactions between bound carbons (in-plane) I was getting huge excess of VDW energy; this was mostly corrected with setting the 1-4 L-J parameters to 0, but possibly all in-plane L-J interactions should be discarded. Basically I use a copy of the parameters for standard CA type (which is also duplicated for CGenFF multi-ring ligands) and it provides all necessary parameters, I only changed the 1-4 part. Note that this type uses regular dihedrals instead of impropers to stiffen the ring plane, so I have generated the PSF with all planar dihedrals but without impropers.

I will be grateful for any insight.

With regards,

Paweł Kędzierski

P.S. Summary of the system for which I reported the numbers above. Note there are no hydrogens so "114 hydrogen groups" is confusing. Here I fixed atoms on the edge of the sheet but without fixing the flood of warnings is still there, only the numbers change.

Info: STRUCTURE SUMMARY:
Info: 603 ATOMS
Info: 867 BONDS
Info: 1659 ANGLES
Info: 3186 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 114 FIXED ATOMS
Info: 1467 DEGREES OF FREEDOM
Info: 603 HYDROGEN GROUPS
Info: 1 ATOMS IN LARGEST HYDROGEN GROUP
Info: 603 MIGRATION GROUPS
Info: 1 ATOMS IN LARGEST MIGRATION GROUP
Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 7242.63 amu
Info: TOTAL CHARGE = 0 e

--Boundary_(ID_t5FM8llxelluh2kCPnvreg)-- --Boundary_(ID_booBYBRwedUZhrz6/n8/SQ) Content-type: text/x-vcard; CHARSET=US-ASCII; name=pawel_kedzierski.vcf Content-transfer-encoding: 7BIT Content-disposition: attachment; filename=pawel_kedzierski.vcf begin:vcard fn;quoted-printable:Pawe=C5=82 K=C4=99dzierski n;quoted-printable;quoted-printable:K=C4=99dzierski;Pawe=C5=82 org;quoted-printable:Wroc=C5=82aw University of Technology, Faculty of Chemistry;Advanced Materials Engineering and Modelling Group adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:Wyb. Wyspia=C5=84skiego 27;;Politechnika Wroc=C5=82awska, Wydzia=C5=82 Chemiczny;Wroc=C5=82aw;dolno=C5=9Bl=C4=85skie;50-370;Poland email;internet:Pawel.Kedzierski@pwr.edu.pl tel;work:+48 71 3203200 tel;fax:+48 71 3203364 version:2.1 end:vcard --Boundary_(ID_booBYBRwedUZhrz6/n8/SQ)-- From owner-namd-l@halifax.ks.uiuc.edu Thu Apr 22 14:15:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13MJFpWN029945; Thu, 22 Apr 2021 14:15:51 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13MJFpH0029944; Thu, 22 Apr 2021 14:15:51 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13MJFpME029940; Thu, 22 Apr 2021 14:15:51 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13MJFoqt029939; Thu, 22 Apr 2021 14:15:50 -0500 (CDT) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13MJFjW4029932 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Thu, 22 Apr 2021 14:15:46 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_C9C4B9E0-9FCB-4E58-9C41-EBF4DA7703F5" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Meaning of the warning: Low global exclusion count! Date: Thu, 22 Apr 2021 14:15:40 -0500 References: <4de7df68-be69-9a93-33f6-ce847e4084db@pwr.edu.pl> <0C396555-F668-419F-BE2D-26AC0596CB30@ks.uiuc.edu> <5b2a7943-f58a-de28-0589-dc6deb7585a5@pwr.edu.pl> To: NAMD list , Pawel Kedzierski In-Reply-To: <5b2a7943-f58a-de28-0589-dc6deb7585a5@pwr.edu.pl> Message-Id: <5C7C962A-F1A6-48AF-B44D-C4735CFA43B8@ks.uiuc.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_C9C4B9E0-9FCB-4E58-9C41-EBF4DA7703F5 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Pawel, I=E2=80=99m glad you found a workaround. However, this does sound like suspicious behavior in NAMD. If you = wouldn=E2=80=99t mind sharing your system with me, I=E2=80=99d be = interested to see why the code isn't handling the Z=3D0 case. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Apr 22, 2021, at 8:21 AM, Pawel Kedzierski = wrote: >=20 > Dear David, >=20 > Thank you for detailed explanation. > Increasing the margin to e.g. 3.0, which is more than ring diameter, = didn't help. > After several more tests I think, I am triggering a bug in this global = exclusion checksum calculation. >=20 > My grafene was generated idealized with all Z coordinates exactly 0.0, = and that was the source of the problem. >=20 > When I started calculations using coordinates from final MD frame of = previous job, so they were slightly distorted, NOT EVEN A SINGLE WARNING = appeared. On the other hand, when I start from ideally flat sheet = aligned to XY plane, I am getting this warning at virtually every step. = The checksum have not to be calculated from scratch, only updated, and = some initial mistake is never corrected later; apparently such update = occurs once per cycle (20 steps in my case). > The warnings are issued both during minimization and dynamics but namd = continues anyway, I run tests for 100ps with no problem. >=20 > I also checked whether the problem is triggered due to zero Z = thickness of the entire system; but adding a sodium ion like 5A above = the graphene did not help. >=20 > So my workaround now is to generate the graphene coordinates with = minimal random distortion (-0.05 to +0.05A range) out of the XY plane = and voila, no more warnings :-D. >=20 > Thank you, > Pawe=C5=82 >=20 > W dniu 21.04.2021 o 22:31, David Hardy pisze: >> Hi Pawel, >>=20 >> NAMD calculates certain checksums to make sure that, due to its = parallel decomposition, no terms are accidentally dropped during force = evaluation. The =E2=80=9Cglobal exclusion=E2=80=9D checksum counts the = total number of non-bonded exclusions evaluated, where the exclusion = policy is set in the config file (usually =E2=80=9Cexclude scaled1-4=E2=80= =9D for CHARMM FF). Before the simulation begins, NAMD counts the total = number of non-bonded exclusions that it should be evaluating when = computing the force. It will then report when an undercount occurs. The = numbers reported are the checksum vs. the number of exclusions that = should have been evaluated. Since this does not end your simulation, = this must be occurring for you during minimization. If this were to = occur during dynamics, NAMD would terminate with an error. >>=20 >> So why would this be occurring? Well, in order for an exclusion to be = calculated, the pair of atoms being excluded must be in an adjacent pair = of patches. It sounds like your graphene sheet has carbons spaced far = enough away, that you have exclusions due to a covalently bonded chain = of 3 or perhaps 4 carbon atoms that extend beyond an entire patch. To = avoid these messages, one thing you might try doing is artificially = increasing the patch size by setting =E2=80=9Cmargin=E2=80=9D to a = nonzero value large enough to pad the patches so that these 3-chains or = 4-chains of carbon atoms are kept in adjacent patches. >>=20 >> As to the =E2=80=9Chydrogen group=E2=80=9D designation, NAMD, for = performance reasons, keeps each hydrogen atom together with its heavy = parent atoms, and refers to the resulting clusters as =E2=80=9Chydrogen = groups.=E2=80=9D In your case, every carbon atom would be its own = hydrogen group (and migration group). Since this has important meaning = for biomolecules, we report aspects of these clusters, such as the = =E2=80=9C114 hydrogen groups with all atoms fixed=E2=80=9D message. >>=20 >> Best regards, >> Dave >>=20 >> -- >> David J. Hardy, Ph.D. >> Beckman Institute >> University of Illinois at Urbana-Champaign >> 405 N. Mathews Ave., Urbana, IL 61801 >> dhardy@ks.uiuc.edu , = http://www.ks.uiuc.edu/~dhardy/ >>=20 >>> On Apr 21, 2021, at 6:01 AM, Pawel Kedzierski = > = wrote: >>>=20 >>> Dear NAMD wizards, >>>=20 >>> The warning from the subject is a topic of many questions appearing = on this list, but I haven't found a single answer which would explain = its exact meaning and the conditions which trigger it. The usual answers = are that it signs some steric or topology problems and such reasons lead = to a quick crash due to divergence of movement integrations. But it does = not apply to my case. >>>=20 >>> In a case I am playing with - a sheet of graphene - NAMD produces = immense numbers of these warnings, which seem to be false. The dynamics = of the system is stable, no crash, setting cutoff and pairlist well = above the system size does not help. These messages are just annoying = filling 90% of the log size. >>>=20 >>> I want to use this graphene example as exercise for my students, and = this flood of warnings not only makes it look unprofessional, but what = troubles me more is that I am unable to explain it. Specifically: >>>=20 >>> what exactly is "excluded globally" and what are the numbers = reported? >>> are there any other conditions apart from cutoff, pairlistdist and = steric problems, which I can change to silence this warning? >>> The first number reported in the warnings changes regularly but the = difference between them is rather huge, from 2340 vs 4593 when they = first appear during minimization to for example 3759 vs 4593 at the end = of dynamics. >>>=20 >>> =46rom my current experience, the combination of graphene and CHARMM = forcefield is not optimal. I already learned that due to L-J = interactions between bound carbons (in-plane) I was getting huge excess = of VDW energy; this was mostly corrected with setting the 1-4 L-J = parameters to 0, but possibly all in-plane L-J interactions should be = discarded. Basically I use a copy of the parameters for standard CA type = (which is also duplicated for CGenFF multi-ring ligands) and it provides = all necessary parameters, I only changed the 1-4 part. Note that this = type uses regular dihedrals instead of impropers to stiffen the ring = plane, so I have generated the PSF with all planar dihedrals but without = impropers. >>>=20 >>> I will be grateful for any insight. >>>=20 >>> With regards, >>>=20 >>> Pawe=C5=82 K=C4=99dzierski >>>=20 >>> P.S. Summary of the system for which I reported the numbers above. = Note there are no hydrogens so "114 hydrogen groups" is confusing. Here = I fixed atoms on the edge of the sheet but without fixing the flood of = warnings is still there, only the numbers change. >>>=20 >>> Info: STRUCTURE SUMMARY: >>> Info: 603 ATOMS >>> Info: 867 BONDS >>> Info: 1659 ANGLES >>> Info: 3186 DIHEDRALS >>> Info: 0 IMPROPERS >>> Info: 0 CROSSTERMS >>> Info: 0 EXCLUSIONS >>> Info: 114 FIXED ATOMS >>> Info: 1467 DEGREES OF FREEDOM >>> Info: 603 HYDROGEN GROUPS >>> Info: 1 ATOMS IN LARGEST HYDROGEN GROUP >>> Info: 603 MIGRATION GROUPS >>> Info: 1 ATOMS IN LARGEST MIGRATION GROUP >>> Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED >>> Info: TOTAL MASS =3D 7242.63 amu >>> Info: TOTAL CHARGE =3D 0 e >>>=20 > --Apple-Mail=_C9C4B9E0-9FCB-4E58-9C41-EBF4DA7703F5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi = Pawel,

I=E2=80=99m = glad you found a workaround.

However, this does sound like = suspicious behavior in NAMD. If you wouldn=E2=80=99t mind sharing your = system with me, I=E2=80=99d be interested to see why the code isn't = handling the Z=3D0 case.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

On Apr 22, 2021, at 8:21 AM, Pawel Kedzierski <pawel.kedzierski@pwr.edu.pl> wrote:

Dear David,

Thank you for detailed explanation.
Increasing the margin to e.g. 3.0, which is more = than ring diameter, didn't help.
After several = more tests I think, I am triggering a bug in this global exclusion = checksum calculation.

My grafene was generated idealized with all Z = coordinates exactly 0.0, and that was the source of the = problem.

When I started calculations using coordinates = from final MD frame of previous job, so they were slightly distorted, = NOT EVEN A SINGLE WARNING appeared. On the other hand, when I start from = ideally flat sheet aligned to XY plane, I am getting this warning at = virtually every step. The checksum have not to be calculated from = scratch, only updated, and some initial mistake is never corrected = later; apparently such update occurs once per cycle (20 steps in my = case).
The warnings are issued both during minimization = and dynamics but namd continues anyway, I run tests for 100ps with no = problem.

I also checked whether the problem is triggered = due to zero Z thickness of the entire system; but adding a sodium ion = like 5A above the graphene did not help.

So my workaround now is to generate the graphene = coordinates with minimal random distortion (-0.05 to +0.05A range) out = of the XY plane and voila, no more warnings :-D.

Thank you,
Pawe=C5=82

W dniu 21.04.2021 o 22:31, David Hardy = pisze:
Hi Pawel,

NAMD calculates certain checksums to = make sure that, due to its parallel decomposition, no terms are = accidentally dropped during force evaluation. The =E2=80=9Cglobal = exclusion=E2=80=9D checksum counts the total number of non-bonded = exclusions evaluated, where the exclusion policy is set in the config = file (usually =E2=80=9Cexclude scaled1-4=E2=80=9D for CHARMM FF). Before = the simulation begins, NAMD counts the total number of non-bonded = exclusions that it should be evaluating when computing the force. It = will then report when an undercount occurs. The numbers reported are the = checksum vs. the number of exclusions that should have been evaluated. = Since this does not end your simulation, this must be occurring for you = during minimization. If this were to occur during dynamics, NAMD would = terminate with an error.

So why would this be occurring? Well, in order for an = exclusion to be calculated, the pair of atoms being excluded must be in = an adjacent pair of patches. It sounds like your graphene sheet has = carbons spaced far enough away, that you have exclusions due to a = covalently bonded chain of 3 or perhaps 4 carbon atoms that extend = beyond an entire patch. To avoid these messages, one thing you might try = doing is artificially increasing the patch size by setting =E2=80=9Cmargin= =E2=80=9D to a nonzero value large enough to pad the patches so that = these 3-chains or 4-chains of carbon atoms are kept in adjacent = patches.

As to = the =E2=80=9Chydrogen group=E2=80=9D designation, NAMD, for performance = reasons, keeps each hydrogen atom together with its heavy parent atoms, = and refers to the resulting clusters as =E2=80=9Chydrogen groups.=E2=80=9D= In your case, every carbon atom would be its own hydrogen group (and = migration group). Since this has important meaning for biomolecules, we = report aspects of these clusters, such as the =E2=80=9C114 hydrogen = groups with all atoms fixed=E2=80=9D message.

Best regards,
Dave

--
David J. Hardy, = Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405= N. Mathews Ave., Urbana, IL 61801

On Apr = 21, 2021, at 6:01 AM, Pawel Kedzierski <pawel.kedzierski@pwr.edu.pl> = wrote:

Dear NAMD wizards,

The warning = from the subject is a topic of many questions appearing on this list, = but I haven't found a single answer which would explain its exact = meaning and the conditions which trigger it. The usual answers are that = it signs some steric or topology problems and such reasons lead to a = quick crash due to divergence of movement integrations. But it does not = apply to my case.

In a case I am playing = with - a sheet of graphene - NAMD produces immense numbers of these = warnings, which seem to be false. The dynamics of the system is stable, = no crash, setting cutoff and pairlist well above the system size does = not help. These messages are just annoying filling 90% of the log = size.

I want to use this graphene example as exercise = for my students, and this flood of warnings not only makes it look = unprofessional, but what troubles me more is that I am unable to explain = it. Specifically:

  • what exactly is = "excluded globally" and what are the numbers reported?
  • are there any other conditions apart from cutoff, = pairlistdist and steric problems, which I can change to silence this = warning?

The first number reported in the = warnings changes regularly but the difference between them is rather = huge, from 2340 vs 4593 when they first appear during minimization to = for example 3759 vs 4593 at the end of dynamics.

=46rom my current experience, the combination of graphene and = CHARMM forcefield is not optimal. I already learned that due to L-J = interactions between bound carbons (in-plane) I was getting huge excess = of VDW energy; this was mostly corrected with setting the 1-4 L-J = parameters to 0, but possibly all in-plane L-J interactions should be = discarded. Basically I use a copy of the parameters for standard CA type = (which is also duplicated for CGenFF multi-ring ligands) and it provides = all necessary parameters, I only changed the 1-4 part. Note that this = type uses regular dihedrals instead of impropers to stiffen the ring = plane, so I have generated the PSF with all planar dihedrals but without = impropers.

I will be grateful for any insight.

With regards,

Pawe=C5=82 K=C4=99dzierski

P.S. Summary of the system for which I reported the numbers = above. Note there are no hydrogens so "114 hydrogen groups" is = confusing. Here I fixed atoms on the edge of the sheet but without = fixing the flood of warnings is still there, only the numbers change.

Info: STRUCTURE SUMMARY:
Info: = 603 ATOMS
Info: 867 BONDS
Info: 1659 = ANGLES
Info: 3186 DIHEDRALS
Info: 0 = IMPROPERS
Info: 0 CROSSTERMS
Info: 0 = EXCLUSIONS
Info: 114 FIXED ATOMS
Info: 1467 = DEGREES OF FREEDOM
Info: 603 HYDROGEN GROUPS
Info: 1 ATOMS IN LARGEST HYDROGEN GROUP
Info: = 603 MIGRATION GROUPS
Info: 1 ATOMS IN LARGEST MIGRATION = GROUP
Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS =3D 7242.63 amu
Info: TOTAL = CHARGE =3D 0 = e

<pa= wel_kedzierski.vcf>

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charset="us-ascii" Content-Transfer-Encoding: Quoted-printable Dear All, I am looking towards upgrading my workstation and would like inputs about h= ardware keeping in view the current NAMD versions and future updates/versio= ns. 1. Does ECC certified versus non-ECC RAM make any difference? 2. RTX 30 series GPUs are hard to find. Looking at the readily available al= ternatives, I wonder what are the things I should look into apart from the = boost speed and number of CUDA cores. Does NAMD benefit from VRAM size, hig= h RT and tensor core counts, etc.? Thanks in advance for your help. Regards, Raman Get Outlook for Android --_000_BMXPR01MB352676A655F70EC5F6CFFC75B3459BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: Quoted-printable
Dear All,

I am looking towards upgrading my workstation and would like inputs about h= ardware keeping in view the current NAMD versions and future updates/versio= ns.

1. Does ECC certified versus non-ECC RAM make any difference?
2. RTX 30 series GPUs are hard to find. Looking at the readily available al= ternatives, I wonder what are the things I should look into apart from the = boost speed and number of CUDA cores. Does NAMD benefit from VRAM size, hig= h RT and tensor core counts, etc.?<= /div>

Thanks in advance for your help.

Regards,
Raman


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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Diship, it highly depends on what error analysis you plan on doing. The approach that I and others use with metadynamics has very few assumptions: after estimating that the systems has explored all relevant states at least once, start collecting the PMF at regular intervals and simulate for additional time such that all states are visited a few more times, i.e. a few more layers of Gaussian hills are added on top of the converged PMF. Then just compute the average and SD of the free-energy over the sample of multiple PMFs, which are only text files, so you can do the following: all_pmfs =3D np.zeros(shape=3D(n_files, n_points)) for i_file in range(n_files): _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue) all_pmfs[i_file,:] =3D pmf[:] pmf_mean =3D all_pmfs.mean(axis=3D0) pmf_SD =3D all_pmfs.std(axis=3D0) The tutorial that Miro has linked uses block averages, where the additional difference is that the length of the blocks is also varied to converge the SD. You should see for yourself that the dependence of the SD on the block length is rather slow (in theory, it should follow a square root). Having said all that, here you're not simulating something trivial like dialanine isomerization: any meaningful error estimate will require that the CV has already visited all states repeatedly during the simulation. If you can see such trajectory, then you're in good shape and any PMF method including metadynamics will give you unbiased results. If you ran long enough for today's review standards, your statistical error bars will be comparable or smaller than the size of the marker used in the plot :-) You ought to be able to explain how you computed the statistical error bars, but these ought to be very small or downright negligible. On the other hand, if the CV is not a good reaction coordinate any error analysis will be uninformative: you need to analyze the atomic trajectory and show that at any given frame the structural properties (e.g. coordination with water or lipids) depend only on the value of the CV, but not on the simulation history. Any inconsistency that you may see there may not easily be solved with longer simulation times. In short, statistical sampling is less of an issue than it used to be (the most common PMF methods are now at least two decades old!), but *picking a good CV* has always been "the big deal", where your insight into the specific problem matters the most. Giacomo On Tue, Apr 20, 2021 at 3:37 AM Miro Astore wrote: > Hi Diship, you should be able to use the code/techniques in this tutorial. > Good luck. > > https://urldefense.com/v3/__https://www.plumed.org/doc-v2.5/user-doc/html= /trieste-4.html__;!!DZ3fjg!oP-_Zk-rfJChIEjBoYdFZ4a-Y4DgRZdCY9AUJTqbm92S-vv-= 5rzsvY3QhKNr8w0SoQ$=20 > > > On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava < > dishipsrivastava@gmail.com> wrote: > >> Hi, >> I have done well tempered metadynamics for a system consisting of a >> molecule insertion into a bilayer using the colvars module. I am >> interested in doing an error analysis for obtained free energy >> preferably using colvars. >> Any help would be most appreciated. >> >> Thanks in advance >> >> >> >> -- >> Diship Srivastava >> JRF >> Department of Chemistry >> IIT(ISM) - Dhanbad >> India >> > > > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney > --000000000000d34c4505c0a5dc82 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Diship, it highly depends on what error analysis you pl= an on doing.=C2=A0 The approach that I and others use with metadynamics has= very few assumptions: after estimating that the systems has explored all r= elevant states at least once, start collecting the PMF at regular intervals= and simulate for additional time such that all states are visited a few mo= re times, i.e. a few more layers of Gaussian hills are added on top of the = converged PMF.=C2=A0 Then just compute the average and SD of the free-energ= y over the sample of multiple PMFs, which are only text files, so you can d= o the following:

all_pmfs =3D np.zeros(shape=3D(n_files,= n_points))
for i_file in range(n_files):
=C2=A0 =C2=A0= _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue)
=C2= =A0 =C2=A0 all_pmfs[i_file,:] =3D pmf[:]
pmf_mean =3D all_pmfs.me= an(axis=3D0)
pmf_SD =3D all_pmfs.std(axis=3D0)

The tutorial that Miro has linked uses block averages, where the a= dditional difference is that the length=C2=A0of the blocks is also varied t= o converge the SD.=C2=A0 You should see for yourself that the dependence of= the SD on the block length is rather slow (in theory, it should follow a s= quare root).

Having said all that, here you're= not simulating something trivial like dialanine isomerization: any meaning= ful error estimate will require that the CV has already visited all states = repeatedly during the simulation.=C2=A0 If you can see such trajectory, the= n you're in good shape and any PMF method including metadynamics will g= ive you unbiased results.=C2=A0 If you ran long enough for today's revi= ew standards, your statistical error bars will be comparable or smaller tha= n the size of the=C2=A0marker used in the plot :-)=C2=A0 You ought to be ab= le to explain how you computed the statistical error bars, but these ought = to be very small or downright negligible.

On the o= ther hand, if the CV is not a good reaction coordinate any error analysis w= ill be uninformative: you need to analyze the atomic trajectory and show th= at at any given frame the structural properties (e.g. coordination with wat= er or lipids) depend only on the value of the CV, but not on the simulation= history.=C2=A0 Any inconsistency that you may see there may not easily be = solved with longer simulation times.

In shor= t, statistical sampling is less of an issue than it used to be (the most co= mmon PMF methods are now at least two decades old!), but picking a good = CV has always been "the big deal", where your insight into th= e specific problem matters the most.

Giacomo
=

= On Tue, Apr 20, 2021 at 3:37 AM Miro Astore <miro.astore@gmail.com> wrote:
= Hi Diship, you should be able to use the code/techniques in this tutorial. = Good luck.


Hi,
I have done well tempered metadynamics for a sys= tem consisting of a molecule insertion into a bilayer using the colvars mod= ule. I am interested=C2=A0in doing an error analysis for obtained free ener= gy preferably=C2=A0using colvars.=C2=A0
Any help would be most ap= preciated.

Thanks in advance

<= br clear=3D"all">

--
Di= ship Srivastava=C2=A0
JRF=C2=A0
Department of Chemistry
=
IIT(ISM) - Dhanbad
India


--
Miro A. As= tore =C2=A0 (he/him)
PhD Candidate | Computational Biophysics
Office = 434 A28 School of Physics
University of Sydney
--000000000000d34c4505c0a5dc82-- From owner-namd-l@halifax.ks.uiuc.edu Fri Apr 23 11:40:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13NGeKpX017369; Fri, 23 Apr 2021 11:40:20 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13NGeKTg017368; Fri, 23 Apr 2021 11:40:20 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13NGeJVB017364; Fri, 23 Apr 2021 11:40:19 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13NGeJfY017363; Fri, 23 Apr 2021 11:40:19 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13NGe9S5017356 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 23 Apr 2021 11:40:10 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13NGXsHO031061 for ; Fri, 23 Apr 2021 16:40:09 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 383abgt57f-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 23 Apr 2021 16:40:08 +0000 Received: from [IPv6:2a02:810c:300:6724:8cfa:5eeb:73d2:1ecb] ([IPv6:2a02:810c:300:6724:8cfa:5eeb:73d2:1ecb]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 13NGe5bm161865 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Fri, 23 Apr 2021 18:40:05 +0200 Subject: Re: namd-l: Error Analysis in Metadynamics To: namd-l@ks.uiuc.edu, Giacomo Fiorin References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <1d7c40e2-3cf2-5422-1f7a-748fb586a45a@physik.uni-kl.de> Date: Fri, 23 Apr 2021 18:40:05 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.9.1 In-Reply-To: Content-Type: multipart/alternative; boundary="------------7FF5ED6CB63A619B1B835412" Content-Language: de-DE X-Spam-Status: No, hits=0.102, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,HTTPS_HTTP_MISMATCH=0.1,NICE_REPLY_A=-0.001,URIBL_BLOCKED=0.001 X-Spam-Score: (0.102) X-Spam-Flag: NO X-CLX-Shades: MLX X-Proofpoint-GUID: ezNhLokiz0p6rHq5QBkhGE6y0bqBy1Mw X-CLX-Response: 1TFkXGxIfEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxkeHREKQ1kXBxscEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF09QZEJmRUFDUBpaHFhiWx97aEFCbW8cUxpIW2hTG2ddEQpYXBcfBBoEGBgSBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JfYBpvEQpNXBcfGxwRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2F6HVlAS0VASHxcEQpCWBdnc2VzQG5hYUxdYhEKWlgX HhEKeUMXYwVkGUJdbmNyWWkRCnBnF2tnaGxmSWJBW19AEBkaEQpwaBdvX0RGQGFTEhxeEhAZGhE KcGgXbHtZe0BdZXBYHgUQGRoRCnBoF2hZXFNHRUgSQEhHEBkaEQpwaBdpU2tQZUR5Rm9mcBAZGh EKcGgXaGQdSEVwUmdhfU4QGRoRCnB9F2VAR2ZFXUVfWkt5EBkaEQpwfRdlXFtyE1AFemYZQxAeE hEKcGcXbBtrHUdzSQUebBwQGRoRCnBnF2xwUAFQREJtHU1pEBkaEQpwfxdrRVJ5bBpQfUF8EhAZ GhEKcF8XekZiWBp9Yl5FTXMQGRoRCnB/F2Fmb1saZ2RCSB1bEBsZGBEKcF8XY2ISUEhjeB98Qn0 QGxoeEQpwbBd6H3h5b3hMQ19wRBAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: ezNhLokiz0p6rHq5QBkhGE6y0bqBy1Mw MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 suspectscore=0 spamscore=0 mlxscore=0 mlxlogscore=999 priorityscore=0 impostorscore=0 clxscore=185 phishscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104230105 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------7FF5ED6CB63A619B1B835412 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Dear Giacomo, a question upon this: =C2=A0=C2=A0=C2=A0 What would you call "long enough for today's review sta= ndards": =C2=A0=C2=A0=C2=A0 Having convergence over serveral runs in the PMF within= <1kcal/mol=20 or rather on the order of (maybe a few) 0.1 kcal/mol? Kind regards Ren=C3=A9 On 4/23/2021 5:57 PM, Giacomo Fiorin wrote: > Hi Diship, it highly depends on what error analysis you plan on=20 > doing.=C2=A0 The approach that I and others use with metadynamics has ver= y=20 > few assumptions: after estimating that the systems has explored all=20 > relevant states at least once, start collecting the PMF at regular=20 > intervals and simulate for additional time such that all states are=20 > visited a few more times, i.e. a few more layers of Gaussian hills are=20 > added on top of the converged PMF.=C2=A0 Then just compute the average an= d=20 > SD of the free-energy over the sample of multiple PMFs, which are only=20 > text files, so you can do the following: > > all_pmfs =3D np.zeros(shape=3D(n_files, n_points)) > for i_file in range(n_files): > =C2=A0 =C2=A0 _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue) > =C2=A0 =C2=A0 all_pmfs[i_file,:] =3D pmf[:] > pmf_mean =3D all_pmfs.mean(axis=3D0) > pmf_SD =3D all_pmfs.std(axis=3D0) > > The tutorial that Miro has linked uses block averages, where the=20 > additional difference is that the length=C2=A0of the blocks is also varie= d=20 > to converge the SD.=C2=A0 You should see for yourself that the dependence= =20 > of the SD on the block length is rather slow (in theory, it should=20 > follow a square root). > > Having said all that, here you're not simulating something trivial=20 > like dialanine isomerization: any meaningful error estimate will=20 > require that the CV has already visited all states repeatedly during=20 > the simulation.=C2=A0 If you can see such trajectory, then you're in good= =20 > shape and any PMF method including metadynamics will give you unbiased=20 > results.=C2=A0 If you ran long enough for today's review standards, your= =20 > statistical error bars will be comparable or smaller than the size of=20 > the=C2=A0marker used in the plot :-)=C2=A0 You ought to be able to explai= n how=20 > you computed the statistical error bars, but these ought to be very=20 > small or downright negligible. > > On the other hand, if the CV is not a good reaction coordinate any=20 > error analysis will be uninformative: you need to analyze the atomic=20 > trajectory and show that at any given frame the structural properties=20 > (e.g. coordination with water or lipids) depend only on the value of=20 > the CV, but not on the simulation history.=C2=A0 Any inconsistency that y= ou=20 > may see there may not easily be solved with longer simulation times. > > In short, statistical sampling is less of an issue than it used to be=20 > (the most common PMF methods are now at least two decades old!), but=20 > /picking a good CV/ has always been "the big deal", where your insight=20 > into the specific problem matters the most. > > Giacomo > > On Tue, Apr 20, 2021 at 3:37 AM Miro Astore > wrote: > > Hi Diship, you should be able to use the code/techniques in this > tutorial. Good luck. > > https://urldefense.com/v3/__https://www.plumed.org/doc-v2.5/user-doc/= html/trieste-4.html__;!!DZ3fjg!oJS1t3i_Uu-bRvPAqzCg71_dwYNFVYB4KeakIoFC_Vc1= 2S1bTzwjSSwpz5LNMNqsvA$=20 > > > On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava > > > wrote: > > Hi, > I have done well tempered metadynamics for a system consisting > of a molecule insertion into a bilayer using the colvars > module. I am interested=C2=A0in doing an error analysis for > obtained free energy preferably=C2=A0using colvars. > Any help would be most appreciated. > > Thanks in advance > > > > --=20 > Diship Srivastava > JRF > Department of Chemistry > IIT(ISM) - Dhanbad > India > > > > --=20 > Miro A. Astore =C2=A0 (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney > --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------7FF5ED6CB63A619B1B835412 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Dear Giacomo,

a question upon this:

    What would you call "long enough for today's review standards":

    Having convergence over serveral runs in the PMF within <1kcal/mol or rather on the order of (maybe a few) 0.1 kcal/mol?

Kind regards

René

On 4/23/2021 5:57 PM, Giacomo Fiorin wrote:
Hi Diship, it highly depends on what error analysis you plan on doing.  The approach that I and others use with metadynamics has very few assumptions: after estimating that the systems has explored all relevant states at least once, start collecting the PMF at regular intervals and simulate for additional time such that all states are visited a few more times, i.e. a few more layers of Gaussian hills are added on top of the converged PMF.  Then just compute the average and SD of the free-energy over the sample of multiple PMFs, which are only text files, so you can do the following:

all_pmfs = np.zeros(shape=(n_files, n_points))
for i_file in range(n_files):
    _, pmf = np.loadtxt(pmf_file_names[i_file], unpack=True)
    all_pmfs[i_file,:] = pmf[:]
pmf_mean = all_pmfs.mean(axis=0)
pmf_SD = all_pmfs.std(axis=0)

The tutorial that Miro has linked uses block averages, where the additional difference is that the length of the blocks is also varied to converge the SD.  You should see for yourself that the dependence of the SD on the block length is rather slow (in theory, it should follow a square root).

Having said all that, here you're not simulating something trivial like dialanine isomerization: any meaningful error estimate will require that the CV has already visited all states repeatedly during the simulation.  If you can see such trajectory, then you're in good shape and any PMF method including metadynamics will give you unbiased results.  If you ran long enough for today's review standards, your statistical error bars will be comparable or smaller than the size of the marker used in the plot :-)  You ought to be able to explain how you computed the statistical error bars, but these ought to be very small or downright negligible.

On the other hand, if the CV is not a good reaction coordinate any error analysis will be uninformative: you need to analyze the atomic trajectory and show that at any given frame the structural properties (e.g. coordination with water or lipids) depend only on the value of the CV, but not on the simulation history.  Any inconsistency that you may see there may not easily be solved with longer simulation times.

In short, statistical sampling is less of an issue than it used to be (the most common PMF methods are now at least two decades old!), but picking a good CV has always been "the big deal", where your insight into the specific problem matters the most.

Giacomo

On Tue, Apr 20, 2021 at 3:37 AM Miro Astore <miro.astore@gmail.com> wrote:
Hi Diship, you should be able to use the code/techniques in this tutorial. Good luck.


On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava <dishipsrivastava@gmail.com> wrote:
Hi,
I have done well tempered metadynamics for a system consisting of a molecule insertion into a bilayer using the colvars module. I am interested in doing an error analysis for obtained free energy preferably using colvars. 
Any help would be most appreciated.

Thanks in advance



--
Diship Srivastava 
JRF 
Department of Chemistry
IIT(ISM) - Dhanbad
India


--
Miro A. Astore   (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=jL6QpGBMQ7uXult2nKURthl1EVuTlKjmOAb4tNs4c/w=; b=jqCZc06fIlfKCdtYjsLjFfeRRievD0pVLzKtwbPLykkRFag8DWHZhitri1mvwF3FIn KhX4lZUjcKOSUdvkoL49Lj8DL91xzHffOnmQ+SYgN47K/NPCBDcrAau5GOPD8hFq0qCr 8KzbWVTgmfMXq3kVQRWSxGCFknsijmPkmhYyOj2C9+Dp9TkS11+maRkx+JV83hPNDSO2 DKqafOHBMf5S8Bx+3maY5kn8bHvAQMrvFLI030NILf+0U5UIlaBAyyXYawGmce9rG+6x ++NAdJK6WE3M7/C9qvup5qunYGWuGpbO58RAUOe0UfDjLCkQfX4BUTjGRzIf3FQ5JXQp Ltkw== X-Gm-Message-State: AOAM530kWhrlB8wAKsDJXogqTf2WtAcSNFyhzk9eiG5MTlcywBzDeUET TDPbAkwuIHeEVMwG8S9E/dDgjuI1RdT7pXiKXjO3W1x5 X-Google-Smtp-Source: ABdhPJyRT5wxwb/BcJDG1GNg9PbQnMVvqOYzyedYFtoju+g6ZEigQl4pV7nka9iVqd4SfYdlnCzXxtFNF2U0FPko5Os= X-Received: by 2002:a25:3f07:: with SMTP id m7mr7515526yba.241.1619221790662; Fri, 23 Apr 2021 16:49:50 -0700 (PDT) References: <1d7c40e2-3cf2-5422-1f7a-748fb586a45a@physik.uni-kl.de> In-Reply-To: <1d7c40e2-3cf2-5422-1f7a-748fb586a45a@physik.uni-kl.de> From: Giacomo Fiorin Date: Fri, 23 Apr 2021 19:49:14 -0400 Message-ID: Subject: Re: namd-l: Error Analysis in Metadynamics To: =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= Cc: NAMD list Content-Type: multipart/alternative; boundary="000000000000a525fd05c0ac731c" X-CLX-Shades: MLX X-Proofpoint-GUID: eP1mjGGwtdSS5MjLpE0t_8XgoGJtlYba X-CLX-Response: 1TFkXGxwcEQpMehcZHh8RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHhMYEQpDWRcHGBkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhxxGBIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XT3obR0BtbV1eTnl5H2dAZlpvGl51EnJNRW1gXkZzSEsRClhcFx8EGgQYGBIF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcl97bRwRCk1cFx8bGBEKTFoXe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRkRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2F6HVlAS0VASHxcEQpCWBdnc2VzQG5hYUxdYhEKWlgXHhEKeUMXYwV kGUJdbmNyWWkRCllLFxMZEh8RCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdjcmJhX2JEUx9JeRAcGh EKcGgXenpzfkUaQE5+bl0QGRoRCnBoF2BeS0BaEh5lEkBeEBkaEQpwaBdtUmlaR3sZHV5BYBAZG hEKcGgXZRpsY0xPeXBrRFAQHBoRCnBnF2tnaGxmSWJBW19AEB4SEQpwfRdlQEdmRV1FX1pLeRAe EhEKcH0XZVxbchNQBXpmGUMQHRoRCnBnF2wbax1Hc0kFHmwcEB4SEQpwfxdrRVJ5bBpQfUF8EhA eEhEKcF8XekZiWBp9Yl5FTXMQHhIRCnB/F2Fmb1saZ2RCSB1bEBsbGREKcF8XY2ISUEhjeB98Qn 0QExgRCnBsF2Yfe1hcYgVLWGQfEBwaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: eP1mjGGwtdSS5MjLpE0t_8XgoGJtlYba MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 suspectscore=0 spamscore=0 mlxscore=0 mlxlogscore=999 priorityscore=345 impostorscore=0 clxscore=166 phishscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104230160 domainage_hfrom=9385 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000a525fd05c0ac731c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Ren=C3=A9, I think it all depends on how expensive is the system to simu= late, how complex the PMF (e.g. dimensionality, number of minima) and most importantly, the intended use of the PMF: qualitative insight, or actual quantification/measurement. If the goal is to estimate the relative probabilities of different states, the relevant scale is dictated by the thermal energy, i.e. ~0.6 kcal/mol in most biological applications. An estimated PMF error of 1 kcal/mol, after exponentiating, means that the corresponding probability can very easily be= *a factor of 5 larger or smaller*. On the other hand, 0.1 kcal/mol means that the relative error on the corresponding probability is just ~15%. Giacomo On Fri, Apr 23, 2021 at 12:40 PM Ren=C3=A9 Hafner TUK wrote: > Dear Giacomo, > > a question upon this: > > What would you call "long enough for today's review standards": > > Having convergence over serveral runs in the PMF within <1kcal/mol or > rather on the order of (maybe a few) 0.1 kcal/mol? > > Kind regards > > Ren=C3=A9 > On 4/23/2021 5:57 PM, Giacomo Fiorin wrote: > > Hi Diship, it highly depends on what error analysis you plan on doing. > The approach that I and others use with metadynamics has very few > assumptions: after estimating that the systems has explored all relevant > states at least once, start collecting the PMF at regular intervals and > simulate for additional time such that all states are visited a few more > times, i.e. a few more layers of Gaussian hills are added on top of the > converged PMF. Then just compute the average and SD of the free-energy > over the sample of multiple PMFs, which are only text files, so you can do > the following: > > all_pmfs =3D np.zeros(shape=3D(n_files, n_points)) > for i_file in range(n_files): > _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue) > all_pmfs[i_file,:] =3D pmf[:] > pmf_mean =3D all_pmfs.mean(axis=3D0) > pmf_SD =3D all_pmfs.std(axis=3D0) > > The tutorial that Miro has linked uses block averages, where the > additional difference is that the length of the blocks is also varied to > converge the SD. You should see for yourself that the dependence of the = SD > on the block length is rather slow (in theory, it should follow a square > root). > > Having said all that, here you're not simulating something trivial like > dialanine isomerization: any meaningful error estimate will require that > the CV has already visited all states repeatedly during the simulation. = If > you can see such trajectory, then you're in good shape and any PMF method > including metadynamics will give you unbiased results. If you ran long > enough for today's review standards, your statistical error bars will be > comparable or smaller than the size of the marker used in the plot :-) Y= ou > ought to be able to explain how you computed the statistical error bars, > but these ought to be very small or downright negligible. > > On the other hand, if the CV is not a good reaction coordinate any error > analysis will be uninformative: you need to analyze the atomic trajectory > and show that at any given frame the structural properties (e.g. > coordination with water or lipids) depend only on the value of the CV, but > not on the simulation history. Any inconsistency that you may see there > may not easily be solved with longer simulation times. > > In short, statistical sampling is less of an issue than it used to be (the > most common PMF methods are now at least two decades old!), but *picking > a good CV* has always been "the big deal", where your insight into the > specific problem matters the most. > > Giacomo > > On Tue, Apr 20, 2021 at 3:37 AM Miro Astore wrote: > >> Hi Diship, you should be able to use the code/techniques in this >> tutorial. Good luck. >> >> https://urldefense.com/v3/__https://www.plumed.org/doc-v2.5/user-doc/htm= l/trieste-4.html__;!!DZ3fjg!oO11QyWtHbxGT-WO97ohc55uoYoxSMDW2Mc608ODkfB0WTN= QkU-dDTPob0qlhTn7fA$=20 >> >> >> On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava < >> dishipsrivastava@gmail.com> wrote: >> >>> Hi, >>> I have done well tempered metadynamics for a system consisting of a >>> molecule insertion into a bilayer using the colvars module. I am >>> interested in doing an error analysis for obtained free energy >>> preferably using colvars. >>> Any help would be most appreciated. >>> >>> Thanks in advance >>> >>> >>> >>> -- >>> Diship Srivastava >>> JRF >>> Department of Chemistry >>> IIT(ISM) - Dhanbad >>> India >>> >> >> >> -- >> Miro A. Astore (he/him) >> PhD Candidate | Computational Biophysics >> Office 434 A28 School of Physics >> University of Sydney >> > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --000000000000a525fd05c0ac731c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Ren=C3=A9, I think it all depends on how expensive is t= he system to simulate, how complex the PMF (e.g. dimensionality, number of = minima) and most importantly, the intended use of the PMF: qualitative insi= ght, or actual quantification/measurement.

If the goal i= s to estimate the relative probabilities of different states, the relevant = scale is dictated by the thermal energy, i.e. ~0.6 kcal/mol in most biologi= cal applications.=C2=A0 An estimated PMF error of 1 kcal/mol, after exponen= tiating, means that the corresponding probability can very=C2=A0easily be= =C2=A0a factor of 5 larger or smaller.=C2=A0 On the other hand, 0.1 = kcal/mol means that the relative error on the corresponding probability=C2= =A0is just ~15%.

Giacomo

=

On Fri, Apr 23, 2021 at 12:40 PM Ren=C3=A9 Hafner TUK <hamburge@physik.uni-kl.de> wrote:<= br>
=20 =20 =20

Dear Giacomo,

a question upon this:

=C2=A0=C2=A0=C2=A0 What would you call "long enough for today&#= 39;s review standards":

=C2=A0=C2=A0=C2=A0 Having convergence over serveral runs in the PMF = within <1kcal/mol or rather on the order of (maybe a few) 0.1 kcal/mol?

Kind regards

Ren=C3=A9

On 4/23/2021 5:57 PM, Giacomo Fiorin wrote:
=20
Hi Diship, it highly depends on what error analysis you plan on doing.=C2=A0 The approach that I and others use with metadynamics has very few assumptions: after estimating that the systems has explored all relevant states at least once, start collecting the PMF at regular intervals and simulate for additional time such that all states are visited a few more times, i.e. a few more layers of Gaussian hills are added on top of the converged PMF.=C2=A0 Then just compute the average and SD of the free-energy over the sample of multiple PMFs, which are only text files, so you can do the following:

all_pmfs =3D np.zeros(shape=3D(n_files, n_points))
for i_file in range(n_files):
=C2=A0 =C2=A0 _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue)
=C2=A0 =C2=A0 all_pmfs[i_file,:] =3D pmf[:]
pmf_mean =3D all_pmfs.mean(axis=3D0)
pmf_SD =3D all_pmfs.std(axis=3D0)

The tutorial that Miro has linked uses block averages, where the additional difference is that the length=C2=A0of the blocks is also varied to converge the SD.=C2=A0 You should see for yourself that the dependence of the SD on the block length is rather slow (in theory, it should follow a square root).

Having said all that, here you're not simulating something trivial like dialanine isomerization: any meaningful error estimate will require that the CV has already visited all states repeatedly during the simulation.=C2=A0 If you can see such trajectory, then you'= re in good shape and any PMF method including metadynamics will give you unbiased results.=C2=A0 If you ran long enough for today's review standards, your statistical error bars will be comparable or smaller than the size of the=C2=A0marker used = in the plot :-)=C2=A0 You ought to be able to explain how you computed the statistical error bars, but these ought to be very small or downright negligible.

On the other hand, if the CV is not a good reaction coordinate any error analysis will be uninformative: you need to analyze the atomic trajectory and show that at any given frame the structural properties (e.g. coordination with water or lipids) depend only on the value of the CV, but not on the simulation history.=C2=A0 Any inconsistency that you may see there may not easily be solved with longer simulation times.

In short, statistical sampling is less of an issue than it used to be (the most common PMF methods are now at least two decades old!), but picking a good CV has always been "the big deal", where your insight into the specific pr= oblem matters the most.

Giacomo

On Tue, Apr 20, 2021 at 3:37 AM Miro Astore <miro.astore@gmail.com> wrote:
Hi Diship, you should be able to use the code/techniques in this tutorial. Good luck.


On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava <dishipsrivastava@gmail.com> wrote:
Hi,
I have done well tempered metadynamics for a system consisting of a molecule insertion into a bilayer using the colvars module. I am interested=C2=A0in doing a= n error analysis for obtained free energy preferably=C2=A0using colvars.=C2=A0
Any help would be most appreciated.

Thanks in advance



--
Diship Srivastava=C2=A0
JRF=C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
India


--
Miro A. Astore =C2=A0 (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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Thanks , Geo. 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boundary="0000000000000e144f05c0cf8260" X-Proofpoint-GUID: DcfZoIfKmYNjO7pz-OkF68mArmP553_E X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRsfEQpMehcZHh4RCllEF2ZbAUJEbk8cW09oEQpYWBdmHxN7GV8bWkV vWBEKeE4XY1Nja3sTWH4aX14RCnlMF2hGWEhJcEZLQAFBEQpDSBcHHhwcEQpDWRcHGBkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFx0ScRsGGx8cdwYdEwYbGhpCGxsGGgYSHQYZGnEbEBp3BhoGGgYaB gccGgYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThduSUxwRWNMYUdzZEBl HVpQB2VBbBwSR2tYR3ofHxl1bxEKWFwXHwQaBBgYEgUbGgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3J fGhlCEQpNXBcbHR4RCkxaF3hpTWtrEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2xrax EKQk8XbhxnHVlyZ2ZeSHIRCkNaFxgaEwQSHwQYGhIEHxgRCkJeFxsRCkReFxgRCkRJFxsRCkJcF xsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXbH9BUkNuYxNkUB4R CkJOF2NTY2t7E1h+Gl9eEQpCTBdmHxN7GV8bWkVvWBEKQmwXYxJOWkFfTGxaHBoRCkJAF2F6HVl AS0VASHxcEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHhEKeUMXYwVkGUJdbmNyWWkRCllLFx MZEh0RCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdjcmJhX2JEUx9JeRAeEhEKcGgXbm9aX3BQXn1oX EYQGRoRCnBoF3p6c35FGkBOfm5dEBkaEQpwaBdgXktAWhIeZRJAXhAZGhEKcGgXbVJpWkd7GR1e QWAQGRoRCnBnF2tnaGxmSWJBW19AEBkaEQpwfRdlQEdmRV1FX1pLeRAZGhEKcH0XZVxbchNQBXp mGUMQHBoRCnB/F2tFUnlsGlB9QXwSEBkaEQpwXxd6RmJYGn1iXkVNcxAZGhEKcH8XYWZvWxpnZE JIHVsQGxoZEQpwXxdjYhJQSGN4H3xCfRASHREKcGwXbXoZe0ZsUm1NZGYQGRoRCm1+FxsRClhNF 0sRIA== X-Proofpoint-ORIG-GUID: DcfZoIfKmYNjO7pz-OkF68mArmP553_E MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 mlxlogscore=999 bulkscore=0 clxscore=315 impostorscore=0 malwarescore=0 adultscore=0 phishscore=0 spamscore=0 mlxscore=0 suspectscore=0 priorityscore=344 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104250134 domainage_hfrom=9387 X-Spam-Score: 0 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --0000000000000e144f05c0cf8260 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks for the answer. I have one more question - since I am doing 2D well tempered metadynamics will the error analysis be done for both cv's separately or is there a method to combine the error analysis for both cv into one? On Sat, 24 Apr 2021, 05:22 Giacomo Fiorin, wrote: > Hi Ren=C3=A9, I think it all depends on how expensive is the system to > simulate, how complex the PMF (e.g. dimensionality, number of minima) and > most importantly, the intended use of the PMF: qualitative insight, or > actual quantification/measurement. > > If the goal is to estimate the relative probabilities of different states, > the relevant scale is dictated by the thermal energy, i.e. ~0.6 kcal/mol = in > most biological applications. An estimated PMF error of 1 kcal/mol, after > exponentiating, means that the corresponding probability can very easily = be *a > factor of 5 larger or smaller*. On the other hand, 0.1 kcal/mol means > that the relative error on the corresponding probability is just ~15%. > > Giacomo > > > On Fri, Apr 23, 2021 at 12:40 PM Ren=C3=A9 Hafner TUK < > hamburge@physik.uni-kl.de> wrote: > >> Dear Giacomo, >> >> a question upon this: >> >> What would you call "long enough for today's review standards": >> >> Having convergence over serveral runs in the PMF within <1kcal/mol or >> rather on the order of (maybe a few) 0.1 kcal/mol? >> >> Kind regards >> >> Ren=C3=A9 >> On 4/23/2021 5:57 PM, Giacomo Fiorin wrote: >> >> Hi Diship, it highly depends on what error analysis you plan on doing. >> The approach that I and others use with metadynamics has very few >> assumptions: after estimating that the systems has explored all relevant >> states at least once, start collecting the PMF at regular intervals and >> simulate for additional time such that all states are visited a few more >> times, i.e. a few more layers of Gaussian hills are added on top of the >> converged PMF. Then just compute the average and SD of the free-energy >> over the sample of multiple PMFs, which are only text files, so you can = do >> the following: >> >> all_pmfs =3D np.zeros(shape=3D(n_files, n_points)) >> for i_file in range(n_files): >> _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue) >> all_pmfs[i_file,:] =3D pmf[:] >> pmf_mean =3D all_pmfs.mean(axis=3D0) >> pmf_SD =3D all_pmfs.std(axis=3D0) >> >> The tutorial that Miro has linked uses block averages, where the >> additional difference is that the length of the blocks is also varied to >> converge the SD. You should see for yourself that the dependence of the= SD >> on the block length is rather slow (in theory, it should follow a square >> root). >> >> Having said all that, here you're not simulating something trivial like >> dialanine isomerization: any meaningful error estimate will require that >> the CV has already visited all states repeatedly during the simulation. = If >> you can see such trajectory, then you're in good shape and any PMF method >> including metadynamics will give you unbiased results. If you ran long >> enough for today's review standards, your statistical error bars will be >> comparable or smaller than the size of the marker used in the plot :-) = You >> ought to be able to explain how you computed the statistical error bars, >> but these ought to be very small or downright negligible. >> >> On the other hand, if the CV is not a good reaction coordinate any error >> analysis will be uninformative: you need to analyze the atomic trajectory >> and show that at any given frame the structural properties (e.g. >> coordination with water or lipids) depend only on the value of the CV, b= ut >> not on the simulation history. Any inconsistency that you may see there >> may not easily be solved with longer simulation times. >> >> In short, statistical sampling is less of an issue than it used to be >> (the most common PMF methods are now at least two decades old!), but *pi= cking >> a good CV* has always been "the big deal", where your insight into the >> specific problem matters the most. >> >> Giacomo >> >> On Tue, Apr 20, 2021 at 3:37 AM Miro Astore >> wrote: >> >>> Hi Diship, you should be able to use the code/techniques in this >>> tutorial. Good luck. >>> >>> https://urldefense.com/v3/__https://www.plumed.org/doc-v2.5/user-doc/ht= ml/trieste-4.html__;!!DZ3fjg!rkoiprliWDa4dAvZ_C6kcdRq2hsiZJ7UaAfB8ieuMj3_8I= qnfaG19QfOwKmL2BTbPw$=20 >>> >>> >>> On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava < >>> dishipsrivastava@gmail.com> wrote: >>> >>>> Hi, >>>> I have done well tempered metadynamics for a system consisting of a >>>> molecule insertion into a bilayer using the colvars module. I am >>>> interested in doing an error analysis for obtained free energy >>>> preferably using colvars. >>>> Any help would be most appreciated. >>>> >>>> Thanks in advance >>>> >>>> >>>> >>>> -- >>>> Diship Srivastava >>>> JRF >>>> Department of Chemistry >>>> IIT(ISM) - Dhanbad >>>> India >>>> >>> >>> >>> -- >>> Miro A. Astore (he/him) >>> PhD Candidate | Computational Biophysics >>> Office 434 A28 School of Physics >>> University of Sydney >>> >> -- >> -- >> Dipl.-Phys. Ren=C3=A9 Hafner >> TU Kaiserslautern >> Germany >> >> --0000000000000e144f05c0cf8260 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thanks for the answer. I have one m= ore question - since I am doing 2D well tempered metadynamics will the erro= r analysis be done for both cv's separately or is there a method to com= bine the error analysis for both cv into one?=C2=A0




On Sat, 24 Apr 2021, 05:22 Giacomo Fiorin, &l= t;giacomo.fiorin@gmail.com> wrote:
Hi Ren=C3=A9, I think it all depen= ds on how expensive is the system to simulate, how complex the PMF (e.g. di= mensionality, number of minima) and most importantly, the intended use of t= he PMF: qualitative insight, or actual quantification/measurement.

=
If the goal is to estimate the relative probabilities of differe= nt states, the relevant scale is dictated by the thermal energy, i.e. ~0.6 = kcal/mol in most biological applications.=C2=A0 An estimated PMF error of 1= kcal/mol, after exponentiating, means that the corresponding probability c= an very=C2=A0easily be=C2=A0a factor of 5 larger or smaller.=C2=A0 O= n the other hand, 0.1 kcal/mol means that the relative error on the corresp= onding probability=C2=A0is just ~15%.

Giacomo


On Fri, Apr 23, 2021 at 12:40 PM Ren=C3=A9 Hafne= r TUK <hamburge@physik.uni-kl.de> wr= ote:
=20 =20 =20

Dear Giacomo,

a question upon this:

=C2=A0=C2=A0=C2=A0 What would you call "long enough for today&#= 39;s review standards":

=C2=A0=C2=A0=C2=A0 Having convergence over serveral runs in the PMF = within <1kcal/mol or rather on the order of (maybe a few) 0.1 kcal/mol?

Kind regards

Ren=C3=A9

On 4/23/2021 5:57 PM, Giacomo Fiorin wrote:
=20
Hi Diship, it highly depends on what error analysis you plan on doing.=C2=A0 The approach that I and others use with metadynamics has very few assumptions: after estimating that the systems has explored all relevant states at least once, start collecting the PMF at regular intervals and simulate for additional time such that all states are visited a few more times, i.e. a few more layers of Gaussian hills are added on top of the converged PMF.=C2=A0 Then just compute the average and SD of the free-energy over the sample of multiple PMFs, which are only text files, so you can do the following:

all_pmfs =3D np.zeros(shape=3D(n_files, n_points))
for i_file in range(n_files):
=C2=A0 =C2=A0 _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue)
=C2=A0 =C2=A0 all_pmfs[i_file,:] =3D pmf[:]
pmf_mean =3D all_pmfs.mean(axis=3D0)
pmf_SD =3D all_pmfs.std(axis=3D0)

The tutorial that Miro has linked uses block averages, where the additional difference is that the length=C2=A0of the blocks is also varied to converge the SD.=C2=A0 You should see for yourself that the dependence of the SD on the block length is rather slow (in theory, it should follow a square root).

Having said all that, here you're not simulating something trivial like dialanine isomerization: any meaningful error estimate will require that the CV has already visited all states repeatedly during the simulation.=C2=A0 If you can see such trajectory, then you'= re in good shape and any PMF method including metadynamics will give you unbiased results.=C2=A0 If you ran long enough for today's review standards, your statistical error bars will be comparable or smaller than the size of the=C2=A0marker used = in the plot :-)=C2=A0 You ought to be able to explain how you computed the statistical error bars, but these ought to be very small or downright negligible.

On the other hand, if the CV is not a good reaction coordinate any error analysis will be uninformative: you need to analyze the atomic trajectory and show that at any given frame the structural properties (e.g. coordination with water or lipids) depend only on the value of the CV, but not on the simulation history.=C2=A0 Any inconsistency that you may see there may not easily be solved with longer simulation times.

In short, statistical sampling is less of an issue than it used to be (the most common PMF methods are now at least two decades old!), but picking a good CV has always been "the big deal", where your insight into the specific pr= oblem matters the most.

Giacomo

On Tue, Apr 20, 2021 at 3:37 AM Miro Astore <miro.astore@gmail.c= om> wrote:
Hi Diship, you should be able to use the code/techniques in this tutorial. Good luck.


On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava <d= ishipsrivastava@gmail.com> wrote:
Hi,
I have done well tempered metadynamics for a system consisting of a molecule insertion into a bilayer using the colvars module. I am interested=C2=A0in doing a= n error analysis for obtained free energy preferably=C2=A0using colvars.=C2=A0
Any help would be most appreciated.

Thanks in advance



--
Diship Srivastava=C2=A0
JRF=C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
India


--
Miro A. Astore =C2=A0 (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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boundary="000000000000bdeb7a05c10a1e13" X-CLX-Response: 1TFkXGxIYEQpMehcZGxoRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHh8SEQpDWRcHEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGHEeGxAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdhellSH05hf2VoHVppc05uQVtEYRkSHwdHUE9Aa39uThEKWFwXHwQaBBgYEgUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdyXFN/HhEKTVwXGBMcEQpMWhd4aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2FZHHkYSAUSG0J4EQpDWhcYGhMEEh8EGBsTBB sdExEKQl4XGxEKREkXGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3IdbmxPWHhgEQpCbBdh X3pTGUNEGnobfhEKQkAXYXodWUBLRUBIfFwRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBceEQp 5QxdjBWQZQl1uY3JZaREKWUsXExkTGhEKcGcXYBlGRXtORxltXEUQGRoRCnBoF2xCTWRse1NDTW 5FEBkaEQpwaBd6eGN4TlobbHhDeBAZGhEKcGgXbE95TBlvRkZbbRIQGRoRCnBoF25ZQE9Nc1xLe 3xpEBkaEQpwaBdtQxpBUmsdWGIYeRAZGhEKcGcXa2dobGZJYkFbX0AQGRoRCnB9F2VAR2ZFXUVf Wkt5EBkaEQpwfRdlXFtyE1AFemYZQxAZGhEKcH8Xa0VSeWwaUH1BfBIQGRoRCnBfF3pGYlgafWJ eRU1zEBkaEQpwfxdhZm9bGmdkQkgdWxAbGRsRCnBfF2NiElBIY3gffEJ9EBsaGBEKcGwXZh97WF xiBUtYZB8QGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: KPsx5dKUOB7pCYdDkqnK385-mzejAUDd X-Proofpoint-ORIG-GUID: KPsx5dKUOB7pCYdDkqnK385-mzejAUDd MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 adultscore=0 mlxlogscore=999 phishscore=0 spamscore=0 lowpriorityscore=0 mlxscore=0 priorityscore=310 clxscore=182 bulkscore=0 suspectscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104280101 domainage_hfrom=9390 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000bdeb7a05c10a1e13 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Diship, sorry, I missed this later one. There is no fundamentally different scenario when increasing dimensionality (1D, 2D, 3D, ...) other than higher dimensionalities usually mean that more bins need to be sampled on average. But the error analysis is done on each grid point individually, regardless of how many dimensions the grid has. With well-tempered metadynamics specifically, it gets a bit trickier. One may still consider different trajectory segments statistically independent as in standard metadynamics (provided that the CVs are "good" i.e. they decorrelate themselves quickly and fully). But because of the WT's scale factor, the statistical weight of later trajectory frames will be on average much lower. The tutorial that Miro linked earlier presumes (without saying it explicitly) that the trajectory being examined is not very different from standard metadynamics, where all segments have equal weight. In practice, you have to accept the potential risk that by using a well-tempered scaling, the later stages of a simulation will always count much less than the earlier ones and may make it appear as if the PMF had converged better than it actually did. Even if interesting stuff is still going on. This complication is somewhat unique to metadynamics, which unlike other methods (umbrella sampling, ABF, etc) doesn't converge asymptotically by design, so you basically are choosing between averaging the incremental PMFs of standard metadynamics yourselves, or use well-tempered to slow the bias down. Or, as you saw, people even use both approaches concurrently. What I really suggest is using a clear and well-defined procedure to quantify the error bars that you mean to plot. But rather than go very sophisticated with the methodology, I feel it much more important to critically examine possible ways that your choices of CVs may be less than ideal. All error analyses that only look at the bias or at the PMF are implicitly assuming that the CVs are ideal. Showing that you actually looked in detail at the atomic trajectory along the simulation will increase the confidence that your purely-statistical error may actually be used as "experimental uncertainty". Giacomo On Sun, Apr 25, 2021 at 1:39 PM Diship Srivastava < dishipsrivastava@gmail.com> wrote: > Thanks for the answer. I have one more question - since I am doing 2D well > tempered metadynamics will the error analysis be done for both cv's > separately or is there a method to combine the error analysis for both cv > into one? > > > > > On Sat, 24 Apr 2021, 05:22 Giacomo Fiorin, > wrote: > >> Hi Ren=C3=A9, I think it all depends on how expensive is the system to >> simulate, how complex the PMF (e.g. dimensionality, number of minima) and >> most importantly, the intended use of the PMF: qualitative insight, or >> actual quantification/measurement. >> >> If the goal is to estimate the relative probabilities of different >> states, the relevant scale is dictated by the thermal energy, i.e. ~0.6 >> kcal/mol in most biological applications. An estimated PMF error of 1 >> kcal/mol, after exponentiating, means that the corresponding probability >> can very easily be *a factor of 5 larger or smaller*. On the other >> hand, 0.1 kcal/mol means that the relative error on the corresponding >> probability is just ~15%. >> >> Giacomo >> >> >> On Fri, Apr 23, 2021 at 12:40 PM Ren=C3=A9 Hafner TUK < >> hamburge@physik.uni-kl.de> wrote: >> >>> Dear Giacomo, >>> >>> a question upon this: >>> >>> What would you call "long enough for today's review standards": >>> >>> Having convergence over serveral runs in the PMF within <1kcal/mol >>> or rather on the order of (maybe a few) 0.1 kcal/mol? >>> >>> Kind regards >>> >>> Ren=C3=A9 >>> On 4/23/2021 5:57 PM, Giacomo Fiorin wrote: >>> >>> Hi Diship, it highly depends on what error analysis you plan on doing. >>> The approach that I and others use with metadynamics has very few >>> assumptions: after estimating that the systems has explored all relevant >>> states at least once, start collecting the PMF at regular intervals and >>> simulate for additional time such that all states are visited a few more >>> times, i.e. a few more layers of Gaussian hills are added on top of the >>> converged PMF. Then just compute the average and SD of the free-energy >>> over the sample of multiple PMFs, which are only text files, so you can= do >>> the following: >>> >>> all_pmfs =3D np.zeros(shape=3D(n_files, n_points)) >>> for i_file in range(n_files): >>> _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue) >>> all_pmfs[i_file,:] =3D pmf[:] >>> pmf_mean =3D all_pmfs.mean(axis=3D0) >>> pmf_SD =3D all_pmfs.std(axis=3D0) >>> >>> The tutorial that Miro has linked uses block averages, where the >>> additional difference is that the length of the blocks is also varied to >>> converge the SD. You should see for yourself that the dependence of th= e SD >>> on the block length is rather slow (in theory, it should follow a square >>> root). >>> >>> Having said all that, here you're not simulating something trivial like >>> dialanine isomerization: any meaningful error estimate will require that >>> the CV has already visited all states repeatedly during the simulation.= If >>> you can see such trajectory, then you're in good shape and any PMF meth= od >>> including metadynamics will give you unbiased results. If you ran long >>> enough for today's review standards, your statistical error bars will be >>> comparable or smaller than the size of the marker used in the plot :-) = You >>> ought to be able to explain how you computed the statistical error bars, >>> but these ought to be very small or downright negligible. >>> >>> On the other hand, if the CV is not a good reaction coordinate any error >>> analysis will be uninformative: you need to analyze the atomic trajecto= ry >>> and show that at any given frame the structural properties (e.g. >>> coordination with water or lipids) depend only on the value of the CV, = but >>> not on the simulation history. Any inconsistency that you may see there >>> may not easily be solved with longer simulation times. >>> >>> In short, statistical sampling is less of an issue than it used to be >>> (the most common PMF methods are now at least two decades old!), but *p= icking >>> a good CV* has always been "the big deal", where your insight into the >>> specific problem matters the most. >>> >>> Giacomo >>> >>> On Tue, Apr 20, 2021 at 3:37 AM Miro Astore >>> wrote: >>> >>>> Hi Diship, you should be able to use the code/techniques in this >>>> tutorial. Good luck. >>>> >>>> https://urldefense.com/v3/__https://www.plumed.org/doc-v2.5/user-doc/h= tml/trieste-4.html__;!!DZ3fjg!qu2_rhPJjAUJMkx_8Wa9l_4t6T1jpu4YBlzw8sa8T06Wz= eT_KcZjWLqFPyLR63eLzQ$=20 >>>> >>>> >>>> On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava < >>>> dishipsrivastava@gmail.com> wrote: >>>> >>>>> Hi, >>>>> I have done well tempered metadynamics for a system consisting of a >>>>> molecule insertion into a bilayer using the colvars module. I am >>>>> interested in doing an error analysis for obtained free energy >>>>> preferably using colvars. >>>>> Any help would be most appreciated. >>>>> >>>>> Thanks in advance >>>>> >>>>> >>>>> >>>>> -- >>>>> Diship Srivastava >>>>> JRF >>>>> Department of Chemistry >>>>> IIT(ISM) - Dhanbad >>>>> India >>>>> >>>> >>>> >>>> -- >>>> Miro A. Astore (he/him) >>>> PhD Candidate | Computational Biophysics >>>> Office 434 A28 School of Physics >>>> University of Sydney >>>> >>> -- >>> -- >>> Dipl.-Phys. Ren=C3=A9 Hafner >>> TU Kaiserslautern >>> Germany >>> >>> --000000000000bdeb7a05c10a1e13 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Diship, sorry, I missed this later one.

<= div>There is no fundamentally different scenario when increasing dimensiona= lity (1D, 2D, 3D, ...) other than higher dimensionalities usually mean that= more bins need to be sampled on average.=C2=A0 But the error analysis is d= one on each grid point individually, regardless of how many dimensions the = grid has.

With well-tempered metadynamics specifically, = it gets a bit trickier.=C2=A0 One may still consider different trajectory s= egments statistically independent as in standard metadynamics (provided tha= t the CVs are "good" i.e. they decorrelate themselves quickly and= fully).=C2=A0 But because of the WT's scale factor, the statistical we= ight of later trajectory frames will be on average much lower.=C2=A0 The tu= torial that Miro linked earlier presumes (without saying it explicitly) tha= t the trajectory being examined is not very different from standard metadyn= amics, where all segments have equal weight.=C2=A0 In practice, you have to= accept the potential risk that by using a well-tempered scaling, the later= stages of a simulation will always count much less than the earlier ones a= nd may make=C2=A0it appear as if the PMF had converged better than it actua= lly did.=C2=A0 Even if interesting stuff is still going on.

<= /div>
This complication is somewhat unique to metadynamics, which unlik= e other methods (umbrella sampling, ABF, etc) doesn't converge asymptot= ically by design, so you basically are choosing between averaging the incre= mental PMFs of standard metadynamics yourselves, or use well-tempered to sl= ow the bias down.=C2=A0 Or, as you saw, people even use both approaches con= currently.

What I really suggest is using a clear = and well-defined procedure to quantify the error bars that you mean to plot= .=C2=A0 But rather than go very sophisticated with the methodology, I feel = it much more important to critically examine possible ways that your choice= s of CVs may be less than ideal.=C2=A0 All error analyses that only look at= the bias or at the PMF are implicitly assuming that the CVs are ideal.=C2= =A0 Showing that you actually looked in detail at the atomic trajectory alo= ng the simulation will increase the confidence that your purely-statistical= error may actually be used as "experimental uncertainty".
<= div>
Giacomo




On Sun, Apr 25, 2021 at 1:39 PM Diship Srivastava <dishipsrivastava@gmail.c= om> wrote:
Thanks for the answer. I have one= more question - since I am doing 2D well tempered metadynamics will the er= ror analysis be done for both cv's separately or is there a method to c= ombine the error analysis for both cv into one?=C2=A0

=



On Sat, 24 Apr 2021, 05:22 Giacomo Fiorin, = <giacomo.fiorin@gmail.com> wrote:
Hi Ren=C3=A9,= I think it all depends on how expensive is the system to simulate, how com= plex the PMF (e.g. dimensionality, number of minima) and most importantly, = the intended use of the PMF: qualitative insight, or actual quantification/= measurement.

If the goal is to estimate the relative pro= babilities of different states, the relevant scale is dictated by the therm= al energy, i.e. ~0.6 kcal/mol in most biological applications.=C2=A0 An est= imated PMF error of 1 kcal/mol, after exponentiating, means that the corres= ponding probability can very=C2=A0easily be=C2=A0a factor of 5 larger or= smaller.=C2=A0 On the other hand, 0.1 kcal/mol means that the relative= error on the corresponding probability=C2=A0is just ~15%.

Giacomo


On Fri, Apr 23, 2021 at 12:= 40 PM Ren=C3=A9 Hafner TUK <hamburge@physik= .uni-kl.de> wrote:
=20 =20 =20

Dear Giacomo,

a question upon this:

=C2=A0=C2=A0=C2=A0 What would you call "long enough for today&#= 39;s review standards":

=C2=A0=C2=A0=C2=A0 Having convergence over serveral runs in the PMF = within <1kcal/mol or rather on the order of (maybe a few) 0.1 kcal/mol?

Kind regards

Ren=C3=A9

On 4/23/2021 5:57 PM, Giacomo Fiorin wrote:
=20
Hi Diship, it highly depends on what error analysis you plan on doing.=C2=A0 The approach that I and others use with metadynamics has very few assumptions: after estimating that the systems has explored all relevant states at least once, start collecting the PMF at regular intervals and simulate for additional time such that all states are visited a few more times, i.e. a few more layers of Gaussian hills are added on top of the converged PMF.=C2=A0 Then just compute the average and SD of the free-energy over the sample of multiple PMFs, which are only text files, so you can do the following:

all_pmfs =3D np.zeros(shape=3D(n_files, n_points))
for i_file in range(n_files):
=C2=A0 =C2=A0 _, pmf =3D np.loadtxt(pmf_file_names[i_file], unpack=3DTrue)
=C2=A0 =C2=A0 all_pmfs[i_file,:] =3D pmf[:]
pmf_mean =3D all_pmfs.mean(axis=3D0)
pmf_SD =3D all_pmfs.std(axis=3D0)

The tutorial that Miro has linked uses block averages, where the additional difference is that the length=C2=A0of the blocks is also varied to converge the SD.=C2=A0 You should see for yourself that the dependence of the SD on the block length is rather slow (in theory, it should follow a square root).

Having said all that, here you're not simulating something trivial like dialanine isomerization: any meaningful error estimate will require that the CV has already visited all states repeatedly during the simulation.=C2=A0 If you can see such trajectory, then you'= re in good shape and any PMF method including metadynamics will give you unbiased results.=C2=A0 If you ran long enough for today's review standards, your statistical error bars will be comparable or smaller than the size of the=C2=A0marker used = in the plot :-)=C2=A0 You ought to be able to explain how you computed the statistical error bars, but these ought to be very small or downright negligible.

On the other hand, if the CV is not a good reaction coordinate any error analysis will be uninformative: you need to analyze the atomic trajectory and show that at any given frame the structural properties (e.g. coordination with water or lipids) depend only on the value of the CV, but not on the simulation history.=C2=A0 Any inconsistency that you may see there may not easily be solved with longer simulation times.

In short, statistical sampling is less of an issue than it used to be (the most common PMF methods are now at least two decades old!), but picking a good CV has always been "the big deal", where your insight into the specific pr= oblem matters the most.

Giacomo

On Tue, Apr 20, 2021 at 3:37 AM Miro Astore <miro.astore@gmail.c= om> wrote:
Hi Diship, you should be able to use the code/techniques in this tutorial. Good luck.


On Tue, Apr 20, 2021 at 4:41 PM Diship Srivastava <d= ishipsrivastava@gmail.com> wrote:
Hi,
I have done well tempered metadynamics for a system consisting of a molecule insertion into a bilayer using the colvars module. I am interested=C2=A0in doing a= n error analysis for obtained free energy preferably=C2=A0using colvars.=C2=A0
Any help would be most appreciated.

Thanks in advance



--
Diship Srivastava=C2=A0
JRF=C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
India


--
Miro A. Astore =C2=A0 (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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boundary="_000_BMXPR01MB3269E5AB6EC30849B6CBEBEFBE409BMXPR01MB3269INDP_" MIME-Version: 1.0 X-OriginatorOrg: iitg.ac.in X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BMXPR01MB3269.INDPRD01.PROD.OUTLOOK.COM X-MS-Exchange-CrossTenant-Network-Message-Id: a8b5d7d0-5307-4bcf-a563-08d90a6c6ba0 X-MS-Exchange-CrossTenant-originalarrivaltime: 28 Apr 2021 17:38:22.7092 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 850aa78d-94e1-4bc6-9cf3-8c11b530701c X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: NSmZMGwTT9rDoJEKPt7SZkfwCeoMSiq9mXcp3UrJauvKOeeYJfBnQ08LXJFS+4KgVwgYqoZQ8k349EBKbitIRw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BM1PR01MB2612 X-Proofpoint-GUID: PjG1VKJQDtB1t0z1P96AATOmnfyF0uQi X-CLX-Response: 1TFkXGxIdEQpMehcaEQpZRBdpf0xlTWVnb256GREKWFgXb2MSUGkFZGViR1A RCnhOF25Tbh9OEmhjG1kBEQp5TBdhHRNdQxNTfW5EGhEKQ0gXBxgfHhEKQ1kXBxsZEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscHXEeHBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThd6QG0bfGFge25eaBteGlAbehMca2t+ZUdETFNsGl97QxEKWFwXHwQaBBgYEgUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3JcGmMYEQpNXBcbGxsRCkxaF3hpa01NEQpFWRdvEQpMXxd 6BQUFBQUFBQUFQxEKTEYXb2tra2traxEKQk8XbHlTQ2hYXWZLSE8RCkNaFx4aBBsaHQQbGRMEGx sSEQpCXhcbEQpCRRdmG1JcY0USQRoaZhEKQk4XblNuH04SaGMbWQERCkJMF29jElBpBWRlYkdQE QpCbBdvf25kf0ZtTFpmYxEKQkAXa0taSXBIWWtJfV0RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpa WBcYEQp5QxdkfVgacxJNaUtDWREKWUsXHB4fGhEKcGgXbWQZHWBPYmhfflgQGRoRCnBoF2FaYH9 bb0QbBXxzEBkaEQpwaBdkYWJOZ1paHlNgUhATGhEKcGgXYG0dQ0hhEhJwcx4QGRoRCnBoF2F/W0 9EextsW35pEBkaEQpwbBdiHFlacgFmT29MXxAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRC lhNF0sRIA== X-Proofpoint-ORIG-GUID: PjG1VKJQDtB1t0z1P96AATOmnfyF0uQi X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 suspectscore=0 malwarescore=0 spamscore=0 priorityscore=0 mlxlogscore=795 impostorscore=0 bulkscore=0 clxscore=187 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104280113 domainage_hfrom=6450 X-Spam-Score: 0 X-Spam-OrigSender: t.shivam@iitg.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, SHIVAM TIWARI --_000_BMXPR01MB3269E5AB6EC30849B6CBEBEFBE409BMXPR01MB3269INDP_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I want to simulate reverse osmosis process on a box of water and ions acros= s a membrane, for which, I am applying a transmembrane pressure on the wate= r box through a graphene sheet (as a piston). I am using tclforces to achie= ve this, the script I am using is as follows: tclForces on tclForcesScript { set linaccel1 {0.0 0.0 -0.0006449914635} set linaccel2 {0.0 0.0 0.0006449914635} set watIdList1 {} set watIdList2 {} for {set i 1} {$i <=3D 5520} {incr i} { lappend watIdList1 $i addatom $i } for {set i 229378} {$i <=3D 234897} {incr i} { lappend watIdList2 $i addatom $i } But the problem with this is that the graphene sheet behaves as a graphene = sheet and not as a rigid piston, that is, the graphene sheet gets deformed = (curled up) as soon as the pressure is applied. Although, the water does ge= t pushed, but I suspect that the pressure applied in this case is much less= er than the desired, since most of the force applied on the graphene sheet = must be getting wasted on the deformation of the graphene sheet. So how can= I achieve a rigid graphene piston? regards shivam --_000_BMXPR01MB3269E5AB6EC30849B6CBEBEFBE409BMXPR01MB3269INDP_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
I want to simulate reverse osmosis process on a box of water and ions acros= s a membrane, for which, I am applying a transmembrane pressure on the wate= r box through a graphene sheet (as a piston). I am using tclforces to achie= ve this, the script I am using is as follows:

tclForces on

tclForcesScript {
  set linaccel1 {0.0 0.0 -0.0006449914635}
  set linaccel2 {0.0 0.0 0.0006449914635}


  set watIdList1 {}
  set watIdList2 {}



  for {set i 1} {$i <=3D 5520} {incr i} {=
    lappend watIdList1 $i
    addatom $i
  }
  for {set i 229378} {$i <=3D 234897} {in= cr i} {
    lappend watIdList2 $i
    addatom $i
  }

But the problem with this is that the graphene sheet behaves as a graphene = sheet and not as a rigid piston, that is, the graphene sheet gets deformed = (curled up) as soon as the pressure is applied. Although, the water does ge= t pushed, but I suspect that the pressure applied in this case is much lesser than the desired, since most = of the force applied on the graphene sheet must be getting wasted on the de= formation of the graphene sheet. So how can I achieve a rigid graphene pist= on?

regards
shivam
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To: NAMD list Subject: namd-l: Efficiency of constant-pH simulations? Thread-Topic: Efficiency of constant-pH simulations? 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charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Hi mailing list, First, does anyone know if there are plans to allow GPU support for constan= t-pH simulations? I read that the computational expense of constant-pH simulations scales as = the number of titratable sites (https://urldefense.com/v3/__https://pubs.ac= s.org/doi/abs/10.1021/acs.jctc.7b00875__;!!DZ3fjg!vkapbFNPDtn9CAiot_Whpx0ne= CWJlTuQyfFd0_biOaoipaJlsBMPzjtqWbF2YntEkQ$ ). My protein of interest has 65= titratable residues (127,352 atoms), but I only care about one. I have sel= ected 8 more in the vicinity and used the keyword "cphExcludeResidue" to pr= event the others from being considered, but my simulation is about the same= speed after adding those exclusions (something like 300 cycles of 5 ps eac= h in 20 hours for 9 replicas on 144 cores -- is this reasonable?). I am run= ning namd2.13b2. The documentation says the maximum number of switch proposal attempts per c= ycle defaults to the number of residues, so I lowered cphMaxProposalAttempt= s to 9. However, my log files all include the lines: TCL: namdcph) CONSTANT pH neMD/MC MOVES: TCL: namdcph) MAX. ATTEMPTS PER CYCLE: 1 TCL: namdcph) ONE RESIDUE MOVES What is going on here? Is the log file wrong? Am I wrong to think that my s= imulations should speed up when less residues are considered for protonatio= n events? Best, Harper Smith --_000_CH2PR01MB5639F2E915F9D22756F3489BFA409CH2PR01MB5639prod_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable
Hi mailing list,

First, does anyone know if there are plans to allow GPU support for constan= t-pH simulations?

I read that the computational expense of constant-pH simulations scales as = the number of titratable sites (h= ttps://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00875). My protein of interest has 65 titratable residues (127,352 atoms), but I only care ab= out one. I have selected 8 more in the vicinity and used the keyword "= cphExcludeResidue" to prevent the others from being considered, but my= simulation is about the same speed after adding those exclusions (something like 300 cycles of 5 ps each in 20 hour= s for 9 replicas on 144 cores -- is this reasonable?). I am running namd2.1= 3b2.

The documentation says the maximum number of switch proposal attempts per c= ycle defaults to the number of residues, so I lowered cphMaxProposalAttempt= s to 9. However, my log files all include the lines:

TCL: namdcph) CONSTANT pH neMD/MC MOVES:
TCL: namdcph) MAX. ATTEMPTS PER CYCLE: 1
TCL: namdcph) ONE RESIDUE MOVES

What is going on here? Is the log file wrong? Am I wrong to think that my s= imulations should speed up when less residues are considered for protonatio= n events? 

Best,
Harper Smith
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Thu, 29 Apr 2021 01:40:57 +0000 Received: from BL0PR05MB4897.namprd05.prod.outlook.com ([fe80::64b2:7864:f9e5:c032]) by BL0PR05MB4897.namprd05.prod.outlook.com ([fe80::64b2:7864:f9e5:c032%6]) with mapi id 15.20.4087.026; Thu, 29 Apr 2021 01:40:57 +0000 From: Ivaylo Nikolaev Ivanov To: "namd-l@ks.uiuc.edu" CC: Ivaylo Nikolaev Ivanov Subject: namd-l: A postdoctoral position in Atlanta, GA, USA Thread-Topic: A postdoctoral position in Atlanta, GA, USA Thread-Index: AQHXPIHVDwKDJpEX00Kn/pfB1H1+PKrKtjdt Date: Thu, 29 Apr 2021 01:40:56 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=gsu.edu; x-originating-ip: [173.54.223.4] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 06865359-ef08-4c76-4173-08d90aafd5b7 x-ms-traffictypediagnostic: MN2PR05MB7183: x-ms-exchange-transport-forked: True x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:9508; 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charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Dear colleagues, I hope this email finds you well! I have an open postdoctoral position in my group. The project is in molecul= ar modeling of protein-nucleic acid assemblies. Details regarding the posit= ion and how to apply are downloadable from my group website at: https://urldefense.com/v3/__https://ivanovgroup.files.wordpress.com/2021/04= /postdoctoral-position-2021.pdf__;!!DZ3fjg!oU-5pO9555aBy5BhJ6VrETRYBmRgyv9O= pJunzIbRG39FF52PnG0gorZgJvq7b8HinQ$=20 Please share the information with suitable applicants or Ph.D. students nea= ring graduation. An ideal candidate will be someone with expertise in molec= ular dynamics, advanced simulation/analysis techniques and some experience = with coding and scripting. Thank you very much in advance. Best wishes, Ivaylo PS I am also looking for motivated Ph.D. students to join my group. Interes= ted candidates are welcome to contact me directly by email and explore the = GSU chemistry graduate program at https://urldefense.com/v3/__http://chemis= try.gsu.edu/graduate__;!!DZ3fjg!oU-5pO9555aBy5BhJ6VrETRYBmRgyv9OpJunzIbRG39= FF52PnG0gorZgJvrtjNTyaw$ . Dr. Ivaylo Ivanov Professor, Georgia State University P.O. Box 3965, Atlanta, Georgia 30302 Phone: (404) 413-5529 https://urldefense.com/v3/__https://ivanov-group.org/__;!!DZ3fjg!oU-5pO9555= aBy5BhJ6VrETRYBmRgyv9OpJunzIbRG39FF52PnG0gorZgJvo-agOIqA$=20 --_000_BL0PR05MB4897C01D14F947F5BC711E45A15F9BL0PR05MB4897namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable
Dear colleagues,

I hope this email finds you well!

I have an open postdoctoral&nbs= p;position in my group. The pro= ject is in molecular modeling of protein-nucleic acid assemblies. Details r= egarding the position and how to apply are downloadable from my group website at:

https://= ivanovgroup.files.wordpress.com/2021/04/postdoctoral-position-2021.pdf<= /div>

Please share the information with suitable applicants or Ph.D. students nea= ring graduation. An ideal candidate will be someone with expertise in molec= ular dynamics, advanced simulation/analysis techniques and some experience = with coding and scripting.

Thank you very much in advance.

Best wishes,
Ivaylo

PS I am also looking for motivated Ph.D. students to join my group. In= terested candidates are welcome to contact me directly by email and explore= the GSU chemistry graduate program at http://chemistry.gsu.edu/graduate.

Dr. Ivaylo Ivanov
Professor, Georgia State University
P.O. Box 3965, Atlanta, Georgia 30302 
Phone: (404) 413-5529 
https= ://ivanov-group.org/

--_000_BL0PR05MB4897C01D14F947F5BC711E45A15F9BL0PR05MB4897namp_-- From owner-namd-l@halifax.ks.uiuc.edu Wed Apr 28 22:05:03 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13T3530g002421; Wed, 28 Apr 2021 22:05:03 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13T353Hi002420; Wed, 28 Apr 2021 22:05:03 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13T352iS002416; Wed, 28 Apr 2021 22:05:02 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13T35214002415; Wed, 28 Apr 2021 22:05:02 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13T34nrx002408 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 28 Apr 2021 22:04:50 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13T32nNx018709 for ; Thu, 29 Apr 2021 03:04:49 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qv1-f45.google.com (mail-qv1-f45.google.com [209.85.219.45]) by mx0a-00007101.pphosted.com with ESMTP id 387aa5pcp0-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 29 Apr 2021 03:04:48 +0000 Received: by mail-qv1-f45.google.com with SMTP id u1so295205qvg.11 for ; Wed, 28 Apr 2021 20:04:48 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=Vg/F+FYxwuIotZ5ZMIhjACbhjFby9xhykQgFXa0rc7o=; b=DN7CaNh5A8mdizUGHcYIcrEFi68fP8p+4tVCDimCYn7EKYizvqXVLf1xoS+J5izKAC 1xDTUOwQvJwZOWmYPBh9HXI5c3z1biEwx8pJfC7iFvuEiTLnjp3QVBPUHXlNhbC48AEb eUQHPJ7h/MS+RYl7k38d1dIMDfCEgMlxcpFqdcoUmo3SkqqCl/wrKRATx/71skeEM9/J S5++QRsYKSxaKgZn7dRe5t+WbdYVOXT46jh1gvxtDL/6N5I77fZT1U/48b7xULlN476F W/DgXobDTXRlIAngRzxjAgHUTtS8m2OE1L9rAJVnsO6eOvFvdHdtdKUJqNRPpSjNh/tW OeWA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=Vg/F+FYxwuIotZ5ZMIhjACbhjFby9xhykQgFXa0rc7o=; b=nLvlk+xejJAfCMt/hU3MyIfDsk3ajUKLzmDeL7r/bvqV6EMR1TettC6B6fP6v54l7r srddjsNysddgCD7pgvbeCAPEqLHSe9DJQVyhUzCdHMzaEKZkCJS7KCa/k05cO3CEn3BX 1898mYasrwnyj6UvrS992ft+g7Cb6fypxWz8nlns6gLUgUUcnjtO+ca3XuHroeuBze76 ZbJn3DyUTemrJbASXc016SLwutWCfDexCinC858jjXaz1kXx5N1vXrU7DxKXIqFtxco2 cveTZlslb3b+cgOInYpO9OP0ZTwBaRTlg0NrYScBOulh9EVBFDaofq98RDGZjJ24/E0M tWmQ== X-Gm-Message-State: AOAM530nceLXpNSoR3IKjVS8yRGL3i8E2vnSx3K+vALa9ilVW+lnYzOQ 6SLL0+by+2w5ocThbxxZXbAJoQr1x5yJ/g== X-Google-Smtp-Source: ABdhPJyoUvaasLOD+V35RseDpMMNNFV4kJ4sl/VyXIfk0yGBB0J4uR72PEYpXJ0FLdRMrgB+mLKWBw== X-Received: by 2002:ad4:4f11:: with SMTP id fb17mr335474qvb.18.1619665487534; Wed, 28 Apr 2021 20:04:47 -0700 (PDT) Received: from [192.168.1.36] ([181.64.231.75]) by smtp.gmail.com with ESMTPSA id d16sm1412884qtr.18.2021.04.28.20.04.46 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Wed, 28 Apr 2021 20:04:47 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Thu, 22 Apr 2021 22:17:15 -0500 Subject: namd-l: Truncated solvate plugin From: "Ropon-Palacios G." To: KS UIUC Message-ID: <36FEAAB1-0D2D-4CFC-B654-CA6C92D2275D@gmail.com> Thread-Topic: Truncated solvate plugin Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3702492286_361559417" X-Proofpoint-GUID: 8GGFb1-X4DtPDfET-fFmZS2D-EMW8-23 X-CLX-Response: 1TFkXGxIZEQpMehcZGhMRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGxwaEQpDWRcHHhIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBlxHhgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XEm1tbEgbB3Iebl56bkxvfgdMbEdweRhuB29nfRIHGBkRClhcFx8EGgQYGBMF GxgdBBoEGgQbEBseGh8aEQpeWRdyXBJIWBEKTVwXGx8bEQpMWhdsaWtNaxEKTEYXb2tra2trEQp CTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEwQeHxEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1 Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja3sTWH4aX 14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXYlBeSx9+W2QeE1wRCkJYF2dz ZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5Qxdof0ZueXMaHhtdbREKWUsXExkTGxEKcGgXZXJkBWh mBUtYSWUQGRoRCnBoF2lSHUQeYxxHG1lSEBkaEQpwaBdlfGBtYWZiSW5MSBAdGhEKcGgXek1eW0 R+SX0bUl0QGRoRCnBoF2FOHxtnGhlsRU58EBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEwXZ35Qf U1rUE9PRmIQGRoRCnBDF29cRHtmckJGQRpoEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 8GGFb1-X4DtPDfET-fFmZS2D-EMW8-23 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 suspectscore=0 malwarescore=0 spamscore=0 priorityscore=309 mlxlogscore=318 impostorscore=0 bulkscore=0 clxscore=183 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104290022 domainage_hfrom=9391 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3702492286_361559417 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear namd users, Where find following packages Toctsolvate and vexpr , for generate truncated octahedron solvate box Best, Geo. --B_3702492286_361559417 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear namd users,

<= p class=3DMsoNormal> 

Where f= ind following packages

 =

Toctsolvate and vexpr , for generate truncated= octahedron solvate box

 =

Best,

 =

Geo.

--B_3702492286_361559417-- From owner-namd-l@halifax.ks.uiuc.edu Thu Apr 29 07:17:47 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13TCHlMh011222; Thu, 29 Apr 2021 07:17:47 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13TCHlqE011221; Thu, 29 Apr 2021 07:17:47 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13TCHkiW011217; Thu, 29 Apr 2021 07:17:46 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13TCHkGu011216; Thu, 29 Apr 2021 07:17:46 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13TCHaCC011207 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 29 Apr 2021 07:17:37 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 13TCERWf012832 for ; Thu, 29 Apr 2021 12:17:36 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=brian.radak@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-io1-f42.google.com (mail-io1-f42.google.com [209.85.166.42]) by mx0a-00007101.pphosted.com with ESMTP id 387aa5sftk-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 29 Apr 2021 12:17:36 +0000 Received: by mail-io1-f42.google.com with SMTP id p11so2084188iob.9 for ; Thu, 29 Apr 2021 05:17:36 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=Sz9Q3D1U5yf8SzSbeNvAiJ3bmuCM8vWiywDXwrPGvFg=; b=VGrG6/IhFoQwTC9SkGrBd4XGLlE57CDdhJktCmP7jToHPo7UAo/2KuwwqHQjdWw25U 1/7t6fPuPeNhOQjVYQ8/UTdGZ5ia5dojrpjQ0Xy8GCzP5t6Me+QdyG2IdJpqukyo6QVh c/ffaoOqCMO23Ba7sD5Tihoh2Cmoen4noJBAQ6HOEFODU6tq2DbhEXR0VqFKy29ty98P ZwBprq6ma2NIiMrkcbJghVk4az3FxziGaTR3hqPa5ZL4BFrO2rX2WX6nYZAfvy9nv18u pkb4iT10g4PgvQBsMjr2rQHhCt/btU66tGHlrpg7/Zhjwg0PE/UZ81XX0eMXSNzKMTLX zKog== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=Sz9Q3D1U5yf8SzSbeNvAiJ3bmuCM8vWiywDXwrPGvFg=; b=meOAyq2YIfyvVWQXaM7h3ucmxCNmi0aa3T++5K6eXJ6nqEWixSTrc08ZQgJqzlib5w YZlLX6vfyADUaQF/Jzfn+9sr4eL7w9vzCVj3YmGyFL7AygvuSmI1h6P3JZeGIaJCFo/3 qkk9RvNOIdNeChh7vKDdlmYTPSqdDKe5eR4GFNkDhqdfk9o1jXjJ7bS8kp0oh6hNzF4Q tL/GWWbXTxhB9SA/9XDdB4U6/BrFSy39ETUSWmbWu7m8MkV/xXO2t1Jt90OSqVhp5kpD NeNxWN9hduPrjW/PUHxQZ+QCMeghXcZ4LZw+Sg2PIRIePtCnB9cYsc6UZPeOREQrQsTL NxyQ== X-Gm-Message-State: AOAM531Qg/kDA/wJ7r/ZPnUPs20V0bDs/eS9hucO2QnoLr1GQLob428O NkMvMVXNyUTFrztGyvhpQ+RsiopN0m+qM/6wz2ij3r7b X-Google-Smtp-Source: ABdhPJwZYr60+NtGQkn9Ijk5CyyLix39nNmkYZ5x7GirnATt41PwU7hHHBJJ9CfWruHhew3ZEMabAYxArtudDXaf0+w= X-Received: by 2002:a05:6602:2bc5:: with SMTP id s5mr27636872iov.91.1619698655629; Thu, 29 Apr 2021 05:17:35 -0700 (PDT) References: In-Reply-To: From: Brian Radak Date: Thu, 29 Apr 2021 08:17:24 -0400 Message-ID: Subject: Re: namd-l: Efficiency of constant-pH simulations? To: namd-l , "Smith, Harper E." Content-Type: multipart/alternative; boundary="00000000000003146505c11b7b44" X-Proofpoint-GUID: w7R4TOj7vs3sInSlTdF1idsEzaz8nCeT X-CLX-Response: 1TFkXGxITEQpMehcZHhIRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHHxwTEQpDWRcbEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwTcRMdEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF10deB5+ZUAdXFkZWWNEeUZ+TmwbQ05Zb1BLUBJEaU9+EQpYXBcfBBoEGBgTBRsY HQQaBBoEGxAbHhofGhEKXlkXcl1vQh0RCk1cFx4eGREKTFoXeGlNTWsRCkVZF29rEQpMXxd6BQU FBQUFBQUFbxEKTEYXb2trbGtrEQpCTxd6UHhka1pSclpGRhEKQ1oXGBoTBBIfBBscHAQeGBEKQl 4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCR RdrExphTl9eWBgdZREKQk4XY1Nja3sTWH4aX14RCkJMF2lJSBpLfmlGG3hzEQpCbBdhHhl4Wm5s Z2NfYhEKQkAXbXkSXnBtR057XH8RCkJYF2dzZXNAbmFhTF1iEQpaWBcdEQp5QxdmS2Byc0JoZl9 7aREKWUsXExkTGxEKcGcXY1lETBlpRxx8E20QHB8RCnBoF2xGGmhZWEZDbn5hEBkaEQpwaBdkTE gbT1MaexhhbBAZGhEKcGgXZURicExLSWxNEkYQGRoRCnBoF2VIZ2ZNfnoafl1MEBkaEQpwaBdgQ V9+GBkTWRoYTxAZGhEKcH0XaEJLH0tbUlhuaWYQGRoRCnB9F3oFaXwZfBwYUGd6EB4SEQpwfxdi HE1Fa2xCYHBoYBASEhEKcF8XYk1eSAUeX0tFe2cQGxsbEQpwfxdhZm9bGmdkQkgdWxAbGRkRCnB fF2NiElBIY3gffEJ9EBMdEQpwbBduHWZ7EksaeBJcbRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: w7R4TOj7vs3sInSlTdF1idsEzaz8nCeT X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 suspectscore=0 malwarescore=0 spamscore=0 priorityscore=348 mlxlogscore=999 impostorscore=0 bulkscore=0 clxscore=189 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104290085 domainage_hfrom=9391 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --00000000000003146505c11b7b44 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Harper, I don't know about namd3 gpu support, but, for what it's worth, namd2 gpu support should already exist. If you are only interested in one residue then constant-pH MD is probably not a very efficient approach - I would just enumerate all protonation states and run standard alchemical FEP. The cost statement about number of residues was meant to reflect overall sampling cost, not computational cost. That latter depends entirely on system size. The cphMaxProposalAttempts keyword is deprecated, bc it usually leads to detailed balance violations - thanks for pointing out that this is still in the manual (it should not be). It's fixed at one because that's the only value that should work. If you want more switch attempts then increase the frequency. HTH, BKR On Wed, Apr 28, 2021, 7:54 PM Smith, Harper E. < smith.12510@buckeyemail.osu.edu> wrote: > Hi mailing list, > > First, does anyone know if there are plans to allow GPU support for > constant-pH simulations? > > I read that the computational expense of constant-pH simulations scales as > the number of titratable sites ( > https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/acs.jctc= .7b00875__;!!DZ3fjg!t4RWmzSEfN9plzIDKomqfXS9-kbGHr8qYllhO8xsaBu_4Kg-4v0gHDg= 6k3Xan3bktg$=20 > ). > My protein of interest has 65 titratable residues (127,352 atoms), but I > only care about one. I have selected 8 more in the vicinity and used the > keyword "cphExcludeResidue" to prevent the others from being considered, > but my simulation is about the same speed after adding those exclusions > (something like 300 cycles of 5 ps each in 20 hours for 9 replicas on 144 > cores -- is this reasonable?). I am running namd2.13b2. > > The documentation says the maximum number of switch proposal attempts per > cycle defaults to the number of residues, so I lowered > cphMaxProposalAttempts to 9. However, my log files all include the lines: > > TCL: namdcph) CONSTANT pH neMD/MC MOVES: > TCL: namdcph) MAX. ATTEMPTS PER CYCLE: 1 > TCL: namdcph) ONE RESIDUE MOVES > > What is going on here? Is the log file wrong? Am I wrong to think that my > simulations should speed up when less residues are considered for > protonation events? > > Best, > Harper Smith > --00000000000003146505c11b7b44 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Harper,=C2=A0

I don't know about namd3 gpu support, but, for what it&= #39;s worth, namd2 gpu support should already exist.=C2=A0

If you are only interested in one residu= e then constant-pH MD is probably not a very efficient approach - I would j= ust enumerate all protonation states and run standard alchemical FEP. The c= ost statement about number of residues was meant to reflect overall samplin= g cost, not computational cost. That latter depends entirely on system size= .=C2=A0

The cphMaxPropos= alAttempts keyword is deprecated, bc it usually leads to detailed balance v= iolations - thanks for pointing out that this is still in the manual (it sh= ould not be). It's fixed at one because that's the only value that = should work. If you want more switch attempts then increase the frequency.= =C2=A0

HTH,=C2=A0
<= div dir=3D"auto">BKR

On Wed, Apr 28, 2021, 7:54 PM Smith, Harper = E. <smith.12510@bucke= yemail.osu.edu> wrote:
Hi mailing list,

First, does anyone know if there are plans to allow GPU support for constan= t-pH simulations?

I read that the computational expense of constant-pH simulations scales as = the number of titratable sites (https://pubs.acs.= org/doi/abs/10.1021/acs.jctc.7b00875). My protein of interest has 65 titratable residues (127,352 atoms), but I only care ab= out one. I have selected 8 more in the vicinity and used the keyword "= cphExcludeResidue" to prevent the others from being considered, but my= simulation is about the same speed after adding those exclusions (something like 300 cycles of 5 ps each in 20 hour= s for 9 replicas on 144 cores -- is this reasonable?). I am running namd2.1= 3b2.

The documentation says the maximum number of switch proposal attempts per c= ycle defaults to the number of residues, so I lowered cphMaxProposalAttempt= s to 9. However, my log files all include the lines:

TCL: namdcph) CONSTANT pH neMD/MC MOVES:
TCL: namdcph) MAX. ATTEMPTS PER CYCLE: 1
TCL: namdcph) ONE RESIDUE MOVES

What is going on here? Is the log file wrong? Am I wrong to think that my s= imulations should speed up when less residues are considered for protonatio= n events?=C2=A0

Best,
Harper Smith
--00000000000003146505c11b7b44-- From owner-namd-l@halifax.ks.uiuc.edu Fri Apr 30 03:54:42 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13U8sg99028417; Fri, 30 Apr 2021 03:54:42 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13U8sggE028416; Fri, 30 Apr 2021 03:54:42 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13U8sfgb028412; Fri, 30 Apr 2021 03:54:41 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13U8sf62028411; Fri, 30 Apr 2021 03:54:41 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13U8sCRO028377 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Fri, 30 Apr 2021 01:54:10 -0700 (PDT) Received: from [10.1.16.80] ([193.147.143.12]) by smtp.gmail.com with ESMTPSA id k188sm15789556wmf.18.2021.04.30.01.54.09 for (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 30 Apr 2021 01:54:09 -0700 (PDT) From: "=?UTF-8?Q?Jos=c3=a9_Villala=c3=adn?=" X-Google-Original-From: =?UTF-8?Q?Jos=c3=a9_Villala=c3=adn?= Subject: namd-l: System with two membranes To: namd-l@ks.uiuc.edu Message-ID: Date: Fri, 30 Apr 2021 10:54:08 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.10.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: en-GB X-CLX-Response: 1TFkXGxkbEQpMehcbGh4RCllEF29NS2NSUGBPXV1pEQpYWBd6cmIfcGFlT1t vYREKeE4XaWNaBU9OHUceH08RCnlMF2Jta0diE2FaTnB7EQpDSBcHGR4bEQpDWRcHHB0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGxtxGxgQGncGGBoGGhEKWV4XaGN5EQpJRhdfQ19Jd UJFWV5PThEKQ04XRX1THlMSUGV9BxsHQVNdZV5aR2d/YURuflBDZk4TZk8RClhcFx8EGgQYGBMF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcl19WnoRCk1cFxgbGxEKTFoXbGlNa2sRCkJPF2h9QWB DWn1zR0ETEQpDWhcYGhMEEh8EGxgSBB4eEQpCXhcbEQpCRRdieV4FR0xEE0lzXBEKQk4XaWNaBU 9OHUceH08RCkJMF3pyYh9wYWVPW29hEQpCbBdoZRJ+RB1uWVsTaREKQkAXZ2xsHxJMS35/f0gRC kJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdmZFt6WGlJHlJzRBEKcGgXZkYYGWFvTWVu bmgQGRoRCnBoF2FdcAUcX2tvZ0B5EBkaEQpwaBdkSU8fE3oeWBwcRxAZGhEKcGgXentpeG9wHk8 Bc2kQGRoRCnBoF2tvGBJwZVJbXRNSEBkaEQpwbBdjGXxSfR9NcH1OARAZGhEKcEMXa1N6QRJiR0 tvS0AQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: oWy4y8zOW-1-kywOtpmMUKnDTziLd9Le X-Proofpoint-ORIG-GUID: oWy4y8zOW-1-kywOtpmMUKnDTziLd9Le X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 mlxlogscore=999 adultscore=0 bulkscore=0 mlxscore=0 impostorscore=0 spamscore=0 priorityscore=104 suspectscore=0 clxscore=131 phishscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104300063 X-Spam-Score: 0 X-Spam-OrigSender: jvillalain@umh.es X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "=?UTF-8?Q?Jos=c3=a9_Villala=c3=adn?=" Dear all, I am trying to build a system with two membranes in order to place different concentrations of ions (inside/outside). To do this, I have minimized, equilibrated and simulated a single membrane system (containing membrane, protein, ions and water). To obtain the system with two membranes, I use the previous system containing one membrane, duplicate it and join the two systems in one. Afterwards, I remove all the water and ions, solvate with water, remove the water inside the membrane and place the ions (different concentrations inside and outside). However, and although I have used several different parameters in the configuration file (different constraints for water, lipids, ions and their combinations, PME, not PME, pressure on /off), whenever I try to equilibrate the system, it shrinks, specially the water molecules, and the water and ions move to the sides and from the sides, move from/to the different compartments . So far it has been impossible for me to continue equilibrating the two membrane system. Could someone give me an idea of what I am doing wrong?. Thank you very much in advance. José IDiBE / UMH From owner-namd-l@halifax.ks.uiuc.edu Fri Apr 30 05:26:06 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13UAQ69Y001816; Fri, 30 Apr 2021 05:26:06 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13UAQ6PK001815; Fri, 30 Apr 2021 05:26:06 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13UAQ59M001811; Fri, 30 Apr 2021 05:26:05 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13UAQ53J001810; Fri, 30 Apr 2021 05:26:05 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13UAPgwY001798 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Fri, 30 Apr 2021 03:25:39 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Hemanth Haridas Date: Fri, 30 Apr 2021 15:58:47 +0530 Message-ID: Subject: Re: namd-l: graphene sheet as a rigid piston To: namd-l@ks.uiuc.edu, SHIVAM TIWARI Content-Type: multipart/alternative; boundary="000000000000884d3905c12e0831" X-CLOUD-SEC-AV-Sent: true X-CLOUD-SEC-AV-Info: iitgn,google_mail,monitor X-Gm-Spam: 0 X-Gm-Phishy: 0 X-CLX-Shades: MLX X-Proofpoint-GUID: rthoi5hByrpijrvEQBMEpLdw2lykL651 X-Proofpoint-ORIG-GUID: rthoi5hByrpijrvEQBMEpLdw2lykL651 X-CLX-Response: 1TFkXGxwfEQpMehcbGxIRCllEF3pMYVlCUmljYEYfEQpYWBdpRVxYeGZmGxh fGREKeE4XZ2lbZm1iX0AbAWMRCnlMF2RsSx5lfhNibGR+EQpDSBcHGRIdEQpDWRcHHB0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHh9xGB0QGncGGBoGGhEKWV4XaGN5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWF5CRUMfQmhTWFpDQFhcb3toZ29aZk5dGEZTQWYcHxsRClhcFx8EGgQYGBMF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXcl1yAQURCk1cFxwYEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF3pMQ0lzaXkBW0B7EQpDWhcYGhMEEh8EGBsaBB4YEQ pCXhcbEQpEXhcYEQpCRRdiR2BvcgFcWlwdbREKQk4XZ2lbZm1iX0AbAWMRCkJMF2lFXFh4ZmYbG F8ZEQpCbBdmR2kFZXhSH2x6ThEKQkAXaFtuW3gZHR5eR2ARCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcYEQp5QxduBXBJTxNlARJ6BREKWUsXHh8ZGREKcGcXZR4FGxJcbh9bZRsQHhIRCnBoF2h /Um9Gc1BFQBtyEBkaEQpwaBdjSF9remZITlNkGRAZGhEKcGgXZRhtW01bGVxhenAQGRoRCnBoF2 dZT2dyG0Z6T19tEBkaEQpwaBdiSEdGU3tnTHsSeBAfGxEKcGwXZ2QFZ3gcSEtvU3AQGRoRCm1+F xsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 impostorscore=0 mlxscore=0 malwarescore=0 phishscore=0 spamscore=0 clxscore=165 priorityscore=118 mlxlogscore=949 bulkscore=0 suspectscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104300073 domainage_hfrom=4533 X-Spam-Score: 0 X-Spam-OrigSender: hemanth.h@iitgn.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hemanth Haridas --000000000000884d3905c12e0831 Content-Type: text/plain; charset="UTF-8" Shivam, I had some luck with using the SMD module to get graphene working as a piston. The trick is to tag one graphene layer as moving (SMD active), and to restrain the layer containing the nanopore with a very high harmonic restraint. Hope this helps, Regards Hemanth On Wed, Apr 28, 2021 at 11:13 PM SHIVAM TIWARI wrote: > Dear all, > I want to simulate reverse osmosis process on a box of water and ions > across a membrane, for which, I am applying a transmembrane pressure on the > water box through a graphene sheet (as a piston). I am using tclforces to > achieve this, the script I am using is as follows: > > tclForces on > > tclForcesScript { > set linaccel1 {0.0 0.0 -0.0006449914635} > set linaccel2 {0.0 0.0 0.0006449914635} > > > set watIdList1 {} > set watIdList2 {} > > > > for {set i 1} {$i <= 5520} {incr i} { > lappend watIdList1 $i > addatom $i > } > for {set i 229378} {$i <= 234897} {incr i} { > lappend watIdList2 $i > addatom $i > } > > But the problem with this is that the graphene sheet behaves as a graphene > sheet and not as a rigid piston, that is, the graphene sheet gets deformed > (curled up) as soon as the pressure is applied. Although, the water does > get pushed, but I suspect that the pressure applied in this case is much > lesser than the desired, since most of the force applied on the graphene > sheet must be getting wasted on the deformation of the graphene sheet. So > how can I achieve a rigid graphene piston? > > regards > shivam > -- *Hemanth H 18310019* Research Scholar IIT Gandhinagar --000000000000884d3905c12e0831 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Shivam,

I had some luck with= using the SMD module to get graphene working as a piston. The trick is to = tag one graphene layer as moving (SMD active), and to restrain the layer co= ntaining the nanopore with a very high harmonic restraint.

Hope this helps,

Regards
Hemant= h

On Wed, Apr 28, 2021 at 11:13 PM SHIVAM TIWARI <t.shivam@iitg.ac.in> wrote:
Dear all,
I want to simulate reverse osmosis process on a box of water and ions acros= s a membrane, for which, I am applying a transmembrane pressure on the wate= r box through a graphene sheet (as a piston). I am using tclforces to achie= ve this, the script I am using is as follows:

tclForces on

tclForcesScript {
=C2=A0 set linaccel1 {0.0 0.0 -0.0006449914635}
=C2=A0 set linaccel2 {0.0 0.0 0.0006449914635}


=C2=A0 set watIdList1 {}
=C2=A0 set watIdList2 {}



=C2=A0 for {set i 1} {$i <=3D 5520} {incr i} {=
=C2=A0 =C2=A0 lappend watIdList1 $i
=C2=A0 =C2=A0 addatom $i
=C2=A0 }
=C2=A0 for {set i 229378} {$i <=3D 234897} {in= cr i} {
=C2=A0 =C2=A0 lappend watIdList2 $i
=C2=A0 =C2=A0 addatom $i
=C2=A0 }

But the problem with this is that the graphene sheet behaves as a graphene = sheet and not as a rigid piston, that is, the graphene sheet gets deformed = (curled up) as soon as the pressure is applied. Although, the water does ge= t pushed, but I suspect that the pressure applied in this case is much lesser than the desired, since most = of the force applied on the graphene sheet must be getting wasted on the de= formation of the graphene sheet. So how can I achieve a rigid graphene pist= on?

regards
shivam


--
Hemanth H 18310019
Research Scholar
IIT Gandhinagar
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Fri, 30 Apr 2021 11:24:39 +0000 Received: from BN8PR02MB5729.namprd02.prod.outlook.com ([fe80::fcba:6ed0:429f:c13e]) by BN8PR02MB5729.namprd02.prod.outlook.com ([fe80::fcba:6ed0:429f:c13e%4]) with mapi id 15.20.4065.033; Fri, 30 Apr 2021 11:24:39 +0000 From: "Dalhaimer, Paul Matthew" To: "namd-l@ks.uiuc.edu" , Hemanth Haridas , SHIVAM TIWARI Subject: Re: namd-l: graphene sheet as a rigid piston Thread-Topic: namd-l: graphene sheet as a rigid piston Thread-Index: AQHXPbJqimg2O4tz50yWhacf03mIzqrM6dtB Date: Fri, 30 Apr 2021 11:24:39 +0000 Message-ID: References: , In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=utk.edu; x-originating-ip: [192.249.3.190] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 5d5525b6-db46-44f6-3134-08d90bca8b27 x-ms-traffictypediagnostic: BN6PR02MB2323: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:8273; 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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Another option, for those who know C++, is to manually change the source co= de in GlobalMasterSMD.C: /** *** Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by *** The Board of Trustees of the University of Illinois. *** All rights reserved. **/ #include "InfoStream.h" #include "Node.h" #include "Molecule.h" #include "NamdTypes.h" #include "GlobalMaster.h" #include "GlobalMasterSMD.h" #include "PDB.h" #include "PDBData.h" /* XXX necessary? #include #if !defined(WIN32) || defined(__CYGWIN__) #include #else #include #endif #include */ //#define DEBUGM #define MIN_DEBUG_LEVEL 1 #include "Debug.h" GlobalMasterSMD::GlobalMasterSMD(BigReal spring_constant, BigReal transverse_spring_constant, BigReal velocity, const Vector direction, int output_frequency, int first_timestep, const char *filename, int numAtoms) { DebugM(3,"initialize called\n"); moveVel =3D velocity; moveDir =3D direction; outputFreq =3D output_frequency; k =3D spring_constant; k2 =3D transverse_spring_constant; currentTime =3D first_timestep; parseAtoms(filename,numAtoms); iout << iINFO << requestedGroups()[0].size() << " SMD ATOMS\n" << endi; DebugM(1,"done with initialize\n"); } void GlobalMasterSMD::parseAtoms(const char *file, int numTotalAtoms) { DebugM(3,"parseAtoms called\n"); PDB smdpdb(file); int numatoms =3D smdpdb.num_atoms(); if (numatoms < 1) NAMD_die("No atoms found in SMDFile\n"); if (numatoms !=3D numTotalAtoms) NAMD_die("The number of atoms in SMDFile must be equal to the total num= ber of atoms in the structure!"); // add a single group modifyRequestedGroups().resize(1); modifyGroupForces().resize(1); // add all the required atoms to the group // also compute the center of mass of these atoms cm.x =3D cm.y =3D cm.z =3D 0; Molecule *mol =3D Node::Object()->molecule; // to get masses BigReal imass =3D 0; for (int i=3D0; ioccupancy()) { // if occupancy is not 0, then add it! // add the atom to the list modifyRequestedGroups()[0].add(i); // compute the center of mass BigReal mass =3D mol->atommass(i); cm.x +=3D atom->xcoor()*mass; cm.y +=3D atom->ycoor()*mass; cm.z +=3D atom->zcoor()*mass; imass +=3D mass; } } if (imass =3D=3D 0) // we didn't find any! NAMD_die("SMDFile contained no SMD atoms (atoms w/ nonzero occupancy)\n= "); // now compute the center of mass cm /=3D imass; DebugM(1,"done with parseAtoms\n"); } GlobalMasterSMD::~GlobalMasterSMD() { } void GlobalMasterSMD::calculate() { DebugM(3,"calculate called\n"); // make extra-sure we have been set up correctly if(!requestedGroups().size() =3D=3D 1) NAMD_die("Internal error: uninitialized!"); // set the correct forces Position curcm =3D *getGroupPositionBegin(); // get the center of mass DebugM(1,"Current CM "< on behalf of Hema= nth Haridas Date: Friday, April 30, 2021 at 7:17 AM To: namd-l@ks.uiuc.edu , SHIVAM TIWARI Subject: Re: namd-l: graphene sheet as a rigid piston Shivam, I had some luck with using the SMD module to get graphene working as a pist= on. The trick is to tag one graphene layer as moving (SMD active), and to r= estrain the layer containing the nanopore with a very high harmonic restrai= nt. Hope this helps, Regards Hemanth On Wed, Apr 28, 2021 at 11:13 PM SHIVAM TIWARI > wrote: Dear all, I want to simulate reverse osmosis process on a box of water and ions acros= s a membrane, for which, I am applying a transmembrane pressure on the wate= r box through a graphene sheet (as a piston). I am using tclforces to achie= ve this, the script I am using is as follows: tclForces on tclForcesScript { set linaccel1 {0.0 0.0 -0.0006449914635} set linaccel2 {0.0 0.0 0.0006449914635} set watIdList1 {} set watIdList2 {} for {set i 1} {$i <=3D 5520} {incr i} { lappend watIdList1 $i addatom $i } for {set i 229378} {$i <=3D 234897} {incr i} { lappend watIdList2 $i addatom $i } But the problem with this is that the graphene sheet behaves as a graphene = sheet and not as a rigid piston, that is, the graphene sheet gets deformed = (curled up) as soon as the pressure is applied. Although, the water does ge= t pushed, but I suspect that the pressure applied in this case is much less= er than the desired, since most of the force applied on the graphene sheet = must be getting wasted on the deformation of the graphene sheet. So how can= I achieve a rigid graphene piston? regards shivam -- Hemanth H 18310019 Research Scholar IIT Gandhinagar --_000_BN8PR02MB57293E96A9DFB5CBC8745B94DE5E9BN8PR02MB5729namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Another option, for those who know C++, is to manual= ly change the source code in GlobalMasterSMD.C:

 

/**

***  Copy= right (c) 1995, 1996, 1997, 1998, 1999, 2000 by

***  The = Board of Trustees of the University of Illinois.

***  All = rights reserved.

**/

 

#include "InfoStream.h"=

#include "Node.h"<= /o:p>

#include "Molecule.h"

#include "NamdTypes.h"<= o:p>

 

#include "GlobalMaster.h&quo= t;

#include "GlobalMasterSMD.h&= quot;

#include "PDB.h"

#include "PDBData.h"

 

/* XXX necessary?

#include <iostream.h>

#if !defined(WIN32) || defined(__CYGWIN__)

#include <strstream.h>

#else

#include <strstrea.h>

#endif

#include <string.h>

*/

 

//#define DEBUGM

#define MIN_DEBUG_LEVEL 1

#include "Debug.h"=

 

GlobalMasterSMD::GlobalMasterSMD(= BigReal spring_constant,

    &nbs= p;        BigReal transverse_spring_constant, BigReal velocity,

     &= nbsp;         const Vector direction, int output_frequency,

    &nbs= p;        int first_timestep, const char *filename,

    &nbs= p;        int numAtoms) {

  DebugM(3,"initialize called\n");=

  moveVel= =3D velocity;

  moveDir= =3D direction;

  outputF= req =3D output_frequency;

  k =3D s= pring_constant;

  k2 =3D = transverse_spring_constant;

  current= Time =3D first_timestep;

 

  parseAt= oms(filename,numAtoms);

  iout &l= t;< iINFO << requestedGroups()[0].size()= << " SMD ATOMS\n" << endi;

  DebugM(1,"done with initialize\n");

}

 

void GlobalMasterSMD::parseAtoms(const char *file, int<= /span> numTotalAtoms) {

  DebugM(3,"parseAtoms called\n");=

  PDB smd= pdb(file);

  int numatoms =3D smdpdb.num_atoms();

  if (numatoms < 1) 

    = NAMD_die("No atoms found in SMDFile\n"<= span class=3D"s6">);

  if (numatoms !=3D numTotalAtoms)

    = NAMD_die("The number of atoms in SMDFile mus= t be equal to the total number of atoms in the structure!");

 

  // add = a single group

  modifyR= equestedGroups().resize(1);

  modifyG= roupForces().resize(1);

 

  // add = all the required atoms to the group

 

  // also= compute the center of mass of these atoms

  cm.x = =3D cm.y =3D cm.z =3D 0;

  Molecul= e *mol =3D Node::Object()->molecule; // to get masses

  BigReal= imass =3D 0; 

 

  for (int i=3D0; i<numatoms; i++) {

#ifdef MEM_OPT_VERSION

    = PDBCoreData *atom =3D smdpdb.atom(i);

#else

    = PDBAtom *atom =3D smdpdb.atom(i); // get an atom from the file

#endif    <= /span>

    = if (atom->occupancy(= )) { // if occupancy is not 0, then add it!

      = // add the atom to the list

      = modifyRequestedGroups()[0].add(i);

 

      = // compute the center of mass

      = BigReal mass =3D mol->atommass(i); 

      = cm.x +=3D atom->xcoor()*mass;

      = cm.y +=3D atom->ycoor()*mass;

      = cm.z +=3D atom->zcoor()*mass;

      = imass +=3D mass; <= o:p>

    = }

  }<= /o:p>

  if (imass =3D=3D 0) // we didn't = find any!

    = NAMD_die("SMDFile contained no SMD atoms (at= oms w/ nonzero occupancy)\n");

 

  // now = compute the center of mass

  cm /=3D= imass;

  DebugM(1,"done with parseAtoms\n");

}

 

GlobalMasterSMD::~GlobalMasterSMD= () { }

 

void GlobalMasterSMD::calculate() {

  DebugM(3,"calculate called\n");<= /p>

 

  // make= extra-sure we have been set up correctly

  if(!requestedGroups().size() =3D=3D 1)

    = NAMD_die("Internal error: uninitialized!&quo= t;);

 

  // set = the correct forces

  Positio= n curcm =3D *getGroupPositionBegin(); // get the center of mass

  DebugM(= 1,"Current CM "<<cm<<"\n");

  //BigReal diff =3D (curcm -= cm)*moveDir;

  // sec= ond term below is along transverse direction: -diff*moveDir + (diff*moveDir= - (curcm-cm)) =3D -(curcm-cm)

  // so = if k =3D k2 and moveVel =3D 0, we see that f =3D -k * (curcm - cm), the des= ired result

  // For= ce f =3D k*(moveVel*currentTime - diff)*moveDir + k2*(diff*moveDir - (curcm= - cm));

       Force = f =3D k*(moveDir-cumcm);

  modify= GroupForces()[0] =3D f;

 

  // prin= t some output sometimes

  if (currentTime % outputFreq =3D=3D 0)

    = output(currentTime, curcm, f);

 

  // keep= track of the number of timesteps

  current= Time++;

 

  DebugM(1,"done with calculate: force: "<<f&l= t;<"\n");

}

 

void GlobalMasterSMD::output(int t, Positi= on p, Force f) {

  DebugM(3,"output called\n");

 

  if (t % (100*outputFreq= ) =3D=3D 0) 

    = iout << "SMDTITLE: TS   CURRENT_POSITION         FO= RCE\n" << endi; 

  iout &l= t;< "SMD CBE 579 " << t << ' '<= /span> << p << ' ' << f*PNPERKCALMOL << '\n' = << endi;

 

  DebugM(1,"done with output\n");<= /p>

}

 

 

 

From: owner-namd-l@ks.uiu= c.edu <owner-namd-l@ks.uiuc.edu> on behalf of Hemanth Haridas <hem= anth.h@iitgn.ac.in>
Date: Friday, April 30, 2021 at 7:17 AM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>, SHIVAM TIWARI <= ;t.shivam@iitg.ac.in>
Subject: Re: namd-l: graphene sheet as a rigid piston

Shivam,

 

I had some luck with using the SMD module to get gra= phene working as a piston. The trick is to tag one graphene layer as moving= (SMD active), and to restrain the layer containing the nanopore with a ver= y high harmonic restraint.

 

Hope this helps,

 

Regards

Hemanth

 

On Wed, Apr 28, 2021 at 11:13 PM SHIVAM TIWARI <<= a href=3D"mailto:t.shivam@iitg.ac.in">t.shivam@iitg.ac.in> wrote:

Dear all,

I want to simulate reverse osmosis process on a box of = water and ions across a membrane, for which, I am applying a transmembrane = pressure on the water box through a graphene sheet (as a piston). I am using tclforces to achieve this, the script I am= using is as follows:

 

tclForces on

 

tclForcesScript {

  set linaccel1 {0.0 0.0 -0.0006449914635}

  set linaccel2 {0.0 0.0 0.0006449914635}

 

 

  set watIdList1 {}

  set watIdList2 {}

 

 

 

  for {set i 1} {$i <=3D 5520} {incr i} {<= /o:p>

    lappend watIdList1 $i

    addatom $i

  }

  for {set i 229378} {$i <=3D 234897} {incr i} = {

    lappend watIdList2 $i

    addatom $i

  }

 

But the problem with this is that the graphene sheet be= haves as a graphene sheet and not as a rigid piston, that is, the graphene = sheet gets deformed (curled up) as soon as the pressure is applied. Although, the water does get pushed, but I sus= pect that the pressure applied in this case is much lesser than the desired= , since most of the force applied on the graphene sheet must be getting was= ted on the deformation of the graphene sheet. So how can I achieve a rigid graphene piston?

 

regards

shivam



--

Hemanth H 18310019

Research Scholar

IIT Gandhinagar

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charset="utf-8" Content-ID: MIME-Version: 1.0 X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR12MB1351.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: eca55203-0601-4878-fd8c-08d90be01c17 X-MS-Exchange-CrossTenant-originalarrivaltime: 30 Apr 2021 13:59:02.0140 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 7IW1fYg28+Sr2PpBa2LhKdvPgLcexjxLVpwK+8pL5Xk29XFNhyqCNMeELSbdfksLBcLdniGQos0UNkirgKTLSQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR12MB1493 X-CLX-Response: 1TFkXGx0TEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxscGxEKQ1kXBx4bEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8TcRkSEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF3lFfV9jWWBCfmNgGV1LZWlPXmFZSHxwB3MZeh9BZFtzEQpYXBcfBBoEGBgTBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3JdSGJuEQpNXBcbEhEKTFoXfGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2tra2xraxEKQk8XZnB/bmJLcn9jXW8RCkNaFx4aBBsaHQQdHAQSGB EKQl4XGxEKRF4XGREKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCTBdvYVgTGktdG 0NBZREKQmwXYXkcHxJce09aaUIRCkJAF21THVpefx0dUGlrEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXGBEKeUMXY21pS1ABbE9bXmMRCllLFxsYHhsZEQpwZxdtR2FrTWMZTFNpbhAcGhEKcGg XZElPHxN6HlgcHEcQGRoRCnBoF2RvAVxgbXxbaWxbEBkaEQpwaBd6e2l4b3AeTwFzaRAZGhEKcG gXZ21tHhtEBV9QSV0QGRoRCnBoF2tvGBJwZVJbXRNSEBkaEQpwbBdneBpAYhhJGn55TRAZGhEKb X4XGxEKWE0XSxEg X-Proofpoint-GUID: SoWuIsJhTIJ3waOCetKsbVZ-Y3P5kNqY X-Proofpoint-ORIG-GUID: SoWuIsJhTIJ3waOCetKsbVZ-Y3P5kNqY X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 mlxlogscore=999 adultscore=0 bulkscore=0 mlxscore=0 impostorscore=0 spamscore=0 priorityscore=0 suspectscore=0 clxscore=179 phishscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104300099 domainage_hfrom=12413 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by halifax.ks.uiuc.edu id 13UDx43q007676 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Hi Jose, What did you do to your periodic box size in the NAMD configuration file, and how is the barostat allowed to change it? Normally, the x-y dimensions are the same between the two membranes, so you use the semi-isotropic ensemble options for the barostat (useflexiblecell yes, useconstantratio yes), and it is quickly impossible for water to cross either membrane without going through it. If you are getting water channels in your membrane, the x-y dimenstions may have been too large in the beginning, and the fast water diffusion formed a stable pore. -Josh On 4/30/21, 5:03 AM, "owner-namd-l@ks.uiuc.edu on behalf of José Villalaín" wrote: Dear all, I am trying to build a system with two membranes in order to place different concentrations of ions (inside/outside). To do this, I have minimized, equilibrated and simulated a single membrane system (containing membrane, protein, ions and water). To obtain the system with two membranes, I use the previous system containing one membrane, duplicate it and join the two systems in one. Afterwards, I remove all the water and ions, solvate with water, remove the water inside the membrane and place the ions (different concentrations inside and outside). However, and although I have used several different parameters in the configuration file (different constraints for water, lipids, ions and their combinations, PME, not PME, pressure on /off), whenever I try to equilibrate the system, it shrinks, specially the water molecules, and the water and ions move to the sides and from the sides, move from/to the different compartments . So far it has been impossible for me to continue equilibrating the two membrane system. Could someone give me an idea of what I am doing wrong?. Thank you very much in advance. José IDiBE / UMH From owner-namd-l@halifax.ks.uiuc.edu Fri Apr 30 10:04:28 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13UF4SKT010234; Fri, 30 Apr 2021 10:04:28 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13UF4S4u010233; Fri, 30 Apr 2021 10:04:28 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13UF4Rjn010229; Fri, 30 Apr 2021 10:04:27 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 13UF4R2o010228; Fri, 30 Apr 2021 10:04:27 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 13UF4Kq3010219 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=nSc1DzMJoDw+U5riEZ7+T1cW9CtedUsv7uDa+9kf5ZA=; b=lVZaG4rWzNdH3Kt1hOzWzI/acUPJ37mztPtSOTaZS9MKHKudwIQjdjqTn4PAqStHVo bDHwt+rdP3m33oUakKbY2QzFHOz2gefkVx3twRnd13J7r2nuPOX38QX+4foR7pzPTSJd qsPSVIoxh+mZjQbPISSxbzHwgc/Xdv4MrdLqBcJs9vNgkQ6W8CYkXcdQlD6tQGCkG3lp BbS6q7Oyn0Exdgt6rQ+7qH6vTm24EKPSY+yzzaDb9xncV1zZDZzm1LNsqnHNDm9mFcOH PpHxarfz27KIkJZUKRwfTlkEKvAeF9W58H9rDqWx7Zi3bIjr5RsDO/ScmeTBakDwf/N4 71oA== X-Gm-Message-State: AOAM531/716BgL4rXyo0W2+SevmPEAIApHMqDprlmdnd57U0qUEqdgB7 ZyA/uhqlxZ1tKPpKJwq68uUAf0TGJQpPqeCHrAXOC/UF X-Google-Smtp-Source: ABdhPJwTz8v+YUqPUZnrAqdgDb1yiJvdNO2UAKGIcCjr05EuZLcE0A0D8hvLQfhimI5U7h/tq6lcGjqj9NsVbqmuyAY= X-Received: by 2002:a25:be09:: with SMTP id h9mr7601751ybk.239.1619795057815; Fri, 30 Apr 2021 08:04:17 -0700 (PDT) MIME-Version: 1.0 References: <74FE90DC-10C3-4372-98E4-445D47B172CA@msu.edu> In-Reply-To: <74FE90DC-10C3-4372-98E4-445D47B172CA@msu.edu> From: Giacomo Fiorin Date: Fri, 30 Apr 2021 11:03:41 -0400 Message-ID: Subject: Re: namd-l: System with two membranes To: NAMD list , "Vermaas, Josh" Cc: =?UTF-8?B?Sm9zw6kgVmlsbGFsYcOtbg==?= Content-Type: multipart/alternative; boundary="00000000000007b51f05c131ed67" X-Proofpoint-ORIG-GUID: 9ZvYAbORD7WjaEB40nPr0Rw_PNxx64Vt X-CLX-Response: 1TFkXGxwZEQpMehcZGRMRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHxwbEQpDWRcHHhsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhlxGBwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XE3Bcc2tIZXhuHX1AS29oHhpEelgaeF11emRSUhwefF4RClhcFx8EGgQYGBMF GxgdBBoEGgQbEBseGh8aEQpeWRdyXUlvZREKTVwXHh0ZEQpMWhdpfGlrTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEwQbHR 8RCkJeFxsRCkReFxgRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2Nre xNYfhpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEK QmwXYV96UxlDRBp6G34RCkJAF21THVpefx0dUGlrEQpCWBdnc2VzQG5hYUxdYhEKWlgXGBEKeUM XY21pS1ABbE9bXmMRCllLFxMZExgRCnBnF21HYWtNYxlMU2luEB0SEQpwaBdkbwFcYG18W2lsWx AdGhEKcGgXentpeG9wHk8Bc2kQExoRCnBoF2dtbR4bRAVfUEldEB0aEQpwaBdrbxgScGVSW10TU hATGhEKcGgXZEMdU3x7UF1kZ2cQGRoRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdtaGUZQVJ9exhF UhAaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: 9ZvYAbORD7WjaEB40nPr0Rw_PNxx64Vt X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 impostorscore=0 lowpriorityscore=0 bulkscore=0 spamscore=0 phishscore=0 malwarescore=0 priorityscore=339 clxscore=163 mlxscore=0 suspectscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2104300103 domainage_hfrom=9392 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000007b51f05c131ed67 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Jos=C3=A9, like Josh said, equilibrating with an anisotropic barostat is= the key (preferably constraining the ratio of the X-Y dimensions). Additionally, although the two bilayers do have similar equilibration times, their exact trajectories will be a bit different and the sporadic mismatch that may occur undesirable. If so, equilibrating each bilayer on its own and merging the two systems *after* equilibration would be the way to go. The interface between the two juxtaposed water layers will vanish very quickly. Giacomo On Fri, Apr 30, 2021 at 10:01 AM Vermaas, Josh wrote: > Hi Jose, > > What did you do to your periodic box size in the NAMD configuration file, > and how is the barostat allowed to change it? Normally, the x-y dimension= s > are the same between the two membranes, so you use the semi-isotropic > ensemble options for the barostat (useflexiblecell yes, useconstantratio > yes), and it is quickly impossible for water to cross either membrane > without going through it. If you are getting water channels in your > membrane, the x-y dimenstions may have been too large in the beginning, a= nd > the fast water diffusion formed a stable pore. > > -Josh > > =EF=BB=BFOn 4/30/21, 5:03 AM, "owner-namd-l@ks.uiuc.edu on behalf of Jos= =C3=A9 > Villala=C3=ADn" > wrote: > > Dear all, > > I am trying to build a system with two membranes in order to place > different concentrations of ions (inside/outside). To do this, I have > minimized, equilibrated and simulated a single membrane system > (containing membrane, protein, ions and water). > > To obtain the system with two membranes, I use the previous system > containing one membrane, duplicate it and join the two systems in one= --00000000000007b51f05c131ed67-- From owner-namd-l@halifax.ks.uiuc.edu Tue May 4 07:31:09 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 144CV9v9005331; Tue, 4 May 2021 07:31:09 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 144CV8os005330; Tue, 4 May 2021 07:31:08 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 144CV8rm005326; Tue, 4 May 2021 07:31:08 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 144CV8uv005325; 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Tue, 4 May 2021 12:30:56 +0000 Date: Tue, 4 May 2021 12:30:53 +0000 (UTC) From: Vidhya Sankar To: NAMD List Message-ID: <1429495276.271184.1620131453516@mail.yahoo.com> Subject: namd-l: Mail about error in Alchemify programme in namd MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_271183_1694137691.1620131453515" References: <1429495276.271184.1620131453516.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18231 YMailNorrin Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:52.0) Gecko/20100101 Firefox/52.0 X-Proofpoint-ORIG-GUID: IV830u6EO6VUnmpAGZmPDEJt_f7Fm3jx X-Proofpoint-GUID: IV830u6EO6VUnmpAGZmPDEJt_f7Fm3jx X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBsSEQpMehcZHxoRCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHExEKQ1kXBxsYEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXHBNxGwYbGRJ3BhgaGgYaBhoGHhMGGnEaEBp3BhoGBxsaGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XY3wSGRpfHG9lHHx/REdaa21w R3pub2BedUwdbEcZQFIRClhcFx8EGgQYGBMFGxgdBBoEGgQbEBseGh8aEQpeWRdyUl9nTxEKTVw XExIRCkxaF2xpa2trEQpMRhdva2tva2sRCkJPF2JJH3pcWB9beRseEQpDWhcbGhwEGxoEGB4aBB seGREKQl4XGxEKQlwXGxEKXk4XGxEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmEQpCR Rd6GW1DW0VfaGl9ZREKQk4XekQcHW9FbG1EQ2YRCkJMF2ZhYhNhbWJrSVxCEQpCbBdrHR9wGWxp RW94XBEKQkAXY2VlZEN4Yk1LaB8RCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGBEKeUMXa05 jax9vTW98HH8RCllLFxMcGhkRCnBoF2trHh9DfG0dZAESEAcZGhEKcGgXYnhYc09+eFpmUGIQBx kaEQpwaBdhSHJwWUB8Qk5eZRAHGRoRCnBoF2VSeXhbR2ASHx9uEAcZGhEKcGgXbWBTQlhMWV5YW m8QBxkaEQpwbBdkb05cRn5TaHxZWhAHGRoRCnBMF2YFYRxHHUZheUN/EAcZGhEKbX4XBxsRClhN F0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=218 phishscore=0 spamscore=0 priorityscore=350 mlxlogscore=754 malwarescore=0 adultscore=0 mlxscore=0 suspectscore=0 lowpriorityscore=0 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2105040093 domainage_hfrom=9603 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_271183_1694137691.1620131453515 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd Users =C2=A0=C2=A0=C2=A0=C2=A0 i am using your alchemify programme for free energ= y of perturbation Nut when i use i got the very output.psf file as output B= ut When i run the the namd using the same psf file generated in your alchem= ify program i got the following error ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: EXCLUSION INDEX -2147483648 LARGER THAN NUMBER OF EXLC= USIONS 19156620 IN PSF FILE, EXCLUSION #9998 Charm++ fatal error: FATAL ERROR: EXCLUSION INDEX -2147483648 LARGER THAN NUMBER OF EXLCUSIONS 1= 9156620 IN PSF FILE, EXCLUSION #9998 It would be highly appreciable if problem solved=20 Thanks in Advance With cheers Vidhya sankar ------=_Part_271183_1694137691.1620131453515 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Na= md Users
     i am using your alchemify progra= mme for free energy of perturbation Nut when i use i got the very output.ps= f file as output But When i run the the namd using the same psf file genera= ted in your alchemify program i got the following error

------------= - Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR:= EXCLUSION INDEX -2147483648 LARGER THAN NUMBER OF EXLCUSIONS 19156620 IN P= SF FILE, EXCLUSION #9998


Charm++ fatal error:
FATAL ERROR: EX= CLUSION INDEX -2147483648 LARGER THAN NUMBER OF EXLCUSIONS 19156620 IN PSF = FILE, EXCLUSION #9998

It would be highly appreciable if problem solv= ed

Thanks in Advance

With cheers
Vidhya sankar




------=_Part_271183_1694137691.1620131453515-- From owner-namd-l@halifax.ks.uiuc.edu Tue May 4 16:08:12 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 144L8C6u013180; Tue, 4 May 2021 16:08:12 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 144L8CfZ013179; Tue, 4 May 2021 16:08:12 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 144L8BTm013175; Tue, 4 May 2021 16:08:11 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 144L8Bcq013174; Tue, 4 May 2021 16:08:11 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 144L7xus013165 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 4 May 2021 16:07:59 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 144L3U1O016723 for ; Tue, 4 May 2021 21:07:59 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0b-00007101.pphosted.com with ESMTP id 38bbvv9kfw-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 04 May 2021 21:07:58 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 090461E4059A; Tue, 4 May 2021 23:07:56 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id cq6q70ikVVXf; Tue, 4 May 2021 23:07:52 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id F31501E40571; Tue, 4 May 2021 23:07:51 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id COeU1v-cesOe; Tue, 4 May 2021 23:07:51 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id 374EC1E4056D; Tue, 4 May 2021 23:07:51 +0200 (CEST) Date: Tue, 4 May 2021 23:07:50 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , Vidhya Sankar Message-ID: <1982171008.1682774.1620162470142.JavaMail.zimbra@ibpc.fr> In-Reply-To: <1429495276.271184.1620131453516@mail.yahoo.com> References: <1429495276.271184.1620131453516.ref@mail.yahoo.com> <1429495276.271184.1620131453516@mail.yahoo.com> Subject: Re: namd-l: Mail about error in Alchemify programme in namd Content-Type: multipart/alternative; boundary="=_9dd0e014-c056-4776-843b-b46e90ddc570" X-Originating-IP: [81.67.142.130] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC88 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Mail about error in Alchemify programme in namd Thread-Index: nCkUkXmJGKAIo/vzuTs+zfvdArJqzQ== X-Proofpoint-ORIG-GUID: t7b-CAAIWBc6A702LvAgCPIUdlnOtWf_ X-CLX-Shades: MLX X-Proofpoint-GUID: t7b-CAAIWBc6A702LvAgCPIUdlnOtWf_ X-CLX-Response: 1TFkXGxIdEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBx4YGREKQ1kXBxkSEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwdcR4cEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF14dSAdpa2tjfWhJHGsdGhhmXGtNaXpjf05GRGVefUx1EQpYXBcfBBoEGBgTBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JSG1JgEQpNXBcZGR4RCkxaF3xta01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XaEBFSBgYfGtbehkRCkNaFxsTGQQeEwQYGR4EGBgbEQ pCXhcbEQpEXhcYEQpCRRdkWFxcTX5SSRtlSREKQk4XZU9+EkNpZlkcAWkRCkJMF3oSZ2lgWXlGQ U9lEQpCbBdhEhJPT0xNf08eBREKQkAXZUdIRF5MGkloeHsRCkJYF2dzZXNAbmFhTF1iEQpaWBcZ EQp5QxdmZkUdYl1ATGYdUBEKcGgXaRJHTH17WFJcSXMQGRoRCnBoF2RCGkx5E1p+fBhmEBkaEQp waBdlUnl4W0dgEh8fbhAeEhEKcGgXaXlCBUMdXnxfXUAQGRoRCnBoF2xMHFJLUE8FWlNfEBkaEQ pwfRdhU1kfenJPAXhmXhAZGhEKcH8Xax1rHlN7Z2NLbXoQGxoZEQpwXxdrQ2d/cx98elNmUxAZG hEKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 clxscore=187 mlxscore=0 bulkscore=0 priorityscore=0 malwarescore=0 adultscore=0 spamscore=0 mlxlogscore=765 suspectscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2105040142 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_9dd0e014-c056-4776-843b-b46e90ddc570 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear Vidhya,=20 Are you using the current version of Alchemify? Is this a CHARMM extended P= SF file?=20 If not, you can update to the latest Alchemify (https://urldefense.com/v3/_= _https://github.com/jhenin/alchemify__;!!DZ3fjg!uQQGU6maAAQzUwsxRu2AzWyRrNi= 6XuZcMd4imPUgvGljG92pVn0nfXLOyaw0S0EEVg$ ) and replace the header line of t= he input PSF with:=20 PSF EXT CMAP=20 which will cause Alchemify to use wider fields in the output, which should = better accommodate the large number of exclusions that are present here.=20 Best=20 Jerome=20 ----- On 4 Mai 21, at 14:30, Vidhya Sankar wrote:=20 > Dear Namd Users > i am using your alchemify programme for free energy of perturbation Nut w= hen i > use i got the very output.psf file as output But When i run the the namd = using > the same psf file generated in your alchemify program i got the following= error > ------------- Processor 0 Exiting: Called CmiAbort ------------ > Reason: FATAL ERROR: EXCLUSION INDEX -2147483648 LARGER THAN NUMBER OF > EXLCUSIONS 19156620 IN PSF FILE, EXCLUSION #9998 > Charm++ fatal error: > FATAL ERROR: EXCLUSION INDEX -2147483648 LARGER THAN NUMBER OF EXLCUSIONS > 19156620 IN PSF FILE, EXCLUSION #9998 > It would be highly appreciable if problem solved > Thanks in Advance > With cheers > Vidhya sankar --=_9dd0e014-c056-4776-843b-b46e90ddc570 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear Vidhya,

Are you using the current version of Alchemify? Is this a= CHARMM extended PSF file? 

<= div>If not, you can update to the latest Alchemify (https://github.com= /jhenin/alchemify) and replace the header line of the input PSF with:
PSF EXT CMAP=

which will cause Alchemify to use wider fi= elds in the output, which should better accommodate the large number of exc= lusions that are present here.

Best
Jerome


<= /div>
----- On 4 Mai 21,= at 14:30, Vidhya Sankar <vidhyasankar7928@REMOVE_yahoo.com> wrote:
Dear Namd Users
 = ;    i am using your alchemify programme for free energy of = perturbation Nut when i use i got the very output.psf file as output But Wh= en i run the the namd using the same psf file generated in your alchemify p= rogram i got the following error

------------- Processor 0 Exiting: = Called CmiAbort ------------
Reason: FATAL ERROR: EXCLUSION INDEX -21474= 83648 LARGER THAN NUMBER OF EXLCUSIONS 19156620 IN PSF FILE, EXCLUSION #999= 8


Charm++ fatal error:
FATAL ERROR: EXCLUSION INDEX -21474836= 48 LARGER THAN NUMBER OF EXLCUSIONS 19156620 IN PSF FILE, EXCLUSION #9998
It would be highly appreciable if problem solved

Thanks in Ad= vance

With cheers
Vidhya sankar





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Wed, 5 May 2021 13:36:18 +0000 Date: Wed, 5 May 2021 13:36:17 +0000 (UTC) From: Vidhya Sankar To: NAMD List , =?UTF-8?Q?J=C3=A9r=C3=B4me_H=C3=A9nin?= Message-ID: <573643040.608732.1620221777510@mail.yahoo.com> Subject: namd-l: Mail about Alchemify error MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_608731_1740502422.1620221777509" References: <573643040.608732.1620221777510.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18231 YMailNorrin Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/90.0.4430.93 Safari/537.36 X-Proofpoint-ORIG-GUID: 6NXBq5--7rEp5AFXI8uc_hgQn-PmDR0a X-CLX-Shades: MLX X-Proofpoint-GUID: 6NXBq5--7rEp5AFXI8uc_hgQn-PmDR0a X-CLX-Response: 1TFkXGRMdEQpMehcZHh4RCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHGxgbEQpDWRcHEhsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwdcRsGGxkZdwYYGhoGGgYaBhsaGgYZGnEbEBp3BhoGGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XHGRyaFsfBwcdWG9aH2tscmMS X0l1Qk17RAd6R254GksRClhcFx8EGgQYGBMFGxgdBBoEGgQbEBseGh8aEQpeWRdyU296XREKTVw XGB0ZEQpMWhdoaWtraxEKTEYXb2trb2trEQpCTxdiSR96XFgfW3kbHhEKQ1oXGxocBBsaBBgeGw QbHhoRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0Vsb URDZhEKQkUXehltQ1tFX2hpfWURCkJOF3pEHB1vRWxtRENmEQpCTBdmYWITYW1ia0lcQhEKQmwX ax0fcBlsaUVveFwRCkJAF2d/RFNAeEMeellEEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXaR4SRFpPQ3kYRVwRCllLFxMcGh4RCnBoF2lbbUEdAUlwS0lTEBkaEQpwaBdnH2dsSBp9b1 oBZhAZGhEKcGgXbVp6YWtDbHhzZGMQGRoRCnBoF2ZCHx1yZmBpHEJJEBkaEQpwaBdheEYca1hAf 0R7ZxAZGhEKcGwXZG9OXEZ+U2h8WVoQGRoRCnBMF2YFYRxHHUZheUN/EBkaEQptfhcbEQpYTRdL ESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=397 phishscore=0 spamscore=0 priorityscore=344 mlxlogscore=554 suspectscore=0 lowpriorityscore=0 bulkscore=0 impostorscore=0 mlxscore=0 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2105050097 domainage_hfrom=9604 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_608731_1740502422.1620221777509 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you sir .=C2=A0Your Hyperlink for u[dated version of alchemify is not= opened in my chrome browser also i am using Namd=C2=A0 PSf file=C2=A0not= =C2=A0CHARMM extended PSF file?=C2=A0 =C2=A0It would be highly helpful to s= olve my problemsThanks in advance ------=_Part_608731_1740502422.1620221777509 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Thank you sir .
 Your Hyperlink for u[dated version of alchemify is not opened in my chrome browser also i am using Namd  PSf file
 not CHARMM extended PSF file?   It would be highly helpful to solve my problems
Thanks in advance

------=_Part_608731_1740502422.1620221777509-- From owner-namd-l@halifax.ks.uiuc.edu Wed May 5 12:57:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 145Hvjuj016294; Wed, 5 May 2021 12:57:45 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 145Hvjro016293; Wed, 5 May 2021 12:57:45 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 145HviGZ016289; Wed, 5 May 2021 12:57:44 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 145HviLb016288; Wed, 5 May 2021 12:57:44 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 145HvXaM016274 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000b5f9ff05c198edb3" X-Proofpoint-ORIG-GUID: KnCJ4NRn0FBtlfmDC2_HCjerjEpkkfOh X-CLX-Response: 1TFkXGxIfEQpMehcZHhMRCllEF2hBb0V/U2YSa2tCEQpYWBdlAU1/ZX1MYRN mHREKeE4XY1Nja3sTWH4aX14RCnlMF3pGWl0eaHp8AWdfEQpDSBcHGB0fEQpDWRcHGxsYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2FEaWAeZHhEGmxoXkZMR25pGHViaUBPWEBvWkFBTGVCEQpYXBcfBBoEGBgT BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3JTY29EEQpNXBcbGBwRCkxaF2hpa01rEQpMRhdva2t ra2sRCkJPF24cZx1ZcmdmXkhyEQpDWhcYGhMEEh8EGBoSBB4SEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF20FQWdCfmRhcmhJEQpCThdjU2Nre xNYfhpfXhEKQkwXZQFNf2V9TGETZh0RCkJsF2lFW0FyRWFJTW5BEQpCQBdpRkZkUHIFax17QBEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2dGEn1HU2ZMQhNdEQpZSxcTGRMdEQpwaBd lX1JJXXsbU3hrGBAZGhEKcGgXYHlZZVJbXUV/ZxoQGRoRCnBoF2RcYwFbe3p9WBpeEBkaEQpwaB d6ZmN7YWEeHnJwGhAZGhEKcGgXZhpJG0IfUlJcfR8QGRoRCnB9F24ZfWVCZxgbGH1SEBkaEQpwf RdtbUdSHWdpEl1YchAZGhEKcH8XZRl5Zl5HaRtkT3MQGxgaEQpwXxduG0BcW2JbQWhacBAZGhEK cGwXaX5EGAV/G1lkSRsQGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: KnCJ4NRn0FBtlfmDC2_HCjerjEpkkfOh X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=349 mlxscore=0 spamscore=0 phishscore=0 adultscore=0 clxscore=185 impostorscore=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 mlxlogscore=824 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2105050124 domainage_hfrom=9397 X-Spam-Score: 0 X-Spam-OrigSender: ecroitoru1@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ethan Croitoru --000000000000b5f9ff05c198edb3 Content-Type: text/plain; charset="UTF-8" Hello, I am trying to quantify my error for free energy calculations. I used the geometrical transformation from this tutorial ( https://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf) which utilizes ABF calculations. I have seen papers talking about the methodology to calculate the errors, but I was wondering if there are resources that illustrate an implementation? Thank you, Ethan Croitoru --000000000000b5f9ff05c198edb3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,

I am trying to quantify my error= for free energy calculations. I used the geometrical transformation from t= his tutorial (https://www.ks.uiuc.edu/Training/Tutorials/n= amd/PLB/tutorial-protein-ligand.pdf) which utilizes ABF calculations. I= have seen papers talking about the methodology to calculate the errors, bu= t I was wondering if there are resources that illustrate an implementation?=

Thank you,
Ethan Croitoru
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policy=cautious_plus_nq score=0 priorityscore=30 mlxscore=0 spamscore=0 phishscore=0 adultscore=0 clxscore=169 impostorscore=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 mlxlogscore=999 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104060000 definitions=main-2105060096 domainage_hfrom=8879 X-Spam-Score: 0 X-Spam-OrigSender: chipot@illinois.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 146DIexB008944 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Chris Chipot Hi, Ethan, I am afraid we do not have a comprehensive, self-contained tool to do error analyses of ABF calculations. The ingredients that you need is an estimation of the correlation length of the force time series in a given bin, and the standard deviation of the force. Once you have these ingredients, you can propagate the error across the PMF, as spelled out in dx.doi.org/10.1021/jp506633n. Chris Chipot On 5/5/21 7:57 PM, Ethan Croitoru wrote: > Hello, > > I am trying to quantify my error for free energy calculations. I used > the geometrical transformation from this tutorial > (https://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf > ) > which utilizes ABF calculations. I have seen papers talking about the > methodology to calculate the errors, but I was wondering if there are > resources that illustrate an implementation? > > Thank you, > Ethan Croitoru -- Chris Chipot, Ph.D. CNRS research director, University of Lorraine Adjunct professor of physics, University of Illinois, Urbana-Champaign _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group 3161 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Urbana, Illinois 61801 Phone: (217) 244-4361 E-mail: chipot@illinois.edu Christophe.Chipot@Univ-Lorraine.fr Web: https://physics.illinois.edu https://urldefense.com/v3/__http://www.lia-uiuc.cnrs.fr__;!!DZ3fjg!qCZxy7gtOE97_3-Ohn2P1Pg5xOIvihqqcMpEd7eVLvdR9NXt94y-dRL0qDfShu2FGw$ http://www.ks.uiuc.edu/~chipot Fiat justitia, et pereat mundus --Heinrich von Kleist _______________________________________________________________________ From owner-namd-l@halifax.ks.uiuc.edu Fri May 14 04:48:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14E9mas4028216; 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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear NAMD comunity, I am running metadynamics on a set of two dihedral angles. I've tried defau= lt metadynamics and well tempered. For both of them after a few hours the r= un stops with errors like the following: namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe44263fa0. B= acktrace: /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_charg= esEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_charg= esEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] and the log file states: mpprun info: Job terminated with error Normal molecular dynamics works well so it must be related to metadynamics.= This is the colvar file that i used: ---------------------------------------------------------------------------= ----------------------------------------------------------- colvarsTrajAppend off colvar { name Psi width 2.5 dihedral { group1 { atomnumbers { 32 } } group2 { atomnumbers { 22 } } group3 { atomnumbers { 20 } } group4 { atomnumbers { 21 } } } lowerBoundary -180 upperBoundary 180 } colvar { name Phi width 2.5 dihedral { group1 { atomnumbers { 33 } } group2 { atomnumbers { 32 } } group3 { atomnumbers { 22 } } group4 { atomnumbers { 20 } } } lowerBoundary -180 upperBoundary 180 } metadynamics { wellTempered on biasTemperature 1490 name metaPhiPsi colvars Phi Psi hillWeight 0.01 hillwidth 1.0 saveFreeEnergyFile no dumpFreeEnergyFile yes #When useGrids and this option are on, the PMF is w= ritten every colvarsRestartFrequency steps to the file outputName.pmf writeHillsTrajectory on newHillFrequency 100 ---------------------------------------------------------------------------= ------------------------------------------------------------ I have tried with different hillWeight values and the problem stays. Can I do something or should I restart from the last step and continue runn= ing and, in doing so, how can I keep the old colvars data so that I restart from the last points = collected? Thank you in advance, All the best, Alex --_000_8dd715e40fba48ac9a543742dce8ed4fsuse_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear NAMD comunity,


I am running metadynamics on a set of two dihedral angles. I've tried de= fault metadynamics and well tempered. For both of them after a few hours&nb= sp;the run stops with errors like the following:


namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe4426= 3fa0.  Backtrace:
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]

and the log file states:

mpprun info:   Job terminated with error=

Normal molecular dynamics works well so it must be related to me= tadynamics. This is the colvar file that i used:
----------------------------------------------------------------------= ----------------------------------------------------------------

colvarsTrajAppend off

colvar {
   name Psi
   width 2.5
   dihedral {
      group1 {
         atomnumbers { 32 }
      }
      group2 {
         atomnumbers { 22 }
      }
      group3 {
         atomnumbers { 20 }
      }
      group4 {
         atomnumbers { 21 }
      }
   }
    lowerBoundary -180
    upperBoundary 180

}

colvar {
   name Phi
   width 2.5
   dihedral {
      group1 {
         atomnumbers { 33 }
      }
      group2 {
         atomnumbers { 32 }
      }
      group3 {
         atomnumbers { 22 }
      }
      group4 {
         atomnumbers { 20 }
      }
   }
 lowerBoundary -180
   upperBoundary 180
}

metadynamics {
wellTempered on
biasTemperature 1490
name metaPhiPsi
colvars Phi Psi
hillWeight 0.01
hillwidth 1.0
saveFreeEnergyFile no
dumpFreeEnergyFile yes  #When useGrids and this option are on,= the PMF is written every colvarsRestartFrequency steps to the file  o= utputName.pmf
writeHillsTrajectory on
newHillFrequency 100 
---------------------------------------------------------------------------= ------------------------------------------------------------

I have tried with different hillWeight values and the problem stays.
Can I do something or should I restart from the last step and continue= running and, in doing so,
how can I keep the old colvars data so that I restart from the last po= ints collected?

Thank you in advance,

All the best,
Alex


--_000_8dd715e40fba48ac9a543742dce8ed4fsuse_-- From owner-namd-l@halifax.ks.uiuc.edu Fri May 14 10:43:59 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EFhxHX003112; Fri, 14 May 2021 10:43:59 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14EFhxUG003111; Fri, 14 May 2021 10:43:59 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EFhwfL003107; Fri, 14 May 2021 10:43:58 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14EFhwsn003106; Fri, 14 May 2021 10:43:58 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EFhkLl003099 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello Alex, if the instability is sporadic you can safely restart and continue running. The instability, however, could be due to the relatively high rate at which you add the Gaussian bias, 1 kcal/mol per 1000 steps. Not knowing the specifics of the system, it would help you to figure out what are the correlation times of the two dihedral angles from an equilibrium MD trajectory, which you should already have. The variables may simply not take up a bias that fast. Lastly, you're using NAMD 2.12, which is more than 4 years old. While it's true that the error is raised from a large force coming from Colvars, later versions like 2.14 may handle it better, or at least clarify more clearly the precise step where things go wrong. For Colvars specifically, there are a few advantages for using metadynamics specifically: https://urldefense.com/v3/__https://colvars.github.io/namd-2.14/colvars-ref= man-namd/colvars-refman-namd.html*sec:colvars_config_changes__;Iw!!DZ3fjg!t= bDVuM83HD_04RzozxgF91FqHs3CWPrENr5oSpILZHhggFg8uG7aB3Ef24YVnREuRA$=20 Giacomo On Fri, May 14, 2021 at 5:50 AM Alessandro Ruda wrote: > Dear *NAMD comunity*, > > > I am running metadynamics on a set of two dihedral angles. I've tried > default metadynamics and well tempered. For both of them after a few > hours the run stops with errors like the following: > > > *namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe44263fa0. > Backtrace:* > > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_ch= argesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_ch= argesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > > and the log file states: > > *mpprun info: Job terminated with error* > > Normal molecular dynamics works well so it must be related to > metadynamics. This is the colvar file that i used: > > -------------------------------------------------------------------------= ------------------------------------------------------------- > > *colvarsTrajAppend off* > > *colvar {* > * name Psi* > * width 2.5* > * dihedral {* > * group1 {* > * atomnumbers { 32 }* > * }* > * group2 {* > * atomnumbers { 22 }* > * }* > * group3 {* > * atomnumbers { 20 }* > * }* > * group4 {* > * atomnumbers { 21 }* > * }* > * }* > * lowerBoundary -180* > * upperBoundary 180* > > *}* > > *colvar {* > * name Phi* > * width 2.5* > * dihedral {* > * group1 {* > * atomnumbers { 33 }* > * }* > * group2 {* > * atomnumbers { 32 }* > * }* > * group3 {* > * atomnumbers { 22 }* > * }* > * group4 {* > * atomnumbers { 20 }* > * }* > * }* > * lowerBoundary -180* > * upperBoundary 180* > *}* > > *metadynamics {* > *wellTempered on* > *biasTemperature 1490* > *name metaPhiPsi* > *colvars Phi Psi* > *hillWeight 0.01* > *hillwidth 1.0* > *saveFreeEnergyFile no* > *dumpFreeEnergyFile yes #When useGrids and this option are on, the PMF is > written every colvarsRestartFrequency steps to the file outputName.pmf* > *writeHillsTrajectory on* > *newHillFrequency 100 * > > -------------------------------------------------------------------------= -------------------------------------------------------------- > > I have tried with different hillWeight values and the problem stays. > Can I do something or should I restart from the last step and continue > running and, in doing so, > how can I keep the old colvars data so that I restart from the last points > collected? > > Thank you in advance, > > All the best, > Alex > > > --000000000000e5e90e05c24c1b1b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello Alex, if the instability is sporadic you can safely = restart and continue running.

The instability, however, = could be due to the relatively high rate at which you add the Gaussian bias= , 1 kcal/mol per 1000 steps.=C2=A0 Not knowing the specifics of the system,= it would help you to figure out what are the correlation times of the two = dihedral angles from an equilibrium MD trajectory, which you should already= =C2=A0have.=C2=A0 The variables may simply not take up a bias that fast.
Lastly, you're using NAMD 2.12, which is more than 4 y= ears old.=C2=A0 While=C2=A0it's true that the error is raised from a la= rge force coming from Colvars, later versions like 2.14 may handle it bette= r, or at least clarify more clearly the precise step where things go wrong.= =C2=A0 For Colvars specifically, there are a few advantages for using metad= ynamics specifically:=C2=A0https://colvars.github.io/namd-2.14/colvars-= refman-namd/colvars-refman-namd.html#sec:colvars_config_changes

Giacomo

<= div dir=3D"ltr" class=3D"gmail_attr">On Fri, May 14, 2021 at 5:50 AM Alessa= ndro Ruda <alessandro.ruda@su.s= e> wrote:

Dear NAMD comunity,


I am running metadynamics on a set of two dihedral angles. I've trie= d default metadynamics and well tempered. For both of them after a few hour= s=C2=A0the run stops with errors like the following:


namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe4426= 3fa0.=C2=A0 Backtrace:
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]

and the log file states:

mpprun info:=C2=A0 =C2=A0Job terminated with error=

Normal molecular dynamics works well so it must be related to me= tadynamics. This is the colvar file that i used:
----------------------------------------------------------------------= ----------------------------------------------------------------

colvarsTrajAppend off

colvar {
=C2=A0 =C2=A0name Psi
=C2=A0 =C2=A0width 2.5
=C2=A0 =C2=A0dihedral {
=C2=A0 =C2=A0 =C2=A0 group1 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 32 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group2 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 22 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group3 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 20 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group4 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 21 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0}
=C2=A0 =C2=A0 lowerBoundary -180
=C2=A0 =C2=A0 upperBoundary 180

}

colvar {
=C2=A0 =C2=A0name Phi
=C2=A0 =C2=A0width 2.5
=C2=A0 =C2=A0dihedral {
=C2=A0 =C2=A0 =C2=A0 group1 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 33 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group2 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 32 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group3 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 22 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group4 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 20 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0}
=C2=A0lowerBoundary -180
=C2=A0 =C2=A0upperBoundary 180
}

metadynamics {
wellTempered on
biasTemperature 1490
name metaPhiPsi
colvars Phi Psi
hillWeight 0.01
hillwidth 1.0
saveFreeEnergyFile no
dumpFreeEnergyFile yes=C2=A0 #When useGrids and this option are on,= the PMF is written every colvarsRestartFrequency steps to the file=C2=A0 o= utputName.pmf
writeHillsTrajectory on
newHillFrequency 100=C2=A0
---------------------------------------------------------------------------= ------------------------------------------------------------

I have tried with different hillWeight values and the problem stays.
Can I do something or should I restart from the last step and continue= running and, in doing so,
how can I keep the old colvars data so that I restart from the last po= ints collected?

Thank you in advance,

All the best,
Alex


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boundary="00000000000045c0e205c24c8495" X-CLX-Shades: MLX X-Proofpoint-GUID: Z6-QfBrDbb033WlbbcBmAvkSd6hOeHxW X-Proofpoint-ORIG-GUID: Z6-QfBrDbb033WlbbcBmAvkSd6hOeHxW X-CLX-Response: 1TFkXGBsYEQpMehcZHxMRCllEF2lSZ35jYHkeSHBrEQpYWBdif29gTWZQRV1 EZhEKeE4XY1Nja3sTWH4aX14RCnlMF2Z/exMeQBprRX4cEQpDSBcHGB0aEQpDWRcHGRoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbExhxEhkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XcBwHe0xoWG5ISBoZGX1GSEhJaEdrXEF5ThxCZU9iUn0RClhcFx8EGgQYGBMF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXchtvc0ERCk1cFxITEQpMWhdpaGlNTWsRCkxGF29ra2t raxEKQk8XZX5cWVtbR2NTYWwRCkNaFxgaEwQSHwQYGxIEHhgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZhsfUHNGQwVJUloRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdif29gTWZQRV1EZhEKQmwXZhlOGxJpYHtgehMRCkJAF2VCWERjbxl5HB1MEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaXtvG1NyR2IeQ2wRCllLFxMeGhwRCnBoF21 LWUdJHlp8TURBEBkaEQpwaBdvcFAbXUBCYRwechAaEQpwaBdpQF9gS31YeFp4QxAaEQpwaBdhfm Qde357eXhCUBAaEQpwaBd6Yx4BaH5gc2laUBAaEQpwfRdheVJCWUhaHBx8WBAZGhEKcH8XYB9DS 21DHhtsE38QGRoRCnBfF2lgehpyfnJ7GGEbEBkaEQpwbBdsGklzSWZ8UllwQhAZGhEKbX4XGxEK WE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 adultscore=0 priorityscore=359 phishscore=1 mlxscore=0 suspectscore=0 impostorscore=0 clxscore=212 spamscore=0 mlxlogscore=573 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140127 domainage_hfrom=9406 X-Spam-Score: 0 X-Spam-OrigSender: joepareti54@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, joseph pareti --00000000000045c0e205c24c8495 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I have a stupid question, but I need to start somewhere: I read that NAMD can do 'nanoseconds simulations' on some supercomputers, but the time step for atomic movements is in the order of femtoseconds. How can this be done? Thanks for any insight. --=20 Regards, Joseph Pareti - Artificial Intelligence consultant Joseph Pareti's AI Consulting Services https://urldefense.com/v3/__https://www.joepareti54-ai.com/__;!!DZ3fjg!owcr= nSrDZrFy6NG87ouIDAtEVGZ3wWXYBlrL_c1qK1Y5Zd45RQd-HlVGU9C5a21haw$=20 cell +49 1520 1600 209 cell +39 339 797 0644 --00000000000045c0e205c24c8495 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
I have a stupid question, but I need to start somewhere: I= read that NAMD can do 'nanoseconds simulations' on some supercompu= ters, but the time step for atomic movements is in the order of femtosecond= s. How can this be done?
Thanks for any insight.
=
--
Regards,
Joseph Pareti - Artificial Intelligence consultant
Joseph Pareti's AI Consulting Services
cell +49 1520 1600 2= 09
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--00000000000045c0e205c24c8495-- From owner-namd-l@halifax.ks.uiuc.edu Fri May 14 12:02:50 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EH2oeZ007885; Fri, 14 May 2021 12:02:50 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14EH2nJ9007884; Fri, 14 May 2021 12:02:49 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EH2nlZ007880; Fri, 14 May 2021 12:02:49 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14EH2nSL007879; Fri, 14 May 2021 12:02:49 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EH2ef4007871 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 14 May 2021 12:02:41 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14EH2UTR005429 for ; Fri, 14 May 2021 17:02:40 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qv1-f52.google.com (mail-qv1-f52.google.com [209.85.219.52]) by mx0a-00007101.pphosted.com with ESMTP id 38hcxst1t0-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 14 May 2021 17:02:39 +0000 Received: by mail-qv1-f52.google.com with SMTP id u1so15764791qvg.11 for ; Fri, 14 May 2021 10:02:39 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=UTo0LKuJgDa9Q3UhR//xE0WkEiTHNqUDpumCddn0fas=; b=jjp8JCW/rCtpCXgK/YNdL7bZej+/XX7W+vc5civsi1U1E5+up48ubdM+hi++6EOmZg vkVGXDeVvVBzj+ajXboPXXJZkA6+Iaqaz8Uz9xUIqlM7h0k0uNShJJ0ercIWqCWrNOoq mNJTL1sulX2pfrBKFm8hn4pzOk5KFRBlrAtOd1DGHBftBWUC1BMEPhXej252Wyo218Cc /guk2QNPqBUUnabF2e2OARkDKoD4sPMlyAFx47DQzgokjLR/WAPjXRPFFFMaC8VO+17Y 6rOXQWUbmOLcZ8nwU7Vnf1pO0+5A8K8zDzx6TPwQ//R3nIwOHZ7a0R/NiP41Ee4SMX1J o2Ow== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=UTo0LKuJgDa9Q3UhR//xE0WkEiTHNqUDpumCddn0fas=; b=XoaZPU/vlxEXYQoQKY5n+P7NP3MN/1z0mNzDM1eZimQGm9RssCDnTlSLwceRiZj8Ic 5os1uYhUslnB0j4w2evw5NbL6tm5ZL+HFuKhCHVJAIK37oV+YHkosijVOyK9wrjxAiVP 8qpFxHPod9A9HUXEC4b0VW0jmUYJTUd+GnBK0oOzzgs3IWG6FxoIMrFdXuY7z8fZRScW WejpERnXKQuBJXPYm7ZwZxgAH/Z6VMHSL9cKrf7Fp34zKjQwrBkygFFtlixMZd3fSSuE x7/4CVBlii674glQg4V2k3wPI78eOCbrmHxuCFwBtb9ahw2lbAYoBpOO4jyVwRfBh2CG mEjA== X-Gm-Message-State: AOAM532ep/RXlXAcI9SrdJ0FbVKeaozERrVdk+PrWZBi6UJ1K5LwAkTX cUk0fABQA5GF8UKTctHIJer+jEkOuGhwPg== X-Google-Smtp-Source: ABdhPJzsd9/vmfrC/VrFBNWO5ZPvos4Sm50cHunqQz6lUEZg130FAgqGXT+pgyETimBVmjbivMNG5A== X-Received: by 2002:a0c:ee81:: with SMTP id u1mr46884192qvr.14.1621011758557; Fri, 14 May 2021 10:02:38 -0700 (PDT) Received: from [192.168.1.39] ([181.64.230.110]) by smtp.gmail.com with ESMTPSA id o12sm5041384qtg.14.2021.05.14.10.02.36 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Fri, 14 May 2021 10:02:37 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 14 May 2021 12:02:34 -0500 Subject: namd-l: Re-center membrane protein From: "Ropon-Palacios G." To: KS UIUC Message-ID: <69FBA301-3D29-4A5A-849B-2BD7AC1ECE8A@gmail.com> Thread-Topic: Re-center membrane protein Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3703838557_1781076734" X-Proofpoint-ORIG-GUID: FTkN6lMm3dg3Xy30pUwkOf6dYu_4CiYT X-Proofpoint-GUID: FTkN6lMm3dg3Xy30pUwkOf6dYu_4CiYT X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0ZEQpMehcZGBIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGBIeEQpDWRcHGx0eEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ZcRkZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2x+QWQcRmdHGU5NGXJTGRpaf11BZUwcTnNfdR5pQ3N+EQpYXBcfBBoEGBgT BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXchtsYmYRCk1cFxgaHhEKTFoXbGlrTWsRCkxGF29ra2t raxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGxMEHxgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaE8dYUVwWXAFTRoRCkJOF2NTY2t7E 1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXY2lZb3pPHXJHT38RCkJAF2dDbRxEUgUaQn9nEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXemlTenIYRGNZQ2wRCllLFxMeGhwRCnBoF2J IXB1hTx9HUHgTEBkaEQpwaBdnGBlIBWRjH1NFTxAZGhEKcGgXekVof0NzXVlMUFkQGRoRCnBoF2 lucAVGQxxaZlxhEBseGBEKcGgXZHBSRFMTUnxbBW0QGRoRCnBsF3pHQGsYWXl/HhtIEBkaEQpwT BdnflB9TWtQT09GYhAZGhEKcEMXbR1He2Z8HnxDaQUQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=173 lowpriorityscore=0 mlxlogscore=659 mlxscore=0 bulkscore=0 phishscore=0 spamscore=0 impostorscore=0 suspectscore=0 priorityscore=328 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140136 domainage_hfrom=9406 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3703838557_1781076734 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Hello namd users, I am running a simulation of a protein in membrane, which after 200 ns of simulation goes to a corner of the membrane and stays there for a long time, I want to perform the analyzes and I want to put it back in the center, how could I do this, without the links crossing the pbc box?. Best, Geo. --B_3703838557_1781076734 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Hello namd = users,

 

I am running a simulation of a protein in membrane, which after 200 ns o= f simulation goes to a corner of the membrane and stays there for a long tim= e, I want to perform the analyzes and I want to put it back in the center, h= ow could I do this, without the links crossing the pbc box?.

 

Best, =

 

Geo.

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boundary="_000_6405a0dc7456c41826cddabd4b7ddb40msuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 91863d69-ec38-4646-9c8d-08d916fa74dc X-MS-Exchange-CrossTenant-originalarrivaltime: 14 May 2021 17:05:20.7189 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: NlZjnJGpsEN22ePSAEP/jQ/x1UZzessz1PP/SfapLBOkCgn+GqzTnkGCJfm4FItUbW3BVXvv2cFOKphi13t57Q== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB4053 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0TEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxsZExEKQ1kXBxseEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8TcRkSEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF20eB3N1B0Fvf2JfdWVCaRtrRl0aE3hwB25ARkt4aEJAEQpYXBcfBBoEGBgTBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3IbbGBfEQpNXBceGh8RCkxaF3xpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF21yaV5uT0wTUh8cEQpDWhceGgQbGh0EGxobBB ISEQpCXhcbEQpEXhcZEQpCRRdobWtgeRJLQFoefREKQk4XaG9MZgFyZmRLXRIRCkJMF29hWBMaS 10bQ0FlEQpCbBdheRwfElx7T1ppQhEKQkAXb11aY1AZQ3lDWBgRCkJYF2dzZXNAbmFhTF1iEQpa WBcfEQp5QxdpRmkZZHNZcHNZWREKWUsXGxgeGB0RCnBnF2BNX29vWUthcGYbEBkaEQpwaBdmZH1 7H319ThlDUBAZGhEKcGgXYhlBbQF+HFNjZH4QGRoRCnBoF2lAX2BLfVh4WnhDEAceGhEKcGgXbX hTZ1pvT1pHElgQGRoRCnBoF2ZPRU9keVBHS3laEBkaEQpwfRdiHEtEchJkGmZzXBAZGhEKcH0Xa 3ocYFMZGG9QRWAQGRoRCnB9F3pBTmdMHn9yHW16EAceGhEKcH8XYB9DS21DHhtsE38QHhIRCnBf F2NrSEZmBWRbRG5LEBkaEQpwfxduH2ddfV5AE3hkeRAbGx0RCnBfF2RjaG0efVBrTFBgEBkaEQp wfxdhZm9bGmdkQkgdWxAbGRoRCnBfF2NiElBIY3gffEJ9EBMTEQpwbBdneBpAYhhJGn55TRAZGh EKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: G4-Y_-kEUHu_OhC1Alw09RZ-DjlaRBhj X-Proofpoint-ORIG-GUID: G4-Y_-kEUHu_OhC1Alw09RZ-DjlaRBhj MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 suspectscore=0 phishscore=0 spamscore=0 impostorscore=0 lowpriorityscore=0 clxscore=179 bulkscore=0 priorityscore=0 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140136 domainage_hfrom=12427 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_6405a0dc7456c41826cddabd4b7ddb40msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Lots and lots of simulation steps. To generate a nanosecond (or microsecond= , or whatever you fancy) trajectory, NAMD calculates the forces experienced= by the atoms in their given configuration, and recalculates the positions = for the atoms a femtosecond later. It then recalculates the forces, and the= n recalculates positions again. Doing this two times, the positions now ref= lect the system 2fs after the start of the simulation. Do this a thousand t= imes, and the simulation reflects 1 picosecond of motion. Do this a million= times, and the simulation reflects 1 nanosecond of motion. Do this a billi= on times, and you get a microsecond worth of trajectory. -Josh On 5/14/21 12:12 PM, joseph pareti wrote: I have a stupid question, but I need to start somewhere: I read that NAMD c= an do 'nanoseconds simulations' on some supercomputers, but the time step f= or atomic movements is in the order of femtoseconds. How can this be done? Thanks for any insight. -- Regards, Joseph Pareti - Artificial Intelligence consultant Joseph Pareti's AI Consulting Services https://urldefense.com/v3/__https://www.joepareti54-ai.com/__;!!DZ3fjg!rIMq= jVS7gQmj9D6BI3gCUtY25ut1PGddRkoOWaYZ0_1gK3th2v0xGHhkYRA6i1W48A$ cell +49 1520 1600 209 cell +39 339 797 0644 -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!rIMqjVS7gQmj9D6BI3gCUtY25ut1PGddRkoOWaYZ0_1gK3th2v0xGHh= kYRDAwbdXww$=20 --_000_6405a0dc7456c41826cddabd4b7ddb40msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <1DF30CBD1989BC45A6BB507DDC67ABA6@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable Lots and lots of simulation steps. To generate a nanosecond (or microsecond= , or whatever you fancy) trajectory, NAMD calculates the forces experienced= by the atoms in their given configuration, and recalculates the positions = for the atoms a femtosecond later. It then recalculates the forces, and then recalculates positions again. Do= ing this two times, the positions now reflect the system 2fs after the star= t of the simulation. Do this a thousand times, and the simulation reflects = 1 picosecond of motion. Do this a million times, and the simulation reflects 1 nanosecond of motion. Do th= is a billion times, and you get a microsecond worth of trajectory.

-Josh

On 5/14/21 12:12 PM, joseph pareti wrote:
I have a stupid question, but I need to start somewhere: I= read that NAMD can do 'nanoseconds simulations' on some supercomputers, bu= t the time step for atomic movements is in the order of femtoseconds. How c= an this be done?
Thanks for any insight.

--
Regards,
Joseph Pareti - Artificial Intelligence consultant
Joseph Pareti's AI Consulting Services
cell +49 1520 1600 209
cell +39 339 797 0644

--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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Subject: namd-l: Re: Re-center membrane protein Thread-Topic: Re-center membrane protein Thread-Index: AQHXSOQeZOSe2CoowkyfareT54u2BKrjN5Ng Date: Fri, 14 May 2021 17:18:13 +0000 Message-ID: References: <69FBA301-3D29-4A5A-849B-2BD7AC1ECE8A@gmail.com> In-Reply-To: <69FBA301-3D29-4A5A-849B-2BD7AC1ECE8A@gmail.com> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=uchicago.edu; x-originating-ip: [158.51.95.201] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: e07fb45e-6578-4376-260d-08d916fc416d x-ms-traffictypediagnostic: BYAPR11MB2887: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:8273; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:BYAPR11MB3160.namprd11.prod.outlook.com;PTR:;CAT:NONE;SFS:(39860400002)(396003)(366004)(136003)(346002)(376002)(122000001)(55016002)(19627405001)(166002)(33656002)(38100700002)(8936002)(5660300002)(52536014)(66446008)(75432002)(4743002)(3480700007)(71200400001)(316002)(7696005)(966005)(786003)(478600001)(66476007)(76116006)(9686003)(186003)(8676002)(53546011)(66946007)(110136005)(4744005)(2906002)(6506007)(66556008)(64756008)(19627235002)(26005)(86362001);DIR:OUT;SFP:1102; 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boundary="_000_BYAPR11MB31608DE6F2FFE52513A809CFD8509BYAPR11MB3160namp_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BYAPR11MB3160.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: e07fb45e-6578-4376-260d-08d916fc416d X-MS-Exchange-CrossTenant-originalarrivaltime: 14 May 2021 17:18:13.4278 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: puKggibK9I6/x4u7HEMntDxUN0tjrah84rEjDfBOW7MNjj3q5dzBJHRRfo7gFbCbUpmw+iJXUkc4ym4l2c5zHQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BYAPR11MB2887 X-Proofpoint-ORIG-GUID: ARgG_QbsFqd2IZO87G-dgDlgpp5DbIj7 X-Proofpoint-GUID: ARgG_QbsFqd2IZO87G-dgDlgpp5DbIj7 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0SEQpMehcZGhEKWUQXYBxaHk0SQVwbX30RClhYF2AFREVpR3BIEhh uEQp4ThdoYwFMf0V/QkFlQBEKeUwXaXJAHUASehhsHx4RCkNIFwccGRoRCkNZFwcbGBgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxJxGR0QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04Xa3hNbXV7SFlsW04YY3BlEh1tB05NbkZNWlofbkhjQB0RClhcFx8EGgQYGBMF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyG2x8UxEKTVwXGx0dEQpMWhdoaU1NTREKTEYXb2tra2x raxEKQk8Xeh5/Zm9CH1Nya30RCkNaFx4aBBsaHQQYHhkEEx0RCkJeFxsRCkReFxkRCkJFF2tEZm kbZGF8a11JEQpCThdoYwFMf0V/QkFlQBEKQkwXYAVERWlHcEgSGG4RCkJsF20Fen15U08BfG4FE QpCQBdkXUNaXxseW0ZPQREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnlDF3ppU3pyGERj WUNsEQpZSxcbGh0cHBEKcGcXbUdha01jGUxTaW4QGRoRCnBoF21CGkNBGhIBAVlyEBkaEQpwaBd pY31BW2NmSUNaYhAZGhEKcGgXYFB7RGhoHXpleFwQGRoRCnBoF2J5ehJAZgVsGF9QEBkaEQpwaB d6XgVeQwF4HBxceRASGhEKcH0XZGhvAUhuaEETWUwQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwf xdlWHIYHUkYXkZpfBAbGx8RCnBfF2J4Q257YkdbcnASEBkaEQpwbBdkThl4EhJPY0h/QhAZGhEK bX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=178 lowpriorityscore=0 mlxlogscore=754 mlxscore=0 bulkscore=0 phishscore=0 spamscore=0 impostorscore=0 suspectscore=0 priorityscore=30 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140136 domainage_hfrom=10766 X-Spam-Score: 0 X-Spam-OrigSender: ramendoza@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ramon Mendoza Uriarte --_000_BYAPR11MB31608DE6F2FFE52513A809CFD8509BYAPR11MB3160namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I would suggest looking at VMD's PBCTools Plugin: http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#:~:text=3DSince%20VMD= %20version%201.8.6%2C%20the%20PBCTools%20plugin%20is,can%20be%20used%20with= in%20VMD%20without%20further%20preparation. ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of Ropo= n-Palacios G. Sent: Friday, May 14, 2021 10:02 AM To: KS UIUC Subject: namd-l: Re-center membrane protein Hello namd users, I am running a simulation of a protein in membrane, which after 200 ns of s= imulation goes to a corner of the membrane and stays there for a long time,= I want to perform the analyzes and I want to put it back in the center, ho= w could I do this, without the links crossing the pbc box?. Best, Geo. --_000_BYAPR11MB31608DE6F2FFE52513A809CFD8509BYAPR11MB3160namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
I would suggest looking at VMD's PBCTools Plugin:


From: owner-namd-l@ks.uiuc.= edu <owner-namd-l@ks.uiuc.edu> on behalf of Ropon-Palacios G. <bio= dano.geo@gmail.com>
Sent: Friday, May 14, 2021 10:02 AM
To: KS UIUC <namd-l@ks.uiuc.edu>
Subject: namd-l: Re-center membrane protein
 

Hello namd users,=

 

I am running a si= mulation of a protein in membrane, which after 200 ns of simulation goes to= a corner of the membrane and stays there for a long time, I want to perfor= m the analyzes and I want to put it back in the center, how could I do this, without the links crossing the pb= c box?.

 

Best,

 

Geo.

--_000_BYAPR11MB31608DE6F2FFE52513A809CFD8509BYAPR11MB3160namp_-- From owner-namd-l@halifax.ks.uiuc.edu Fri May 14 12:21:33 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EHLXiN012841; Fri, 14 May 2021 12:21:33 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14EHLXOV012840; Fri, 14 May 2021 12:21:33 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EHLWnq012836; Fri, 14 May 2021 12:21:32 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14EHLWWb012835; Fri, 14 May 2021 12:21:32 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14EHLPtD012827 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 14 May 2021 12:21:25 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14EH2sQ8024197 for ; Fri, 14 May 2021 17:21:25 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qv1-f44.google.com (mail-qv1-f44.google.com [209.85.219.44]) by mx0b-00007101.pphosted.com with ESMTP id 38hcmskd1m-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 14 May 2021 17:21:24 +0000 Received: by mail-qv1-f44.google.com with SMTP id 5so45765qvk.0 for ; Fri, 14 May 2021 10:21:24 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=Vvf8+kVM5bAHkIhj2WArgn5dWk931zuw+w4EMryGhQw=; b=LPnB8AGOqX7V3qaDt49VmUjUlGg2L/LolRvMrTtUQYp4O4SW7QhyRP8O33PdQBBi0X KC8HhRmute6dkv445jjyRjyyO/0SIQJWqBA//G1tD1JrXjFmfpQFua8SFUU11MiC40O+ FB7u2dcLvrGnDnGs9mbfkaqKuI7MgLHKDsImmslWmhWu75AYjrBF/Y4+O1JhJWWNL1Xg uCDF2OBUUZf9+LzMRpgGHAUyIw0JU9qPKbtPqc0Yt3FTJ/7gv/E2p/W587JAQ4C3JanH dCBKz/N+yfaaWs9GHHj1cdqoIVwJYfpfCA52NHkLC0AiggaU0BuodOPhCovb+fEC9BCd hkaQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=Vvf8+kVM5bAHkIhj2WArgn5dWk931zuw+w4EMryGhQw=; b=R9WherWGA2Z8eH86SLe8y3/Q2VIumTXdNffNVvkhV4MjMTc7+1VdAsnGfTf0nbYIXh GYp2VvLqozWABqk8HcLeL7B0HskxbqeZOrz0egzw7Hx1mYWg5cMwQ3SoPGzVqnVnF1QR E7TqOcW2JTNzVnF60aXxsNBfRZcATIt8JAEY8L7XYH7oXMrbcli/nsin7f3G/J59SoAH eDecYIiIKuUESS1OzC/gKiBgjpOnN84+Y+JTy3ZOKJ0wxtcneeB37TyhjB9zOGOjPATg M4XtC8e8ueuKBkwhDJiw0GgvRf99701tQ+PDGUx/dUBMglaAdrNLx5rIOfsBOVbTN8a4 kpyw== X-Gm-Message-State: AOAM531vvjnyVOBIdHMg36xicbuyoNgipwHfWQbRV1nI4Cj4fcWngOHQ AnObQx5AgwdY17McIg5gIX2QfSceldbhJA== X-Google-Smtp-Source: ABdhPJyhurZBisDG77YheQNfJ8nYuNy2sbJgQc0EWg4XQ4vF3RtgYd7XqoGPYqfEd4J/rBaPMaoqWA== X-Received: by 2002:a05:6214:e82:: with SMTP id hf2mr47862670qvb.22.1621012883972; Fri, 14 May 2021 10:21:23 -0700 (PDT) Received: from [192.168.1.39] ([181.64.64.40]) by smtp.gmail.com with ESMTPSA id b7sm5392736qkj.126.2021.05.14.10.21.22 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Fri, 14 May 2021 10:21:23 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 14 May 2021 12:21:20 -0500 Subject: Re: namd-l: Re: Re-center membrane protein From: "Ropon-Palacios G." To: , Ramon Mendoza Uriarte Message-ID: Thread-Topic: namd-l: Re: Re-center membrane protein Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3703839683_556445154" X-CLX-Shades: MLX X-Proofpoint-GUID: sYPJxS-fQ2gI7IrYqXcohBggq5SV37-3 X-Proofpoint-ORIG-GUID: sYPJxS-fQ2gI7IrYqXcohBggq5SV37-3 X-CLX-Response: 1TFkXGx0TEQpMehcZHBsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHhwSEQpDWRcZEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfE3EZEhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdZc3pgUnkHTHsYTWMdY1hzW3JJRUJoTU1bH3l8GR0HGREKWFwXHwQaBBgYEwUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdyG2xzXBEKTVwXGx0aEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tra2sRCkJPF21ScxJBW2lEEx5MEQpDWhcYGhMEEh8EGBsTBB 4eEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2Np WW96Tx1yR09/EQpCQBdhXW1/bmJrQXsBQREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnl DF2ZiQhhvQBleZ054EQpZSxcTHhocEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXY1hfYnJpfXpaTk sQGRoRCnBoF2F8bl1EXHpAeXsaEBkaEQpwaBdue0tpXR9sWU9mRhAZGhEKcGgXbGViTmQdXGhBW 3IQGRoRCnBoF2RgaHBBW1JjTV5IEBkaEQpwZxdpQ25QAVlzRwEeUxAZGhEKcH0XZGhvAUhuaEET WUwQGRoRCnB/F2VYchgdSRheRml8EBsbExEKcF8XYnhDbntiR1tycBIQGRoRCnBsF3pHQGsYWXl /HhtIEB0aEQpwQxdpQmt7ZnJYfFBEaBAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 adultscore=0 priorityscore=361 phishscore=0 mlxscore=0 suspectscore=0 impostorscore=0 clxscore=179 spamscore=0 mlxlogscore=760 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140136 domainage_hfrom=9406 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3703839683_556445154 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable I=E2=80=99m using pbctools,=20 =20 Following command :=C2=A0 pbc wrap -compound fragment -center com -centersel "p= rotein" -all -shiftcenter {0 1 0} =20 But bond of atoms crossing pbc box, how fix it bug?=20 =20 From: on behalf of Ramon Mendoza Uriarte Reply-To: , Ramon Mendoza Uriarte Date: Friday, May 14, 2021 at 12:19 PM To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." Subject: namd-l: Re: Re-center membrane protein=20 =20 I would suggest looking at VMD's PBCTools Plugin: =20 http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#:~:text=3DSince%20VMD%2= 0version%201.8.6%2C%20the%20PBCTools%20plugin%20is,can%20be%20used%20within%= 20VMD%20without%20further%20preparation. From: owner-namd-l@ks.uiuc.edu on behalf of Ropo= n-Palacios G. Sent: Friday, May 14, 2021 10:02 AM To: KS UIUC Subject: namd-l: Re-center membrane protein=20 =20 Hello namd users, =20 I am running a simulation of a protein in membrane, which after 200 ns of s= imulation goes to a corner of the membrane and stays there for a long time, = I want to perform the analyzes and I want to put it back in the center, how = could I do this, without the links crossing the pbc box?.=20 =20 Best,=20 =20 Geo.=20 --B_3703839683_556445154 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable <= meta http-equiv=3DContent-Type content=3D"text/html; charset=3Dutf-8">

I=E2=80=99m using pbctool= s,

 

Following command :=C2=A0 pbc wrap -compound fragment -center com -centersel "protein&qu= ot; -all -shiftcenter {0 1 0}

&= nbsp;

But bond of atoms crossing pbc box, how fi= x it bug?

 

From: <owner-namd-l@ks.uiuc.edu>= on behalf of Ramon Mendoza Uriarte <ramendoza@uchicago.edu>
Rep= ly-To: <namd-l@ks.uiuc.edu>, Ramon Mendoza Uriarte <ramendoza@u= chicago.edu>
Date: Friday, May 14, 2021 at 12:19 PM
To: <= /b>"namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, "Ropon-Pa= lacios G." <biodano.geo@gmail.com>
Subject: namd-l: Re:= Re-center membrane protein

 

I would suggest looking at VMD's PBCTools Plugin:=

 

From: = owner-namd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.edu> on behalf of Ropon= -Palacios G. <biodano.geo@gmail.com>
Sent: Friday, May 14, 2= 021 10:02 AM
To: KS UIUC <namd-l@ks.uiuc.edu>
Subject:= namd-l: Re-center membrane protein

 

Hello namd users,

 

I am running a simulation of a = protein in membrane, which after 200 ns of simulation goes to a corner of th= e membrane and stays there for a long time, I want to perform the analyzes a= nd I want to put it back in the center, how could I do this, without the lin= ks crossing the pbc box?.

 

Best,

 

Geo.

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boundary="_000_BYAPR11MB3160650C6D6102B966EC5280D8509BYAPR11MB3160namp_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BYAPR11MB3160.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 34b0ee8b-a7d0-48fc-b666-08d91700ee25 X-MS-Exchange-CrossTenant-originalarrivaltime: 14 May 2021 17:51:41.1814 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: E2JCg3bFF+BdeeV0sv+xwLUVdIWpJO7oY5gaa8W5SIIxm0DpzGexe+i74hVh0w4JYMnroypJsJ4SIjvGHo5fCg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SJ0PR11MB4927 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIbEQpMehceEhEKWUQXYBxaHk0SQVwbX30RClhYF2AFREVpR3BIEhh uEQp4ThdoYwFMf0V/QkFlQBEKeUwXaXJAHUASehhsHx4RCkNIFwccGx0RCkNZFxkSEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwbcR4aEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0RtB1BAWEB8RkBic0J/GHpFRR9TeV8dfBliY0dETFhgEQpYXBcfBBoEGBgTBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3IbbBtgEQpNXBcYHxkRCkxaF2l7aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxd6Hn9mb0IfU3JrfREKQ1oXHhoEGxodBBMZBB saExEKQl4XGxEKRF4XGREKQkUXa0RmaRtkYXxrXUkRCkJOF2hjAUx/RX9CQWVAEQpCTBdgBURFa UdwSBIYbhEKQmwXbQV6fXlTTwF8bgURCkJAF2FdbX9uYmtBewFBEQpCWBdnc2VzQG5hYUxdYhEK TV4XGxEKWlgXHxEKeUMXZmJCGG9AGV5nTngRCllLFxsaHRwcEQpwZxdpQ25QAVlzRwEeUxAZGhE KcGgXYX5pSGNBUBx5aRsQGhEKcGgXZ315SGxIAVNsU1kQGhEKcGgXaFpfXlpTE10cblAQHhkRCn BoF21zWnprf1xIfWxeEBoRCnBoF2FkX0FjcF5JWB8YEBMfEQpwZxdtR2FrTWMZTFNpbhAZGhEKc H0XZlxGZWd5GR5QRG0QGhEKcH0XbX0FEmsTe2JFYksQGhEKcH8XZVhyGB1JGF5GaXwQGxgaEQpw XxdieENue2JHW3JwEhAcGhEKcH8XYWZvWxpnZEJIHVsQGxkZEQpwXxdjYhJQSGN4H3xCfRAbGhs RCnBsF2ROGXgSEk9jSH9CEB4SEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: nG-zjrjVljHYhU2Poo5ySu7V3HImnfrJ X-Proofpoint-ORIG-GUID: nG-zjrjVljHYhU2Poo5ySu7V3HImnfrJ X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 suspectscore=0 phishscore=0 spamscore=0 impostorscore=0 lowpriorityscore=0 clxscore=181 bulkscore=0 priorityscore=48 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140139 domainage_hfrom=10766 X-Spam-Score: 0 X-Spam-OrigSender: ramendoza@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ramon Mendoza Uriarte --_000_BYAPR11MB3160650C6D6102B966EC5280D8509BYAPR11MB3160namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable For the future use the VMD mailing list for VMD related questions. You can maybe try a different center first and then com: pbc wrap -all -compound fragment -center origin pbc wrap -all -compound fragment -center com -centersel "protein" ________________________________ From: Ropon-Palacios G. Sent: Friday, May 14, 2021 10:21 AM To: namd-l@ks.uiuc.edu ; Ramon Mendoza Uriarte Subject: Re: namd-l: Re: Re-center membrane protein I=92m using pbctools, Following command : pbc wrap -compound fragment -center com -centersel "pr= otein" -all -shiftcenter {0 1 0} But bond of atoms crossing pbc box, how fix it bug? From: on behalf of Ramon Mendoza Uriarte Reply-To: , Ramon Mendoza Uriarte Date: Friday, May 14, 2021 at 12:19 PM To: "namd-l@ks.uiuc.edu" , "Ropon-Palacios G." Subject: namd-l: Re: Re-center membrane protein I would suggest looking at VMD's PBCTools Plugin: http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#:~:text=3DSince%20VMD= %20version%201.8.6%2C%20the%20PBCTools%20plugin%20is,can%20be%20used%20with= in%20VMD%20without%20further%20preparation. ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of Ropo= n-Palacios G. Sent: Friday, May 14, 2021 10:02 AM To: KS UIUC Subject: namd-l: Re-center membrane protein Hello namd users, I am running a simulation of a protein in membrane, which after 200 ns of s= imulation goes to a corner of the membrane and stays there for a long time,= I want to perform the analyzes and I want to put it back in the center, ho= w could I do this, without the links crossing the pbc box?. Best, Geo. --_000_BYAPR11MB3160650C6D6102B966EC5280D8509BYAPR11MB3160namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
For the future use the VMD mailing list for VMD related questions.

You can maybe try a different center first and then com:

pbc wrap -all -compound fragment -center origin
pbc wrap -all -compound fragment -center com -centersel "protein"=

From: Ropon-Palacios G. <= ;biodano.geo@gmail.com>
Sent: Friday, May 14, 2021 10:21 AM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>; Ramon Mendoza Uri= arte <ramendoza@uchicago.edu>
Subject: Re: namd-l: Re: Re-center membrane protein
 

I=92m using pbctools,

 

Following command :  pbc wrap -compound fragment -center com -centersel "protein" -all= -shiftcenter {0 1 0}

 

But bond of atoms crossing pbc box, how fix it bug= ?

 

F= rom: <owner-namd-l@ks.uiuc.= edu> on behalf of Ramon Mendoza Uriarte <ramendoza@uchicago.edu> Reply-To: <namd-l@ks.uiuc.edu>, Ramon Mendoza Uriarte <rame= ndoza@uchicago.edu>
Date: Friday, May 14, 2021 at 12:19 PM
To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, "= ;Ropon-Palacios G." <biodano.geo@gmail.com>
Subject: namd-l: Re: Re-center membrane protein

 

I wo= uld suggest looking at VMD's PBCTools Plugin:

&nbs= p;


From: owner-namd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc= .edu> on behalf of Ropon-Palacios G. <biodano.geo@gmail.com>
Sent: Friday, May 14, 2021 10:02 AM
To: KS UIUC <namd-l@ks.uiuc.edu>
Subject: namd-l: Re-center membrane protein

 

Hello namd users= ,

 

I am running a s= imulation of a protein in membrane, which after 200 ns of simulation goes t= o a corner of the membrane and stays there for a long time, I want to perfo= rm the analyzes and I want to put it back in the center, how could I do this, without the links crossing the pb= c box?.

 

Best,

 

Geo.

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boundary="0000000000009d1cf405c24e9c2c" X-Proofpoint-ORIG-GUID: 97c7H-g-cqCrY1_pH_9W0cVrLxC-Ixo5 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIZEQpMehcbHBIRCllEF2dMU0cZaBJoR0x7EQpYWBdjWGZBfmxIWGB SexEKeE4XYX5mSUN9fVxYHUARCnlMF29Pf24BGnlLH1NlEQpDSBcHGRoeEQpDWRcHGx8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBlxEh4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XEx1JHWIHTQdJW2lYcxt1WmJ1E30aSXxYZlJpB2NSRR8RClhcFx8EGgQYGBMF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyG21GYREKTVwXGxofEQpMWhd4aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2R+WE9mbnNJcFtPEQpDWhcYGhMEEh8EGBscBB 4TEQpCXhcbEQpEXhcZEQpCXBcbEQpeThcbEQpCSxdhfmZJQ319XFgdQBEKQkkXYX5mSUN9fVxYH UARCkJFF2YYHn1uYEhLZkVyEQpCThdhfmZJQ319XFgdQBEKQkwXY1hmQX5sSFhgUnsRCkJsF21v Zhxcb35fW2NcEQpCQBdvXVpjUBlDeUNYGBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnl DF2lGaRlkc1lwc1lZEQpZSxcbGRoaGREKcGcXYmZBHWtYbkRcc1sQGRoRCnBoF2l8enhpS0gBf2 NYEBkaEQpwaBdvEkRfWll4ZR9vEhAZGhEKcGgXaB9lQm1fYWBTQlgQGRoRCnBoF2lGaxhBZWhLU 1hFEBkaEQpwaBdsYEtDY3hYYUxhchAZGhEKcH0XYXlSQllIWhwcfFgQGRoRCnB9F3pBTmdMHn9y HW16EBoRCnB/F2AfQ0ttQx4bbBN/EBkaEQpwXxdpYHoacn5yexhhGxAZGhEKcH8XYWZvWxpnZEJ IHVsQGxgfEQpwXxdjYhJQSGN4H3xCfRATHxEKcGwXZkxhGkh4cB98Ym8QGRoRCm1+FxsRClhNF0 sRIA== X-Proofpoint-GUID: 97c7H-g-cqCrY1_pH_9W0cVrLxC-Ixo5 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 priorityscore=168 lowpriorityscore=0 impostorscore=0 mlxlogscore=836 spamscore=0 phishscore=0 bulkscore=0 clxscore=183 mlxscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105140145 domainage_hfrom=13003 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --0000000000009d1cf405c24e9c2c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Run 1 million timesteps... Best, Peter On Fri, May 14, 2021 at 1:19 PM joseph pareti wrote: > I have a stupid question, but I need to start somewhere: I read that NAMD > can do 'nanoseconds simulations' on some supercomputers, but the time step > for atomic movements is in the order of femtoseconds. How can this be don= e? > Thanks for any insight. > > -- > Regards, > Joseph Pareti - Artificial Intelligence consultant > Joseph Pareti's AI Consulting Services > https://urldefense.com/v3/__https://www.joepareti54-ai.com/__;!!DZ3fjg!sQ= Q-8VScxVLBfxdqoMxuFtLjiuYGacTqX1A9Gi5pHT3Vtm72lITG3Pwq0ZMGMbRDhA$=20 > > cell +49 1520 1600 209 > cell +39 339 797 0644 > --0000000000009d1cf405c24e9c2c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Run 1 million timesteps...
Best,
<= div>Peter

On Fri, May 14, 2021 at 1:19 PM joseph pareti <joepareti54@gmail.com> wrote:
=
I = have a stupid question, but I need to start somewhere: I read that NAMD can= do 'nanoseconds simulations' on some supercomputers, but the time = step for atomic movements is in the order of femtoseconds. How can this be = done?
Thanks for any insight.

--
Regards,
Joseph Pareti - Artificial Intelligence consultant
= Joseph Pareti's AI Consulting Services
cell +49 1520 1600 209
=
cell +39 339 797 0644
<= /div>
--0000000000009d1cf405c24e9c2c-- From owner-namd-l@halifax.ks.uiuc.edu Mon May 17 10:59:46 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14HFxk53026644; Mon, 17 May 2021 10:59:46 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14HFxk7b026643; Mon, 17 May 2021 10:59:46 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14HFxj7E026639; Mon, 17 May 2021 10:59:45 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14HFxjhK026638; Mon, 17 May 2021 10:59:45 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14HFxZF8026630 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000f890a405c288ada1" X-CLX-Response: 1TFkXGxMbEQpMehcZGRwRCllEF2ZhbmV9XmdIbBhzEQpYWBduWkBEenASH0x dRBEKeE4XY1Nja3sTWH4aX14RCnlMF2ZuQ0BLZl9ub01dEQpDSBcHGR4TEQpDWRcHGRkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHRtxGxobEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3VFZQcZSXocW25eWmVaRmYZXB5rYxkeeHNNQmB/EkNsEQpYXBcfBBoEGBgT BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXchhuT2gRCk1cFx0dEQpMWhdsaU1NaxEKTEYXb2tra2t rEQpCTxdmTB9NaW1BQB8TcxEKQ1oXGBoTBBIfBBscHQQbEhgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXbk5wfkBwZ20ZUBwRCkJOF2NTY2t7E 1h+Gl9eEQpCTBduWkBEenASH0xdRBEKQmwXblB+G2lwExxMEwERCkJAF25eTR5OUENgTxljEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXZmMTRE1zW1gbG2cRCllLFxMeGhMRCnBoF2V 7RAVnfFJHeWduEBkaEQpwaBdgfFhdfhJ5Sx1FXRAZGhEKcGgXZmZwQVpzTRpHQx8QGRoRCnBoF2 B+UkIeHxIfc2FyEBkaEQpwaBdkQBhrRnpmfHpgaxAZGhEKcGwXY2toTXh/H20bX0IQGRoRCm1+F xsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: _oO-3cP6qDtpOplL3v4AI34RYghJU8iF X-CLX-Shades: MLX X-Proofpoint-GUID: _oO-3cP6qDtpOplL3v4AI34RYghJU8iF X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=336 bulkscore=0 malwarescore=0 impostorscore=0 suspectscore=0 clxscore=191 lowpriorityscore=0 mlxlogscore=576 adultscore=0 spamscore=0 phishscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105170109 domainage_hfrom=9409 X-Spam-Score: 0 X-Spam-OrigSender: iasarekwaku@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Isaac Asare Kwaku --000000000000f890a405c288ada1 Content-Type: text/plain; charset="UTF-8" Hello guys, This is more of a tcl script problem but I was hoping I could get some help. I am measuring the center of mass of two different residues of a protein in VMD. Now I want to find the difference between only the z coordinates of the center of mass of the residues. The command "measure center $sel weight mass" gives me the x,y,z coordinates of the center of mass but I am looking for a way to store just the z coordinates so I can find the difference between them. I have tried to assign the value of "measure center $sel weight mass" to a variable as a list so I use "lindex listname 2" to get the z coordinate. However the assignment of the output of the "measure" command has proved futile. How do I get only the z coordinate of the center of mass? Regards, Isaac. --000000000000f890a405c288ada1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello guys,

This is more of a tcl scrip= t problem but I was hoping I could get some help. I am measuring the center= of mass of two different residues of a protein in VMD. Now I want to find = the difference between only the z coordinates of the center of mass of the = residues. The command "measure center $sel weight mass" gives me = the x,y,z coordinates of the center of mass but I am looking for a way to s= tore just the z coordinates so I can find the difference between them. I ha= ve tried to assign the value of=C2=A0"measure center $sel weight mass&= quot; to a variable as a list so I use "lindex listname 2" to get= the z coordinate. However the assignment of the output of the "measur= e" command has proved futile. How do I get only the z coordinate=C2=A0= of the center of mass?

Regards,
Isaac.
--000000000000f890a405c288ada1-- From owner-namd-l@halifax.ks.uiuc.edu Mon May 17 11:51:29 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14HGpTLE029122; Mon, 17 May 2021 11:51:29 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14HGpTsJ029121; Mon, 17 May 2021 11:51:29 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14HGpSTT029117; Mon, 17 May 2021 11:51:28 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14HGpS7l029116; Mon, 17 May 2021 11:51:28 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14HGpG5m029107 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Mon, 17 May 2021 18:51:11 +0200 Received: from EBOX-PROD-SRV17.win.su.se (ebox-prod-srv17.win.su.se [IPv6:2001:6b0:5:1462:5102:4de3:b90f:2e2d]) by smtp.su.se (Postfix) with ESMTPS id 4FkQBQ5fPfz2V; Mon, 17 May 2021 18:51:10 +0200 (CEST) Received: from ebox-prod-srv13.win.su.se (2001:6b0:5:1162:f071:3d85:b2d0:c2f6) by EBOX-PROD-SRV17.win.su.se (2001:6b0:5:1462:5102:4de3:b90f:2e2d) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.2242.10; Mon, 17 May 2021 18:51:10 +0200 Received: from ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6]) by ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6%2]) with mapi id 15.01.2242.010; Mon, 17 May 2021 18:51:10 +0200 From: Alessandro Ruda To: Giacomo Fiorin , "namd-l@ks.uiuc.edu" Subject: Re: namd-l: Metadynamics problems Thread-Topic: namd-l: Metadynamics problems Thread-Index: AQHXSKSzS8cNRHVYRUSVHrn3dHeTCqri/NsAgATnmyo= Date: Mon, 17 May 2021 16:51:10 +0000 Message-ID: <18db5ec5ffaa4322958ad2eaad1f95c0@su.se> References: <8dd715e40fba48ac9a543742dce8ed4f@su.se>, In-Reply-To: Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [130.237.154.251] Content-Type: multipart/alternative; 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charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Thanks Giacomo for the prompt reply, Restarting the run didn't really work since it stopped again after 20 minut= es (after running for 11 h though). Doesn't look stable at all. The correlation time for the torsions I am looking at is around 100 ps. What value would you suggest to be the optimal one in such case? All the best, Alex ________________________________ From: Giacomo Fiorin Sent: 14 May 2021 17:43:08 To: NAMD list; Alessandro Ruda Subject: Re: namd-l: Metadynamics problems Hello Alex, if the instability is sporadic you can safely restart and conti= nue running. The instability, however, could be due to the relatively high rate at which= you add the Gaussian bias, 1 kcal/mol per 1000 steps. Not knowing the spe= cifics of the system, it would help you to figure out what are the correlat= ion times of the two dihedral angles from an equilibrium MD trajectory, whi= ch you should already have. The variables may simply not take up a bias th= at fast. Lastly, you're using NAMD 2.12, which is more than 4 years old. While it's= true that the error is raised from a large force coming from Colvars, late= r versions like 2.14 may handle it better, or at least clarify more clearly= the precise step where things go wrong. For Colvars specifically, there a= re a few advantages for using metadynamics specifically: https://urldefense= .com/v3/__https://colvars.github.io/namd-2.14/colvars-refman-namd/colvars-r= efman-namd.html*sec:colvars_config_changes__;Iw!!DZ3fjg!rjaeCr5aC3536OV2G4_= FTzSKIEA6WZlT-zoXvc1VHCTUZDGKcghFS0LbSI8rSP1OpA$ Giacomo On Fri, May 14, 2021 at 5:50 AM Alessandro Ruda > wrote: Dear NAMD comunity, I am running metadynamics on a set of two dihedral angles. I've tried defau= lt metadynamics and well tempered. For both of them after a few hours the r= un stops with errors like the following: namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe44263fa0. B= acktrace: /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_charg= esEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_charg= esEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] and the log file states: mpprun info: Job terminated with error Normal molecular dynamics works well so it must be related to metadynamics.= This is the colvar file that i used: ---------------------------------------------------------------------------= ----------------------------------------------------------- colvarsTrajAppend off colvar { name Psi width 2.5 dihedral { group1 { atomnumbers { 32 } } group2 { atomnumbers { 22 } } group3 { atomnumbers { 20 } } group4 { atomnumbers { 21 } } } lowerBoundary -180 upperBoundary 180 } colvar { name Phi width 2.5 dihedral { group1 { atomnumbers { 33 } } group2 { atomnumbers { 32 } } group3 { atomnumbers { 22 } } group4 { atomnumbers { 20 } } } lowerBoundary -180 upperBoundary 180 } metadynamics { wellTempered on biasTemperature 1490 name metaPhiPsi colvars Phi Psi hillWeight 0.01 hillwidth 1.0 saveFreeEnergyFile no dumpFreeEnergyFile yes #When useGrids and this option are on, the PMF is w= ritten every colvarsRestartFrequency steps to the file outputName.pmf writeHillsTrajectory on newHillFrequency 100 ---------------------------------------------------------------------------= ------------------------------------------------------------ I have tried with different hillWeight values and the problem stays. Can I do something or should I restart from the last step and continue runn= ing and, in doing so, how can I keep the old colvars data so that I restart from the last points = collected? Thank you in advance, All the best, Alex o, how can I keep the old colvars data so that I restart from the last points = collected? Thank you in advance, All the best, Alex --_000_18db5ec5ffaa4322958ad2eaad1f95c0suse_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable

Thanks Giacomo for the prompt reply,


Restarting the run didn't really work since it stopped again after = 20 minutes (after running for 11 h though). Doesn't look stable at all.&nbs= p;


The correlation time for the torsions I am looking at is around 100 ps. 

What value would you suggest to be the optimal one in such case?


All the best,

Alex


From: Giacomo Fiorin <gi= acomo.fiorin@gmail.com>
Sent: 14 May 2021 17:43:08
To: NAMD list; Alessandro Ruda
Subject: Re: namd-l: Metadynamics problems
 
Hello Alex, if the instability is sporadic you can safely = restart and continue running.

The instability, however, could be due to the relatively high rate at = which you add the Gaussian bias, 1 kcal/mol per 1000 steps.  Not knowi= ng the specifics of the system, it would help you to figure out what are th= e correlation times of the two dihedral angles from an equilibrium MD trajectory, which you should already ha= ve.  The variables may simply not take up a bias that fast.

Lastly, you're using NAMD 2.12, which is more than 4 years old.  = While it's true that the error is raised from a large force coming fro= m Colvars, later versions like 2.14 may handle it better, or at least clari= fy more clearly the precise step where things go wrong.  For Colvars specifically, there are a few advantages for u= sing metadynamics specifically: https://colvars.github.io/namd-2.1= 4/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_config_changes

Giacomo

Dear NAMD comunity,


I am running metadynamics on a set of two dihedral angles. I've tried de= fault metadynamics and well tempered. For both of them after a few hours&nb= sp;the run stops with errors like the following:


namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe4426= 3fa0.  Backtrace:
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]

and the log file states:

mpprun info:   Job terminated with error=

Normal molecular dynamics works well so it must be related to me= tadynamics. This is the colvar file that i used:
----------------------------------------------------------------------= ----------------------------------------------------------------

colvarsTrajAppend off

colvar {
   name Psi
   width 2.5
   dihedral {
      group1 {
         atomnumbers { 32 }
      }
      group2 {
         atomnumbers { 22 }
      }
      group3 {
         atomnumbers { 20 }
      }
      group4 {
         atomnumbers { 21 }
      }
   }
    lowerBoundary -180
    upperBoundary 180

}

colvar {
   name Phi
   width 2.5
   dihedral {
      group1 {
         atomnumbers { 33 }
      }
      group2 {
         atomnumbers { 32 }
      }
      group3 {
         atomnumbers { 22 }
      }
      group4 {
         atomnumbers { 20 }
      }
   }
 lowerBoundary -180
   upperBoundary 180
}

metadynamics {
wellTempered on
biasTemperature 1490
name metaPhiPsi
colvars Phi Psi
hillWeight 0.01
hillwidth 1.0
saveFreeEnergyFile no
dumpFreeEnergyFile yes  #When useGrids and this option are on,= the PMF is written every colvarsRestartFrequency steps to the file  o= utputName.pmf
writeHillsTrajectory on
newHillFrequency 100 
---------------------------------------------------------------------------= ------------------------------------------------------------

I have tried with different hillWeight values and the problem stays.
Can I do something or should I restart from the last step and continue= running and, in doing so,
how can I keep the old colvars data so that I restart from the last po= ints collected?

Thank you in advance,

All the best,
Alex



All the best,
Alex


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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi, You can use the colvars module for this measurement. The required function is distanceZ. For more information https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-namd/co= lvars-refman-namd.html*x1-60002.3__;Iw!!DZ3fjg!onu4K8K6kVG8Bxqux-PfbwcfZXA_= kMrVqjXT4ySPxFBFKBMsF3zk7Lj9dUFCIr-dbQ$=20 On Mon, 17 May 2021, 21:32 Isaac Asare Kwaku, wrote: > Hello guys, > > This is more of a tcl script problem but I was hoping I could get some > help. I am measuring the center of mass of two different residues of a > protein in VMD. Now I want to find the difference between only the z > coordinates of the center of mass of the residues. The command "measure > center $sel weight mass" gives me the x,y,z coordinates of the center of > mass but I am looking for a way to store just the z coordinates so I can > find the difference between them. I have tried to assign the value > of "measure center $sel weight mass" to a variable as a list so I use > "lindex listname 2" to get the z coordinate. However the assignment of the > output of the "measure" command has proved futile. How do I get only the z > coordinate of the center of mass? > > Regards, > Isaac. > --=20 Diship Srivastava JRF Department of Chemistry IIT(ISM) - Dhanbad India --000000000000e94ce305c289ad23 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi,=C2=A0
You can use t= he colvars module for this=C2=A0 measurement. The required function is dist= anceZ. For more information=C2=A0http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.= html#x1-60002.3

On Mon, 17 May 2021, 21:32 Isaac Asare Kwaku= , <iasarekwak= u@gmail.com> wrote:
Hello guys,

This is more of = a tcl script problem but I was hoping I could get some help. I am measuring= the center of mass of two different residues of a protein in VMD. Now I wa= nt to find the difference between only the z coordinates of the center of m= ass of the residues. The command "measure center $sel weight mass"= ; gives me the x,y,z coordinates of the center of mass but I am looking for= a way to store just the z coordinates so I can find the difference between= them. I have tried to assign the value of=C2=A0"measure center $sel w= eight mass" to a variable as a list so I use "lindex listname 2&q= uot; to get the z coordinate. However the assignment of the output of the &= quot;measure" command has proved futile. How do I get only the z coord= inate=C2=A0of the center of mass?

Regards,
Isaac.


--
Diship Srivastava=C2=A0
JRF=C2=A0
De= partment of Chemistry
IIT(ISM) - Dhanbad
India
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Mon, 17 May 2021 19:17:32 +0200 (CEST) X-PMX-Spam: Gauge=IIIIIIII, Probability=8%, Report=' HTML_NO_HTTP 0.1, BODYTEXTH_SIZE_10000_LESS 0, BODYTEXTP_SIZE_3000_LESS 0, BODY_SIZE_4000_4999 0, BODY_SIZE_5000_LESS 0, BODY_SIZE_7000_LESS 0, FROM_EDU_TLD 0, IN_REP_TO 0, LEGITIMATE_SIGNS 0, MSG_THREAD 0, NO_CTA_URI_FOUND 0, NO_URI_HTTPS 0, RDNS_GENERIC_POOLED 0, RDNS_SUSP 0, RDNS_SUSP_GENERIC 0, REFERENCES 0, SENDER_NO_AUTH 0, TEXT_DIRECTION 0, TEXT_DIR_LTR_ONLY 0, __ANY_URI 0, __ATTACHMENT_NOT_IMG 0, __BAT_BOUNDARY 0, __BODY_NO_MAILTO 0, __BODY_TEXT_X4 0, __BOUNCE_CHALLENGE_SUBJ 0, __BOUNCE_NDR_SUBJ_EXEMPT 0, __CT 0, __CTYPE_HAS_BOUNDARY 0, __CTYPE_MULTIPART 0, __CTYPE_MULTIPART_MIXED 0, __DQ_NEG_HEUR 0, __DQ_NEG_IP 0, __FORWARDED_MSG 0, __FRAUD_MONEY_CURRENCY 0, __FRAUD_MONEY_CURRENCY_DOLLAR 0, __FROM_DOMAIN_NOT_IN_BODY 0, __FROM_NAME_NOT_IN_BODY 0, __HAS_ATTACHMENT 0, __HAS_ATTACHMENT1 0, __HAS_FROM 0, __HAS_HTML 0, __HAS_MSGID 0, __HAS_REFERENCES 0, __HTML_ATTR_DIR 0, __HTML_DIR_LTR 0, __HTML_TAG_DIV 0, __IN_REP_TO 0, __MIME_HTML 0, __M X-PMX-Version: 6.4.9.2830568, Antispam-Engine: 2.7.2.2107409, Antispam-Data: 2021.5.17.170915, AntiVirus-Engine: 5.82.0, AntiVirus-Data: 2021.5.17.5820001 Subject: Re: namd-l: Getting the z coordinate To: namd-l@ks.uiuc.edu, Isaac Asare Kwaku References: From: Pawel Kedzierski Organization: Wroclaw University of Technology Message-id: Date: Mon, 17 May 2021 19:17:31 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 In-reply-to: Content-language: pl-PL X-Proofpoint-ORIG-GUID: OyIj31BjybFeksNXxAf81RvZkaV7Cx0G X-Proofpoint-GUID: OlerfFVoBDvbHD-yvVd09CdUrRRtEvLe X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0SEQpMehcaEQpZRBdtbHwZfXNCc31PbREKWFgXYEZFTEB+RGN7Znw RCnhOF21zZGBIE054GxJoEQp5TBdhHVNeHwVOa1keaREKQ0gXBx4aHBEKQ1kXGBIRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHxJxGR0QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XZVNjQBkbaEBTSGxPQVlkclJrTBIbeFxwQUt8HWlSGm0RClhcFx8EGgQYGBMFGxoE GxsaBB8aBBseHxAbHhofGhEKXlkXchhvRWIRCk1cFxkeEhEKTFoXe2lNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdvRUVkaGATbB1/SxEKQ1oXGx8cBBsdBBsTGQQbHhsRCk JeFxsRCkReFxgRCkJFF2QYZGNZE2ZtYkgBEQpCThdtc2RgSBNOeBsSaBEKQkwXYEZFTEB+RGN7Z nwRCkJsF2NZTUJpekgcHm56EQpCQBdpeGRcBUseaF5mZREKQlgXZ3Nlc0BuYWFMXWIRClpYFxgR CnlDF2hFW3paHWNgfwFfEQpZSxcfExMfEQpwZxdsX3htWV5gf3kaWhAZGhEKcGgXZXtEBWd8Ukd 5Z24QBxkaEQpwaBdgfFhdfhJ5Sx1FXRAHGRoRCnBoF3pfHmhJWG5PE115EBkaEQpwaBdrX25JYF AcbWhhRBAZGhEKcGgXbm9BQE1Pc01uZR0QGRoRCnBrF2l/Um9oAUFpW2gdEBkaEQpwSxdkGmlLH HJ8YBp5QxAZGhEKcGsXek9SSV1EXXJjaV4QGRoRCnBsF2VYR3p4RmxPTUBeEBkaEQpwQxdme1Nz G0l7ckBcARAZGhEKbX4XGhEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=178 phishscore=0 mlxscore=0 lowpriorityscore=0 bulkscore=0 priorityscore=0 suspectscore=0 impostorscore=0 spamscore=0 malwarescore=0 adultscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=2 engine=8.12.0-2104190000 definitions=main-2105170118 domainage_hfrom=5995 X-Spam-Score: 0 X-Spam-OrigSender: pawel.kedzierski@pwr.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Pawel Kedzierski This is a multi-part message in MIME format. --Boundary_(ID_dYbZ/GSlfBaTry5zICaSKg) Content-type: multipart/alternative; boundary="Boundary_(ID_6L0HTNs77+ah3Z+uD7leBg)" --Boundary_(ID_6L0HTNs77+ah3Z+uD7leBg) Content-type: text/plain; charset=utf-8; format=flowed Content-transfer-encoding: 8BIT W dniu 17.05.2021 o 17:59, Isaac Asare Kwaku pisze: > Hello guys, > > This is more of a tcl script problem but I was hoping I could get some > help. I am measuring the center of mass of two different residues of a > protein in VMD. Now I want to find the difference between only the z > coordinates of the center of mass of the residues. The command > "measure center $sel weight mass" gives me the x,y,z coordinates of > the center of mass but I am looking for a way to store just the z > coordinates so I can find the difference between them. I have tried to > assign the value of "measure center $sel weight mass" to a variable as > a list so I use "lindex listname 2" to get the z coordinate. However > the assignment of the output of the "measure" command has proved > futile. How do I get only the z coordinate of the center of mass? > > Regards, > Isaac. Dear Isaac, Likely you have some Tcl syntax mistake. It works for me like this: vmd > set all [atomselect top all] atomselect0 vmd > set cent [measure center $all] 29.005212783813477 17.393484115600586 12.841275215148926 vmd > lindex $cent 2 12.841275215148926 Cheers, Paweł --Boundary_(ID_6L0HTNs77+ah3Z+uD7leBg) Content-type: text/html; charset=utf-8 Content-transfer-encoding: 8BIT
W dniu 17.05.2021 o 17:59, Isaac Asare Kwaku pisze:
Hello guys,

This is more of a tcl script problem but I was hoping I could get some help. I am measuring the center of mass of two different residues of a protein in VMD. Now I want to find the difference between only the z coordinates of the center of mass of the residues. The command "measure center $sel weight mass" gives me the x,y,z coordinates of the center of mass but I am looking for a way to store just the z coordinates so I can find the difference between them. I have tried to assign the value of "measure center $sel weight mass" to a variable as a list so I use "lindex listname 2" to get the z coordinate. However the assignment of the output of the "measure" command has proved futile. How do I get only the z coordinate of the center of mass?

Regards,
Isaac.

Dear Isaac,

Likely you have some Tcl syntax mistake. It works for me like this:

vmd > set all [atomselect top all]
atomselect0
vmd > set cent [measure center $all]
29.005212783813477 17.393484115600586 12.841275215148926
vmd > lindex $cent 2
12.841275215148926

Cheers,

Paweł


  


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From: Isaac Asare Kwaku 
Date: Mon, 17 May 2021 13:21:14 -0400
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Subject: Re: namd-l: Getting the z coordinate
To: Pawel Kedzierski 
Cc: namd-l@ks.uiuc.edu
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Reply-To: namd-l@ks.uiuc.edu, Isaac Asare Kwaku 

--000000000000bee99605c289d2ab
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

Thank you very much! it worked!

On Mon, May 17, 2021 at 1:17 PM Pawel Kedzierski <
pawel.kedzierski@pwr.edu.pl> wrote:

> W dniu 17.05.2021 o 17:59, Isaac Asare Kwaku pisze:
>
> Hello guys,
>
> This is more of a tcl script problem but I was hoping I could get some
> help. I am measuring the center of mass of two different residues of a
> protein in VMD. Now I want to find the difference between only the z
> coordinates of the center of mass of the residues. The command "measure
> center $sel weight mass" gives me the x,y,z coordinates of the center of
> mass but I am looking for a way to store just the z coordinates so I can
> find the difference between them. I have tried to assign the value
> of "measure center $sel weight mass" to a variable as a list so I use
> "lindex listname 2" to get the z coordinate. However the assignment of th=
e
> output of the "measure" command has proved futile. How do I get only the =
z
> coordinate of the center of mass?
>
> Regards,
> Isaac.
>
> Dear Isaac,
>
> Likely you have some Tcl syntax mistake. It works for me like this:
>
> vmd > set all [atomselect top all]
> atomselect0
> vmd > set cent [measure center $all]
> 29.005212783813477 17.393484115600586 12.841275215148926
> vmd > lindex $cent 2
> 12.841275215148926
>
> Cheers,
>
> Pawe=C5=82
>
>

--000000000000bee99605c289d2ab
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

Thank you very much! it worked!

On Mon, May 17, 2021= at 1:17 PM Pawel Kedzierski <pawel.kedzierski@pwr.edu.pl> wrote:
=20 =20 =20
W dniu 17.05.2021 o=C2=A017:59, Isaac Asare Kwaku pisze:
=20
Hello guys,

This is more of a tcl script problem but I was hoping I could get some help. I am measuring the center of mass of two different residues of a protein in VMD. Now I want to find the difference between only the z coordinates of the center of mass of the residues. The command "measure center $sel weigh= t mass" gives me the x,y,z coordinates of the center of mass b= ut I am looking for a way to store just the z coordinates so I can find the difference between them. I have tried to assign the value of=C2=A0"measure center $sel weight mass" to = a variable as a list so I use "lindex listname 2" to get the z coordinate. However the assignment of the output of the "measure" command has proved futile. How do I get only = the z coordinate=C2=A0of the center of mass?

Regards,
Isaac.

Dear Isaac,

Likely you have some Tcl syntax mistake. It works for me like this:

vmd > set all [atomselect top a=
ll]
atomselect0
vmd > set cent [measure center $all]
29.005212783813477 17.393484115600586 12.841275215148926
vmd > lindex $cent 2
12.841275215148926

Cheers,

Pawe=C5=82


  
--000000000000bee99605c289d2ab-- From owner-namd-l@halifax.ks.uiuc.edu Tue May 18 08:42:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14IDgeKb018838; Tue, 18 May 2021 08:42:40 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14IDgeNo018837; Tue, 18 May 2021 08:42:40 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14IDgdaj018832; Tue, 18 May 2021 08:42:39 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14IDgdpD018831; Tue, 18 May 2021 08:42:39 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14IDgM48018823 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000136bc005c29ae1d5" X-Proofpoint-ORIG-GUID: 2fXFItEmWVC6W5yIMP6-I6g93GgMk_-N X-CLX-Response: 1TFkXGR4aEQpMehcZGBIRCllEF3poR1wfbxtYXF5jEQpYWBdoWXhyHl5raGE TehEKeE4XY1Nja3sTWH4aX14RCnlMF2lZAW1lHW1wSWxaEQpDSBcHHxgdEQpDWRcHGBMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsYHXETBhgSdwYbGBsGGRpCGwYaBh8aBhsYGXEbHBAadwYaBgcfG gYaBgccGgYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThcYTHJsY15vR318 aRx9H1NjZ3ocB2McTRMZbU1nQXUHZBEKWFwXHwQaBBgYEwUbGgQbGhoEHhIEGBkQGx4aHxoRCl5 ZF3IYfUBwEQpNXBcbGhoRCkxaF3xpTWtNEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2 xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx0bEQpCXhcbEQpEXhcYEQpCXBcbE QpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF29PeEMdZl5NY0JOEQpC ThdjU2NrexNYfhpfXhEKQkwXaFl4ch5ea2hhE3oRCkJsF2FfQEZGf11LaGRGEQpCQBdkfEZjeVx QGwUbTBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnlDF3ptX0tgHm1IAUMYEQpZSxcTHh saEQpwaBdvSQVyGBlOaFx+WBAeEhEKcGgXbkhPekFZBUNAcH0QHhIRCnBoF29eRkxiclJ8fGtTE BkaEQpwaBdgYBtZWWVTTFgdXBAZGhEKcGgXbXNBGxlvTURjeE8QGRoRCnB9F2NgaRoTemtLfhNb EBkaEQpwfRdjZlxoWxMTE05ITxAZGhEKcH0XZRwZW2t+f11AXHAQGRoRCnB/F2JuaElNYFJOEh1 PEBsaHhEKcF8XYxtOf0JlZmAcG0IQGRoRCnB/F21AZlxlU2xAHW9LEBISEQpwXxduGksFYVhQGF 9DYxAZGhEKcH8XZR9fWkN+QHlBU0AQGRoRCnBsF2R/aGlhU2JoQht/EBkaEQptfhcbEQpYTRdLE SA= X-Proofpoint-GUID: 2fXFItEmWVC6W5yIMP6-I6g93GgMk_-N X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=328 clxscore=340 impostorscore=0 mlxlogscore=999 spamscore=0 mlxscore=0 malwarescore=0 suspectscore=0 adultscore=0 bulkscore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105180096 domainage_hfrom=9410 X-Spam-Score: 0 X-Spam-OrigSender: kushalrajroyfc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kushal Raj Roy --000000000000136bc005c29ae1d5 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thank you Professor for such opportunities. I'm interested to join in your laboratory if my previous research experiences in MD simulation matches with your requirements. I am eagerly waiting for your response. Kind regards, Kushal Raj Roy MSc Biochemistry Fergusson College (Autonomous) Pune, India. On Thu, 29 Apr 2021 at 07:42, Ivaylo Nikolaev Ivanov wrote: > Dear colleagues, > > I hope this email finds you well! > > I have an open postdoctoral position in my group. The project is in > molecular modeling of protein-nucleic acid assemblies. Details regarding > the position and how to apply are downloadable from my group website at: > > > https://urldefense.com/v3/__https://ivanovgroup.files.wordpress.com/2021/= 04/postdoctoral-position-2021.pdf__;!!DZ3fjg!tMxhNvO_wCzDWA8GhSxTCDkPr9DzYY= Z060t3sZMdFvTATnjMI8er3YLMg_ET4fclIg$=20 > > Please share the information with suitable applicants or Ph.D. students > nearing graduation. An ideal candidate will be someone with expertise in > molecular dynamics, advanced simulation/analysis techniques and some > experience with coding and scripting. > > Thank you very much in advance. > > Best wishes, > Ivaylo > > PS I am also looking for motivated Ph.D. students to join my group. > Interested candidates are welcome to contact me directly by email and > explore the GSU chemistry graduate program at > https://urldefense.com/v3/__http://chemistry.gsu.edu/graduate__;!!DZ3fjg!= tMxhNvO_wCzDWA8GhSxTCDkPr9DzYYZ060t3sZMdFvTATnjMI8er3YLMg_HkP6COGg$ . > > Dr. Ivaylo Ivanov > Professor, Georgia State University > P.O. Box 3965, Atlanta, Georgia 30302 > Phone: (404) 413-5529 > https://urldefense.com/v3/__https://ivanov-group.org/__;!!DZ3fjg!tMxhNvO_= wCzDWA8GhSxTCDkPr9DzYYZ060t3sZMdFvTATnjMI8er3YLMg_HFPij7Ew$=20 > --000000000000136bc005c29ae1d5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thank you Professor for such oppor= tunities. I'm interested to join in your laboratory if my previous rese= arch experiences in MD simulation matches with your requirements. I am eage= rly waiting for your response.=C2=A0

Kind regards,

Kus= hal Raj Roy
MSc Biochemistry=C2=A0
Fergusson College (Autonomous)
Pune, India.
On Thu, 29 Apr 2021 at 07:42, Iva= ylo Nikolaev Ivanov <iivanov@gsu.edu> wrote:
Dear colleagues,

I hope this email finds you well!

I have an open=C2=A0postdoctoral=C2=A0position=C2= =A0in my group. The project is in molecular modeling of protein-nucleic aci= d assemblies. Details regarding the=C2=A0position=C2=A0and how to apply are downloadable from my group website at:


Please share the information with suitable applicants or Ph.D. students nea= ring graduation. An ideal candidate will be someone with expertise in molec= ular dynamics, advanced simulation/analysis techniques and some experience = with coding and scripting.

Thank you very much in advance.

Best wishes,
Ivaylo

PS I am also=C2=A0looking for motivated Ph.D. students to join my group. In= terested candidates are welcome to contact me directly by email and explore= the GSU chemistry graduate program at http://chemistry.gsu.edu/gradua= te.

Dr. Ivaylo Ivanov
Professor, Georgia State University
P.O. Box 3965, Atlanta, Georgia 30302=C2=A0
Phone: (404) 413-5529=C2=A0
https://ivanov-group.org/
=
--000000000000136bc005c29ae1d5-- From owner-namd-l@halifax.ks.uiuc.edu Tue May 18 14:27:14 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14IJREsh024445; Tue, 18 May 2021 14:27:14 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14IJREYN024444; Tue, 18 May 2021 14:27:14 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14IJRDAg024440; Tue, 18 May 2021 14:27:13 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14IJRDnd024439; Tue, 18 May 2021 14:27:13 -0500 (CDT) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14IJR5jM024424 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 18 May 2021 14:27:07 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_96B891C7-5A76-4873-B159-DB497C754E2F" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: namd-l: VMD and NAMD surveys will be coming soon Message-Id: <95CC7CC3-E3E1-492F-9CB2-C8D4300532B8@ks.uiuc.edu> Date: Tue, 18 May 2021 14:26:59 -0500 Cc: vmdsurvey@ks.uiuc.edu, namdsurvey@ks.uiuc.edu To: NAMD list X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_96B891C7-5A76-4873-B159-DB497C754E2F Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Dear NAMD-L, Many of you that have registered and downloaded VMD and NAMD, or that are members of their respective mailing lists, should expect to receive an invitation for a survey for one or both of VMD and NAMD. The current funding for NAMD and VMD development ends in the next year, and the funding mechanism that has historically supported NAMD and VMD development is no longer available. We're applying to a new NIH funding mechanism, and we need input from our user community to demonstrate the number and diversity of our users, the types of research being served by the software programs we develop, and the development areas that are most responsive to users' needs. Due to limits on the total number of survey responses that we're allowed to collect per month using commercial survey tools, not every VMD or NAMD user will receive a survey invitation (more than 75,000 unique users have downloaded VMD in the past year, but we're only permitted to collect 5,000 survery responses per month). If you receive a survey invitation, we ask that you take the time to fill it out as completely as possible and submit it (be sure to press the "Done" button at the bottom). We expect that most users should be able to complete the survey in less than 5 minutes. All of the survey questions are visible on a single page, so it should be easy to use. The surveys for VMD and NAMD are distinct, so if you happen to receive an invitation for both programs, we do ask that you fill both of them out. If by chance you receive more than one survey invitation for the same software -- as a result of using multiple email addresses in recent years, or through some mistake on our side -- please feel free to disregard any duplicative invitations once you've submitted your survey. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ --Apple-Mail=_96B891C7-5A76-4873-B159-DB497C754E2F Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = NAMD-L,

Many of you = that have registered and downloaded VMD and NAMD,
or that = are members of their respective mailing lists, should
expect= to receive an invitation for a survey for one or
both of = VMD and NAMD.

The current funding for NAMD = and VMD development ends in
the next year, and the funding = mechanism that has historically 
supported NAMD and = VMD development is no longer available. 
We're = applying to a new NIH funding mechanism, and we need
input = from our user community to demonstrate the number and 
diversity of our users, the types of research being = served 
by the software programs we develop, and the = development areas
that are most responsive to users' = needs. 

Due to limits on the total = number of survey responses that we're 
allowed to = collect per month using commercial survey tools, 
not = every VMD or NAMD user will receive a survey invitation
(more than 75,000 unique users have downloaded VMD in the = past year, 
but we're only permitted to collect 5,000 = survery responses per month).

If you = receive a survey invitation, we ask that you take the
time = to fill it out as completely as possible and submit it
(be = sure to press the "Done" button at the bottom).  We expect
that most users should be able to complete the survey in = less
than 5 minutes.  All of the survey questions are = visible on a 
single page, so it should be easy to = use.

The surveys for VMD and NAMD are = distinct, so if you happen to
receive an invitation for = both programs, we do ask that you 
fill both of them = out.  

If by chance you receive more = than one survey invitation for the 
same software -- = as a result of using multiple email addresses in 
recent years, or through some mistake on our side -- please = feel
free to disregard any duplicative invitations once = you've submitted
your survey.

Best regards,
Dave

=
--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801

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boundary="000000000000e3167c05c2a6b4a6" X-Proofpoint-ORIG-GUID: qqsGk9Fem53H0Sm8EQzVH4OC4goVppVM X-CLX-Shades: MLX X-Proofpoint-GUID: qqsGk9Fem53H0Sm8EQzVH4OC4goVppVM X-CLX-Response: 1TFkXGxwdEQpMehcbHB8RCllEF2YaHkZ+fEBlSWVIEQpYWBdrE31cRXBIfRJ IbREKeE4XZEdZZnNmX3tASxwRCnlMF2FmX1BCSXhuWRNHEQpDSBcHGxsfEQpDWRcHGxodEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRccHXEbBhsZHncGGx8cBhoGGgYHGBwGGnEaEBp3BhoGGgYaBgcZG gYaBhpxGhAadwYaEQpZXhdoY3kRCklGF19DX0l1QkVZXk9OEQpDThdbW1ltQRNsT0cfGWIaeUcS b3tQfGIeZWkeTUV8Wlp8ZxEKWFwXHwQaBBgYEwUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3IYQxN jEQpNXBcHHxkRCkxaF3hpTWtrEQpFWRdvEQpMXxd6BQUFBQUFBQUFQxEKQk8XZX5cWVtbR2NTYW wRCkNaFxgaEwQSHwQYGxIEHxgRCkJeFxsRCkJFF29uH21SHW9maAFQEQpCThdkR1lmc2Zfe0BLH BEKQkwXaxN9XEVwSH0SSG0RCkJsF2MTHxlwUmJuTWcTEQpCQBdieEdDX0J6eVtERxEKQlgXZ3Nl c0BuYWFMXWIRCk1eFwcbEQpaWBcbEQp5QxdhXlBOY0gfAWt6GBEKcGgXaR5JWnhfGn1lTH8QBxk aEQpwaBdiZlhaXUtoHHNdGRAHGRoRCnBoF2FzXl1ESVhrXhxCEAcZGhEKcGgXYhtAQXBmUlxAQF kQBxkaEQpwaBdrR1BMTUlHHFl+WRAHGRoRCnBsF2AFT3lMcgVgZkhsEAcZGhEKbX4XBxsRClhNF 0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=167 spamscore=0 priorityscore=165 phishscore=0 malwarescore=0 adultscore=0 suspectscore=0 impostorscore=0 mlxlogscore=602 mlxscore=0 lowpriorityscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105190025 X-Spam-Score: 0 X-Spam-OrigSender: sheyla.carmen@unmsm.edu.pe X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, SHEYLA ESTHER CARMEN SIFUENTES --000000000000e3167c05c2a6b4a6 Content-Type: text/plain; charset="UTF-8" Hi guys I have made a dynamic of a membrane protein, however almost all the simulation goes to the end of the box, I have already tried to center it with the pcb commands, however it is not centered, I think it is a problem of my simulation, I do not know if at all In case I have to change parameters, it is a protein in a membrane only with POPC, I gave it 10 ns of equilibration, I do not know if in any case I better add other lipids to the membrane, it should equilibrate it longer, or there is some kind of restriction that can be added in these cases, I hope you can help me. Regards Sheyla --000000000000e3167c05c2a6b4a6 Content-Type: text/html; charset="UTF-8"
Hi guys
I have made a dynamic of a membrane protein, however almost all the simulation goes to the end of the box, I have already tried to center it with the pcb commands, however it is not centered, I think it is a problem of my simulation, I do not know if at all In case I have to change parameters, it is a protein in a membrane only with POPC, I gave it 10 ns of equilibration, I do not know if in any case I better add other lipids to the membrane, it should equilibrate it longer, or there is some kind of restriction that can be added in these cases, I hope you can help me.
Regards
Sheyla
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charset="UTF-8" Greetings, When I try to minimize my system composed of a protein complex solvated in OPC water (Amber parameters - and I set watermodel to tip4 and rigidatoms in the config file), I get 'Nan' values in the output when running on NAMD3 CUDA version. I do not get this issue when running the system on NAMD2.14 and the system gets minimized successfully. Any suggestions? Kindest regards, Sara --0000000000002539c205c2bb543e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Greetings,

When I try to minimize my sy= stem composed of a protein complex solvated in OPC water (Amber parameters = - and I set watermodel to tip4 and rigidatoms in the config file), I get &#= 39;Nan' values in the output when running on NAMD3 CUDA version.
<= div>I do not get this issue when running the system on NAMD2.14 and the sys= tem gets minimized successfully.

Any=C2=A0suggesti= ons?

Kindest regards,
Sara=

--0000000000002539c205c2bb543e-- From owner-namd-l@halifax.ks.uiuc.edu Fri May 21 00:43:46 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14L5hjfZ003939; Fri, 21 May 2021 00:43:45 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14L5hj9q003938; Fri, 21 May 2021 00:43:45 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14L5hj9O003934; Fri, 21 May 2021 00:43:45 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14L5hi94003933; Fri, 21 May 2021 00:43:44 -0500 (CDT) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14L5hdRw003925 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Fri, 21 May 2021 00:43:40 -0500 (CDT) From: David Hardy Content-Type: multipart/alternative; boundary="Apple-Mail=_B52BAA50-975C-4EB0-95DC-EE27D4A6D19F" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: Cannot run OPC solvated system on NAMD3 Date: Fri, 21 May 2021 00:43:32 -0500 References: To: NAMD list , Sara Omar In-Reply-To: Message-Id: X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_B52BAA50-975C-4EB0-95DC-EE27D4A6D19F Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 [Resending my reply to Sara from earlier today so that it is received by = namd-l =E2=80=94 had unintentionally sent from my non-list-subscribed = Illinois.edu address.] Hi Sara, I expect that you are talking about using the GPU-resident mode of NAMD = 3, with =E2=80=9CCUDASOAintegrate on=E2=80=9D? The constraint routines = and dummy atom site needed for the TIP4P water model are not yet = supported on the GPU. We do have plans to support as many features as we = can for GPU-resident NAMD, including TIP4P water, but it will take time = for us to do so. I do appreciate you pointing out this issue to us -- one would hope that = NAMD would immediately terminate with an error message rather than = compute invalid results. Best regards, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On May 19, 2021, at 11:24 PM, Sara Omar = wrote: >=20 > Greetings, >=20 > When I try to minimize my system composed of a protein complex = solvated in OPC water (Amber parameters - and I set watermodel to tip4 = and rigidatoms in the config file), I get 'Nan' values in the output = when running on NAMD3 CUDA version. > I do not get this issue when running the system on NAMD2.14 and the = system gets minimized successfully. >=20 > Any suggestions? >=20 > Kindest regards, > Sara >=20 --Apple-Mail=_B52BAA50-975C-4EB0-95DC-EE27D4A6D19F Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 [Resending my reply to Sara from earlier today so that it is = received by namd-l =E2=80=94 had unintentionally sent from my = non-list-subscribed Illinois.edu address.]


Hi = Sara,

I expect that = you are talking about using the GPU-resident mode of NAMD 3, with = =E2=80=9CCUDASOAintegrate on=E2=80=9D? The constraint routines and dummy = atom site needed for the TIP4P water model are not yet supported on the = GPU. We do have plans to support as many features as we can for = GPU-resident NAMD, including TIP4P water, but it will take time for us = to do so.

I do = appreciate you pointing out this issue to us -- one would hope that NAMD = would immediately terminate with an error message rather than compute = invalid results.

Best regards,
Dave

--
David J. = Hardy, Ph.D.
Beckman = Institute
University of = Illinois at Urbana-Champaign
405 N. = Mathews Ave., Urbana, IL 61801


On May 19, 2021, at 11:24 PM, Sara Omar = <sara.ibrahim.omar@gmail.com> wrote:

Greetings,

When I try to minimize my system composed of a protein = complex solvated in OPC water (Amber parameters - and I set watermodel = to tip4 and rigidatoms in the config file), I get 'Nan' values in the = output when running on NAMD3 CUDA version.
I do not = get this issue when running the system on NAMD2.14 and the system gets = minimized successfully.

Any suggestions?

Kindest = regards,
Sara


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To: KS UIUC Message-ID: <70F2FDCF-9A8C-4D9C-A1A3-C5AA3A809627@gmail.com> Thread-Topic: Tclforces Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3704473514_358734482" X-Proofpoint-ORIG-GUID: jYdP8i7aF_lt3O0lR0vc5u4UYuBE1RVu X-CLX-Response: 1TFkXGxIbEQpMehcZGRkRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGRIbEQpDWRcHHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscG3EeGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdAc056EkMdS2x1Rl4ZZRpGeBpcSR9fHn9zX2hvG3h8XxEKWFwXHwQaBBgZGgUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3IZTWNzEQpNXBcZGBoRCkxaF2hpa01rEQpMRhdva2tra2s RCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBBsSGBEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja3sTW H4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXYmBiSFBuHHpFRBsRCkJY F2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdiYGJIUG4cekVEGxEKWUsXEx4bHhEKcGgXaEN4TV5TTB1 iaUwQGRoRCnBoF2AScAFnXnJkc0RcEBkaEQpwaBdlWkdBfhNlH35BbhAZGhEKcGgXY31LbFNObE RCfGEQGRoRCnBoF2Z9e2lta2RTRGkTEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEwXZ35QfU1rU E9PRmIQGRoRCnBDF2ROZWEdH3lDWBoYEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: jYdP8i7aF_lt3O0lR0vc5u4UYuBE1RVu X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 phishscore=0 clxscore=181 impostorscore=0 spamscore=0 lowpriorityscore=0 adultscore=0 bulkscore=0 priorityscore=333 suspectscore=0 mlxlogscore=740 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105220003 domainage_hfrom=9414 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3704473514_358734482 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear user, =20 I am simulating a membrane protein that has a long lateral displacement, wh= ich I have not been able to correct with pbctool, so I would like to do the = simulation again, trying to be able to use a circular barrier of force to ke= ep the protein in its center of mass with a freedom of move 5 Angstroms on t= he XY axis, without compromising its secondary structure or conformational c= hanges. Could you please help me solve this with tcl? =20 =20 I leave my script below. =20 =20 =C2=A0=C2=A0 proc calcforces {} { =C2=A0=C2=A0=C2=A0 global grp xc0 yc0 zc0 =C2=A0 =C2=A0=C2=A0global kforce =C2=A0=C2=A0=C2=A0 global freq fout ofile =20 =C2=A0=C2=A0=C2=A0 loadcoords coords =20 =C2=A0=C2=A0=C2=A0 set rc $coords($grp) =C2=A0=C2=A0=C2=A0 set xc [lindex $rc 0] =C2=A0=C2=A0=C2=A0 set yc [lindex $rc 1] =C2=A0=C2=A0=C2=A0 set zc [lindex $rc 2] =20 =C2=A0=C2=A0=C2=A0 set diffx [expr {$xc0 - $xc}] =C2=A0=C2=A0=C2=A0 set diffy [expr {$yc0 - $yc}] =C2=A0=C2=A0=C2=A0 #set diffz [expr {$zc0 - $zc}] =C2=A0=C2=A0=C2=A0 set f {} =C2=A0=C2=A0=C2=A0 set fx [expr {$kforce*$diffx}] =C2=A0=C2=A0=C2=A0 set fy [expr {$kforce*$diffy}] =C2=A0=C2=A0=C2=A0 #set fz [expr {$kforce*$diffz}] =C2=A0=C2=A0=C2=A0 lappend f $fx $fy ; #$fz =20 =C2=A0=C2=A0=C2=A0 addforce $grp $f =20 =C2=A0=C2=A0=C2=A0 addenergy [expr {0.5*$kforce*$diffx*$diffx}] =C2=A0=C2=A0=C2=A0 addenergy [expr {0.5*$kforce*$diffy*$diffy}] =C2=A0=C2=A0=C2=A0 #addenergy [expr {0.5*$kforce*$diffz*$diffz}] =20 #=C2=A0=C2=A0=C2=A0 set currstep [getstep] #=C2=A0=C2=A0=C2=A0 if {[expr {$currstep % $freq}] =3D=3D 0} { #=C2=A0=C2=A0=C2=A0 set fout [open $ofile a+] #=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 puts $fout [format "%f %f %f %f" $currstep $xc $yc $zc] #=C2=A0=C2=A0=C2=A0 close $fout #=C2=A0=C2=A0=C2=A0 } =20 =C2=A0=C2=A0=C2=A0 return =C2=A0=C2=A0=C2=A0 } } --B_3704473514_358734482 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear user,

 

I am simulating a membrane protein tha= t has a long lateral displacement, which I have not been able to correct wit= h pbctool, so I would like to do the simulation again, trying to be able to = use a circular barrier of force to keep the protein in its center of mass wi= th a freedom of move 5 Angstroms on the XY axis, without compromising its se= condary structure or conformational changes. Could you please help me solve = this with tcl?

 

I leave my script bel= ow.

<= o:p> 

 

=C2=A0=C2=A0 proc calcforces {} {

=C2=A0=C2=A0=C2=A0 global grp xc0 yc0 zc0

=C2=A0 =C2=A0=C2=A0global kforce

=C2=A0=C2=A0=C2=A0 global freq fout ofile=

 <= /o:p>

= =C2=A0=C2=A0=C2=A0 loadcoords coords

 

=C2=A0=C2=A0=C2=A0 set rc $coords($grp)

=C2= =A0=C2=A0=C2=A0 set xc [lindex $rc 0]

=C2=A0=C2=A0=C2=A0 set yc [lindex $rc 1]

=C2=A0=C2=A0=C2=A0 se= t zc [lindex $rc 2]

 

=C2=A0=C2=A0=C2=A0 set diffx [expr {$xc0 - $xc}]

=C2=A0=C2=A0=C2=A0 set diffy [expr {$yc0 - $yc}]

=C2=A0=C2=A0=C2=A0 #set diffz [expr {$zc0 -= $zc}]

=C2=A0=C2=A0=C2=A0 set f {}

=C2=A0=C2=A0=C2=A0 set fx [expr {$kforce*$diffx}]<= /o:p>

= =C2=A0=C2=A0=C2=A0 set fy [expr {$kforce*$diffy}]

=C2=A0=C2=A0=C2=A0 #set fz [expr {$kforce*$di= ffz}]

=C2=A0=C2=A0=C2=A0 lappend f $fx $fy ; #$fz

 

=

=C2=A0=C2=A0=C2=A0 addforce = $grp $f

 

=C2=A0=C2=A0=C2=A0 addenergy [expr {0.5*$kforce*$diffx*$diffx}]=

=C2=A0=C2=A0=C2=A0 addenergy [expr {0.5*$kforce*$diffy*$diffy}]<= /p>

=C2=A0=C2=A0=C2=A0 #adden= ergy [expr {0.5*$kforce*$diffz*$diffz}]

 

#=C2=A0=C2=A0=C2=A0 set currste= p [getstep]

#=C2=A0=C2=A0=C2=A0 if {[expr {$currstep % $freq}] =3D=3D 0} {

#=C2=A0=C2=A0=C2=A0= set fout [open $ofile a+]

#=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 puts $fout [format "%f = %f %f %f" $currstep $xc $yc $zc]

#=C2=A0=C2=A0=C2=A0 close $fout

#=C2=A0=C2=A0=C2=A0 = }

 

=C2=A0=C2=A0=C2=A0 return

=C2=A0=C2=A0=C2=A0 }

}

<= /div> --B_3704473514_358734482-- From owner-namd-l@halifax.ks.uiuc.edu Sun May 23 12:15:05 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14NHF5Ok003832; Sun, 23 May 2021 12:15:05 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14NHF5oV003831; Sun, 23 May 2021 12:15:05 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14NHF48h003827; Sun, 23 May 2021 12:15:04 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14NHF4rj003826; Sun, 23 May 2021 12:15:04 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14NHEmEZ003813 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Sun, 23 May 2021 22:44:39 +0530 (IST) Received: from [47.9.156.82] by webmail.iitd.ac.in with HTTP (HTTP/1.1 POST); Sun, 23 May 2021 22:44:39 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit Date: Sun, 23 May 2021 22:44:39 +0530 From: Nadira Khatoon To: namd-l@ks.uiuc.edu Subject: namd-l: Regarding Parameter file User-Agent: Roundcube Webmail/1.4.2 Message-ID: X-Sender: Nadira.Khatoon@bioschool.iitd.ac.in X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBMaEQpMehcaEQpZRBdhfVhhHG5NBVtobhEKWFgXZmAaAUUfGhtkTkw RCnhOF2BBYlBvWkFvfmVSEQp5TBd6S3hvRB5DWkxTZhEKQ0gXBxscExEKQ1kXGxMRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxwdcRsGGxkedwYbHRsGGgYaBh0YBhkacRsQGncGGgYHHxoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF11mbxtLQXgcS1BNe0lpbVxQdR5y Uml4eGlFa197cG9tEQpYXBcfBBoEGBkaBRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXch5uY0MRCk1 cFxseHxEKTFoXbGlNa2sRCkxGF29ra2traxEKQk8XY0VCaQF8XmUSWBkRCkNaFxsaGQQYHQQTBB 4fEQpCXhcbEQpCXBcbEQpCSxdjYWxcck15WEIZHxEKQkkXYEFiUG9aQW9+ZVIRCkJFF24Ye1twT BJDSVlhEQpCThdgQWJQb1pBb35lUhEKQkwXZmAaAUUfGhtkTkwRCkJsF2BJe2RJRWJnX39oEQpC QBdoZX4Fe2BmSH5LWREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxsRCnlDF2ROY0l6cGJYf0F LEQpZSxccHB8TEQpwaBdpEhwbT0UFbnoFchAZGhEKcGgXaU1EZBxDS28cYlMQGRoRCnBsF2VmUG Z5ZkJ6SUAYEBkaEQpwQxdsYUlpeRN7R2VnHBAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: wLE1akR6azgQcCGvz_4XxCRRCoAuQZEG X-Proofpoint-GUID: wLE1akR6azgQcCGvz_4XxCRRCoAuQZEG X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 priorityscore=0 malwarescore=0 mlxscore=0 adultscore=0 mlxlogscore=636 spamscore=0 suspectscore=0 impostorscore=0 clxscore=290 bulkscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105230129 domainage_hfrom=6659 X-Spam-Score: 0 X-Spam-OrigSender: Nadira.Khatoon@bioschool.iitd.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nadira Khatoon Hi, I am new at learning NAMD for simulating membrane embedded proteins. Will use of different versions of Charmm parameter files cause errors in the simulation? Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE ON3", is coming, but there are no ON3 atoms in both pdb and psf files. I am unable to find a solution to this. Could you please help me with this? For running this simulation, I have used parameter files as mentioned below: parameters par_all36_lipid.prm parameters par_all36m_prot.prm parameters toppar_water_ions.str From owner-namd-l@halifax.ks.uiuc.edu Mon May 24 03:51:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14O8peYF011825; Mon, 24 May 2021 03:51:40 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14O8pe7X011824; Mon, 24 May 2021 03:51:40 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14O8pciv011818; Mon, 24 May 2021 03:51:38 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14O8pcdY011817; Mon, 24 May 2021 03:51:38 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14O8pSDx011806 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 24 May 2021 03:51:29 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14O8obr6001325 for ; Mon, 24 May 2021 08:51:23 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0a-00007101.pphosted.com with ESMTP id 38prf0w3ay-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 24 May 2021 08:51:22 +0000 Received: from [IPv6:2a02:810c:300:6724:38e1:15f3:6d42:6653] ([IPv6:2a02:810c:300:6724:38e1:15f3:6d42:6653]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 14O8p5Lt119756 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 24 May 2021 10:51:11 +0200 Subject: Re: namd-l: Regarding Parameter file To: namd-l@ks.uiuc.edu, Nadira Khatoon References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <1e21c848-bd49-8dd2-1eae-44b2f74504eb@physik.uni-kl.de> Date: Mon, 24 May 2021 10:51:05 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.10.2 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: de-DE X-Spam-Status: No, hits=0, tests=HELO_NO_DOMAIN=0.001,NICE_REPLY_A=-0.001 X-Spam-Score: (0) X-Spam-Flag: NO X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwbEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsSGBEKQ1kXEhMRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHhtxHxoQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XHlMHenJGZhJpckEdfhxme3VZXE17fHpFRkFvemVEbU4RClhcFx8EGgQYGRoFGxoE GxoaBB4SBBgYEBseGh8aEQpeWRdyHnsYRxEKTVwXGx8eEQpMWhd4aU1NTREKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2xfbGZfcExLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGBoRCk JeFxsRCkReFxgRCkJFF2wdWHJFHxxHSQVuEQpCThdkGkluenp4GmR9XBEKQkwXYGAbUhkdGBpSc gURCkJsF2ZrYmQYWWJtSH5sEQpCQBdlSRlOUn1HblBdXREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsR ClpYFxgRCnlDF2x+TFtbHVsfQVNeEQpwaBdkbXBDc2VPW3lNQRAZGhEKcGgXa1McYxl5XGsbRx8 QGRoRCnBoF2RrWlpEbmAbH3tfEBkaEQpwaBdsYmUBGElJH2NgcxAZGhEKcGgXYXpDTBhPSHgSfH IQGRoRCnBsF3ofeHlveExDX3BEEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 4y-PXlL8CXk7T6LQ_svgQVPolkEPOnGd X-Proofpoint-GUID: 4y-PXlL8CXk7T6LQ_svgQVPolkEPOnGd X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 priorityscore=0 malwarescore=0 mlxscore=0 adultscore=0 mlxlogscore=983 spamscore=0 suspectscore=0 impostorscore=0 clxscore=161 bulkscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105240068 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Hi,     ON3 is an atom type from par_all36_na.prm     Inside toppar_water_ions.str you only need to comment out any NBFIXes Lines where "ON3" occurs; may happen for more atom types but should be solvable the same way. Cheers René On 5/23/2021 7:14 PM, Nadira Khatoon wrote: > Hi, > I am new at learning NAMD for simulating membrane embedded proteins. > Will use of different versions of Charmm parameter files cause errors > in the simulation? > Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR > ATOM TYPE ON3", is coming, but there are no ON3 atoms in both pdb and > psf files. I am unable to find a solution to this. Could you please > help me with this? > For running this simulation, I have used parameter files as mentioned > below: > parameters par_all36_lipid.prm > parameters par_all36m_prot.prm > parameters toppar_water_ions.str > -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany From owner-namd-l@halifax.ks.uiuc.edu Mon May 24 09:27:10 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14OERAiK016062; Mon, 24 May 2021 09:27:10 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14OERAm5016061; Mon, 24 May 2021 09:27:10 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14OER9Qp016056; Mon, 24 May 2021 09:27:09 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14OER90O016055; Mon, 24 May 2021 09:27:09 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14OEQx8n016048 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Mon, 24 May 2021 19:56:49 +0530 (IST) Received: from [47.8.75.160] by webmail.iitd.ac.in with HTTP (HTTP/1.1 POST); Mon, 24 May 2021 19:56:49 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 24 May 2021 19:56:49 +0530 From: Nadira Khatoon To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= Subject: Re: namd-l: Regarding Parameter file In-Reply-To: <1e21c848-bd49-8dd2-1eae-44b2f74504eb@physik.uni-kl.de> References: <1e21c848-bd49-8dd2-1eae-44b2f74504eb@physik.uni-kl.de> User-Agent: Roundcube Webmail/1.4.2 Message-ID: <6575479beed3ebb9943f1a59c06663ef@bioschool.iitd.ac.in> X-Sender: Nadira.Khatoon@bioschool.iitd.ac.in X-CLX-Response: 1TFkXGxsaEQpMehcaEQpZRBdhfVhhHG5NBVtobhEKWFgXZmAaAUUfGhtkTkw RCnhOF2BBYlBvWkFvfmVSEQp5TBd6S3hvRB5DWkxTZhEKQ0gXBxsYEhEKQ1kXExoRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYTGnEdEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCRVleT 04RCkNOF0hOeBxjHx1JHllOB1NGHWVfQ18cUnVbcEMbEnNMYXhEEQpYXBcfBBoEGBkaBRsaBBsb GgQfGgQbHh8QGx4aHxoRCl5ZF3IefFJkEQpNXBcZHB8RCkxaF3hpTWtrEQpFWRdvaxEKTF8XegU FBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XY0VCaQF8XmUSWBkRCkNaFxsaGQQYHQQTBB4fEQpCXh cbEQpEXhcYEQpCXBcbEQpCSxdjYWxcck15WEIZHxEKQkkXYEFiUG9aQW9+ZVIRCkJFF24Ye1twT BJDSVlhEQpCThdgQWJQb1pBb35lUhEKQkwXZmAaAUUfGhtkTkwRCkJsF2BJe2RJRWJnX39oEQpC QBdlSRlOUn1HblBdXREKQlgXZ3Nlc0BuYWFMXWIRClpYFxsRCnlDF2x+TFtbHVsfQVNeEQpZSxc cHBwaEQpwZxdgGUZFe05HGW1cRRAZGhEKcGgXYxJkGVJ8ZF8cQWQQGRoRCnBoF2RrWlpEbmAbH3 tfEBwaEQpwaBdhY0IbHXJLQBhGXxAZGhEKcGgXaRIcG09FBW56BXIQGRoRCnBoF2F6Q0wYT0h4E nxyEBwaEQpwZxdpQ25QAVlzRwEeUxAZGhEKcGcXblhdfU5mQgUeS0wQGRoRCnBsF2VmUGZ5ZkJ6 SUAYEBkaEQpwQxdhaGZpaRNzX08ZSBAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: bdR6I57c4sd-yl7Ouiu6x_qZi18YfKRn X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: bdR6I57c4sd-yl7Ouiu6x_qZi18YfKRn X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 spamscore=0 clxscore=110 priorityscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 malwarescore=0 bulkscore=0 phishscore=0 mlxscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105240091 domainage_hfrom=6660 X-Spam-Score: 0 X-Spam-OrigSender: Nadira.Khatoon@bioschool.iitd.ac.in X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 14OER08m016049 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nadira Khatoon Thanks for the help René. Your suggestion solved the issue. However, now I am getting a new error stating, "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CTL2 OSL PL OSL (ATOMS 17 23 20 24)". This gets solved if I use toppar_all36_lipid_sphingo.str as one of my parameter file in addition to the par_all36_lipid.prm , par_all36m_prot.prm, and toppar_water_ions.str. I am unable to understand the reason behind it. Will unnecessary parameter file affect simulation results? -------- Original Message -------- Subject: Re: namd-l: Regarding Parameter file Date: 24.05.2021 14:21 From: René Hafner TUK To: namd-l@ks.uiuc.edu, Nadira Khatoon Hi,     ON3 is an atom type from par_all36_na.prm     Inside toppar_water_ions.str you only need to comment out any NBFIXes Lines where "ON3" occurs; may happen for more atom types but should be solvable the same way. Cheers René On 5/23/2021 7:14 PM, Nadira Khatoon wrote: > Hi, > I am new at learning NAMD for simulating membrane embedded proteins. > Will use of different versions of Charmm parameter files cause errors > in the simulation? > Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM > TYPE ON3", is coming, but there are no ON3 atoms in both pdb and psf > files. I am unable to find a solution to this. Could you please help me > with this? > For running this simulation, I have used parameter files as mentioned > below: > parameters par_all36_lipid.prm > parameters par_all36m_prot.prm > parameters toppar_water_ions.str > From owner-namd-l@halifax.ks.uiuc.edu Mon May 24 09:51:33 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14OEpX05017948; Mon, 24 May 2021 09:51:33 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14OEpXvk017947; Mon, 24 May 2021 09:51:33 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14OEpWTq017943; Mon, 24 May 2021 09:51:32 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14OEpWBq017942; Mon, 24 May 2021 09:51:32 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14OEpOYg017928 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 24 May 2021 09:51:25 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14OEn3BX029789 for ; Mon, 24 May 2021 14:51:24 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0a-00007101.pphosted.com with ESMTP id 38prf0yyw0-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 24 May 2021 14:51:23 +0000 Received: from [IPv6:2a02:810c:300:6724:f538:244c:e679:8f5e] ([IPv6:2a02:810c:300:6724:f538:244c:e679:8f5e]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 14OEpEF2070956 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 24 May 2021 16:51:15 +0200 Subject: Re: namd-l: Regarding Parameter file To: Nadira Khatoon , namd-l@ks.uiuc.edu References: <1e21c848-bd49-8dd2-1eae-44b2f74504eb@physik.uni-kl.de> <6575479beed3ebb9943f1a59c06663ef@bioschool.iitd.ac.in> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <05d52e07-c61b-6e17-c62a-dc35f3276a74@physik.uni-kl.de> Date: Mon, 24 May 2021 16:51:14 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.10.2 In-Reply-To: <6575479beed3ebb9943f1a59c06663ef@bioschool.iitd.ac.in> Content-Type: multipart/alternative; boundary="------------EAC53BB0590723D90EE010CB" Content-Language: de-DE X-Spam-Status: No, hits=0.001, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.001 X-Spam-Score: (0.001) X-Spam-Flag: NO X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0cEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsfHhEKQ1kXExsRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHxxxGR8QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XQXhjH2BFS1xLXH1tQVN7GE1gUFAbT3xBXVt+elpseFARClhcFx8EGgQYGRoFGxoE GxoaBB4SBBgYEBseGh8aEQpeWRdyHn1jYhEKTVwXGR8fEQpMWhd7aU1NTREKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2xfbGZfcExLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGBoRCk JeFxsRCkReFxgRCkJFF2wdWHJFHxxHSQVuEQpCThdkGkluenp4GmR9XBEKQkwXYGAbUhkdGBpSc gURCkJsF2ZrYmQYWWJtSH5sEQpCQBdlSRlOUn1HblBdXREKQlgXZ3Nlc0BuYWFMXWIRClpYFxkR CnlDF2x+TFtbHVsfQVNeEQpwZxdgGUZFe05HGW1cRRAZGhEKcGgXelgTTkgbRx1OH0gQGhEKcGg XZUZ+bR16HVMFS3IQGhEKcGgXYGRdE0dEG1IeUm8QGhEKcGgXZ2JzGH4cc01/ZEYQGhEKcGgXaR NfYVhzexJAXEgQGhEKcH0XZW9TQERuXntcGkYQGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnBnF25YX X1OZkIFHktMEBkaEQpwfRdrG0h/GEcZWk56QxAaEQpwZxdmfW8Fa2ZkT2FCRBAaEQpwfxdubmga Ex1DYB9dbRAdGREKcF8XblxjZ1NTZxwcfEYQGhEKcGwXeh94eW94TENfcEQQGRoRCm1+FxoRClh NF0sRIA== X-Proofpoint-ORIG-GUID: kRI5JoavavWGkyQ2gJzz1eVkwqTPpFRz X-Proofpoint-GUID: kRI5JoavavWGkyQ2gJzz1eVkwqTPpFRz MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 priorityscore=0 malwarescore=0 mlxscore=0 adultscore=0 mlxlogscore=999 spamscore=0 suspectscore=0 impostorscore=0 clxscore=176 bulkscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105240093 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------EAC53BB0590723D90EE010CB Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Nadira, no, atom types NOT present while present in the prm file in the simulation will not influence it. BUT the NBFIX part that might contain atom of yours at the very end will still be applied (which might not be what you want). *BUT this error *indicates that your structure HAS this DIHEDRAL and REQUIRES to have it defined inside a parameter file you pass to NAMD. Though it seems you have a (https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Sphingolipid= __;!!DZ3fjg!vdCetnlO5lhkwRgRUyAats6ukszTSchq4yPSapx7P-jlml2aAV4jeEDEQ0rg88Z= T_w$ ) lipid there that cannot be describe by "par_all36_lipid.prm" only. That's why you need the "toppar_all36_lipid_sphingo.str" . Make sure that this the kind of lipid you actually want to simulate. Ren=C3=A9 On 5/24/2021 4:26 PM, Nadira Khatoon wrote: > Thanks for the help Ren=C3=A9. Your suggestion solved the issue. However,= =20 > now I am getting a new error stating, "FATAL ERROR: UNABLE TO FIND=20 > DIHEDRAL PARAMETERS FOR CTL2 OSL PL OSL (ATOMS 17 23 20 24)". This=20 > gets solved if I use toppar_all36_lipid_sphingo.str as one of my=20 > parameter file in addition to the par_all36_lipid.prm ,=20 > par_all36m_prot.prm, and toppar_water_ions.str. > I am unable to understand the reason behind it. Will unnecessary=20 > parameter file affect simulation results? > > > -------- Original Message -------- > Subject: Re: namd-l: Regarding Parameter file > Date: 24.05.2021 14:21 > From: Ren=C3=A9 Hafner TUK > To: namd-l@ks.uiuc.edu, Nadira Khatoon=20 > > > Hi, > =C2=A0=C2=A0=C2=A0 ON3 is an atom type from par_all36_na.prm > > =C2=A0=C2=A0=C2=A0 Inside toppar_water_ions.str you only need to comment = out any > NBFIXes Lines where "ON3" occurs; may happen for more atom types but > should be solvable the same way. > > Cheers > Ren=C3=A9 > > On 5/23/2021 7:14 PM, Nadira Khatoon wrote: >> Hi, >> I am new at learning NAMD for simulating membrane embedded proteins.=20 >> Will use of different versions of Charmm parameter files cause errors=20 >> in the simulation? >> Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR=20 >> ATOM TYPE ON3", is coming, but there are no ON3 atoms in both pdb and=20 >> psf files. I am unable to find a solution to this. Could you please=20 >> help me with this? >> For running this simulation, I have used parameter files as mentioned=20 >> below: >> parameters par_all36_lipid.prm >> parameters par_all36m_prot.prm >> parameters toppar_water_ions.str >> --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------EAC53BB0590723D90EE010CB Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable

Hi Nadira,

no, atom types NOT present while present in the prm file in the simulation will not influence it. BUT the NBFIX part that might contain atom of yours at the very end will still be applied (which might not be what you want).

BUT this error indicates that your structure HAS this DIHEDRAL and REQUIRES to have it defined inside a parameter file you pass to NAMD.

Though it seems you have a (https://en.wikipedia.o= rg/wiki/Sphingolipid) lipid there that cannot be describe by "par_all36_lipid.prm" only.

That's why you need the "toppar_all36_lipid_sphingo.str" .

Make sure that this the kind of lipid you actually want to simulate.

Ren=C3=A9



On 5/24/2021 4:26 PM, Nadira Khatoon wrote:
Th= anks for the help Ren=C3=A9. Your suggestion solved the issue. However, now I am getting a new error stating, "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CTL2 OSL PL OSL (ATOMS 17 23 20 24)". This gets solved if I use toppar_all36_lipid_sphingo.str as one of my parameter file in addition to the par_all36_lipid.prm , par_all36m_prot.prm, and toppar_water_ions.str.
I am unable to understand the reason behind it. Will unnecessary parameter file affect simulation results?


-------- Original Message --------
Subject: Re: namd-l: Regarding Parameter file
Date: 24.05.2021 14:21
From: Ren=C3=A9 Hafner TUK <hamburge@physik.uni-kl.de>
To: namd-l@ks.uiuc.edu, Nadira Khatoon <Nadira.Khatoon@bioschool.iitd.ac.in>

Hi,
=C2=A0=C2=A0=C2=A0 ON3 is an atom type from par_all36_na.prm

=C2=A0=C2=A0=C2=A0 Inside toppar_water_ions.str you only need to comm= ent out any
NBFIXes Lines where "ON3" occurs; may happen for more atom types but
should be solvable the same way.

Cheers
Ren=C3=A9

On 5/23/2021 7:14 PM, Nadira Khatoon wrote:
Hi,
I am new at learning NAMD for simulating membrane embedded proteins. Will use of different versions of Charmm parameter files cause errors in the simulation?
Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE ON3", is coming, but there are no ON3 atoms in both pdb and psf files. I am unable to find a solution to this. Could you please help me with this?
For running this simulation, I have used parameter files as mentioned below:
parameters par_all36_lipid.prm
parameters par_all36m_prot.prm
parameters toppar_water_ions.str

--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--------------EAC53BB0590723D90EE010CB-- From owner-namd-l@halifax.ks.uiuc.edu Tue May 25 08:40:13 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14PDeDAH001175; Tue, 25 May 2021 08:40:13 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14PDeD2v001174; Tue, 25 May 2021 08:40:13 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14PDeCGM001170; Tue, 25 May 2021 08:40:12 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14PDeC02001169; Tue, 25 May 2021 08:40:12 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14PDdxwL001161 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 25 May 2021 08:39:59 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14PDXZKZ028157 for ; Tue, 25 May 2021 13:39:58 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=kevin@skblnw.com Received: from mta-11-4.privateemail.com (mta-11-4.privateemail.com [198.54.127.104]) by mx0a-00007101.pphosted.com with ESMTP id 38rsc8bqvn-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 25 May 2021 13:39:58 +0000 Received: from mta-11.privateemail.com (localhost [127.0.0.1]) by mta-11.privateemail.com (Postfix) with ESMTP id 079FA80054 for ; Tue, 25 May 2021 09:39:58 -0400 (EDT) Received: from APP-09 (unknown [10.50.14.159]) by mta-11.privateemail.com (Postfix) with ESMTPA id E41D080050 for ; Tue, 25 May 2021 09:39:57 -0400 (EDT) Date: Tue, 25 May 2021 09:39:57 -0400 (EDT) From: Kevin Chan To: "namd-l@ks.uiuc.edu" Message-ID: <1333379885.257237.1621949997892@privateemail.com> Subject: namd-l: FEP with cudaSOAIntegrate in NAMD 3.0alph9 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_257236_907109580.1621949997889" X-Priority: 3 Importance: Normal X-Mailer: Open-Xchange Mailer v7.10.4-Rev23 X-Originating-Client: open-xchange-appsuite X-Virus-Scanned: ClamAV using ClamSMTP X-Proofpoint-GUID: 9Ef8jv8caTsybuwZxovQEDGZjOxv87uW X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 9Ef8jv8caTsybuwZxovQEDGZjOxv87uW X-CLX-Response: 1TFkXGRoaEQpMehcaEQpZRBdjXwF5c1pgZ28ZUhEKWFgXY3JfW3xYG2hgZW4 RCnhOF24bTX4cbhN7Ym56EQp5TBdhHEEaQF0aTnlveBEKQ0gXBxsdGxEKQ1kXBxsbGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXHBxxGwYbGRh3BhsZHgYaBhoGGxoaBhpxGhAadwYaBhoGGgYaBhoGG nEaEBp3BhoRClleF2NjeREKSUYXX0NfSXVCRVleT04RCkNOFxNvTBJAXBJJS35ZU0hfXXBSRVx7 b25tcEBlUlwSHV99EQpYXBcfBBoEGBkaBRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXch5bZmARCk1 cFxkaGREKTFoXaGlNa2sRCkJPF2huUxx8ekhPGFlpEQpDWhcbExIEHx4EGxgdBBsaHhEKQl4XGx EKRF4XGBEKQkUXZkFzX0gYYk1jH2sRCkJOF24bTX4cbhN7Ym56EQpCTBdjcl9bfFgbaGBlbhEKQ mwXZWVhc3h9Z018b1kRCkJAF2x+QE1oH2xPeFoBEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpY FxgRCnlDF2NlGE5iYkhMSU1IEQpwaBdpX1JAGlgfExh/fhAHGRoRCnBoF3p/Z0tuGX4YTlp6EAc ZGhEKcGgXenBSe28TXmQFHUkQBxkaEQpwaBdkS3oeGkhrcGIFbxAHGRoRCnBoF2JHYV1eHXJGe0 weEAcZGhEKcGwXaVgZUmBOGH9Pc2gQEh8RCm1+FwcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 bulkscore=0 impostorscore=0 mlxscore=0 mlxlogscore=903 spamscore=0 suspectscore=0 lowpriorityscore=0 clxscore=300 phishscore=0 priorityscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105250084 X-Spam-Score: 0 X-Spam-OrigSender: kevin@skblnw.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kevin Chan ------=_Part_257236_907109580.1621949997889 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Dear Users, I am trying to speed up an FEP calculation using cudaSOAIntegrate with NAMD 3.0alpha9 single-node path, however, failed by getting either FATAL ERROR: Periodic cell has become too small for original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation. or FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813) System unstable or pairlistdist or cutoff too small. The system has been tested with NAMD2.14 and NAMD3.0alpha9 without cudaSOAIntegrate and worked perfectly fine. So I have tried to tackle the errors by 1. pairlistdist 13.5 to 16 2. margin 4, 8, 16, 20 3. LangevinPistonDecay 100 to 1000 None of the combination worked. Sometimes first 1 or 2 windows (lambda 0 to 0.001) got finished (500k+ steps), but I never got the middle windows (lambda > 0.1) running. I also tried the alpha8 version and had the same results. I set stepsPerCycle to 400 and pairlistsPerCycle to 40 all the time. The run command is simply "namd3 +p1 +devices 0". I understand that FEP with CUDA speedup is still in alpha, so any experience shared will be greatly appreciated. Thanks, Kevin Zhejiang University ------=_Part_257236_907109580.1621949997889 MIME-Version: 1.0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Dear Users,

I am trying to speed up an FEP calculation using cudaSOAIntegrate with NAMD 3.0alpha9 single-node path, however, failed by getting either 

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

or

FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813) System unstable or pairlistdist or cutoff too small.

The system has been tested with NAMD2.14 and NAMD3.0alpha9 without cudaSOAIntegrate and worked perfectly fine. 

So I have tried to tackle the errors by 

1. pairlistdist 13.5 to 16
2. margin 4, 8, 16, 20
3. LangevinPistonDecay 100 to 1000

None of the combination worked. Sometimes first 1 or 2 windows (lambda 0 to 0.001) got finished (500k+ steps), but I never got the middle windows (lambda > 0.1) running. I also tried the alpha8 version and had the same results. I set stepsPerCycle to 400 and pairlistsPerCycle to 40 all the time. The run command is simply "namd3 +p1 +devices 0".

I understand that FEP with CUDA speedup is still in alpha, so any experience shared will be greatly appreciated. 

Thanks,
Kevin
Zhejiang University 
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boundary="000000000000b7392d05c3285b50" X-CLX-Response: 1TFkXGxITEQpMehcZGxgRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHxsTEQpDWRcbGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscE3EeEhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdlZHJCZk1vU2RpZB5ZGERPaWBscn8SE10HeU1ZWn5QfxEKWFwXHwQaBBgZGgUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3IeWx8eEQpNXBceHBkRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx 0cEQpCXhcbEQpESRcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9YeGARCkJsF2Ff elMZQ0Qaeht+EQpCQBdma31gXUNlc11kZREKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF2x8XmF OQmEaR0NBEQpZSxcTHhsdEQpwaBdjbVxbTRJJRmBmcxAZGhEKcGgXZlMBYX9ZHnpwWRkQGRoRCn BoF29cS35Dbh5hbx1YEBkaEQpwaBdreGJBcnt9E0dMSRAZGhEKcGgXZH5ATBhFR2x8RHoQGRoRC nB9F2BaHH1GSGJyGWB5EBkaEQpwfxdiTgUBcEReaUR7ZRATEhEKcF8XZktYGnkbZHlCR0sQGRoR CnBsF2Yfe1hcYgVLWGQfEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: ONXhLgEyNCN4s2neCJFXU89w-SgspTzU X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: ONXhLgEyNCN4s2neCJFXU89w-SgspTzU MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 adultscore=0 spamscore=0 lowpriorityscore=0 phishscore=0 priorityscore=312 impostorscore=0 bulkscore=0 clxscore=189 mlxscore=0 mlxlogscore=999 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105250090 domainage_hfrom=9417 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000b7392d05c3285b50 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Sorry, I left the reply in draft accidentally. I would try not to exceed ~0.6 kcal/mol (thermal energy at 300 K) added every correlation time of the variables, and ideally stay well below that rate. Giacomo On Mon, May 17, 2021 at 12:51 PM Alessandro Ruda wrote: > Thanks Giacomo for the prompt reply, > > > Restarting the run didn't really work since it stopped again after 20 > minutes (after running for 11 h though). Doesn't look stable at all. > > > The correlation time for the torsions I am looking at is around 100 ps. > > What value would you suggest to be the optimal one in such case? > > > All the best, > > Alex > ------------------------------ > *From:* Giacomo Fiorin > *Sent:* 14 May 2021 17:43:08 > *To:* NAMD list; Alessandro Ruda > *Subject:* Re: namd-l: Metadynamics problems > > Hello Alex, if the instability is sporadic you can safely restart and > continue running. > > The instability, however, could be due to the relatively high rate at > which you add the Gaussian bias, 1 kcal/mol per 1000 steps. Not knowing > the specifics of the system, it would help you to figure out what are the > correlation times of the two dihedral angles from an equilibrium MD > trajectory, which you should already have. The variables may simply not > take up a bias that fast. > > Lastly, you're using NAMD 2.12, which is more than 4 years old. > While it's true that the error is raised from a large force coming from > Colvars, later versions like 2.14 may handle it better, or at least clari= fy > more clearly the precise step where things go wrong. For Colvars > specifically, there are a few advantages for using metadynamics > specifically: > https://urldefense.com/v3/__https://colvars.github.io/namd-2.14/colvars-r= efman-namd/colvars-refman-namd.html*sec:colvars_config_changes__;Iw!!DZ3fjg= !qOhlt2m9TYK7BRGsQiGuJiq3akA1iqhn-By0VCKkmL4dndq0_mT4Vui3UsJXPHGwmA$=20 > > Giacomo > > On Fri, May 14, 2021 at 5:50 AM Alessandro Ruda > wrote: > >> Dear *NAMD comunity*, >> >> >> I am running metadynamics on a set of two dihedral angles. I've tried >> default metadynamics and well tempered. For both of them after a few >> hours the run stops with errors like the following: >> >> >> *namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe44263fa0. >> Backtrace:* >> >> */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_c= hargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* >> >> */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_c= hargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* >> >> and the log file states: >> >> *mpprun info: Job terminated with error* >> >> Normal molecular dynamics works well so it must be related to >> metadynamics. This is the colvar file that i used: >> >> ------------------------------------------------------------------------= -------------------------------------------------------------- >> >> *colvarsTrajAppend off* >> >> *colvar {* >> * name Psi* >> * width 2.5* >> * dihedral {* >> * group1 {* >> * atomnumbers { 32 }* >> * }* >> * group2 {* >> * atomnumbers { 22 }* >> * }* >> * group3 {* >> * atomnumbers { 20 }* >> * }* >> * group4 {* >> * atomnumbers { 21 }* >> * }* >> * }* >> * lowerBoundary -180* >> * upperBoundary 180* >> >> *}* >> >> *colvar {* >> * name Phi* >> * width 2.5* >> * dihedral {* >> * group1 {* >> * atomnumbers { 33 }* >> * }* >> * group2 {* >> * atomnumbers { 32 }* >> * }* >> * group3 {* >> * atomnumbers { 22 }* >> * }* >> * group4 {* >> * atomnumbers { 20 }* >> * }* >> * }* >> * lowerBoundary -180* >> * upperBoundary 180* >> *}* >> >> *metadynamics {* >> *wellTempered on* >> *biasTemperature 1490* >> *name metaPhiPsi* >> *colvars Phi Psi* >> *hillWeight 0.01* >> *hillwidth 1.0* >> *saveFreeEnergyFile no* >> *dumpFreeEnergyFile yes #When useGrids and this option are on, the PMF >> is written every colvarsRestartFrequency steps to the file outputName.p= mf* >> *writeHillsTrajectory on* >> *newHillFrequency 100 * >> >> ------------------------------------------------------------------------= --------------------------------------------------------------- >> >> I have tried with different hillWeight values and the problem stays. >> Can I do something or should I restart from the last step and continue >> running and, in doing so, >> how can I keep the old colvars data so that I restart from the last >> points collected? >> >> Thank you in advance, >> >> All the best, >> Alex >> >> >> > All the best, > Alex > > > --000000000000b7392d05c3285b50 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Sorry, I left the reply in draft accidentally.

I would try not to exceed ~0.6 kcal/mol (thermal energy at 300 K) a= dded every correlation time of the variables, and ideally stay well below t= hat rate.

Giacomo

On Mon, May 17, 2021 at 12:= 51 PM Alessandro Ruda <alessand= ro.ruda@su.se> wrote:

Thanks Giacomo for the prompt reply,


Restarting the run didn't really work since=C2=A0it stopped again af= ter 20 minutes (after running for 11 h though). Doesn't look stable at = all.=C2=A0

<= br>

T= he correlation time for the torsions I am looking at is around 100 ps.=C2=A0

What value would you suggest to be the optimal one in such case?


All the best,

Alex


Fro= m: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Sent: 14 May 2021 17:43:08
To: NAMD list; Alessandro Ruda
Subject: Re: namd-l: Metadynamics problems
=C2=A0
Hello Alex, if the instability is sporadic you can safely = restart and continue running.

The instability, however, could be due to the relatively high rate at = which you add the Gaussian bias, 1 kcal/mol per 1000 steps.=C2=A0 Not knowi= ng the specifics of the system, it would help you to figure out what are th= e correlation times of the two dihedral angles from an equilibrium MD trajectory, which you should already=C2=A0ha= ve.=C2=A0 The variables may simply not take up a bias that fast.

Lastly, you're using NAMD 2.12, which is more than 4 years old.=C2= =A0 While=C2=A0it's true that the error is raised from a large force co= ming from Colvars, later versions like 2.14 may handle it better, or at lea= st clarify more clearly the precise step where things go wrong.=C2=A0 For Colvars specifically, there are a few advantages for u= sing metadynamics specifically:=C2=A0https://colvars.= github.io/namd-2.14/colvars-refman-namd/colvars-refman-namd.html#sec:colvar= s_config_changes

Giacomo

On Fri, May 14, 2021 at 5:50 AM Aless= andro Ruda <a= lessandro.ruda@su.se> wrote:

Dear NAMD comunity,


I am running metadynamics on a set of two dihedral angles. I've trie= d default metadynamics and well tempered. For both of them after a few hour= s=C2=A0the run stops with errors like the following:


namd2:207125 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe4426= 3fa0.=C2=A0 Backtrace:
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
/software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fi= ll_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]

and the log file states:

mpprun info:=C2=A0 =C2=A0Job terminated with error=

Normal molecular dynamics works well so it must be related to me= tadynamics. This is the colvar file that i used:
----------------------------------------------------------------------= ----------------------------------------------------------------

colvarsTrajAppend off

colvar {
=C2=A0 =C2=A0name Psi
=C2=A0 =C2=A0width 2.5
=C2=A0 =C2=A0dihedral {
=C2=A0 =C2=A0 =C2=A0 group1 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 32 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group2 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 22 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group3 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 20 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group4 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 21 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0}
=C2=A0 =C2=A0 lowerBoundary -180
=C2=A0 =C2=A0 upperBoundary 180

}

colvar {
=C2=A0 =C2=A0name Phi
=C2=A0 =C2=A0width 2.5
=C2=A0 =C2=A0dihedral {
=C2=A0 =C2=A0 =C2=A0 group1 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 33 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group2 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 32 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group3 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 22 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 group4 {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers { 20 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0}
=C2=A0lowerBoundary -180
=C2=A0 =C2=A0upperBoundary 180
}

metadynamics {
wellTempered on
biasTemperature 1490
name metaPhiPsi
colvars Phi Psi
hillWeight 0.01
hillwidth 1.0
saveFreeEnergyFile no
dumpFreeEnergyFile yes=C2=A0 #When useGrids and this option are on,= the PMF is written every colvarsRestartFrequency steps to the file=C2=A0 o= utputName.pmf
writeHillsTrajectory on
newHillFrequency 100=C2=A0
---------------------------------------------------------------------------= ------------------------------------------------------------

I have tried with different hillWeight values and the problem stays.
Can I do something or should I restart from the last step and continue= running and, in doing so,
how can I keep the old colvars data so that I restart from the last po= ints collected?

Thank you in advance,

All the best,
Alex



All the best,
Alex


--000000000000b7392d05c3285b50-- From owner-namd-l@halifax.ks.uiuc.edu Wed May 26 05:19:43 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14QAJhvx015700; Wed, 26 May 2021 05:19:43 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14QAJhdT015699; Wed, 26 May 2021 05:19:43 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14QAJgYn015695; Wed, 26 May 2021 05:19:42 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14QAJgC6015694; Wed, 26 May 2021 05:19:42 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14QAJVOm015685 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 26 May 2021 05:19:32 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14QADo6x003417 for ; Wed, 26 May 2021 10:19:31 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=xzhfood@njau.edu.cn Received: from mail-m176237.qiye.163.com (mail-m176237.qiye.163.com [59.111.176.237]) by mx0b-00007101.pphosted.com with ESMTP id 38re7dbmre-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 26 May 2021 10:19:31 +0000 Received: from njau.edu.cn (localhost [127.0.0.1]) by mail-m176237.qiye.163.com (Hmail) with ESMTP id 03D64C40169 for ; Wed, 26 May 2021 18:19:28 +0800 (CST) Content-Type: multipart/alternative; BOUNDARY="=_Part_313111_28978199.1622024368004" Message-ID: To: namd-l@ks.uiuc.edu Subject: namd-l: =?UTF-8?B?RkFUQUwgRVJST1I6IEVycm9yIGluIHRoZSBjb2xsZWN0aXZlIHZhcmlhYmxlcyBtb2R1bGUgIA==?= X-Priority: 3 X-Mailer: HMail Webmail Server V2.0 Copyright (c) 2016-163.com X-Originating-IP: 112.4.142.139 Received: from xzhfood@njau.edu.cn( [112.4.142.139) ] by ajax-webmail ( [127.0.0.1] ) ; Wed, 26 May 2021 18:19:28 +0800 (GMT+08:00) From: =?UTF-8?B?6L6b5b+X5a6P?= Date: Wed, 26 May 2021 18:19:28 +0800 (GMT+08:00) X-HM-Spam-Status: e1kfGhgUHx5ZQUtXWQgYFAkeWUFZS1VLWVdZKFlBSE83V1ktWUFJV1kPCR oVCBIfWUFZQh8YQ1YfGRhKTBlDQxpCSh9VEwETFhoSFyQUDg9ZV1kWGg8SFR0UWUFZT0tIVUpKS0 hKTFVLWQY+ X-HM-Sender-Digest: e1kMHhlZQQ8JDh5XWRIfHhUPWUFZRzo0DDocKjgxPxMJGTAaQhZCMB8C ShoLF1VKVUpNSUlLSU9ITUNJQ09VMxYaEhdVAwETHRQUHzsVERoOVR4fDlUYFUVZV1kSC1lBWUpK SVVPVUpPSVVKSEJZV1kIAVlBSk9JTUM3Bg++ X-HM-Tid: 0a79a82faf90d9afkuws03d64c40169 X-CLX-Response: 1TFkXGxIbEQpMehcaEQpZRBdrSBpwYXxYaG1OXBEKWFgXZ3ocGFJJYm4ecE4 RCnhOF2dsb0tEZ3kTYhpjEQp5TBdlZUNwYW0dbF1NEhEKQ0gXBxseHREKQ1kXBx4cEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwbcR4aEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxpHGBJuXEVJH2Z4SRtNZEtvSBJBWEVweV8dQX98QxxJEQpYXBcfBBoEGBkaBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3IeEnxlEQpNXBceHxMRCkxaF2hpTU1rEQpCTxdkTWBfTF9 yQR58XhEKQ1oXHxMEGxsbBBsdHAQYGR0RCkJeFxsRCkJFF2R5YkcYZXhAHkBfEQpCThdnbG9LRG d5E2IaYxEKQkwXZ3ocGFJJYm4ecE4RCkJsF2loTBgFb0MdWGgBEQpCQBdoZXBLBXhsG3xpfxEKQ lgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2EFb1pZbmhmY0VSEQpwaBdjcFBrZWN9WF4eThAZGhEK cGgXZnhnbmlAcGAZZEUQGRoRCnBoF2IfbG4FTEtNBUsbEBkaEQpwaBdva1pZRUtbaHtpWhAZGhE KcGgXZEF9BX8aYhtQTxwQGRoRCnB9F2QSb2BaZXkaT0Z9EBkaEQpwfxdsXH9pE01BS2dfGBATEh EKcF8Xb08TaV5QAXNDHGcQHhIRCnBsF29pX39dWmccT0kTEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 0m28Dvoc5LRc1gNaEb8kroZSu7kUVi6c X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 0m28Dvoc5LRc1gNaEb8kroZSu7kUVi6c MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 impostorscore=0 adultscore=0 clxscore=181 phishscore=0 lowpriorityscore=0 malwarescore=0 priorityscore=0 bulkscore=0 spamscore=0 mlxscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105260069 X-Spam-Score: 0 X-Spam-OrigSender: xzhfood@njau.edu.cn X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?B?6L6b5b+X5a6P?= --=_Part_313111_28978199.1622024368004 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear namd, I came across a issue when I run an example according to the namd offical t= utorial "Methods for calculating Potentials of Mean Force" by namd3 as foll= ows: I use NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA How to fix the issue? It will be highly appreciate if there are any suggestion. Zhihong Xin ......... colvars: ------------------------------------------------------------------= ---- colvars: Initializing the collective variables module, version "2020-02-27". colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: https://urldefense.com/v3/__https://dx.doi.org/10.1080/00268976.2= 013.813594__;!!DZ3fjg!tb9uE3bYl5Bfibz8wQRgWaLBW41ITMHSu2NTGRK-qGDGSSmwZONB2= m5FTHhpkLQudw$=20 colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override t= his. colvars: This version was built with the C++11 standard or higher. colvars: Using NAMD interface, version "2019-12-04". colvars: ------------------------------------------------------------------= ---- colvars: Reading new configuration from file "restrain.in": colvars: # units =3D "" [default] colvars: # smp =3D on [default] colvars: # colvarsTrajFrequency =3D 1000 colvars: # colvarsRestartFrequency =3D 1000 colvars: # scriptedColvarForces =3D off [default] colvars: # scriptingAfterBiases =3D off [default] colvars: ------------------------------------------------------------------= ---- colvars: Initializing a new collective variable. colvars: # name =3D "restrain01" colvars: Initializing a new "distanceXY" component. colvars: # name =3D "" [default] colvars: # componentCoeff =3D 1 [default] colvars: # componentExp =3D 1 [default] colvars: # period =3D 0 [default] colvars: # wrapAround =3D 0 [default] colvars: # forceNoPBC =3D off [default] colvars: # scalable =3D on [default] colvars: Initializing atom group "main". colvars: # name =3D "" [default] colvars: # centerReference =3D off [default] colvars: # rotateReference =3D off [default] colvars: # atomsOfGroup =3D "" [default] colvars: # indexGroup =3D "" [default] colvars: # psfSegID =3D [default] colvars: # atomsFile =3D "" [default] colvars: # dummyAtom =3D ( 0 , 0 , 0 ) [default] colvars: # enableForces =3D on [default] colvars: # enableFitGradients =3D on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs =3D off [default] colvars: Atom group "main" defined with 1 atoms requested: total mass= =3D 14.007, total charge =3D -1.125. colvars: Initializing atom group "ref". colvars: # name =3D "" [default] colvars: # centerReference =3D off [default] colvars: # rotateReference =3D off [default] colvars: # atomsOfGroup =3D "" [default] colvars: # indexGroup =3D "" [default] colvars: # psfSegID =3D [default] colvars: # atomsFile =3D "" [default] colvars: # dummyAtom =3D ( 0 , 0 , 0 ) [default] colvars: # enableForces =3D on [default] colvars: # enableFitGradients =3D on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs =3D off [default] colvars: Atom group "ref" defined with 383 atoms requested: total mas= s =3D 4600.21, total charge =3D 21.42. colvars: # axis =3D ( 0 , 0 , 1 ) colvars: # oneSiteSystemForce =3D off [default] colvars: # oneSiteTotalForce =3D off [default] colvars: All components initialized. colvars: # timeStepFactor =3D 1 [default] colvars: # width =3D 0.5 colvars: # lowerBoundary =3D 0 colvars: # upperBoundary =3D 8 colvars: Reading legacy options lowerWall and lowerWallConstant: consider= using a harmonicWalls restraint (caution: force constant would then be sca= led by width^2). colvars: # lowerWall =3D 0 [default] FATAL ERROR: Error in the collective variables module (see above for detail= s) colvars: Error: the value of lowerWall must be set explicitly. FATAL ERROR: Error in the collective variables module (see above for detail= s) [Partition 0][Node 0] End of program --=_Part_313111_28978199.1622024368004 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear namd,
I came across a issue when I run an example ac= cording to the namd offical tutorial "Methods for calculating Potentials of= Mean Force" by namd3 as follows:

I use NAM= D_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA

How to= fix the issue?
It will be highly appreciate if there are any sug= gestion.

Zhihong Xin

=
..........
colvars: ----------------------------= ------------------------------------------

colvars: Initializing th= e collective variables module, version "2020-02-27".

colvars: Please = cite Fiorin et al, Mol Phys 2013:

colvars:  htt= ps://dx.doi.org/10.1080/00268976.2013.813594

colvars: in any publ= ication based on this calculation.

colvars: SMP parallelism is enable= d; if needed, use "smp off" to override this.

colvars: This version w= as built with the C++11 standard or higher.

colvars: Using NAMD inter= face, version "2019-12-04".

colvars: --------------------------------= --------------------------------------

colvars: Reading new configura= tion from file "restrain.in":

colvars: # units =3D "" [default]

colvars: # smp =3D on [default]

colvars: # colvarsTrajFrequency =3D = 1000

colvars: # colvarsRestartFrequency =3D 1000

colvars: # scr= iptedColvarForces =3D off [default]

colvars: # scriptingAfterBiases = =3D off [default]

colvars: ------------------------------------------= ----------------------------

colvars:   Initializing a new = collective variable.

colvars:   # name =3D "restrain01"

=

colvars:   Initializing a new "distanceXY" component.

co= lvars:     # name =3D "" [default]

colvars:  &nbs= p;  # componentCoeff =3D 1 [default]

colvars:     = ;# componentExp =3D 1 [default]

colvars:     # period = =3D 0 [default]

colvars:     # wrapAround =3D 0 [defau= lt]

colvars:     # forceNoPBC =3D off [default]

= colvars:     # scalable =3D on [default]

colvars: = ;      Initializing atom group "main".

colvars:  =      # name =3D "" [default]

colvars:    &nb= sp;  # centerReference =3D off [default]

colvars:    &= nbsp;  # rotateReference =3D off [default]

colvars:   =    # atomsOfGroup =3D "" [default]

colvars:    &= nbsp;  # indexGroup =3D "" [default]

colvars:     = ;  # psfSegID =3D  [default]

colvars:      &= nbsp;# atomsFile =3D "" [default]

colvars:       = # dummyAtom =3D ( 0 , 0 , 0 ) [default]

colvars:      =  # enableForces =3D on [default]

colvars:      &n= bsp;# enableFitGradients =3D on [default]

colvars:     = ;  Enabling scalable calculation for group "main".

colvars: = ;      # printAtomIDs =3D off [default]

colvars: =      Atom group "main" defined with 1 atoms requested: tota= l mass =3D 14.007, total charge =3D -1.125.

colvars:    &nb= sp;  Initializing atom group "ref".

colvars:     =  # name =3D "" [default]

colvars:       # c= enterReference =3D off [default]

colvars:       #= rotateReference =3D off [default]

colvars:       = ;# atomsOfGroup =3D "" [default]

colvars:       #= indexGroup =3D "" [default]

colvars:       # psf= SegID =3D  [default]

colvars:       # atomsF= ile =3D "" [default]

colvars:       # dummyAtom = =3D ( 0 , 0 , 0 ) [default]

colvars:       # enab= leForces =3D on [default]

colvars:       # enable= FitGradients =3D on [default]

colvars:       Enab= ling scalable calculation for group "ref".

colvars:    &nbs= p;  # printAtomIDs =3D off [default]

colvars:     = ;  Atom group "ref" defined with 383 atoms requested: total mass =3D 4= 600.21, total charge =3D 21.42.

colvars:     # axis = =3D ( 0 , 0 , 1 )

colvars:     # oneSiteSystemForce = =3D off [default]

colvars:     # oneSiteTotalForce =3D= off [default]

colvars:   All components initialized.

colvars:   # timeStepFactor =3D 1 [default]

colvars: =  # width =3D 0.5

colvars:   # lowerBoundary =3D 0

=

colvars:   # upperBoundary =3D 8

colvars:   Re= ading legacy options lowerWall and lowerWallConstant: consider using a harm= onicWalls restraint (caution: force constant would then be scaled by width^= 2).

colvars:   # lowerWall =3D 0 [default]

FATAL ERRO= R: Error in the collective variables module (see above for details)

c= olvars: Error: the value of lowerWall must be set explicitly.

FATAL E= RROR: Error in the collective variables module (see above for details)

<= p>[Partition 0][Node 0] End of program



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[51.81.154.37]) by smtp.gmail.com with ESMTPSA id u12sm14482500pfm.2.2021.05.26.03.43.26 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Wed, 26 May 2021 03:43:28 -0700 (PDT) Subject: Re: namd-l: FATAL ERROR: Error in the collective variables module To: namd-l@ks.uiuc.edu, =?UTF-8?B?6L6b5b+X5a6P?= References: From: yjcoshc Message-ID: <627a0a55-d711-a13d-12e3-816b34314d8d@gmail.com> Date: Wed, 26 May 2021 05:43:20 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.10.2 In-Reply-To: Content-Type: multipart/alternative; boundary="------------624207936F13FDA5E9694F71" Content-Language: en-US X-CLX-Response: 1TFkXGxMaEQpMehcZGhoRCllEF2ZkX1pvRRJLb1hmEQpYWBdmW3x/R0hvHwV PZREKeE4XY1Nja3sTWH4aX14RCkNIFwcbHxwRCkNZFx4fEQpDSRcaBBoaGhEKWU0XZ2ZyEQpZSR cacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF3hYGR9SZ 0YTb2FcbkZ5YUlgZUJiax9eZG8cfU9HZEZMEQpYXBcfBBoEGBkaBRsaBBsbGgQfGgQbHhsQGx4a HxoRCl5ZF3IeElheEQpNXBcYHRgRCkxaF3hpTU1NEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkx GF29ra2xraxEKQk8XZH5YT2Zuc0lwW08RCkNaFxgaEwQSHwQYGxwEHhsRCkJeFxsRCkReFxgRCk JcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZFJCBRpYGl57Q 3gRCkJOF2NTY2t7E1h+Gl9eEQpCTBdmW3x/R0hvHwVPZREKQmwXYk9iRBpLQBtSX10RCkJAF21O c1hwWmVofQVbEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHxEKeUMXbF1IeGYaThpgZBoRCll LFxMeGxIRCnBnF2x7QWJHT2cBc0JNEBkaEQpwaBdmfXscRRpQGx4dehAZGhEKcGgXZGIbbUMfYB 15ZksQGRoRCnBoF3pkS3NQZVhBTVB9EBkaEQpwaBdnZBlnX1l5YEZzZhAZGhEKcGgXbQVSXxp6c BtuE3gQGRoRCnB9F2QSb2BaZXkaT0Z9EB4SEQpwfRdofngdX2dMcHobUhAZGhEKcH8XbFx/aRNN QUtnXxgQExIRCnBfF29PE2leUAFzQxxnEBwaEQpwfxdhZm9bGmdkQkgdWxAbGhMRCnBfF2NiElB IY3gffEJ9EB0TEQpwbBdmHmlFG0hITWRoXxAZGhEKcEMXaX1Lf35lBW1GfE8QGRoRCm1+FxsRCl hNF0sRIA== X-Proofpoint-GUID: Rr35xMl9EKvDlSKcJOhHA5tNE6WemNlf X-Proofpoint-ORIG-GUID: Rr35xMl9EKvDlSKcJOhHA5tNE6WemNlf X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=300 phishscore=0 clxscore=190 mlxscore=0 malwarescore=0 impostorscore=0 mlxlogscore=999 suspectscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105260071 domainage_hfrom=9418 X-Spam-Score: 0 X-Spam-OrigSender: yjcoshc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, yjcoshc This is a multi-part message in MIME format. --------------624207936F13FDA5E9694F71 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Zhihong, I suspect you are trying to use ABF or metadynamics to determine the=20 PMF. Both of the methods require histograms to discretize the CVs, and=20 in general wall potentials are necessary to keep the CVs inside the=20 histograms. Historically, the Colvars module implicitly set the wall=20 boundaries the same as the histogram boundaries (lowerBoundary and=20 upperBoundary), but recently this behavior has changed, so explicitly=20 specifying the wall boundaries (lowerWall and upperWall) is mandatory. In your case, I think you can just add the following lines in your=20 "restrain01" colvar component: lowerWall 0 upperWall 8 Best regards, Haochuan Chen On 5/26/21 5:19 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote: > Dear namd, > I came across a issue when I run an example according to the namd=20 > offical tutorial "Methods for calculating Potentials of Mean Force" by=20 > namd3 as follows: > > I use=C2=A0NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA > > How to fix the issue? > It will be highly appreciate if there are any suggestion. > > Zhihong Xin > > > .......... > colvars:=20 > ---------------------------------------------------------------------- > > colvars: Initializing the collective variables module, version=20 > "2020-02-27". > > colvars: Please cite Fiorin et al, Mol Phys 2013: > > colvars: https://urldefense.com/v3/__https://dx.doi.org/10.1080/00268976.= 2013.813594__;!!DZ3fjg!pyVmqjC0qROsYdjEB66MLGSYAJwywH2H7QADwSFLtcGg0CXN2z4n= KVEftHbyQCQC9A$=20=20 > > > colvars: in any publication based on this calculation. > > colvars: SMP parallelism is enabled; if needed, use "smp off" to=20 > override this. > > colvars: This version was built with the C++11 standard or higher. > > colvars: Using NAMD interface, version "2019-12-04". > > colvars:=20 > ---------------------------------------------------------------------- > > colvars: Reading new configuration from file "restrain.in": > > colvars: # units =3D "" [default] > > colvars: # smp =3D on [default] > > colvars: # colvarsTrajFrequency =3D 1000 > > colvars: # colvarsRestartFrequency =3D 1000 > > colvars: # scriptedColvarForces =3D off [default] > > colvars: # scriptingAfterBiases =3D off [default] > > colvars:=20 > ---------------------------------------------------------------------- > > colvars:=C2=A0 =C2=A0Initializing a new collective variable. > > colvars:=C2=A0 =C2=A0# name =3D "restrain01" > > colvars:=C2=A0 =C2=A0Initializing a new "distanceXY" component. > > colvars:=C2=A0 =C2=A0 =C2=A0# name =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# componentCoeff =3D 1 [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# componentExp =3D 1 [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# period =3D 0 [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# wrapAround =3D 0 [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# forceNoPBC =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# scalable =3D on [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0Initializing atom group "main". > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# name =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# centerReference =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# rotateReference =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# atomsOfGroup =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# indexGroup =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# psfSegID =3D=C2=A0 [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# atomsFile =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# dummyAtom =3D ( 0 , 0 , 0 ) [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# enableForces =3D on [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# enableFitGradients =3D on [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0Enabling scalable calculation for grou= p "main". > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# printAtomIDs =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0Atom group "main" defined with 1 atoms= requested: total=20 > mass =3D 14.007, total charge =3D -1.125. > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0Initializing atom group "ref". > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# name =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# centerReference =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# rotateReference =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# atomsOfGroup =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# indexGroup =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# psfSegID =3D=C2=A0 [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# atomsFile =3D "" [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# dummyAtom =3D ( 0 , 0 , 0 ) [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# enableForces =3D on [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# enableFitGradients =3D on [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0Enabling scalable calculation for grou= p "ref". > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0# printAtomIDs =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0 =C2=A0Atom group "ref" defined with 383 atom= s requested:=20 > total mass =3D 4600.21, total charge =3D 21.42. > > colvars:=C2=A0 =C2=A0 =C2=A0# axis =3D ( 0 , 0 , 1 ) > > colvars:=C2=A0 =C2=A0 =C2=A0# oneSiteSystemForce =3D off [default] > > colvars:=C2=A0 =C2=A0 =C2=A0# oneSiteTotalForce =3D off [default] > > colvars:=C2=A0 =C2=A0All components initialized. > > colvars:=C2=A0 =C2=A0# timeStepFactor =3D 1 [default] > > colvars:=C2=A0 =C2=A0# width =3D 0.5 > > colvars:=C2=A0 =C2=A0# lowerBoundary =3D 0 > > colvars:=C2=A0 =C2=A0# upperBoundary =3D 8 > > colvars:=C2=A0 =C2=A0Reading legacy options lowerWall and lowerWallConsta= nt:=20 > consider using a harmonicWalls restraint (caution: force constant=20 > would then be scaled by width^2). > > colvars:=C2=A0 =C2=A0# lowerWall =3D 0 [default] > > FATAL ERROR: Error in the collective variables module (see above for=20 > details) > > colvars: Error: the value of lowerWall must be set explicitly. > > FATAL ERROR: Error in the collective variables module (see above for=20 > details) > > [Partition 0][Node 0] End of program > > > --------------624207936F13FDA5E9694F71 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Zhihong,

I suspect you are trying to use ABF or metadynamics to determine the PMF. Both of the methods require histograms to discretize the CVs, and in general wall potentials are necessary to keep the CVs inside the histograms. Historically, the Colvars module implicitly set the wall boundaries the same as the histogram boundaries (lowerBoundary and upperBoundary), but recently this behavior has changed, so explicitly specifying the wall boundaries (lowerWall and upperWall) is mandatory.

In your case, I think you can just add the following lines in your "restrain01" colvar component:

lowerWall 0

upperWall 8

Best regards,

Haochuan Chen


On 5/26/21 5:19 AM, è¾›å¿—å® wrote:
Dear namd,
I came across a issue when I run an example according to the namd offical tutorial "Methods for calculating Potentials of Mean Force" by namd3 as follows:

I use NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA

How to fix the issue?
It will be highly appreciate if there are any suggestion.

Zhihong Xin


..........
colvars: ----------------------------------------------------------------------

colvars: Initializing the collective variables module, version "2020-02-27".

colvars: Please cite Fiorin et al, Mol Phys 2013:

colvars:  https://dx.doi.org/10.1080/00268976.2013.813594

colvars: in any publication based on this calculation.

colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.

colvars: This version was built with the C++11 standard or higher.

colvars: Using NAMD interface, version "2019-12-04".

colvars: ----------------------------------------------------------------------

colvars: Reading new configuration from file "restrain.in":

colvars: # units = "" [default]

colvars: # smp = on [default]

colvars: # colvarsTrajFrequency = 1000

colvars: # colvarsRestartFrequency = 1000

colvars: # scriptedColvarForces = off [default]

colvars: # scriptingAfterBiases = off [default]

colvars: ----------------------------------------------------------------------

colvars:   Initializing a new collective variable.

colvars:   # name = "restrain01"

colvars:   Initializing a new "distanceXY" component.

colvars:     # name = "" [default]

colvars:     # componentCoeff = 1 [default]

colvars:     # componentExp = 1 [default]

colvars:     # period = 0 [default]

colvars:     # wrapAround = 0 [default]

colvars:     # forceNoPBC = off [default]

colvars:     # scalable = on [default]

colvars:       Initializing atom group "main".

colvars:       # name = "" [default]

colvars:       # centerReference = off [default]

colvars:       # rotateReference = off [default]

colvars:       # atomsOfGroup = "" [default]

colvars:       # indexGroup = "" [default]

colvars:       # psfSegID =  [default]

colvars:       # atomsFile = "" [default]

colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]

colvars:       # enableForces = on [default]

colvars:       # enableFitGradients = on [default]

colvars:       Enabling scalable calculation for group "main".

colvars:       # printAtomIDs = off [default]

colvars:       Atom group "main" defined with 1 atoms requested: total mass = 14.007, total charge = -1.125.

colvars:       Initializing atom group "ref".

colvars:       # name = "" [default]

colvars:       # centerReference = off [default]

colvars:       # rotateReference = off [default]

colvars:       # atomsOfGroup = "" [default]

colvars:       # indexGroup = "" [default]

colvars:       # psfSegID =  [default]

colvars:       # atomsFile = "" [default]

colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]

colvars:       # enableForces = on [default]

colvars:       # enableFitGradients = on [default]

colvars:       Enabling scalable calculation for group "ref".

colvars:       # printAtomIDs = off [default]

colvars:       Atom group "ref" defined with 383 atoms requested: total mass = 4600.21, total charge = 21.42.

colvars:     # axis = ( 0 , 0 , 1 )

colvars:     # oneSiteSystemForce = off [default]

colvars:     # oneSiteTotalForce = off [default]

colvars:   All components initialized.

colvars:   # timeStepFactor = 1 [default]

colvars:   # width = 0.5

colvars:   # lowerBoundary = 0

colvars:   # upperBoundary = 8

colvars:   Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).

colvars:   # lowerWall = 0 [default]

FATAL ERROR: Error in the collective variables module (see above for details)

colvars: Error: the value of lowerWall must be set explicitly.

FATAL ERROR: Error in the collective variables module (see above for details)

[Partition 0][Node 0] End of program



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[51.81.154.37]) by smtp.gmail.com with ESMTPSA id ft19sm4195746pjb.48.2021.05.26.04.43.18 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Wed, 26 May 2021 04:43:20 -0700 (PDT) Subject: Re: namd-l: FEP with cudaSOAIntegrate in NAMD 3.0alph9 To: namd-l@ks.uiuc.edu, Kevin Chan References: <1333379885.257237.1621949997892@privateemail.com> From: yjcoshc Message-ID: <5533ea2f-6e66-fa1d-1773-fb5a147cc305@gmail.com> Date: Wed, 26 May 2021 06:43:16 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.10.2 MIME-Version: 1.0 In-Reply-To: <1333379885.257237.1621949997892@privateemail.com> Content-Type: multipart/alternative; boundary="------------803BA532917E28119AC7E376" Content-Language: en-US X-CLX-Response: 1TFkXGx0ZEQpMehcZHh8RCllEF2ZkX1pvRRJLb1hmEQpYWBdmW3x/R0hvHwV PZREKeE4XY1Nja3sTWH4aX14RCkNIFwcbEx8RCkNZFxkfEQpDSRcaBBoaGhEKWU0XZ2ZyEQpZSR cacRoQGncGGx8ZcRkZEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF3J6dV4aQ UBwYxgeHgcaXH8YfX5nZhx/H0AfG1hQYHB4EQpYXBcfBBoEGBkaBRsaBBsaGgQeEgQYGRAbHhof GhEKXlkXch4TQBsRCk1cFxkdHxEKTFoXfGlNTU0RCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEY Xb2trbGtrEQpCTxdkflhPZm5zSXBbTxEKQ1oXGBoTBBIfBBgbHAQfGBEKQl4XGxEKRF4XGBEKQl wXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdkUkIFGlgaXntDe BEKQk4XY1Nja3sTWH4aX14RCkJMF2ZbfH9HSG8fBU9lEQpCbBdiT2JEGktAG1JfXREKQkAXaV5T HkN/Hk1tG1sRCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxd6Q0ZuQxhCQV4BehEKWUsXEx4bEhE KcGcXZH1gbwUZQG5NfmMQGRoRCnBoF2t+HFATXhJOfUJgEBkaEQpwaBd6f2dLbhl+GE5aehAZGh EKcGgXbhtDTxplcn0feV8QGRoRCnBoF2ZSe01FUhkcUF1vEBkaEQpwaBdnZGNfehxNaHlkSBAZG hEKcGwXZh5pRRtISE1kaF8QBxsSEQpwQxdpfUt/fmUFbUZ8TxAHGxIRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: XP_t0kjZI244-0vU2WTML6U5j51rzJZR X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: XP_t0kjZI244-0vU2WTML6U5j51rzJZR X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 adultscore=0 spamscore=0 lowpriorityscore=0 phishscore=0 priorityscore=345 impostorscore=0 bulkscore=0 clxscore=173 mlxscore=0 mlxlogscore=999 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105260079 domainage_hfrom=9418 X-Spam-Score: 0 X-Spam-OrigSender: yjcoshc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, yjcoshc This is a multi-part message in MIME format. --------------803BA532917E28119AC7E376 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Kevin, Could you share some test input files for testing and debugging? Thanks, Haochuan Chen On 5/25/21 8:39 AM, Kevin Chan wrote: > Dear Users, > > I am trying to speed up an FEP calculation using /cudaSOAIntegrate > /with NAMD 3.0alpha9 single-node path, however, failed by getting either > > FATAL ERROR: Periodic cell has become too small for original patch grid! > Possible solutions are to restart from a recent checkpoint, > increase margin, or disable useFlexibleCell for liquid simulation. > > or > > FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813) > System unstable or pairlistdist or cutoff too small. > > The system has been tested with NAMD2.14 and NAMD3.0alpha9 without > /cudaSOAIntegrate /and worked perfectly fine. > > So I have tried to tackle the errors by > > 1. pairlistdist 13.5 to 16 > 2. margin 4, 8, 16, 20 > 3. /LangevinPistonDecay /100 to 1000 > > None of the combination worked. Sometimes first 1 or 2 windows (lambda > 0 to 0.001) got finished (500k+ steps), but I never got the middle > windows (lambda > 0.1) running. I also tried the alpha8 version and > had the same results. I set stepsPerCycle to 400 and pairlistsPerCycle > to 40 all the time. The run command is simply "namd3 +p1 +devices 0". > > I understand that FEP with CUDA speedup is still in alpha, so any > experience shared will be greatly appreciated. > > Thanks, > Kevin > Zhejiang University --------------803BA532917E28119AC7E376 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Kevin,

Could you share some test input files for testing and debugging?

Thanks,

Haochuan Chen


On 5/25/21 8:39 AM, Kevin Chan wrote:
Dear Users,

I am trying to speed up an FEP calculation using cudaSOAIntegrate with NAMD 3.0alpha9 single-node path, however, failed by getting either 

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

or

FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813) System unstable or pairlistdist or cutoff too small.

The system has been tested with NAMD2.14 and NAMD3.0alpha9 without cudaSOAIntegrate and worked perfectly fine. 

So I have tried to tackle the errors by 

1. pairlistdist 13.5 to 16
2. margin 4, 8, 16, 20
3. LangevinPistonDecay 100 to 1000

None of the combination worked. Sometimes first 1 or 2 windows (lambda 0 to 0.001) got finished (500k+ steps), but I never got the middle windows (lambda > 0.1) running. I also tried the alpha8 version and had the same results. I set stepsPerCycle to 400 and pairlistsPerCycle to 40 all the time. The run command is simply "namd3 +p1 +devices 0".

I understand that FEP with CUDA speedup is still in alpha, so any experience shared will be greatly appreciated. 

Thanks,
Kevin
Zhejiang University 
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A" Date: Thu, 27 May 2021 12:00:54 +0430 Message-ID: Subject: namd-l: question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD To: NAMD Content-Type: multipart/alternative; boundary="0000000000000c1e3b05c34abe45" X-CLX-Shades: MLX X-Proofpoint-GUID: Qq5V7eTN8oHnU2JPMbGytSb591wYRiFx X-Proofpoint-ORIG-GUID: Qq5V7eTN8oHnU2JPMbGytSb591wYRiFx X-CLX-Response: 1TFkXGx0SEQpMehcZHxkRCllEF2xoH2xzXEYbehoYEQpYWBdvWU9DRXNFZUt SXREKeE4XY1Nja3sTWH4aX14RCnlMF2Ede2NlWE1OekBhEQpDSBcHGxkdEQpDWRcHGx4YEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ScRkdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3tbH3wdT35kEkViRH8YYHpnSG1TXnlIHxMbXXN4Q2xSEQpYXBcfBBoEGBka BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXch9lE3IRCk1cFxsbHxEKTFoXbGlNTU0RCkxGF29ra2t raxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGxMEHh0RCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZx0fSRhOWURgW1IRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdvWU9DRXNFZUtSXREKQmwXbF9OYB9hbWABARgRCkJAF2hPcB9pHEBwRRlLEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXbmdYR0NoXnl+AV4RCllLFxMeGxMRCnBoF2x MSWdDS158ekxrEBkaEQpwaBdtSGhnRAUdYB5mXxAZGhEKcGgXbEdYSXNIWngefFIQGRoRCnBoF2 dnZBxtWEBuTG9bEBkaEQpwaBdvQnwBZB1uaUFBHhAZGhEKcGwXax18ZRJ9GVNEcE4QGRoRCm1+F xsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=807 suspectscore=0 lowpriorityscore=0 clxscore=178 malwarescore=0 phishscore=0 impostorscore=0 adultscore=0 mlxscore=0 spamscore=0 priorityscore=353 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105270050 domainage_hfrom=9419 X-Spam-Score: 0 X-Spam-OrigSender: matabay2010@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "M. A" --0000000000000c1e3b05c34abe45 Content-Type: text/plain; charset="UTF-8" Dear All, I am running MD simulation of ligand and protein interaction with the FEP method for calculation of free energy parameter. As is mentioned in page 36 of the related tutorial (In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD), we can measure the free-energy cost incurred for fading out pseudo bonds by zeroing out reversibly the associated force constants, until the aforementioned contribution due to the loss of translational entropy be recovered. Does anybody know how we can decrease the value of K in the extrabond section of namd config file? I need the exact script for decreasing K in every window (for example k=3 to k=0 with dK= 0.09) and simultaneously use it for measuring free energy in constant lambda. bests Maryam -- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology --0000000000000c1e3b05c34abe45 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear All,

I=C2=A0 am running MD simulation of ligan= d and protein interaction with the FEP method for calculation of free energ= y parameter. As is mentioned in page 36 of the related tutorial (In silico = alchemy: tutorial for alchemical free-energy perturbation calculations with= NAMD), we can measure the free-energy cost incurred for fading out pseudo = bonds by zeroing out reversibly the associated force constants, until the a= forementioned contribution due to the loss of translational entropy=C2=A0 b= e recovered. Does anybody know how we can decrease the value of K in the ex= trabond section of namd config file? I need the exact script for decreasing= K in every window (for example k=3D3 to k=3D0 with dK=3D 0.09) and simult= aneously use it for measuring free energy in constant lambda.


bests
Maryam

--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology

--0000000000000c1e3b05c34abe45-- From owner-namd-l@halifax.ks.uiuc.edu Thu May 27 04:29:14 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14R9TEc5004130; Thu, 27 May 2021 04:29:14 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14R9TEMm004129; Thu, 27 May 2021 04:29:14 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14R9TDgF004125; Thu, 27 May 2021 04:29:13 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 14R9TDFY004124; Thu, 27 May 2021 04:29:13 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 14R9Sx5l004114 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 27 May 2021 04:28:59 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 14R9JPnC010014 for ; Thu, 27 May 2021 09:28:58 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0a-00007101.pphosted.com with ESMTP id 38spvth6xd-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Thu, 27 May 2021 09:28:58 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 6603E1E4058B; Thu, 27 May 2021 11:28:55 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id 8lQI-7Jt0AlW; Thu, 27 May 2021 11:28:50 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 6D5F71E4058C; Thu, 27 May 2021 11:28:50 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id 3cq0rXg1g6ZV; Thu, 27 May 2021 11:28:50 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id A5AD61E4058B; Thu, 27 May 2021 11:28:49 +0200 (CEST) Date: Thu, 27 May 2021 11:28:37 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , "M. A" Message-ID: <1385149371.5764732.1622107717648.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: Re: namd-l: question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_ec1a175e-ce72-4171-985b-ca0e3f9ee3b8" X-Originating-IP: [81.67.142.130] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC90 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD Thread-Index: yyNnWmgxvE+Sr1DF8XZ/SJz8pXmR3Q== X-CLX-Shades: MLX X-Proofpoint-GUID: 7CkdSPMbeWc4_LI3kT73h2czzJ3yOhCa X-Proofpoint-ORIG-GUID: 7CkdSPMbeWc4_LI3kT73h2czzJ3yOhCa X-CLX-Response: 1TFkXGxwbEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxgeEQpDWRcHGxsSEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4bcR8aEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFx1pQU55emdIT31JHnVmYxlBfh0ZQhhJUFBgGVNlQmlLEQpYXBcfBBoEGBkaBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXch97WBsRCk1cFxkSEhEKTFoXeG1rTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdoQEVIGBh8a1t6GREKQ1oXGxMZBB4TBBgZHgQYGBsRCk JeFxsRCkReFxgRCkJFF2RYXFxNflJJG2VJEQpCThdlT34SQ2lmWRwBaREKQkwXehJnaWBZeUZBT 2URCkJsF2ESEk9PTE1/Tx4FEQpCQBdtRX9yb29me3NwaREKQlgXZ3Nlc0BuYWFMXWIRClpYFxgR CnlDF2xHUEkFZW9fbmVAEQpwZxdmYBhZRk5ZEx1ZfxAZGhEKcGgXYnlrWVBJQkRsZEYQGRoRCnB oF2xvZk1MfE5mGER4EBkaEQpwaBdgGmtyenB/UnBlXhAbGhkRCnBoF2VdE356RAVtc3lEEBkaEQ pwaBdoTWd7WRN+ZHtIGxAZGhEKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17GEVSEBkaE QptfhcaEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 impostorscore=0 clxscore=161 suspectscore=0 mlxscore=0 adultscore=0 lowpriorityscore=0 spamscore=0 phishscore=0 bulkscore=0 mlxlogscore=726 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105270062 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_ec1a175e-ce72-4171-985b-ca0e3f9ee3b8 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Maryam,=20 ----- On 27 Mai 21, at 9:30, M. A wrote:=20 > Dear All, > I am running MD simulation of ligand and protein interaction with the FEP= method > for calculation of free energy parameter. As is mentioned in page 36 of t= he > related tutorial (In silico alchemy: tutorial for alchemical free-energy > perturbation calculations with NAMD), we can measure the free-energy cost > incurred for fading out pseudo bonds by zeroing out reversibly the associ= ated > force constants, until the aforementioned contribution due to the loss of > translational entropy be recovered. Does anybody know how we can decrease= the > value of K in the extrabond section of namd config file? The force constant is part of the extrabonds file. You will need a differen= t extrabonds file for each value of the force constant. You can generate th= em with the scripting language of your choice. Then you need to run a NAMD = simulation using each of the extrabonds files.=20 > I need the exact script How much are you willing to pay someone to do that for you?=20 Best,=20 J=C3=A9r=C3=B4me=20 --=_ec1a175e-ce72-4171-985b-ca0e3f9ee3b8 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Maryam,

----- On 2= 7 Mai 21, at 9:30, M. A <matabay2010@gmail.com> wrote:
Dear All,

I  am running= MD simulation of ligand and protein interaction with the FEP method for ca= lculation of free energy parameter. As is mentioned in page 36 of the relat= ed tutorial (In silico alchemy: tutorial for alchemical free-energy perturb= ation calculations with NAMD), we can measure the free-energy cost incurred= for fading out pseudo bonds by zeroing out reversibly the associated force= constants, until the aforementioned contribution due to the loss of transl= ational entropy  be recovered. Does anybody know how we can decrease t= he value of K in the extrabond section of namd config file?
The force constant is part of the extrabonds file. You will n= eed a different extrabonds file for each value of the force constant. You c= an generate them with the scripting language of your choice. Then you need = to run a NAMD simulation using each of the extrabonds files.
I need the exact script
How much are you willing to pay someone to do that for you?


Best,
J=C3=A9r=C3=B4me
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boundary="000000000000cb693b05c353b25e" X-Proofpoint-GUID: KC_g62G7NSSXzrh_9ekdbP3Su3LEBvm0 X-CLX-Response: 1TFkXGxwSEQpMehcYEx8RCllEF2tcUF9tcwUTQmBgEQpYWBdlSEgZYm5sYWR cehEKeE4XY1Nja3sTWH4aX14RCnlMF25eHUVEWWJJQAEfEQpDSBcHGxwbEQpDWRcHGx4bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ScRgTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2FpdU0cGG0dZHl5clBYQnUTT0FOSHoZeV8ZZm9oXEcaEQpYXBcfBBoEGBka BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3Ifc31LEQpNXBcYGRMRCkxaF2lsaU1NaxEKTEYXb2t ra2trEQpCTxdlflxZW1tHY1NhbBEKQ1oXGBoTBBIfBBgbEgQfHhEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdvbmZibnNwUmddWhEKQk4XY1Nja 3sTWH4aX14RCkJMF2VISBlibmxhZFx6EQpCbBduU15/e01GYnpGeBEKQkAXZGxuXxtPHmxrf3wR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdsGxpGeRx/em1sSxEKWUsXEx4bExEKcGg XaE4dHVxAWUldH34QGhEKcGgXbH1GYAVvAWdzXEsQGhEKcGgXZWMcW2hFGlheSGgQGhEKcGgXZn AbYn9BU19Pa1oQGhEKcGgXaW1aaVtPHBpiZQUQGhEKcH0XYENjfkx6AWtZEwUQGhEKcH0XaXJBG 0NEQG9YGHsQHhIRCnB/F2h6eWtoel9OS15cEAcbExEKcF8Xb2dlBQUcaVIaaAEQGhEKcH8Xb04T R09lW1BiHV8QHhIRCnBfF2lyQRtDREBvWBh7EB4SEQpwbBdme2JIY3B7GBNHSRAZGhEKbX4XGxE KWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: KC_g62G7NSSXzrh_9ekdbP3Su3LEBvm0 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 clxscore=168 malwarescore=0 adultscore=0 mlxscore=0 phishscore=0 suspectscore=0 priorityscore=295 mlxlogscore=999 lowpriorityscore=0 spamscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105270118 domainage_hfrom=9419 X-Spam-Score: 0 X-Spam-OrigSender: abalaeff@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alexander Balaeff --000000000000cb693b05c353b25e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear NAMD community: Black Diamond Therapeutics, a precision oncology medicine company, is looking for a creative and self-motivated computational chemist with broad experience to apply her/his expertise and knowledge in the art of computational chemistry to drug discovery programs. The position is located= in Cambridge, MA, USA. The advertisement is forwarded below. Feel free to share it with your friends & colleagues, or apply yourself at the link: https://urldefense.com/v3/__https://careers-bdtherapeutics.icims.com/jobs/1= 046/computational-chemist/job__;!!DZ3fjg!qvclj8WsbaJG6quYfY6nYcMKd-qX9a-gi_= 6e6iHsLHxqkxlnJBbFN86YDFB1dj6SIA$=20 As a current employee, I highly recommend this fun and dynamic company as a great place to work :-) Best, Alexander. ** Computational Chemist ** Job Locations US-MA-Cambridge ID 2020-1046 Category Research - Chemistry Type Regular Full-Time Overview Black Diamond Therapeutics is a precision oncology medicine company pioneering the discovery and development of small molecule, tumor-agnostic therapies. Black Diamond targets undrugged mutations in patients with genetically defined cancers for whom limited treatment options currently exist. Black Diamond is built upon a deep understanding of cancer genetics, protein structure and function, and medicinal chemistry. The Company=E2=80= =99s proprietary technology platform, Mutation-Allostery-Pharmacology, or MAP, platform, is designed to allow Black Diamond to analyze population-level genetic sequencing data to identify oncogenic mutations that promote cancer across tumor types, group these mutations into families and develop a single small molecule therapy in a tumor-agnostic manner that targets a specific family of mutations. The Discovery Team at Black Diamond Therapeutics is looking for a creative and self-motivated scientist with broad experience to apply her/his expertise and knowledge in the art of computational chemistry to drug discovery programs. Reporting to the Director of Computational Chemistry, and based in our office in Cambridge, USA, the right candidate will support projects across all stages of discovery from early target selection through to development candidate nomination. She/he will interact and collaborate cross-functionally with scientists across the drug discovery organization. Responsibilities Apply computational techniques to advance projects at all phases of drug discovery, from target validation and hit generation to lead optimization and candidate selection Collaborate with discovery chemists and bioinformaticians to maximize computational impact on structure-, ligand-, and property-based design of selective molecules targeting allosteric mutant proteins Contribute, assist, and advise in the design, evaluation, and prioritization of new analogues for medicinal chemistry projects. Build and drive computational strategies to guide the design of small molecules with improved potency, selectivity, and ADME properties Develop testable hypotheses and deliver computational tools for predicting mutant selectivity, ADME, and in vivo pharmacokinetics. Propose and develop new modeling approaches to enhance existing workflows. Develop and enhance the cheminformatics and database systems at Black Diamond. Qualifications A Ph.D. in Computational Chemistry or a related discipline You have spent several years in industry developing and applying modern computational chemistry and cheminformatics to drug design. You are an expert in using virtual screening, data mining, machine learning, pharmacophore development, homology modeling, structure-based and ligand-based drug design, molecular dynamics. You are familiar with ORION and software from OpenEye, Python programing, statistical analysis, and artificial intelligence. You have a working knowledge of medicinal chemistry and drug discovery You thrive in a fast-paced, rapidly changing environment. Excellent written, verbal and presentation skills are required. You=E2=80=99re an honest communicator with the ability to present data clea= rly to experts and non-experts alike. You have demonstrated your impact by supporting publications, presentations, and/or patents. You have a strategic perspective and demonstrated ability to work in a rapidly changing, fast-paced environment. Your interpersonal and communication skills allow you to work effectively as part of cross functional teams. You are committed to building and maintaining an energetic, collaborative, and open culture. Work Environment: This job operates in a professional office environment. This role routinely uses standard office equipment. Physical Demands: The physical demands described here are representative of those that must be met by an employee to successfully perform he essential functions of this job. While performing the duties of this job, the employee is occasionally required to stand; walk; sit; used hands to fingers, handle, or feel objects, tools, or controls; reach with hands and arms; climb be stairs; talk or hear. The employee must occasionally lift or move office products and supplies, up to 20 lbs. Black Diamond Therapeutics is an equal opportunity employer and welcomes and encourages all applications. Diversity and inclusion are important core values and will encourage our creativity and growth as a company. Accommodations are available on request for candidates taking part in all aspects of the selection process. We thank all applicants for their interest, however, only those selected will be invited for an interview. Black Diamond Therapeutics values our relationships with our Recruitment Partners and will only accept resumes from those partners who have been contracted by a member of our Human Resources team to collaborate with us. Black Diamond is not responsible for any fees related to resumes that are unsolicited or are received by any employee of Black Diamond who is not a member of the Human Resources team =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D Dr. Alexander Balaeff Black Diamond Therapeutics abalaeff@gmail.com https://urldefense.com/v3/__http:/= /www.blackdiamondtherapeutics.com__;!!DZ3fjg!qvclj8WsbaJG6quYfY6nYcMKd-qX9a= -gi_6e6iHsLHxqkxlnJBbFN86YDFAutxajFw$=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D --000000000000cb693b05c353b25e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear NAMD co= mmunity:

Black Diamond Therapeutics= , a precision oncology medicine company, = is looking for a creative and self-motivated computational chemist with broad experience to apply her/his = expertise and knowledge in the art of computational chemistry to drug disco= very programs. The position is located in Cambridge, MA, USA. The advertisement= is forwarded below. Feel free to share it with your friends & colleagu= es, or apply yourself at the link:

https://careers-bdtherapeutics.icims.com/jobs/1046/computational-ch= emist/job

As a current employee, I highly recommend this fun and d= ynamic company as a great place to work :-)

Best,

Alexander.
=

** Comp= utational Chemist **

Job Locati= ons US-MA-Cambridge
ID 2020-1046 Category Research - Chemistry Type Regu= lar Full-Time

Overview

Black Diamond Therapeutics is a precis= ion oncology medicine company pioneering the discovery and development of s= mall molecule, tumor-agnostic therapies. Black Diamond targets undrugged mu= tations in patients with genetically defined cancers for whom limited treat= ment options currently exist. Black Diamond is built upon a deep understand= ing of cancer genetics, protein structure and function, and medicinal chemi= stry. The Company=E2=80=99s proprietary technology platform, Mutation-Allos= tery-Pharmacology, or MAP, platform, is designed to allow Black Diamond to = analyze population-level genetic sequencing data to identify oncogenic muta= tions that promote cancer across tumor types, group these mutations into fa= milies and develop a single small molecule therapy in a tumor-agnostic mann= er that targets a specific family of mutations.

The Discovery Team a= t Black Diamond Therapeutics is looking for a creative and self-motivated s= cientist with broad experience to apply her/his expertise and knowledge in = the art of computational chemistry to drug discovery programs. Reporting to= the Director of Computational Chemistry, and based in our office in Cambri= dge, USA, the right candidate will support projects across all stages of di= scovery from early target selection through to development candidate nomina= tion. She/he will interact and collaborate cross-functionally with scientis= ts across the drug discovery organization.

=C2=A0

Responsibil= ities

Apply computational techniques to advance projects at all phas= es of drug discovery, from target validation and hit generation to lead opt= imization and candidate selection
Collaborate with discovery chemists an= d bioinformaticians to maximize computational impact on structure-, ligand-= , and property-based design of selective molecules targeting allosteric mut= ant proteins
Contribute, assist, and advise in the design, evaluation, a= nd prioritization of new analogues for medicinal chemistry projects.
Bui= ld and drive computational strategies to guide the design of small molecule= s with improved potency, selectivity, and ADME properties
Develop testab= le hypotheses and deliver computational tools for predicting mutant selecti= vity, ADME, and in vivo pharmacokinetics.
Propose and develop new modeli= ng approaches to enhance existing workflows.
Develop and enhance the che= minformatics and database systems at Black Diamond.

Qualifications
A Ph.D. in Computational Chemistry or a related discipline
You hav= e spent several years in industry developing and applying modern computatio= nal chemistry and cheminformatics to drug design.
You are an expert in u= sing virtual screening, data mining, machine learning, pharmacophore develo= pment, homology modeling, structure-based and ligand-based drug design, mol= ecular dynamics.
You are familiar with ORION and software from OpenEye, = Python programing, statistical analysis, and artificial intelligence.
Yo= u have a working knowledge of medicinal chemistry and drug discovery
You= thrive in a fast-paced, rapidly changing environment.
Excellent written= , verbal and presentation skills are required.
You=E2=80=99re an honest = communicator with the ability to present data clearly to experts and non-ex= perts alike.
You have demonstrated your impact by supporting publication= s, presentations, and/or patents.
You have a strategic perspective and d= emonstrated ability to work in a rapidly changing, fast-paced environment.<= br>Your interpersonal and communication skills allow you to work effectivel= y as part of cross functional teams.
You are committed to building and m= aintaining an energetic, collaborative, and open culture.

Work Envir= onment:

This job operates in a professional office environment. This= role routinely uses standard office equipment.

Physical Demands:
The physical demands described here are representative of those that m= ust be met by an employee to successfully perform he essential functions of= this job.

While performing the duties of this job, the employee is = occasionally required to stand; walk; sit; used hands to fingers, handle, o= r feel objects, tools, or controls; reach with hands and arms; climb be sta= irs; talk or hear. The employee must occasionally lift or move office produ= cts and supplies, up to 20 lbs.

Black Diamond Therapeutics is an equ= al opportunity employer and welcomes and encourages all applications.=C2=A0= Diversity and inclusion are important core values and will encourage our c= reativity and growth as a company.=C2=A0 Accommodations are available on re= quest for candidates taking part in all aspects of the selection process.= =C2=A0 We thank all applicants for their interest, however, only those sele= cted will be invited for an interview.

Black Diamond Therapeutics va= lues our relationships with our Recruitment Partners and will only accept r= esumes from those partners who have been contracted by a member of our Huma= n Resources team to collaborate with us. Black Diamond is not responsible f= or any fees related to resumes that are unsolicited or are received by any = employee of Black Diamond who is not a member of the Human Resources team
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=C2=A0 =C2=A0Dr. Alexander Balaeff =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Black Diamond Ther= apeutics
=C2=A0 =C2=A0abalaeff@gma= il.com =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0www.blackdiamondtherapeutics.com
=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D
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A" Date: Fri, 28 May 2021 19:14:14 +0430 Message-ID: Subject: Re: namd-l: question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD To: =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= Cc: NAMD list Content-Type: multipart/alternative; boundary="000000000000a59bbe05c364e969" X-CLX-Shades: MLX X-Proofpoint-GUID: MBpK4AwmlUVV6oeJ6EjaMw3nV7yjxAeI X-CLX-Response: 1TFkXGxIZEQpMehcZGh4RCllEF2xoH2xzXEYbehoYEQpYWBdvWU9DRXNFZUt SXREKeE4XY1Nja3sTWH4aX14RCnlMF2Ede2NlWE1OekBhEQpDSBcHGRsdEQpDWRcHGxgeEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwZcR4YEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2doWmEea11HRn98fBxFT2Acb0BLZ10ZRHwdU0BSa09jEQpYXBcfBBoEGBka BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXch9bcEURCk1cFxsTEhEKTFoXe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEw QfGxEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdnHR9JGE5ZRGBbUhEKQk4XY1Nja3sTWH4aX14RCkJMF29ZT0NFc0VlS1JdEQpCbBds X05gH2FtYAEBGBEKQkAXbUV/cm9vZntzcGkRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdsR1BJBWVvX25lQBEKWUsXEx4YGhEKcGgXaHIdRWBLGx5jYmgQGRoRCnBoF3pjeV9IEnl9RG RPEBkaEQpwaBdnUx5BGGZ7UE1kWBAZGhEKcGgXa3pOX0llH2dFRVkQGRoRCnBoF2t/GQFze0JeZ 2JCEBkaEQpwbBdrHXxlEn0ZU0RwThAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sR IA== X-Proofpoint-ORIG-GUID: MBpK4AwmlUVV6oeJ6EjaMw3nV7yjxAeI X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=183 suspectscore=0 bulkscore=0 spamscore=0 malwarescore=0 adultscore=0 mlxscore=0 priorityscore=304 impostorscore=0 mlxlogscore=987 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2105280098 domainage_hfrom=9420 X-Spam-Score: 0 X-Spam-OrigSender: matabay2010@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "M. A" --000000000000a59bbe05c364e969 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi J=C3=A9r=C3=B4me, Thank you for your reply . I understood but unfortunately I can not pay and I need help. I prepared the extrabond files separately, but now I don't know how to write the script in the config file to use these extrabond files one after the other. If you can help me it would be kind of you. my config file is: # MD SETUP timestep 2.0 ##numsteps 1 # FLEXIBLE CELL useflexiblecell no # INPUT structure ionized.psf parameters par_all36_lipid.prm parameters par_all36_prot.prm parameters par_all22_prot.prm parameters par_all27_prot_lipid_na.inp parameters par_all36_cgenff.prm parameters par_all36_na.prm parameters par_all36_carb.prm paraTypeCharmm on coordinates ionized.pdb bincoordinates equilibration.coor binvelocities equilibration.vel extendedsystem equilibration.xsc # OUTPUT outputenergies 500 outputtiming 500 outputpressure 500 binaryoutput yes outputname forward restartname forward restartfreq 500 binaryrestart yes XSTFreq 500 # DCD DCDfreq 5000 DCDfile forward.dcd # PME PME yes PMETolerance 10e-6 PMEInterpOrder 4 PMEGridSizeX 60 PMEGridSizeY 60 PMEGridSizeZ 110 # WRAP WATER FOR OUTPUT wrapAll on # CONSTANT-T langevin on langevinTemp 300.0 langevinDamping 1.0 # CONSTANT-P LangevinPiston on LangevinPistonTarget 1 LangevinPistonPeriod 75 LangevinPistonDecay 25 LangevinPistonTemp 300 StrainRate 0.0 0.0 0.0 useGroupPressure yes # SPACE PARTITIONING splitpatch hydrogen hgroupcutoff 2.8 stepspercycle 10 margin 1.0 # CUT-OFFS switching on switchdist 10.0 cutoff 12.0 pairlistdist 14.0 limitDist 1.3 # RESPA fullElectFrequency 2 nonbondedFreq 1 # 1-4 NON-BONDED exclude scaled1-4 1-4scaling 1.0 # COM commotion no # SHAKE rigidbonds all rigidtolerance 0.000001 rigiditerations 400 # COLVARS SECTION extraBonds on #extraBondsCosAngles off extraBondsFile rest.pdb # FEP PARAMETERS source fep.tcl alch on alchType FEP alchFile solvate.fep alchCol B alchOutFreq 2500 alchOutFile forward.fepout alchElecLambdaStart 0.1 alchVdwLambdaEnd 1.0 alchVdwShiftCoeff 5.0 alchdecouple on alchEquilSteps 5000 set numSteps 500000 set dLambda 0.0 runFEP 1.0 1.0 $dLambda $numSteps best regards Maryam On Thu, May 27, 2021 at 1:58 PM J=C3=A9r=C3=B4me H=C3=A9nin wrote: > Dear Maryam, > > ----- On 27 Mai 21, at 9:30, M. A wrote: > > Dear All, > > I am running MD simulation of ligand and protein interaction with the FE= P > method for calculation of free energy parameter. As is mentioned in page = 36 > of the related tutorial (In silico alchemy: tutorial for alchemical > free-energy perturbation calculations with NAMD), we can measure the > free-energy cost incurred for fading out pseudo bonds by zeroing out > reversibly the associated force constants, until the aforementioned > contribution due to the loss of translational entropy be recovered. Does > anybody know how we can decrease the value of K in the extrabond section = of > namd config file? > > The force constant is part of the extrabonds file. You will need a > different extrabonds file for each value of the force constant. You can > generate them with the scripting language of your choice. Then you need t= o > run a NAMD simulation using each of the extrabonds files. > > I need the exact script > > How much are you willing to pay someone to do that for you? > > > Best, > J=C3=A9r=C3=B4me > --=20 Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology --000000000000a59bbe05c364e969 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi J=C3=A9r=C3=B4me,

Thank y= ou for your reply . I understood=C2=A0 but unfortunately I can not pay and = I need help. I prepared the extrabond files separately, but now I don't= know how to write the script in the config file to use these extrabond fil= es one after the other. If you can help me it would be kind of you. my conf= ig file is:
# MD SETUP
timestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A02.0
##numsteps =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A01
# FLEXIBLE CELL
useflexiblecell =C2=A0 = =C2=A0 =C2=A0 =C2=A0 no
# INPUT
structure =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 ionized.psf
parameters =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all36_lipid.prm
= parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0par_all36_prot.prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all22_prot.prm
param= eters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0par_all27_prot_lipid_na.inp
parameters =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all36_cgenff.prmparameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0par_all36_na.prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all36_carb.prm
paraType= Charmm =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on
coordinates =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0ionized.pdb
bincoordinates =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0equilibration.coor
binvelocities =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 equilibration.vel
extendedsystem =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0equilibration.xsc
# OUTPUT
outputenergies =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0500
outputtiming =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0500
outputpressure =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0500
binaryout= put =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0yes
outputname =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0forward
restartname =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 forward
restartfreq =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 500
binaryrestart =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 y= es
XSTFreq =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 500# DCD
DCDfreq =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = 5000
DCDfile =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 for= ward.dcd
# PME
PME =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 yes
PMETolerance =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A010e-6
PMEInterpOrder =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A04
PMEGr= idSizeX =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A060
PMEGridSizeY =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A060
PMEGridSizeZ =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0110
# WRAP WATER FOR OUTPUT
wrapAll =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on
# CONSTANT-T
langevin = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on
langevinTemp = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0300.0
langevinDamping =C2=A0 = =C2=A0 =C2=A0 =C2=A0 1.0
# CONSTANT-P
LangevinPiston =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0on
LangevinPistonTarget =C2=A0 =C2=A01
LangevinPi= stonPeriod =C2=A0 =C2=A075
LangevinPistonDecay =C2=A0 =C2=A0 25
Lange= vinPistonTemp =C2=A0 =C2=A0 =C2=A0300
StrainRate =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A00.0 0.0 0.0
useGroupPressure =C2=A0 =C2=A0 = =C2=A0 =C2=A0yes
# SPACE PARTITIONING
splitpatch =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0hydrogen
hgroupcutoff =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A02.8
stepspercycle =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 10
margin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A01.0
# CUT-OFFS
switching =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 on
switchdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1= 0.0
cutoff =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A012.0
pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A014.0
li= mitDist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.3
# RES= PA
fullElectFrequency =C2=A0 =C2=A0 =C2=A02
nonbondedFreq =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 1
# 1-4 NON-BONDED
exclude =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scaled1-4
1-4scaling =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
# COM
commotion =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 no
# SHAKE
rigidbonds =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0all
rigidtolerance =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A00.000001
rigiditerations =C2=A0 =C2=A0 =C2=A0 = =C2=A0 400
# COLVARS SECTION
extraBonds on
#extraBondsCosAngles of= f
extraBondsFile rest.pdb
# FEP PARAMETERS
source =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0fep.tcl=C2=A0=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0
alch =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on
alchType =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0FEP
alchFile =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0solvate.fep
alchCol =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 B
alchOutFreq =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 2500
alchOutFile =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= forward.fepout
alchElecLambdaStart =C2=A0 =C2=A0 0.1
alchVdwLambdaEn= d =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
alchVdwShiftCoeff =C2=A0 =C2=A0 =C2=A0 = 5.0
alchdecouple =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on
alchEqui= lSteps =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A05000
set numSteps =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0500000
set dLambda =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A00.0
runFEP 1.0 1.0 $dLambda $numSteps

best regards
Maryam

On Thu, May 27, 2021 at 1:58= PM J=C3=A9r=C3=B4me H=C3=A9nin <jerome.henin@ibpc.fr> wrote:
Dear Maryam,

=
----- On 27 Mai 21, at = 9:30, M. A <m= atabay2010@gmail.com> wrote:
Dear All,

I=C2=A0 am running MD simulation of ligand and protein interac= tion with the FEP method for calculation of free energy parameter. As is me= ntioned in page 36 of the related tutorial (In silico alchemy: tutorial for= alchemical free-energy perturbation calculations with NAMD), we can measur= e the free-energy cost incurred for fading out pseudo bonds by zeroing out = reversibly the associated force constants, until the aforementioned contrib= ution due to the loss of translational entropy=C2=A0 be recovered. Does any= body know how we can decrease the value of K in the extrabond section of na= md config file?
The force constant is part of = the extrabonds file. You will need a different extrabonds file for each val= ue of the force constant. You can generate them with the scripting language= of your choice. Then you need to run a NAMD simulation using each of the e= xtrabonds files.
I need th= e exact script
How much are you willing to pay= someone to do that for you?


Best,<= /div>
J=C3=A9r=C3=B4me


--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology

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Wed, 2 Jun 2021 12:44:09 +0000 Date: Wed, 2 Jun 2021 12:44:06 +0000 (UTC) From: "oivalf_nix@yahoo.com" To: NAMD DISCUSSION LIST Message-ID: <549467314.1465490.1622637846963@mail.yahoo.com> Subject: namd-l: Glycoprotein-flavonoid complex MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1465489_549164187.1622637846962" References: <549467314.1465490.1622637846963.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18368 YMailNorrin X-CLX-Shades: MLX X-Proofpoint-GUID: _Bkx85LQb0OF6iCLaZ09nAByYxAQptU6 X-Proofpoint-ORIG-GUID: _Bkx85LQb0OF6iCLaZ09nAByYxAQptU6 X-CLX-Response: 1TFkXGRwTEQpMehcZGxwRCllEF21rUB4ZSWBhfnxIEQpYWBdvH0R5W0FsGk1 5ehEKeE4XekQcHW9FbG1EQ2YRCnlMF2kBXWMTXUdbb2ZHEQpDSBcHHhMRCkNZFwcbGRkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwTcRsGGxkSdwYYGhoGGgYaBhsaGgYacRoQGncGGgYaBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThd1aEFSEh9me0gaZWwcQ2lmS3Aa E0RraFNzUmt7Wl5/HBEKWFwXHwQaBBgZGgUbGgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3IdeW0YEQp NXBcYHhkRCkxaF2hta2trEQpMRhdva2tva2sRCkJPF2hGeUdMAUwcW3JuEQpDWhcdHgQcBBsZGw QbGBkRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0VsbURDZhEKQ kUXbX54WV57fkIcEhwRCkJOF3pEHB1vRWxtRENmEQpCTBdvH0R5W0FsGk15ehEKQmwXbx9EeVtB bBpNeXoRCkJAF2NlUHscRhNge01nEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxkRCnlDF2x ta3NOGkceEh8aEQpZSxcTHBkYEQpwaBdjEmVDTGUcW2hPZxAdGREKcGgXZk99Xxpff39AHFkQBx kaEQpwaBdkS2Z7Zx1EAX4BfRAHGRoRCnBoF2dAQR1HemdmAUBOEAcZGhEKcGgXY3tPRHpGHFJub HoQBxkaEQpwbBdhZF8bbnB9bkRkZxAHGRoRCnBMF2BOE1ATRENmaXhfEAcZGhEKbX4XBxsRClhN F0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 mlxlogscore=922 lowpriorityscore=0 phishscore=0 impostorscore=0 bulkscore=0 malwarescore=0 clxscore=369 spamscore=0 adultscore=0 priorityscore=316 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106020082 domainage_hfrom=9632 X-Spam-Score: 0 X-Spam-OrigSender: oivalf_nix@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "oivalf_nix@yahoo.com" ------=_Part_1465489_549164187.1622637846962 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Hi I have a glycoprotein complex (pentasaccharide) bonded to a flavonoid ligand, which also has a D-glucose group. I used the Charmm-gui webserver to generate the inputs for namd. For the protein-oligosaccharide group it worked very well. However, the interface automatically recognizes the D-glucose group of the ligand and deletes the rest of the flavonoid. Ideally, the interface would have the option of not modeling the glycan group for a given chain. In this case, I would upload the ligand's force field, but this is not yet possible. My question is: Does anyone have any tips on how I could generate the .psf and .coor files for this glycoprotein-flavonoid complex? NOTE: I have already generated topology and parameter files for the flavonoid. Regards, Flavio ------=_Part_1465489_549164187.1622637846962 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi
I have a glycoprotein complex (pe= ntasaccharide) bonded to a flavonoid ligand, which also has a D-glucose gro= up.
I used the Charmm-gui webserver to generate the inputs for namd.
= For the protein-oligosaccharide group it worked very well.
However, the = interface automatically recognizes the D-glucose group of the ligand and de= letes the rest of the flavonoid.
Ideally, the interface would have the o= ption of not modeling the glycan group for a given chain. In this case, I w= ould upload the ligand's force field, but this is not yet possible.
My q= uestion is: Does anyone have any tips on how I could generate the .psf and = .coor files for this glycoprotein-flavonoid complex?
NOTE: I have alread= y generated topology and parameter files for the flavonoid.

<= /div>
Regards,

Flav= io
------=_Part_1465489_549164187.1622637846962-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jun 4 12:10:15 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154HAFHa020231; Fri, 4 Jun 2021 12:10:15 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 154HAFXD020230; Fri, 4 Jun 2021 12:10:15 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154HAEUT020226; Fri, 4 Jun 2021 12:10:14 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 154HAExo020225; Fri, 4 Jun 2021 12:10:14 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154HA5p4020217 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 4 Jun 2021 12:10:06 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 154H4jJW028572 for ; Fri, 4 Jun 2021 17:10:04 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=max.ebert@me.com; dkim=pass header.s=1a1hai header.d=me.com Received: from st43p00im-ztdg10061801.me.com (st43p00im-ztdg10061801.me.com [17.58.63.170]) by mx0a-00007101.pphosted.com with ESMTP id 38xj3exasp-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 04 Jun 2021 17:10:03 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=me.com; s=1a1hai; t=1622826602; bh=7i6TiSmikHni/JedwOulCiNI8x8ohDHZ/Pw8+ztWWyk=; h=From:Content-Type:Mime-Version:Subject:Message-Id:Date:To; b=AhdoK944k0DgL4A6F8xYBczIoIv6oXlcExO2JnvmI8xYHhy4T4hg72N4mSBj6ZQAs yuHkqvEnYEHAYyH+kLlqHdERZ7E2nG74ixS5IhUOIPFsaDIJofLXhc+cMJaKLu5sfH y3s+AIn7qdhLOqynBiMDtQviJ6AYUkhx2/ztcBkUjSGhmUc52meD7DfTQnTjGA/CO5 im/7+7/flkgClhVNX2lzONihhwm7gfBejmfjqzd8pBZUvFuQ3+e8Zsj0aQYMUmi8xc 4jswM3SVDS8lu9MueM/1sDPtycMiVGCtsUA1sGKaKHuwIVGBwtScrYlBALyqi4T6sN 1zeWHTsUhuNcw== Received: from smtpclient.apple (modemcable134.58-83-70.mc.videotron.ca [70.83.58.134]) by st43p00im-ztdg10061801.me.com (Postfix) with ESMTPSA id 361B88C03E1 for ; Fri, 4 Jun 2021 17:10:02 +0000 (UTC) From: Maximilian Ebert Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.100.0.2.22\)) Subject: namd-l: PSF file format Message-Id: <1E2F69EE-71A7-4E14-9183-BF0143152CE2@me.com> Date: Fri, 4 Jun 2021 13:10:00 -0400 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3654.100.0.2.22) X-Proofpoint-Virus-Version: =?UTF-8?Q?vendor=3Dfsecure_engine=3D1.1.170-22c6f66c430a71ce266a39bfe25bc?= =?UTF-8?Q?2903e8d5c8f:6.0.391,18.0.761,17.0.607.475.0000000_definitions?= =?UTF-8?Q?=3D2021-06-04=5F08:2021-06-04=5F01,2021-06-04=5F08,2020-04-07?= =?UTF-8?Q?=5F01_signatures=3D0?= X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 mlxscore=0 clxscore=1011 spamscore=0 adultscore=0 mlxlogscore=646 malwarescore=0 suspectscore=0 phishscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2106040122 X-Proofpoint-GUID: J1wpfEAL9UA9ZASK_zYt0x3rHn0Pa2J5 X-CLX-Response: 1TFkXGBseEQpMehcYHB4RCllEF2IdbU9wXVISE2VvEQpYWBdlWFJIQW1aaWV hbhEKeE4XbHBgeUAdYlJpGmIRCnlMF2tIZE9iZllmeUleEQpDSBcHHhkRCkNZFwcfExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsTHnEbHR8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYBtdWkxva2YTf2sTcGt5YXVQc14aUhlYYkQaeksYYB8RClhcFx8EGgQYGRoF GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdyEmtnbREKTVwXGxgcEQpMWhdsaU1NaxEKTEYXb2tra2t rEQpCTxdrBRwFTH59Y0BsbREKQ1oXGx0EHxIEHBkEGx0aEQpCXhcbEQpCXBcbEQpeThcbEQpCSx dscGB5QB1iUmkaYhEKQkkXbHBgeUAdYlJpGmIRCkJFF3obfUkeQWl8f2MbEQpCThdscGB5QB1iU mkaYhEKQkwXZVhSSEFtWmllYW4RCkJsF2REEkZmXVh7R2lOEQpCQBdmax9QZWcfUFpTSBEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF24YcB1ZZ0JJf2R8EQpZSxcTHRIYEQpwaBdma0Q dAWdEE2ZyQRAZGhEKcGgXbFAaYn4YWV8BRRsQGRoRCnBsF2JhZXpNT30bUEhMEBkaEQpwQxdjcx x/GkhyX31NbRAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: J1wpfEAL9UA9ZASK_zYt0x3rHn0Pa2J5 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 spamscore=0 lowpriorityscore=0 mlxlogscore=731 impostorscore=0 phishscore=0 clxscore=214 bulkscore=0 mlxscore=0 adultscore=0 suspectscore=0 priorityscore=264 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106040123 domainage_hfrom=9782 X-Spam-Score: 0 X-Spam-OrigSender: max.ebert@me.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 154HA6p3020218 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maximilian Ebert Dear list, Is there a resource which describes the PSF file format? I am many wondering about the max column width and if the width needs to be fixed or can changed when numbers get larger. 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engine=8.12.0-2104190000 definitions=main-2106040126 domainage_hfrom=12448 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 154HmjcW022553 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Josh Vermaas The best documentation on the format is *probably* the CHARMM documentation, which is actually rather sparse. https://urldefense.com/v3/__https://academiccharmm.org/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$ Basically, the first line of the PSF file dictates the field width. For regular, non-extended PSFs, the header will look like: PSF In these files, you are limited to 4 characters for segnames and atomtypes. CHARMM can also write (and VMD/NAMD can also read/write) "extended" PSF files. The headers for these will look like: PSF EXT This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows: PSF NAMD The NAMD/VMD version is the most flexible, since fields just need to be separated by spaces, and for the most part psfgen/VMD will select this option if the contents of the psf file demand it. -Josh On 6/4/21 1:10 PM, Maximilian Ebert wrote: > Dear list, > > Is there a resource which describes the PSF file format? I am many wondering about the max column width and if the width needs to be fixed or can changed when numbers get larger. > > Thanks > -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$ From owner-namd-l@halifax.ks.uiuc.edu Fri Jun 4 13:00:12 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154I0C8V024376; Fri, 4 Jun 2021 13:00:12 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 154I0B42024375; Fri, 4 Jun 2021 13:00:11 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154I0Bb5024371; 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Fri, 04 Jun 2021 10:59:59 -0700 (PDT) References: <1E2F69EE-71A7-4E14-9183-BF0143152CE2@me.com> In-Reply-To: From: Axel Kohlmeyer Date: Fri, 4 Jun 2021 13:59:48 -0400 Message-ID: Subject: Re: namd-l: PSF file format To: NAMD list , Josh Vermaas Cc: Maximilian Ebert Content-Type: multipart/alternative; boundary="000000000000cb5cd005c3f47594" X-CLX-Response: 1TFkXGxIaEQpMehcZGRIRCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGBIaEQpDWRcHHh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBpxGRMQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xe3pLQU1bZU5ZXE5JT11CGEwac11PTRkaExllbU1HGUcRClhcFx8EGgQYGRoF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXchJrHBIRCk1cFxwYHhEKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrfFlQWBlpXhhmWhEKQ1oXGBoTBBIfBBgaEg QbHRwRCkJeFxsRCkReFxgRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXYGBLGWZEY15eUHgRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6WGtMY2VdWwVE cBEKQmwXZnhufhhkZUESWH8RCkJAF2UeXGBERH8YRltnEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxE KeUMXYVBOa11+eHpERkARCllLFxMeGB0RCnBoF25sSUVeYn1GQGRSEBkaEQpwaBdnUxltZGQFAR xuRRAZGhEKcGgXZFtrWUJdGX1laFIQGRoRCnBoF21bR394Rl5FSXhLEBkaEQpwaBdtGFNGREsSY 2JmTxAcGhEKcH0XZ25/XUZ4GFt9Z2wQHBoRCnB9F2tHZl5CSAEdQntjEBwaEQpwfRdgGEUbAUga Exp5UhAeEhEKcH8XYWZvWxpnZEJIHVsQGxgYEQpwXxdjYhJQSGN4H3xCfRASEhEKcH8XaHpfYh5 +WwVkUhsQGxsaEQpwXxdgExlmS05sTkVTexAeEhEKcGwXYGlHZ2lSX39feEwQHhIRCnBMF21oZR lBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: QPakgqOdsvdcewh2f0Yweg3093OGgm3m X-CLX-Shades: MLX X-Proofpoint-GUID: QPakgqOdsvdcewh2f0Yweg3093OGgm3m MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 clxscore=180 malwarescore=0 priorityscore=338 suspectscore=0 spamscore=0 lowpriorityscore=0 phishscore=0 mlxscore=0 impostorscore=0 bulkscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106040126 domainage_hfrom=9427 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --000000000000cb5cd005c3f47594 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable lore has it that the *authoritative* documentation of the CHARMM file formats is the CHARMM source code. one important point to note is that PSF (and PDB) are file formats based on Fortran style formatting, which has fixed widths and does not need spaces as separators. so it can be legal to have something like: 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 but if you would write out 1001 1002 1003 1004 in would be read as 1001, 100, 210, 31 that is different from how C/C++ and Python process input. So what it now boils down to is what you are after: do you want to write out or edit PSF files to be fully conforming, or do they just have to be read by NAMD. Axel. P.S.: there are some more possible flags to appear in the first line to indicate the use of the PSF for specific purposes On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas wrote: > The best documentation on the format is *probably* the CHARMM > documentation, which is actually rather sparse. > > https://urldefense.com/v3/__https://academiccharmm.org/documentation/vers= ion/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx= 66nLOh7NH4vymgTxHM9_y3qw$ > > Basically, the first line of the PSF file dictates the field width. For > regular, non-extended PSFs, the header will look like: > > PSF > > In these files, you are limited to 4 characters for segnames and > atomtypes. CHARMM can also write (and VMD/NAMD can also read/write) > "extended" PSF files. The headers for these will look like: > > PSF EXT > > This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can > write space-delimited psf files, which are tagged as follows: > > PSF NAMD > > The NAMD/VMD version is the most flexible, since fields just need to be > separated by spaces, and for the most part psfgen/VMD will select this > option if the contents of the psf file demand it. > > -Josh > > On 6/4/21 1:10 PM, Maximilian Ebert wrote: > > Dear list, > > > > Is there a resource which describes the PSF file format? I am many > wondering about the max column width and if the width needs to be fixed or > can changed when numbers get larger. > > > > Thanks > > > -- > Josh Vermaas > > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and > Molecular Biology > Michigan State University > > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4v= ymgTxF1980Jig$ > > > --=20 Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!p-wNAv3ovVg_nB2ZTNtCw1YI1YgEhtCqEwvmhNx5kIZ70jVHlH8z= ck9jETJ9ZMFntw$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. --000000000000cb5cd005c3f47594 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
lore has it that the *authoritative* documentati= on of the CHARMM file formats is the CHARMM source code.

one important poi= nt to note is that PSF (and PDB) are file formats based on Fortran style fo= rmatting, which has fixed widths and does not need spaces as separators.
so i= t can be legal to have something like:

1001100210031004 (for a 4I4 format)= being read as 1001, 1002, 1003, 1004 but if you would write out 1001 1002 = 1003 1004=C2=A0 in would be read as 1001, 100,=C2=A0 210, 31
that is differen= t from how C/C++ and Python process input.

So what it now boils down to is= what you are after: do you want to write out or edit PSF files to be fully= conforming, or do they just have to be read by NAMD.

Axel.

P.S.: there a= re some more possible flags to appear in the first line to indicate the use= of the PSF for specific purposes


On Fri, Jun 4, 2021 at 1:49 PM = Josh Vermaas <vermaasj@msu.edu&g= t; wrote:
The be= st documentation on the format is *probably* the CHARMM
documentation, which is actually rather sparse.
ht= tps://urldefense.com/v3/__https://academiccharmm.org/documentation/version/= c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nL= Oh7NH4vymgTxHM9_y3qw$

Basically, the first line of the PSF file dictates the field width. For
regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:

PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be
separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@msu.edu<= br> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
https://urlde= fense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!= DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$<= /a>




--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://= goo.gl/1wk0
College of Science & Technology, Temple University, = Philadelphia PA, USA
International Centre for Theoretical Physics, Tries= te. Italy.
--000000000000cb5cd005c3f47594-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jun 4 13:52:01 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154Iq1nG026868; Fri, 4 Jun 2021 13:52:01 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 154Iq0BG026867; Fri, 4 Jun 2021 13:52:00 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154Iq01f026863; Fri, 4 Jun 2021 13:52:00 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 154Iq0kB026862; Fri, 4 Jun 2021 13:52:00 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 154Ipr5u026851 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Fri, 4 Jun 2021 18:51:50 +0000 (UTC) From: Maximilian Ebert Message-Id: <1C53D749-0CDE-41DA-8438-830A21B720EB@me.com> Content-Type: multipart/alternative; boundary="Apple-Mail=_95B1746C-F9E3-49A5-A07A-11CCA6BA3A91" Subject: Re: namd-l: PSF file format Date: Fri, 4 Jun 2021 14:51:49 -0400 In-Reply-To: Cc: NAMD list , Josh Vermaas To: Axel Kohlmeyer References: <1E2F69EE-71A7-4E14-9183-BF0143152CE2@me.com> X-Mailer: Apple Mail (2.3654.100.0.2.22) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:6.0.391,18.0.761 definitions=2021-06-04_12:2021-06-04,2021-06-04 signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=0 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1011 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-2009150000 definitions=main-2106040133 X-Proofpoint-GUID: HYW7ysM72aJhOAueRM7PgQxHrNddFhQ5 X-Proofpoint-ORIG-GUID: HYW7ysM72aJhOAueRM7PgQxHrNddFhQ5 X-CLX-Response: 1TFkXGx0TEQpMehcYEhwRCllEF2IdbU9wXVISE2VvEQpYWBdlWFJIQW1aaWV hbhEKeE4XbHBgeUAdYlJpGmIRCnlMF2tIZE9iZllmeUleEQpDSBcHGRMYEQpDWRcHHh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxNxHRwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYnN9HVNZZx0YS2BCZWtfT3hnHXpNe1JiWGROTmxCex8RClhcFx8EGgQYGRoF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyEmhYQBEKTVwXGB4dEQpMWhd8aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2Niengbb39JQU5rEQpDWhcbHQQfEgQcGQQbHR MRCkJeFxsRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2xwYHlAHWJSaRpiEQpCSRdscGB5QB1iUmkaY hEKQkUXeht9SR5BaXx/YxsRCkJOF2xwYHlAHWJSaRpiEQpCTBdlWFJIQW1aaWVhbhEKQmwXZEQS RmZdWHtHaU4RCkJAF2UeXGBERH8YRltnEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHxEKeUM XYVBOa11+eHpERkARCllLFxMdEhgRCnBoF2FFYVNbYWxpZx5rEBkaEQpwaBdkS19rQW1wfXN6QB AZGhEKcGgXb3hSZkNeQ0t6Yk8QGRoRCnBoF2Bga2ZHAWB4ekFeEBkaEQpwaBdsa08BXWFYQxlPW RAZGhEKcH0XZ25/XUZ4GFt9Z2wQHBoRCnB9F2tHZl5CSAEdQntjEBwaEQpwfRdgGEUbAUgaExp5 UhAcGhEKcH8XYWZvWxpnZEJIHVsQGxsTEQpwXxdjYhJQSGN4H3xCfRASGBEKcH8XaHpfYh5+WwV kUhsQGxsTEQpwXxdgExlmS05sTkVTexAcGhEKcGwXYmFlek1PfRtQSEwQGhEKcEwXbWhlGUFSfX sYRVIQGRoRCnBDF2NzHH8aSHJffU1tEBoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 malwarescore=0 bulkscore=0 priorityscore=286 mlxscore=0 spamscore=0 suspectscore=0 lowpriorityscore=0 mlxlogscore=999 adultscore=0 clxscore=179 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106040132 domainage_hfrom=9782 X-Spam-Score: 0 X-Spam-OrigSender: max.ebert@me.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maximilian Ebert --Apple-Mail=_95B1746C-F9E3-49A5-A07A-11CCA6BA3A91 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Thanks for the answer. I am trying to write out a compliment PSF file for s= ystem with over 1 million atoms. I want to be sure to not bust any field wi= dth and get into trouble with the NAMD PSF parser. So I guess you can=E2=80= =99t be fully compliant for system which go over a certain number of atoms = correct? Is my assumption correct that NAMD uses the space as a separator a= nd that VMD for example has fixed field width? Max > On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer wrote: >=20 > lore has it that the *authoritative* documentation of the CHARMM file for= mats is the CHARMM source code. >=20 > one important point to note is that PSF (and PDB) are file formats based = on Fortran style formatting, which has fixed widths and does not need space= s as separators. > so it can be legal to have something like: >=20 > 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 = but if you would write out 1001 1002 1003 1004 in would be read as 1001, 1= 00, 210, 31 > that is different from how C/C++ and Python process input. >=20 > So what it now boils down to is what you are after: do you want to write = out or edit PSF files to be fully conforming, or do they just have to be re= ad by NAMD. >=20 > Axel. >=20 > P.S.: there are some more possible flags to appear in the first line to i= ndicate the use of the PSF for specific purposes >=20 >=20 > On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas > wrote: > The best documentation on the format is *probably* the CHARMM=20 > documentation, which is actually rather sparse.=20 > https://urldefense.com/v3/__https://academiccharmm.org/documentation/vers= ion/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx= 66nLOh7NH4vymgTxHM9_y3qw$ =20 >=20 > Basically, the first line of the PSF file dictates the field width. For=20 > regular, non-extended PSFs, the header will look like: >=20 > PSF >=20 > In these files, you are limited to 4 characters for segnames and=20 > atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)=20 > "extended" PSF files. The headers for these will look like: >=20 > PSF EXT >=20 > This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can= =20 > write space-delimited psf files, which are tagged as follows: >=20 > PSF NAMD >=20 > The NAMD/VMD version is the most flexible, since fields just need to be=20 > separated by spaces, and for the most part psfgen/VMD will select this=20 > option if the contents of the psf file demand it. >=20 > -Josh >=20 > On 6/4/21 1:10 PM, Maximilian Ebert wrote: > > Dear list, > > > > Is there a resource which describes the PSF file format? I am many wond= ering about the max column width and if the width needs to be fixed or can = changed when numbers get larger. > > > > Thanks > > > --=20 > Josh Vermaas >=20 > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State University > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4v= ymgTxF1980Jig$ =20 >=20 >=20 >=20 >=20 > --=20 > Dr. Axel Kohlmeyer akohlmey@gmail.com https= ://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!rEJu6_H8cDKYNH3kS6pdPB= lDfMIMi7LjGo_8KKGxFUzUh-nlF9KJXxO51I66IS-5Rw$ > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy. --Apple-Mail=_95B1746C-F9E3-49A5-A07A-11CCA6BA3A91 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Thanks for the answer. I a= m trying to write out a compliment PSF file for system with over 1 million = atoms. I want to be sure to not bust any field width and get into trouble w= ith the NAMD PSF parser. So I guess you can=E2=80=99t be fully compliant fo= r system which go over a certain number of atoms correct? Is my assumption = correct that NAMD uses the space as a separator and that VMD for example ha= s fixed field width?

Ma= x


On Jun 4, 2021, at 1:59 PM, Axel Kohlm= eyer <akohlmey@gmail.co= m> wrote:

lore has it that the *a= uthoritative* documentation of the CHARMM file formats is the CHARMM source= code.

one important point to note is that PSF (and PDB) are fi= le formats based on Fortran style formatting, which has fixed widths and do= es not need spaces as separators.
so it can be legal to have something like= :
=
1001100210031004 (for a 4I4 format) being read as 1001, 1002,= 1003, 1004 but if you would write out 1001 1002 1003 1004  in would b= e read as 1001, 100,  210, 31
that is different from how C/C++ and Pyth= on process input.

So what it now boils down to is what you are = after: do you want to write out or edit PSF files to be fully conforming, o= r do they just have to be read by NAMD.

Axel.

P.S= .: there are some more possible flags to appear in the first line to indica= te the use of the PSF for specific purposes


O= n Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas <vermaasj@msu.edu> wrote:
The best documentation on the= format is *probably* the CHARMM
documentation, which is actually rather sparse.
https://urldefense.com/v3/__https://academiccharmm.org/documentati= on/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2= pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$

Basically, the first line of the PSF file dictates the field width. For regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:

PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@m= su.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
ht= tps://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-ve= rmaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgT= xF1980Jig$




--
Dr= . Axel Kohlmeyer  akohlmey@gmail.com  http://goo.gl/= 1wk0
College of Science & Technology, Temple Universi= ty, Philadelphia PA, USA
International Centre for Theoretical= Physics, Trieste. Italy.

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boundary="000000000000a2991f05c3f5407b" X-CLX-Response: 1TFkXGxwcEQpMehcZHx8RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHh8YEQpDWRcHHhIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhxxGBIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XREl1RRhyB3V+UkVDHHhEWH1NXWRnSE1PXBleH1BzeEERClhcFx8EGgQYGRoF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXchJoXW0RCk1cFx8eEhEKTFoXe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbEhgRCkJeFxsRCkReFxgRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4 YBEKQmwXYV96UxlDRBp6G34RCkJAF2UeXGBERH8YRltnEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxE KeUMXYVBOa11+eHpERkARCllLFxMeGB0RCnBoF2dTGW1kZAUBHG5FEB0aEQpwaBdkW2tZQl0ZfW VoUhAdGhEKcGgXbVtHf3hGXkVJeEsQHRoRCnBoF20YU0ZESxJjYmZPEBIfEQpwaBdiYGd8Y0cSc h5zeBAZGhEKcH0XbhxJUxxscHxmXxIQGRoRCnB9F2duf11GeBhbfWdsEBIfEQpwfRdrR2ZeQkgB HUJ7YxASHxEKcH0XYBhFGwFIGhMaeVIQHBoRCnB/F2UZeWZeR2kbZE9zEBsaGhEKcF8XZGsTW3k TYm1yeksQGRoRCnB/F2Fmb1saZ2RCSB1bEBsYHxEKcF8XY2ISUEhjeB98Qn0QEh0RCnB/F2h6X2 IeflsFZFIbEBsbGhEKcF8XYBMZZktObE5FU3sQHBoRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdta GUZQVJ9exhFUhAeEhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: nc_o2X-_Txoi6RnrWgwNMbgev3t5zYRk X-CLX-Shades: MLX X-Proofpoint-GUID: nc_o2X-_Txoi6RnrWgwNMbgev3t5zYRk MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 clxscore=166 malwarescore=0 priorityscore=355 suspectscore=0 spamscore=0 lowpriorityscore=0 phishscore=0 mlxscore=0 impostorscore=0 bulkscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106040133 domainage_hfrom=9427 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000a2991f05c3f5407b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Max, for large systems the recommended format in VMD/NAMD is "JS": https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert wrote: > Thanks for the answer. I am trying to write out a compliment PSF file for > system with over 1 million atoms. I want to be sure to not bust any field > width and get into trouble with the NAMD PSF parser. So I guess you can= =E2=80=99t > be fully compliant for system which go over a certain number of atoms > correct? Is my assumption correct that NAMD uses the space as a separator > and that VMD for example has fixed field width? > > Max > > > On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer wrote: > > lore has it that the *authoritative* documentation of the CHARMM file > formats is the CHARMM source code. > > one important point to note is that PSF (and PDB) are file formats based > on Fortran style formatting, which has fixed widths and does not need > spaces as separators. > so it can be legal to have something like: > > 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 > but if you would write out 1001 1002 1003 1004 in would be read as 1001, > 100, 210, 31 > that is different from how C/C++ and Python process input. > > So what it now boils down to is what you are after: do you want to write > out or edit PSF files to be fully conforming, or do they just have to be > read by NAMD. > > Axel. > > P.S.: there are some more possible flags to appear in the first line to > indicate the use of the PSF for specific purposes > > > On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas wrote: > >> The best documentation on the format is *probably* the CHARMM >> documentation, which is actually rather sparse. >> >> https://urldefense.com/v3/__https://academiccharmm.org/documentation/ver= sion/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsK= x66nLOh7NH4vymgTxHM9_y3qw$ >> >> Basically, the first line of the PSF file dictates the field width. For >> regular, non-extended PSFs, the header will look like: >> >> PSF >> >> In these files, you are limited to 4 characters for segnames and >> atomtypes. CHARMM can also write (and VMD/NAMD can also read/write) >> "extended" PSF files. The headers for these will look like: >> >> PSF EXT >> >> This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can >> write space-delimited psf files, which are tagged as follows: >> >> PSF NAMD >> >> The NAMD/VMD version is the most flexible, since fields just need to be >> separated by spaces, and for the most part psfgen/VMD will select this >> option if the contents of the psf file demand it. >> >> -Josh >> >> On 6/4/21 1:10 PM, Maximilian Ebert wrote: >> > Dear list, >> > >> > Is there a resource which describes the PSF file format? I am many >> wondering about the max column width and if the width needs to be fixed = or >> can changed when numbers get larger. >> > >> > Thanks >> > >> -- >> Josh Vermaas >> >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and >> Molecular Biology >> Michigan State University >> >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4= vymgTxF1980Jig$ >> >> >> > > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http:= //goo.gl/1wk0__;!!DZ3fjg!vEskiYZs4uWQTl-q6HIFaq3vUrz4LU7wgXThKKXY1Je_RzZ9at= 1d7ZNw_ZqE3Na-bg$=20 > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy. > > > --000000000000a2991f05c3f5407b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Max, for large systems the recommended=C2=A0format in V= MD/NAMD is "JS":

On Fri, Jun 4, 2021 at = 2:53 PM Maximilian Ebert <max.ebert@= me.com> wrote:
Thanks for the answer. I am= trying to write out a compliment PSF file for system with over 1 million a= toms. I want to be sure to not bust any field width and get into trouble wi= th the NAMD PSF parser. So I guess you can=E2=80=99t be fully compliant for= system which go over a certain number of atoms correct? Is my assumption c= orrect that NAMD uses the space as a separator and that VMD for example has= fixed field width?

Max


On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer <ako= hlmey@gmail.com> wrote:

lor= e has it that the *authoritative* documentation of the CHARMM file formats = is the CHARMM source code.

one important point to note is that PSF (and PD= B) are file formats based on Fortran style formatting, which has fixed widt= hs and does not need spaces as separators.
so it can be legal to have somethi= ng like:

1001100210031004 (for a 4I4 format) being read as 1001, 1002, 100= 3, 1004 but if you would write out 1001 1002 1003 1004=C2=A0 in would be re= ad as 1001, 100,=C2=A0 210, 31
that is different from how C/C++ and Python pr= ocess input.

So what it now boils down to is what you are after: do you wa= nt to write out or edit PSF files to be fully conforming, or do they just h= ave to be read by NAMD.

Axel.

P.S.: there are some more possible flags = to appear in the first line to indicate the use of the PSF for specific pur= poses


On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas <vermaasj= @msu.edu> wrote:
The best documentation on the format is *probably* the CHARMM
documentation, which is actually rather sparse.
https://urldefense.com/v3/__https://academiccharmm.or= g/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55= ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$

Basically, the first line of the PSF file dictates the field width. For
regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:

PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be
separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.ed= u/people/faculty/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHL= a2pb7HsKx66nLOh7NH4vymgTxF1980Jig$




--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://goo.gl/1wk0=
College of Science & Technology, Temple University, Philadelphia PA= , USA
International Centre for Theoretical Physics, Trieste. Italy.

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Fri, 4 Jun 2021 21:38:04 +0000 (UTC) From: Maximilian Ebert Message-Id: <33AC0F04-2DBA-4368-9D26-47B27258B8B1@me.com> Content-Type: multipart/alternative; boundary="Apple-Mail=_6C008BE5-00CD-4D93-83AC-24BFB6A6FD9C" Subject: Re: namd-l: PSF file format Date: Fri, 4 Jun 2021 17:38:03 -0400 In-Reply-To: Cc: NAMD list , Axel Kohlmeyer , Josh Vermaas To: Giacomo Fiorin References: <1E2F69EE-71A7-4E14-9183-BF0143152CE2@me.com> <1C53D749-0CDE-41DA-8438-830A21B720EB@me.com> X-Mailer: Apple Mail (2.3654.100.0.2.22) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:6.0.391,18.0.761 definitions=2021-06-04_16:2021-06-04,2021-06-04 signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=0 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1011 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-2009150000 definitions=main-2106040148 X-Proofpoint-GUID: XhbjSjsZSXxK7A4Yub0L4gZvRWO2ZcIj X-Proofpoint-ORIG-GUID: XhbjSjsZSXxK7A4Yub0L4gZvRWO2ZcIj X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBseEQpMehcYEhkRCllEF2IdbU9wXVISE2VvEQpYWBdlWFJIQW1aaWV hbhEKeE4XbHBgeUAdYlJpGmIRCnlMF2tIZE9iZllmeUleEQpDSBcHHhsSEQpDWRcHHhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEx5xGx0fEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3JCSEB5QFlweXJSYR1rHnNfSBpmHk1wXHh9ZRhwSWNAEQpYXBcfBBoEGBka BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3ISb2JwEQpNXBcYGRIRCkxaF3tpa01rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XawUcBUx+fWNAbG0RCkNaFxsdBB8SBBwZBB sdHREKQl4XGxEKREkXGREKQlwXGxEKXk4XGxEKQksXbHBgeUAdYlJpGmIRCkJJF2xwYHlAHWJSa RpiEQpCRRd6G31JHkFpfH9jGxEKQk4XbHBgeUAdYlJpGmIRCkJMF2VYUkhBbVppZWFuEQpCbBdk RBJGZl1Ye0dpThEKQkAXZR5cYEREfxhGW2cRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcfEQp 5QxdhUE5rXX54ekRGQBEKWUsXEx0SGBEKcGgXbklkQ0FITEQZBRoQGRoRCnBoF2BoGWR6G25de3 0YEBkaEQpwaBdmR09MaXttG1lsQBAZGhEKcGgXaFxiYkRuHH5ZfmMQGRoRCnBoF2ZOaGgfHmhvf mkaEBkaEQpwfRduHElTHGxwfGZfEhAcGhEKcH0XZ25/XUZ4GFt9Z2wQGRoRCnB9F2tHZl5CSAEd QntjEBkaEQpwfRdgGEUbAUgaExp5UhAcGhEKcH8XZRl5Zl5HaRtkT3MQGxgaEQpwXxdkaxNbeRN ibXJ6SxAcGhEKcH8XYWZvWxpnZEJIHVsQGxsZEQpwXxdjYhJQSGN4H3xCfRASGREKcH8XaHpfYh 5+WwVkUhsQGxscEQpwXxdgExlmS05sTkVTexAdEhEKcGwXYmFlek1PfRtQSEwQBxsSEQpwTBdta GUZQVJ9exhFUhAZGhEKcEMXY3McfxpIcl99TW0QBxsSEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=283 bulkscore=0 phishscore=0 lowpriorityscore=0 suspectscore=0 impostorscore=0 clxscore=214 mlxscore=0 mlxlogscore=999 adultscore=0 spamscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106040148 domainage_hfrom=9782 X-Spam-Score: 0 X-Spam-OrigSender: max.ebert@me.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maximilian Ebert --Apple-Mail=_6C008BE5-00CD-4D93-83AC-24BFB6A6FD9C Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Giacomo, This is a bit concerning: Due to the lack of full structure data on every node, various features not = normally needed for large simulations are non-functional or restricted. The= se limits, combined with the small number of projects using memory-optimize= d NAMD, cause us to caution users that this capability should be considered= experimental. Also is there a full documentation of the JS and namdbin format? Where can = I find the Fortran style formatting for PSFs? And how are they different wh= en read into NAMD? Max > On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin wro= te: >=20 > Hi Max, for large systems the recommended format in VMD/NAMD is "JS": > https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction = >=20 > On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert > wrote: > Thanks for the answer. I am trying to write out a compliment PSF file for= system with over 1 million atoms. I want to be sure to not bust any field = width and get into trouble with the NAMD PSF parser. So I guess you can=E2= =80=99t be fully compliant for system which go over a certain number of ato= ms correct? Is my assumption correct that NAMD uses the space as a separato= r and that VMD for example has fixed field width? >=20 > Max >=20 >=20 >> On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer > wrote: >>=20 >> lore has it that the *authoritative* documentation of the CHARMM file fo= rmats is the CHARMM source code. >>=20 >> one important point to note is that PSF (and PDB) are file formats based= on Fortran style formatting, which has fixed widths and does not need spac= es as separators. >> so it can be legal to have something like: >>=20 >> 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004= but if you would write out 1001 1002 1003 1004 in would be read as 1001, = 100, 210, 31 >> that is different from how C/C++ and Python process input. >>=20 >> So what it now boils down to is what you are after: do you want to write= out or edit PSF files to be fully conforming, or do they just have to be r= ead by NAMD. >>=20 >> Axel. >>=20 >> P.S.: there are some more possible flags to appear in the first line to = indicate the use of the PSF for specific purposes >>=20 >>=20 >> On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas > wrote: >> The best documentation on the format is *probably* the CHARMM=20 >> documentation, which is actually rather sparse.=20 >> https://urldefense.com/v3/__https://academiccharmm.org/documentation/ver= sion/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsK= x66nLOh7NH4vymgTxHM9_y3qw$ <>=20 >>=20 >> Basically, the first line of the PSF file dictates the field width. For= =20 >> regular, non-extended PSFs, the header will look like: >>=20 >> PSF >>=20 >> In these files, you are limited to 4 characters for segnames and=20 >> atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)=20 >> "extended" PSF files. The headers for these will look like: >>=20 >> PSF EXT >>=20 >> This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can= =20 >> write space-delimited psf files, which are tagged as follows: >>=20 >> PSF NAMD >>=20 >> The NAMD/VMD version is the most flexible, since fields just need to be= =20 >> separated by spaces, and for the most part psfgen/VMD will select this=20 >> option if the contents of the psf file demand it. >>=20 >> -Josh >>=20 >> On 6/4/21 1:10 PM, Maximilian Ebert wrote: >> > Dear list, >> > >> > Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger. >> > >> > Thanks >> > >> --=20 >> Josh Vermaas >>=20 >> vermaasj@msu.edu <> >> Assistant Professor, Plant Research Laboratory and Biochemistry and Mole= cular Biology >> Michigan State University >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4= vymgTxF1980Jig$ <>=20 >>=20 >>=20 >>=20 >>=20 >> --=20 >> Dr. Axel Kohlmeyer akohlmey@gmail.com <> https://urldefense.com/v3/__h= ttp://goo.gl/1wk0__;!!DZ3fjg!pDAF--74IildTv1UlAQlsAQ3Bi_p55e0sWNSWHOILBijfi= 5RwBOBN_aoQTKNabMAyw$ <> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >=20 --Apple-Mail=_6C008BE5-00CD-4D93-83AC-24BFB6A6FD9C Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Giacomo,

This is a bit concerning:

Due to the lack of full stru= cture data on every node, various features not normally needed for large si= mulations are non-functional or restricted. These limits, combined wit= h the small number of projects using memory-optimized NAMD, cause us to cau= tion users that this capability should be considered experimental.

Also is there a full= documentation of the JS and namdbin format? Where can I find the = ;Fortran style formatting for PSFs? And how are they different when read in= to NAMD?

Max

<= div class=3D"">On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin <giacomo.fiorin@gmail.com> = wrote:

Hi Max, for large systems the recommended format = in VMD/NAMD is "JS":
On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert <max.ebert@me.com> wrote:
Thanks for the answer. I am tr= ying to write out a compliment PSF file for system with over 1 million atom= s. I want to be sure to not bust any field width and get into trouble with = the NAMD PSF parser. So I guess you can=E2=80=99t be fully compliant for sy= stem which go over a certain number of atoms correct? Is my assumption corr= ect that NAMD uses the space as a separator and that VMD for example has fi= xed field width?

Max


On Jun 4, 2021, at 1:59 PM, Axel= Kohlmeyer <akohlmey@gmail.com> wrote:

l= ore has it that the *authoritative* documentation of the CHARMM file format= s is the CHARMM source code.

one important point to note is tha= t PSF (and PDB) are file formats based on Fortran style formatting, which h= as fixed widths and does not need spaces as separators.
so it can be legal to= have something like:

1001100210031004 (for a 4I4 format) being= read as 1001, 1002, 1003, 1004 but if you would write out 1001 1002 1003 1= 004  in would be read as 1001, 100,  210, 31
that is different from= how C/C++ and Python process input.

So what it now boils down = to is what you are after: do you want to write out or edit PSF files to be = fully conforming, or do they just have to be read by NAMD.

Axe= l.

P.S.: there are some more possible flags to appear in the fi= rst line to indicate the use of the PSF for specific purposes

=

On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas <vermaasj@msu.edu> wrote:
The best documentation on the format is *p= robably* the CHARMM
documentation, which is actually rather sparse.
https://urldefense.com/v3/__https://academ= iccharmm.org/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW17= 80p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$

Basically, the first line of the PSF file dictates the field width. For regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:

PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
https://urldefense.com/v3/__https://prl.na= tsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55= ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$




--
Dr. Axel Kohlmeye= r  akohlmey@gmail.com  http://goo.gl/1wk0=
College of Science & Technology, Temple University, = Philadelphia PA, USA
International Centre for Theoretical Phy= sics, Trieste. Italy.


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boundary="_000_ea12d04b9c07d338d56b105ae38aa942msuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: a0910a3a-e0b5-4fe7-42e0-08d92807f4d9 X-MS-Exchange-CrossTenant-originalarrivaltime: 05 Jun 2021 09:54:48.6560 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: d6BJhaiTk0Tgg3ue16LxU3/79+Z2izQoloEWmRJKlVJbRuc6w6hL5EbpjVocl2I8j/u5gzAzndCjc81QUXE8Sg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB4278 X-Proofpoint-GUID: 0aMpBdsR3vDdftke0fAzoDVcdzcoKAzI X-CLX-Response: 1TFkXGx0eEQpMehcbGhIRCllEF2l7Un5kbBlQYGFkEQpYWBdvYVgTGktdG0N BZREKeE4XaG9MZgFyZmRLXRIRCnlMF2BlU2BNHU8eZxhcEQpDSBcHGRscEQpDWRcHHhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHx5xGR4QGncGGBoGGhEKWV4XaGN5EQpJRhdfQ19Jd UJFWV5PThEKQ04XGktnWmhOWXgZXG5OTF5BTxpMa1BFbnxJTlBJRWFrUGMRClhcFx8EGgQYGRoF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdyEmUcchEKTVwXGB8ZEQpMWhd7aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxd6XnNBEk8baRxGcxEKQ1oXHhoEGxodBBgbGA QcGhEKQl4XGxEKRF4XGBEKREkXGBEKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCT BdvYVgTGktdG0NBZREKQmwXYXkcHxJce09aaUIRCkJAF2UeXGBERH8YRltnEQpCWBdnc2VzQG5h YUxdYhEKTV4XGxEKWlgXHBEKeUMXYVBOa11+eHpERkARCllLFxsYHh4TEQpwaBdsR2gZbWJnQRx kaBAZGhEKcGgXZ1MZbWRkBQEcbkUQHBoRCnBoF2Rba1lCXRl9ZWhSEBwaEQpwaBduE2ZgREUTcw VaZxAZGhEKcGgXYwVkTBtSenAdcxoQGRoRCnB9F2xpAUAeWXpbc01fEBkaEQpwfRdnbn9dRngYW 31nbBAdGhEKcH0Xa0dmXkJIAR1Ce2MQHRoRCnB9F2AYRRsBSBoTGnlSEBwaEQpwfRdrehxgUxkY b1BFYBAZGhEKcH8XZRl5Zl5HaRtkT3MQGxoaEQpwXxdkaxNbeRNibXJ6SxAeEhEKcH8XYWZvWxp nZEJIHVsQEh4RCnBfF2NiElBIY3gffEJ9EBwcEQpwfxdoel9iHn5bBWRSGxAbGxIRCnBfF2ATGW ZLTmxORVN7EBwaEQpwfxduH2ddfV5AE3hkeRAbGBkRCnBfF2RjaG0efVBrTFBgEBkaEQpwbBdne BpAYhhJGn55TRAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: 0aMpBdsR3vDdftke0fAzoDVcdzcoKAzI X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=108 suspectscore=0 adultscore=0 spamscore=0 mlxscore=0 malwarescore=0 phishscore=0 clxscore=174 mlxlogscore=999 bulkscore=0 impostorscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106050071 domainage_hfrom=12449 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_ea12d04b9c07d338d56b105ae38aa942msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable For the fortran style formatting, the VMD source code or the CHARMM source = code. These are the lines from psfplugin.c: Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n" EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n" The NAMD format just overruns the specified field widths, which is perfectl= y allowable in C but not in fortran. In terms of using the js format, I think what you are seeing was more true = when that warning was written (~2015, 2016), than it is now. -Josh On 6/4/21 5:38 PM, Maximilian Ebert wrote: Hi Giacomo, This is a bit concerning: Due to the lack of full structure data on every node, various features not = normally needed for large simulations are non-functional or restricted. The= se limits, combined with the small number of projects using memory-optimize= d NAMD, cause us to caution users that this capability should be considered= experimental. Also is there a full documentation of the JS and namdbin format? Where can = I find the Fortran style formatting for PSFs? And how are they different wh= en read into NAMD? Max On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin > wrote: Hi Max, for large systems the recommended format in VMD/NAMD is "JS": https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert > wrote: Thanks for the answer. I am trying to write out a compliment PSF file for s= ystem with over 1 million atoms. I want to be sure to not bust any field wi= dth and get into trouble with the NAMD PSF parser. So I guess you can=E2=80= =99t be fully compliant for system which go over a certain number of atoms = correct? Is my assumption correct that NAMD uses the space as a separator a= nd that VMD for example has fixed field width? Max On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer wrote: lore has it that the *authoritative* documentation of the CHARMM file forma= ts is the CHARMM source code. one important point to note is that PSF (and PDB) are file formats based on= Fortran style formatting, which has fixed widths and does not need spaces = as separators. so it can be legal to have something like: 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 bu= t if you would write out 1001 1002 1003 1004 in would be read as 1001, 100= , 210, 31 that is different from how C/C++ and Python process input. So what it now boils down to is what you are after: do you want to write ou= t or edit PSF files to be fully conforming, or do they just have to be read= by NAMD. Axel. P.S.: there are some more possible flags to appear in the first line to ind= icate the use of the PSF for specific purposes On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas wrote: The best documentation on the format is *probably* the CHARMM documentation, which is actually rather sparse. https://urldefense.com/v3/__https://academiccharmm.org/documentation/versio= n/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66= nLOh7NH4vymgTxHM9_y3qw$ Basically, the first line of the PSF file dictates the field width. For regular, non-extended PSFs, the header will look like: PSF In these files, you are limited to 4 characters for segnames and atomtypes. CHARMM can also write (and VMD/NAMD can also read/write) "extended" PSF files. The headers for these will look like: PSF EXT This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows: PSF NAMD The NAMD/VMD version is the most flexible, since fields just need to be separated by spaces, and for the most part psfgen/VMD will select this option if the contents of the psf file demand it. -Josh On 6/4/21 1:10 PM, Maximilian Ebert wrote: > Dear list, > > Is there a resource which describes the PSF file format? I am many wonder= ing about the max column width and if the width needs to be fixed or can ch= anged when numbers get larger. > > Thanks > -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vym= gTxF1980Jig$ -- Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!tca8shL5MNjPvKe0WQ2CuKt_WzZHsbdeZOJRaXxyIaLAg4TDr1Ak= lyLLa9o-tCCMkQ$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis= ty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!tca8shL5MNjPvKe0WQ2CuKt_WzZHsbdeZOJRaXxyIaLAg4TDr1AklyL= La9rskPyosA$=20 --_000_ea12d04b9c07d338d56b105ae38aa942msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <178A3FB5C3964B48A219EF54D419FB63@namprd12.prod.outlook.com> Content-Transfer-Encoding: Quoted-printable For the fortran style formatting, the VMD source code or the CHARMM source = code. These are the lines from psfplugin.c:

Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n"
EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n"

The NAMD format just overruns the specified field widths, which is perfectl= y allowable in C but not in fortran.

In terms of using the js format, I think what you are seeing was more true = when that warning was written (~2015, 2016), than it is now.

-Josh

On 6/4/21 5:38 PM, Maximilian Ebert wrote:
Hi Giacomo,

This is a bit concerning:

Due to the lack of full structure data on every node, vario= us features not normally needed for large simulations are non-functional or=  restricted. These limits, combined with the small number of projects = using memory-optimized NAMD, cause us to caution users that this capability should be considered experimental.=

Also is there a full documentation of the JS and namdb= in format? Where can I find the Fortran style formatting for PSFs? And= how are they different when read into NAMD?

Max

On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin <giacomo= .fiorin@gmail.com> wrote:

Hi Max, for large systems the recommended = format in VMD/NAMD is "JS":

On Fri, Jun 4, 2021 at 2:53 PM Maximi= lian Ebert <max.ebert@me.com> wrote:
Thanks for the answer.= I am trying to write out a compliment PSF file for system with over 1 mill= ion atoms. I want to be sure to not bust any field width and get into troub= le with the NAMD PSF parser. So I guess you can=E2=80=99t be fully compliant for system which go over a certain nu= mber of atoms correct? Is my assumption correct that NAMD uses the space as= a separator and that VMD for example has fixed field width?

Max


On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:

lore ha= s it that the *authoritative* documentation of the CHARMM file formats is t= he CHARMM source code.

one imp= ortant point to note is that PSF (and PDB) are file formats based on Fortra= n style formatting, which has fixed widths and does not need spaces as sepa= rators.
so it c= an be legal to have something like:

1001100= 210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 but if yo= u would write out 1001 1002 1003 1004  in would be read as 1001, 100,&= nbsp; 210, 31
that is= different from how C/C++ and Python process input.

So what= it now boils down to is what you are after: do you want to write out or ed= it PSF files to be fully conforming, or do they just have to be read by NAM= D.

Axel.

P.S.: t= here are some more possible flags to appear in the first line to indicate t= he use of the PSF for specific purposes


On Fri, Jun 4, 2021 at 1:49 PM Josh V= ermaas <vermaasj@msu.edu> = wrote:
The best documentation on the format is *probably* the CHARMM
documentation, which is actually rather sparse.
https://urldefens= e.com/v3/__https://academiccharmm.org/documentation/version/c45b2/io*IOFORM= __;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9= _y3qw$

Basically, the first line of the PSF file dictates the field width. For regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:

PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
https://urldefens= e.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3f= jg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$




--
Dr. Axel Kohlmeyer  akohlmey@gmail.com  ht= tp://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, US= A
International Centre for Theoretical Physics, Trieste. Italy.



--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
verm=
aasj@msu.edu
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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Sat, 5 Jun 2021 12:55:36 +0000 (UTC) Content-Type: multipart/alternative; boundary=Apple-Mail-C9D7699C-7BF1-4F78-9CC6-86F020DE5E3D Content-Transfer-Encoding: 7bit From: Maximilian Ebert Subject: Re: namd-l: PSF file format Date: Sat, 5 Jun 2021 08:55:19 -0400 Message-Id: References: Cc: Giacomo Fiorin , Axel Kohlmeyer In-Reply-To: To: namd-l@ks.uiuc.edu, "Vermaas, Josh" X-Mailer: iPad Mail (18F72) X-Proofpoint-Virus-Version: =?UTF-8?Q?vendor=3Dfsecure_engine=3D1.1.170-22c6f66c430a71ce266a39bfe25bc?= =?UTF-8?Q?2903e8d5c8f:6.0.391,18.0.761,17.0.607.475.0000000_definitions?= =?UTF-8?Q?=3D2021-06-05=5F04:2021-06-04=5F01,2021-06-05=5F04,2020-04-07?= =?UTF-8?Q?=5F01_signatures=3D0?= X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 adultscore=0 malwarescore=0 suspectscore=0 mlxlogscore=999 spamscore=0 phishscore=0 bulkscore=0 mlxscore=0 clxscore=1015 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2009150000 definitions=main-2106050093 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehcYHxsRCllEF2IdbU9wXVISE2VvEQpYWBdlWFJIQW1aaWV hbhEKeE4XbHBgeUAdYlJpGmIRCnlMF2tIZE9iZllmeUleEQpDSBcHHhwdEQpDWRcHHhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBNxHhIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XXlNFGB4baXxCdVNtZE9iXGUaT1oSTmt/UEhMHGBYQRoRClhcFx8EGgQYGRoF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdyEnhARhEKTVwXGBweEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2hQUE4FQmUeZXxdEQpDWhcbHQQfEgQcGQQbEh sRCkJeFxsRCkReFxgRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2xwYHlAHWJSaRpiEQpCSRdscGB5Q B1iUmkaYhEKQkUXeht9SR5BaXx/YxsRCkJOF2xwYHlAHWJSaRpiEQpCTBdlWFJIQW1aaWVhbhEK QmwXZEQSRmZdWHtHaU4RCkJAF2UeXGBERH8YRltnEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlg XHBEKeUMXYVBOa11+eHpERkARCllLFxMdEhkRCnBnF2tMHUFafFhEchNeEB4SEQpwaBdnWHBoaE VjUhtQbhAZGhEKcGgXbn5Df0ZQa2Fzc1MQGRoRCnBoF2V6YkVjGgUfSGdOEBkaEQpwaBdjQUJte 0dFXGdsHRAeEhEKcGgXaWlwY0dBbmRwcxoQGRoRCnB9F24cSVMcbHB8Zl8SEB4SEQpwfRdnbn9d RngYW31nbBASHxEKcH0Xa0dmXkJIAR1Ce2MQEh8RCnB9F2AYRRsBSBoTGnlSEBwaEQpwfRdrehx gUxkYb1BFYBAZGhEKcH0XYhNjHRhbfmkbfF8QHhIRCnB9F2gYRElgWXlsWn9oEB4SEQpwfRdsE0 1cYG1YbX1gRBAeEhEKcH8XZRl5Zl5HaRtkT3MQExoRCnBfF2RrE1t5E2JtcnpLEBwaEQpwfxdhZ m9bGmdkQkgdWxATHBEKcF8XY2ISUEhjeB98Qn0QHR8RCnB/F2h6X2IeflsFZFIbEBsbHBEKcF8X YBMZZktObE5FU3sQHRoRCnB/F24fZ119XkATeGR5EBsbExEKcF8XZGNobR59UGtMUGAQGRoRCnB sF2JhZXpNT30bUEhMEBsSEQpwQxdpfx9/GnNeYnhYRBAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: tyo241CVh_yGNeHvO0ep8dAUzbf6Jrk0 X-Proofpoint-GUID: tyo241CVh_yGNeHvO0ep8dAUzbf6Jrk0 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 clxscore=189 phishscore=0 malwarescore=0 suspectscore=0 priorityscore=251 impostorscore=0 mlxlogscore=999 mlxscore=0 bulkscore=0 adultscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106050093 domainage_hfrom=9783 X-Spam-Score: 0 X-Spam-OrigSender: max.ebert@me.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maximilian Ebert --Apple-Mail-C9D7699C-7BF1-4F78-9CC6-86F020DE5E3D Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Thanks everyone. That is super helpful. We could implement JS writing for s= ystems over 1mio atoms, which would also be helpful to write out fully comp= liant coordinate files I guess. Since we have a native writer i would like = to implement this as well. Do i need to go through the C code or is there a= full spec of the file format somewhere? Max > On Jun 5, 2021, at 5:56 AM, Vermaas, Josh wrote: >=20 > =EF=BB=BF For the fortran style formatting, the VMD source code or the CH= ARMM source code. These are the lines from psfplugin.c: >=20 > Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n" > EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n" >=20 > The NAMD format just overruns the specified field widths, which is perfec= tly allowable in C but not in fortran. >=20 > In terms of using the js format, I think what you are seeing was more tru= e when that warning was written (~2015, 2016), than it is now. >=20 > -Josh >=20 >> On 6/4/21 5:38 PM, Maximilian Ebert wrote: >> Hi Giacomo, >>=20 >> This is a bit concerning: >>=20 >> Due to the lack of full structure data on every node, various features n= ot normally needed for large simulations are non-functional or restricted. = These limits, combined with the small number of projects using memory-optim= ized NAMD, cause us to caution users that this capability should be conside= red experimental. >>=20 >> Also is there a full documentation of the JS and namdbin format? Where c= an I find the Fortran style formatting for PSFs? And how are they different= when read into NAMD? >>=20 >> Max >>=20 >>> On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin w= rote: >>>=20 >>> Hi Max, for large systems the recommended format in VMD/NAMD is "JS": >>> https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction >>>=20 >>>> On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert wro= te: >>>> Thanks for the answer. I am trying to write out a compliment PSF file = for system with over 1 million atoms. I want to be sure to not bust any fie= ld width and get into trouble with the NAMD PSF parser. So I guess you can= =E2=80=99t be fully compliant for system which go over a certain number of = atoms correct? Is my assumption correct that NAMD uses the space as a separ= ator and that VMD for example has fixed field width? >>>>=20 >>>> Max >>>>=20 >>>>=20 >>>>> On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer wrote: >>>>>=20 >>>>> lore has it that the *authoritative* documentation of the CHARMM file= formats is the CHARMM source code. >>>>>=20 >>>>> one important point to note is that PSF (and PDB) are file formats ba= sed on Fortran style formatting, which has fixed widths and does not need s= paces as separators. >>>>> so it can be legal to have something like: >>>>>=20 >>>>> 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1= 004 but if you would write out 1001 1002 1003 1004 in would be read as 100= 1, 100, 210, 31 >>>>> that is different from how C/C++ and Python process input. >>>>>=20 >>>>> So what it now boils down to is what you are after: do you want to wr= ite out or edit PSF files to be fully conforming, or do they just have to b= e read by NAMD. >>>>>=20 >>>>> Axel. >>>>>=20 >>>>> P.S.: there are some more possible flags to appear in the first line = to indicate the use of the PSF for specific purposes >>>>>=20 >>>>>=20 >>>>>> On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas wrote: >>>>>> The best documentation on the format is *probably* the CHARMM=20 >>>>>> documentation, which is actually rather sparse.=20 >>>>>> https://urldefense.com/v3/__https://academiccharmm.org/documentation= /version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb= 7HsKx66nLOh7NH4vymgTxHM9_y3qw$=20 >>>>>>=20 >>>>>> Basically, the first line of the PSF file dictates the field width. = For=20 >>>>>> regular, non-extended PSFs, the header will look like: >>>>>>=20 >>>>>> PSF >>>>>>=20 >>>>>> In these files, you are limited to 4 characters for segnames and=20 >>>>>> atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)= =20 >>>>>> "extended" PSF files. The headers for these will look like: >>>>>>=20 >>>>>> PSF EXT >>>>>>=20 >>>>>> This buys you 8 characters for segnames and atomtypes. NAMD/VMD also= can=20 >>>>>> write space-delimited psf files, which are tagged as follows: >>>>>>=20 >>>>>> PSF NAMD >>>>>>=20 >>>>>> The NAMD/VMD version is the most flexible, since fields just need to= be=20 >>>>>> separated by spaces, and for the most part psfgen/VMD will select th= is=20 >>>>>> option if the contents of the psf file demand it. >>>>>>=20 >>>>>> -Josh >>>>>>=20 >>>>>> On 6/4/21 1:10 PM, Maximilian Ebert wrote: >>>>>> > Dear list, >>>>>> > >>>>>> > Is there a resource which describes the PSF file format? I am many= wondering about the max column width and if the width needs to be fixed or= can changed when numbers get larger. >>>>>> > >>>>>> > Thanks >>>>>> > >>>>>> --=20 >>>>>> Josh Vermaas >>>>>>=20 >>>>>> vermaasj@msu.edu >>>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and = Molecular Biology >>>>>> Michigan State University >>>>>> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/facult= y/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh= 7NH4vymgTxF1980Jig$=20 >>>>>>=20 >>>>>>=20 >>>>>=20 >>>>>=20 >>>>> --=20 >>>>> Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__h= ttp://goo.gl/1wk0__;!!DZ3fjg!uRefTsOJu_lE1cCqZFtx8q7ivz16yB9C6w-hEDWgEhBjYF= 9qWEEKh05gOTXIpNtclQ$=20 >>>>> College of Science & Technology, Temple University, Philadelphia PA, = USA >>>>> International Centre for Theoretical Physics, Trieste. Italy. >>>>=20 >>=20 >=20 > --=20 > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochem= isty and Molecular Biology > vermaasj@msu.edu > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/__;!!DZ3fjg!uRefTsOJu_lE1cCqZFtx8q7ivz16yB9C6w-hEDWgEhBjYF9qWEEKh= 05gOTV_26L4cQ$=20 --Apple-Mail-C9D7699C-7BF1-4F78-9CC6-86F020DE5E3D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Thanks everyone. That is super helpful. We c= ould implement JS writing for systems over 1mio atoms, which would also be h= elpful to write out fully compliant coordinate files I guess. Since we have a= native writer i would like to implement this as well. Do i need to go throu= gh the C code or is there a full spec of the file format somewhere?

Max

On Jun 5, 2021, at 5:56 AM, Vermaas, Josh &= lt;vermaasj@msu.edu> wrote:

=EF=BB=BF For the fortran style formatting, the VMD source code or the CHARMM source c= ode. These are the lines from psfplugin.c:

Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n"
EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n"

The NAMD format just overruns the specified field widths, which is perfectly= allowable in C but not in fortran.

In terms of using the js format, I think what you are seeing was more true w= hen that warning was written (~2015, 2016), than it is now.

-Josh

On 6/4/21 5:38 PM, Maximilian Ebert wrote:
Hi Giacomo,

This is a bit concerning:

Due to the lack of full structure data on every node, variou= s features not normally needed for large simulations are non-functional or&n= bsp;restricted. These limits, combined with the small number of projects usi= ng memory-optimized NAMD, cause us to caution users that this capability should be considered experimental.<= /div>

Also is there a full documentation of the JS and namdbi= n format? Where can I find the Fortran style formatting for PSFs? And h= ow are they different when read into NAMD?

Max

On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin <giacomo.f= iorin@gmail.com> wrote:

Hi Max, for large systems the recommended f= ormat in VMD/NAMD is "JS":

On Fri, Jun 4, 2021 at 2:53 PM Maximil= ian Ebert <max.ebert@me.com> wrote:
Thanks for the answer. I= am trying to write out a compliment PSF file for system with over 1 million= atoms. I want to be sure to not bust any field width and get into trouble w= ith the NAMD PSF parser. So I guess you can=E2=80=99t be fully compliant for system which go over a certain num= ber of atoms correct? Is my assumption correct that NAMD uses the space as a= separator and that VMD for example has fixed field width?

Max


On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:

lore has= it that the *authoritative* documentation of the CHARMM file formats is the= CHARMM source code.

one impo= rtant point to note is that PSF (and PDB) are file formats based on Fortran s= tyle formatting, which has fixed widths and does not need spaces as separato= rs.
so it ca= n be legal to have something like:

10011002= 10031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 but if you w= ould write out 1001 1002 1003 1004  in would be read as 1001, 100, = ; 210, 31
that is d= ifferent from how C/C++ and Python process input.

So what i= t now boils down to is what you are after: do you want to write out or edit P= SF files to be fully conforming, or do they just have to be read by NAMD.

Axel.

P.S.: th= ere are some more possible flags to appear in the first line to indicate the= use of the PSF for specific purposes


On Fri, Jun 4, 2021 at 1:49 PM Josh Ve= rmaas <vermaasj@msu.edu> wr= ote:
The best documentation on the format is *probably* the CHARMM
documentation, which is actually rather sparse.
https://urldefense= .com/v3/__https://academiccharmm.org/documentation/version/c45b2/io*IOFORM__= ;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3= qw$

Basically, the first line of the PSF file dictates the field width. For
regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:
=
PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be
separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many wond= ering about the max column width and if the width needs to be fixed or can c= hanged when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecula= r Biology
Michigan State University
https://urldefense= .com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg= !uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$




--
Dr. Axel Kohlmeyer  akohlmey@gmail.com  htt= p://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA=
International Centre for Theoretical Physics, Trieste. Italy.



--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemist=
y and Molecular Biology
verma=
asj@msu.edu
https://prl.natsci.ms=
u.edu/people/faculty/josh-vermaas/
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boundary="000000000000c9749205c4052fce" X-Proofpoint-GUID: MZ-BeiW44g3zlN7vX5p75g7fh0oLEafn X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIbEQpMehcYEhwRCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGRwaEQpDWRcHHhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBtxHhoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XZ3AHaE9DfR4eTRlQRmQdXHIfWh0fTR1MQhpFZm9LTEQRClhcFx8EGgQYGRoF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXchJ5TkkRCk1cFxkfGBEKTFoXe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrfFlQWBlpXhhmWhEKQ1oXGBoTBBIfBBgaEg QbEhgRCkJeFxsRCkRJFxkRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXYGBLGWZEY15eUHgRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6WGtMY2VdWwVEcBEKQmwX ZnhufhhkZUESWH8RCkJAF2UeXGBERH8YRltnEQpCWBdnc2VzQG5hYUxdYhEKWlgXHREKeUMXYVB Oa11+eHpERkARCllLFxMeGBIRCnBnF2AeRWxCZmtHGl9gEBkaEQpwaBdlU1JfYW19XFliQhAZGh EKcGgXbhNmYERFE3MFWmcQGRoRCnBoF2JmHl1TGH5ZZWIfEBkaEQpwaBdoa3xFTRJQb0cBUxAZG hEKcGgXYwVkTBtSenAdcxoQGRoRCnB9F2cBS09IZ2N7bFNEEBkaEQpwfRduHElTHGxwfGZfEhAc GhEKcH0XYhNjHRhbfmkbfF8QHRIRCnB9F2duf11GeBhbfWdsEBsaGhEKcH0Xa0dmXkJIAR1Ce2M QGxoaEQpwfRdgGEUbAUgaExp5UhAcGhEKcH0XZh4FZltsQEVGW2QQHBoRCnB9F2wTTVxgbVhtfW BEEB0SEQpwfRdoGERJYFl5bFp/aBAdEhEKcH8XZRl5Zl5HaRtkT3MQEx8RCnBfF2NHZ09memByb RNaEBkaEQpwXxdkaxNbeRNibXJ6SxAdGhEKcH8XYWZvWxpnZEJIHVsQGxoaEQpwXxdjYhJQSGN4 H3xCfRASGREKcH8XaHpfYh5+WwVkUhsQGxoTEQpwXxdgExlmS05sTkVTexAcGhEKcH8XbURfRkV tfUh5GW4QGxgaEQpwXxdrRksTeWhpbnwTeBATGREKcGwXYGlHZ2lSX39feEwQHBoRCnBMF21oZR lBUn17GEVSEB4SEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: MZ-BeiW44g3zlN7vX5p75g7fh0oLEafn MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 spamscore=0 clxscore=181 mlxscore=0 impostorscore=0 priorityscore=286 lowpriorityscore=0 mlxlogscore=999 suspectscore=0 phishscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106050100 domainage_hfrom=9428 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --000000000000c9749205c4052fce Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable The best way to have a native writer for the format (and a whole bunch of additional file formats) would be to add an interface to using molfile plugins in general and then load/use the plugin directly. Otherwise you can also incorporate the source (molfile plugins are under a more liberal license than VMD and NAMD). Most molfile plugins can be compiled as standalone executables for testing and benchmarking, so that is a starting point. https://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/index.html There are several software packages that have implemented molfile plugin interfaces. There is the original in VMD, I wrote one for LAMMPS, I know there is one in Plumed2.x and Pymol and there are likely more. Axel. On Sat, Jun 5, 2021 at 8:55 AM Maximilian Ebert wrote: > Thanks everyone. That is super helpful. We could implement JS writing for > systems over 1mio atoms, which would also be helpful to write out fully > compliant coordinate files I guess. Since we have a native writer i would > like to implement this as well. Do i need to go through the C code or is > there a full spec of the file format somewhere? > > Max > > On Jun 5, 2021, at 5:56 AM, Vermaas, Josh wrote: > > =EF=BB=BF For the fortran style formatting, the VMD source code or the CH= ARMM > source code. These are the lines from psfplugin.c: > > Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n" > EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n" > > The NAMD format just overruns the specified field widths, which is > perfectly allowable in C but not in fortran. > > In terms of using the js format, I think what you are seeing was more true > when that warning was written (~2015, 2016), than it is now. > > -Josh > > On 6/4/21 5:38 PM, Maximilian Ebert wrote: > > Hi Giacomo, > > This is a bit concerning: > > Due to the lack of full structure data on every node, various features not > normally needed for large simulations are non-functional or restricted. > These limits, combined with the small number of projects using > memory-optimized NAMD, cause us to caution users that this capability > should be considered experimental. > > Also is there a full documentation of the JS and namdbin format? Where can > I find the Fortran style formatting for PSFs? And how are they different > when read into NAMD? > > Max > > On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin > wrote: > > Hi Max, for large systems the recommended format in VMD/NAMD is "JS": > https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction > > > On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert wrote: > >> Thanks for the answer. I am trying to write out a compliment PSF file for >> system with over 1 million atoms. I want to be sure to not bust any field >> width and get into trouble with the NAMD PSF parser. So I guess you can= =E2=80=99t >> be fully compliant for system which go over a certain number of atoms >> correct? Is my assumption correct that NAMD uses the space as a separator >> and that VMD for example has fixed field width? >> >> Max >> >> >> On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer wrote: >> >> lore has it that the *authoritative* documentation of the CHARMM file >> formats is the CHARMM source code. >> >> one important point to note is that PSF (and PDB) are file formats based >> on Fortran style formatting, which has fixed widths and does not need >> spaces as separators. >> so it can be legal to have something like: >> >> 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 >> but if you would write out 1001 1002 1003 1004 in would be read as 1001, >> 100, 210, 31 >> that is different from how C/C++ and Python process input. >> >> So what it now boils down to is what you are after: do you want to write >> out or edit PSF files to be fully conforming, or do they just have to be >> read by NAMD. >> >> Axel. >> >> P.S.: there are some more possible flags to appear in the first line to >> indicate the use of the PSF for specific purposes >> >> >> On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas wrote: >> >>> The best documentation on the format is *probably* the CHARMM >>> documentation, which is actually rather sparse. >>> >>> https://urldefense.com/v3/__https://academiccharmm.org/documentation/ve= rsion/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7Hs= Kx66nLOh7NH4vymgTxHM9_y3qw$ >>> >>> Basically, the first line of the PSF file dictates the field width. For >>> regular, non-extended PSFs, the header will look like: >>> >>> PSF >>> >>> In these files, you are limited to 4 characters for segnames and >>> atomtypes. CHARMM can also write (and VMD/NAMD can also read/write) >>> "extended" PSF files. The headers for these will look like: >>> >>> PSF EXT >>> >>> This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can >>> write space-delimited psf files, which are tagged as follows: >>> >>> PSF NAMD >>> >>> The NAMD/VMD version is the most flexible, since fields just need to be >>> separated by spaces, and for the most part psfgen/VMD will select this >>> option if the contents of the psf file demand it. >>> >>> -Josh >>> >>> On 6/4/21 1:10 PM, Maximilian Ebert wrote: >>> > Dear list, >>> > >>> > Is there a resource which describes the PSF file format? I am many >>> wondering about the max column width and if the width needs to be fixed= or >>> can changed when numbers get larger. >>> > >>> > Thanks >>> > >>> -- >>> Josh Vermaas >>> >>> vermaasj@msu.edu >>> Assistant Professor, Plant Research Laboratory and Biochemistry and >>> Molecular Biology >>> Michigan State University >>> >>> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/j= osh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH= 4vymgTxF1980Jig$ >>> >>> >>> >> >> -- >> Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http= ://goo.gl/1wk0__;!!DZ3fjg!qcEpve0sF0dqYedKaMDLsMdRfYakMguBBq4Vc5YFTb35B9bYe= g_f_pAvwvdTbR1ttw$=20 >> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >> >> >> > > -- > Josh Vermaas > Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochem= isty and Molecular Biologyvermaasj@msu.eduhttps://prl.natsci.msu.edu/people= /faculty/josh-vermaas/ > > --=20 Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!qcEpve0sF0dqYedKaMDLsMdRfYakMguBBq4Vc5YFTb35B9bYeg_f= _pAvwvdTbR1ttw$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. --000000000000c9749205c4052fce Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
The best way to have a native writer for the for= mat (and a whole bunch of additional file formats) would be to add an inter= face to using molfile plugins in general and then load/use the plugin direc= tly. Otherwise you can also incorporate the source (molfile plugins are und= er a more liberal license than VMD and NAMD). Most molfile plugins can be c= ompiled as standalone executables for testing and benchmarking, so that is = a starting point. https://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/ind= ex.html

There are several software packages that have implemented molf= ile plugin interfaces. There is the original in VMD, I wrote one for LAMMPS= , I know there is one in Plumed2.x and Pymol and there are likely more.

<= /div>
Ax= el.

On Sat, Jun 5, 2021 at 8:55 AM Maximilian Ebert <max.ebert@me.com> wrote:
Thanks everyone. That is super helpful. We could implement JS writing= for systems over 1mio atoms, which would also be helpful to write out full= y compliant coordinate files I guess. Since we have a native writer i would= like to implement this as well. Do i need to go through the C code or is t= here a full spec of the file format somewhere?

Max

On Jun 5, = 2021, at 5:56 AM, Vermaas, Josh <vermaasj@msu.edu> wrote:

=EF=BB=BF For the fortran style formatting, the VMD source code or the CHARMM source = code. These are the lines from psfplugin.c:

Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n"
EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n"

The NAMD format just overruns the specified field widths, which is perfectl= y allowable in C but not in fortran.

In terms of using the js format, I think what you are seeing was more true = when that warning was written (~2015, 2016), than it is now.

-Josh

On 6/4/21 5:38 PM, Maximilian Ebert wrote:
Hi Giacomo,

This is a bit concerning:

Due to the lack of full structure data on every node, various features= not normally needed for large simulations are non-functional or=C2=A0restr= icted. These limits, combined with the small number of projects using memor= y-optimized NAMD, cause us to caution users that this=C2=A0capability should be considered experimental.=

Also is there a full documentation of the JS and=C2=A0namdbin format? = Where can I find the=C2=A0Fortran style formatting for PSFs? And how are th= ey different when read into NAMD?

Max

On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin <giacomo.fiorin@gmail.com> wro= te:

Hi Max, for large systems the recommended=C2=A0format in V= MD/NAMD is "JS":

On Fri, Jun 4, 2021 at 2:53 PM Maximi= lian Ebert <max.eb= ert@me.com> wrote:
Thanks for the answer. I am trying to write out a compliment PSF file = for system with over 1 million atoms. I want to be sure to not bust any fie= ld width and get into trouble with the NAMD PSF parser. So I guess you can=E2=80=99t be fully compliant for system which go over a certain nu= mber of atoms correct? Is my assumption correct that NAMD uses the space as= a separator and that VMD for example has fixed field width?

Max


On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:

lore has it that the *authorita= tive* documentation of the CHARMM file formats is the CHARMM source code.

one important point to note is = that PSF (and PDB) are file formats based on Fortran style formatting, whic= h has fixed widths and does not need spaces as separators.
so it can be legal to have some= thing like:

1001100210031004 (for a 4I4 for= mat) being read as 1001, 1002, 1003, 1004 but if you would write out 1001 1= 002 1003 1004=C2=A0 in would be read as 1001, 100,=C2=A0 210, 31
that is different from how C/C+= + and Python process input.

So what it now boils down to is= what you are after: do you want to write out or edit PSF files to be fully= conforming, or do they just have to be read by NAMD.

Axel.

P.S.: there are some more possi= ble flags to appear in the first line to indicate the use of the PSF for sp= ecific purposes


The best documentation on the format is *probably* the CHARMM
documentation, which is actually rather sparse.
https://urldefense.com/v3/__https://academiccharmm.or= g/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55= ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$

Basically, the first line of the PSF file dictates the field width. For
regular, non-extended PSFs, the header will look like:

PSF

In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:

PSF EXT

This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can write space-delimited psf files, which are tagged as follows:

PSF NAMD

The NAMD/VMD version is the most flexible, since fields just need to be
separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.

-Josh

On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many won= dering about the max column width and if the width needs to be fixed or can= changed when numbers get larger.
>
> Thanks
>
--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.ed= u/people/faculty/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHL= a2pb7HsKx66nLOh7NH4vymgTxF1980Jig$




--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0<= a>http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, US= A
International Centre for Theoretical Physics, Trieste. Italy.



--=20
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemis=
ty and Molecular Biology
vermaasj@msu.edu
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/


--
Dr. Axel Kohlmeyer =C2= =A0akohlmey@gmail.c= om =C2=A0http://goo.gl/1wk0
College of Science & Techn= ology, Temple University, Philadelphia PA, USA
International Centre for = Theoretical Physics, Trieste. Italy.
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boundary="000000000000cbaf0105c423a924" X-Proofpoint-GUID: hJ19DD1IpdV3T0IikeHnI5n2yJvjZaGx X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwfEQpMehcZGx0RCllEF2xtEhJzGXB+ek4bEQpYWBdnXBJPY38YTkt GeBEKeE4XY1Nja3sTWH4aX14RCnlMF25CUBpsYhNyfExBEQpDSBcHGBobEQpDWRcHGx8TEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcbGXEbBhgfdwYSGQYaBhoGGxoaBgcZGnEaEBt3BhoGGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XQmAbE25uG2NaTnwZfhpjQ0FP YkRjH0QYU2BcQHBLbVIRClhcFx8EGgQYGRoFGxoEGxsaBB8aBBseGBAbHhofGhEKXlkXchJTS1k RCk1cFxgaGhEKTFoXaG5Na2sRCkxGF29ra2traxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHw QYGhIEGxIYEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF3pyS3BMUmEFSEcSEQpCThdjU2NrexNYfhpfXhEKQkwXZ1wST2N/GE5LRngRCkJsF2tl cBlMYhlhfkZNEQpCQBdiRh94HWZ4a1NgexEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnl DF2d+WnJwbWVbaUhkEQpZSxcTHhkaEQpwaBdoc1oZUltyXEBeYBAZGhEKcGgXbkVvG3xtbh1sHk AQGRoRCnBoF2NYBWFdSRwaQ3lMEBkaEQpwaBdmG0ZkZl1venpibxAZGhEKcGgXb35PSRodexIZX lwQGRoRCnBsF3prTkxlQRgaTU4YEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: hJ19DD1IpdV3T0IikeHnI5n2yJvjZaGx X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 spamscore=0 clxscore=165 mlxscore=0 impostorscore=0 priorityscore=317 lowpriorityscore=0 mlxlogscore=853 suspectscore=0 phishscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106070013 domainage_hfrom=9430 X-Spam-Score: 0 X-Spam-OrigSender: namong456@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Namho Kim --000000000000cbaf0105c423a924 Content-Type: text/plain; charset="UTF-8" Dear NAMD users We wanted to determine free energy change upon rotation of a molecule using 'angle' colvar sampled by extended ABF but we couldn't get valuable results. So we tested our methodology on an only-water system which consist of 251 water molecules in 20 X 20 X 20 A sized box. In the system the center of mass of a selected water molecule was fixed at the center of the simulation box using harmonic constraint and was only allowed to rotate freely. We were trying to calculate the free energy change as a function of angle between the selected water dipole and the z axis using eABF. It is obvious that the free energy change should be negligible with respect to the angle because the system is isotropic. However, we obtained unexpected result where the free energy difference is quite large (upto ~3,5 kcal/mol) and we couldn;t find any certain reason. Below is the colvar file we used. colvar { name wat_fix width 1.0 distance { group1 { atomnumbers { 4 5 6 } ##centered water molecule } group2 { dummyAtom (0.0, 0.0, 0) } } } colvar { name Theta width 2.00 lowerboundary 0.0 upperboundary 180.0 extendedLagrangian on extendedFluctuation 0.05 angle { group1 { atomnumbers {5 6} ##H-molecules of centered water } group2 { atomnumbers {4 5 6} ##centered water molecule } group3 { dummyAtom (0.0, 0.0, 1.0) } } } harmonic { colvars wat_fix forceConstant 10.0 centers 0.0 } abf { colvars Theta fullSamples 50000 historyFreq 100 } Thank you. -Namho- --000000000000cbaf0105c423a924 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD users

We wan= ted to determine free energy change upon rotation of a molecule using '= angle' colvar sampled by extended ABF but we couldn't get valuable = results.

So we tested our methodology=C2=A0on an o= nly-water system which consist of 251 water molecules in 20 X 20 X 20 A siz= ed box.

In the system the center of mass of a sele= cted water molecule was fixed at the center of the simulation box using har= monic constraint and was only allowed to rotate freely. We were trying to c= alculate the free energy change as a function of angle between the selected= water dipole and the z axis using eABF.

It is obv= ious that the free energy change should be negligible with respect to the a= ngle because the system is isotropic. However, we obtained unexpected resul= t where the free energy difference is quite large (upto ~3,5 kcal/mol) and = we couldn;t find any certain reason.

Below is= the colvar file we used.

colvar {

=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0name wat_fix

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0

<= p align=3D"left" style=3D"margin:0cm;padding:0px;font-size:10pt;line-height= :normal;color:rgb(51,51,51);font-family:"\00b9d1\00c740 \00ace0\00b51= 5";word-break:keep-all">=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0width 1.0

=C2=A0

=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0distance {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0group1 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0atomnumbers { 4 5 6 } ##centered water = molecule

=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= }

=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0group2 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0dummyAtom (0.0, 0.0, 0)

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0}

=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0}

}<= /span>

=C2=A0

colvar {

= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0name Theta

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0width 2.00

=C2= =A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0lowerboundary=C2=A0=C2=A00.0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0upperbou= ndary=C2=A0=C2=A0180.0

=C2=A0=

=C2=A0=C2=A0=C2=A0=C2=A0extend= edLagrangian=C2=A0=C2=A0on

=C2= =A0=C2=A0=C2=A0=C2=A0extendedFluctuation 0.05

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0angle {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0group1 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0atomnumbers {5 6} ##H-molecules of cent= ered water

=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0}=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0group2 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0atomnumbers {4 5 6} ##centered water molecule

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0}

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0group3 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0dummyAtom (0.0, 0.0, 1.0)

= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0}

=C2=A0=

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0}

}=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0

=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0

=C2=A0

harmonic {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0colvars wat_fix<= /span>

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0forceConstant=C2=A0=C2=A010.0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0centers=C2= =A0=C2=A00.0=C2=A0

}

=

=C2=A0

abf {

=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0colvars Theta

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 fullSamples 50000=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0historyFreq 100

=C2=A0

}

=C2=A0

=C2=A0

Thank you.

-= Namho-

--000000000000cbaf0105c423a924-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jun 7 05:30:42 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 157AUgsn019649; Mon, 7 Jun 2021 05:30:42 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 157AUfCS019648; Mon, 7 Jun 2021 05:30:41 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 157AUf3j019644; Mon, 7 Jun 2021 05:30:41 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 157AUfxR019643; Mon, 7 Jun 2021 05:30:41 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 157AUVFE019635 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 7 Jun 2021 05:30:32 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 157AFBoG028875 for ; Mon, 7 Jun 2021 10:30:31 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0b-00007101.pphosted.com with ESMTP id 39003tjyq1-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 07 Jun 2021 10:30:31 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 0A1361E423AA; Mon, 7 Jun 2021 12:30:30 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id YTwFdl38FCLd; Mon, 7 Jun 2021 12:30:29 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id DB5D41E426E5; Mon, 7 Jun 2021 12:30:28 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id tLdDN4WGj464; Mon, 7 Jun 2021 12:30:28 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id 749951E423AA; Mon, 7 Jun 2021 12:30:28 +0200 (CEST) Date: Mon, 7 Jun 2021 12:30:26 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , Namho Kim Message-ID: <339430770.8774316.1623061826479.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: Re: namd-l: Problem of calculating PMF changed by tilt angle using extended ABF MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_db91a189-d517-47ce-ade4-13e3fb34f404" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Problem of calculating PMF changed by tilt angle using extended ABF Thread-Index: Hha7ZS2TTO8cmKy70YTPxeDfw7QUZw== X-Proofpoint-ORIG-GUID: OtRT7FlZ2uDxP3LKm8crF7pDO8L6D4zh X-Proofpoint-GUID: OtRT7FlZ2uDxP3LKm8crF7pDO8L6D4zh X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxISEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxgaEQpDWRcHExoRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHBJxHh0QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XZV54fh1sRnAYX25SehlmYUcSSVhsHVpuZRJmHG4eUEIRClhcFx8EGgQYGRoFGxoE GxsaBB8aBBseHxAbHhofGhEKXlkXchIfREMRCk1cFxgdHhEKTFoXfG1rTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdoQEVIGBh8a1t6GREKQ1oXGxMZBB4TBBgZHgQYGBsRCk JeFxsRCkReFxgRCkJFF2RYXFxNflJJG2VJEQpCThdlT34SQ2lmWRwBaREKQkwXehJnaWBZeUZBT 2URCkJsF2ESEk9PTE1/Tx4FEQpCQBdlfkReHW1hS0ZHTREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsR ClpYFxkRCnlDF2ABc15iYF4SAXxPEQpwaBdmZVseAVMaXGloXhAZGhEKcGgXZEN9ewFBHWdNaGA QGRoRCnBoF2RSXUlNYVxQEmdzEBkaEQpwaBdtG1lzWm9iTGdeWRAZGhEKcGgXYBprcnpwf1JwZV 4QHxwRCnBsF2ZgE2RcTRpnT3pQEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 malwarescore=0 spamscore=0 clxscore=188 adultscore=0 bulkscore=0 mlxscore=0 impostorscore=0 priorityscore=0 mlxlogscore=999 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106070080 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_db91a189-d517-47ce-ade4-13e3fb34f404 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Namho,=20 > We wanted to determine free energy change upon rotation of a molecule usi= ng > 'angle' colvar sampled by extended ABF I don't think you need the extended-system version of ABF for this, standar= d ABF should work for an angle coordinate. That said, it will become necess= ary if you switch to more complicated coordinates, so you can keep it.=20 > So we tested our methodology on an only-water system which consist of 251= water > molecules in 20 X 20 X 20 A sized box. > In the system the center of mass of a selected water molecule was fixed a= t the > center of the simulation box using harmonic constraint and was only allow= ed to > rotate freely. I don't know how will-defined the angle will be, since the center of mass i= s not really fixed, but will fluctuate around the center of the restraint, = giving a noisy version of the angle.=20 > We were trying to calculate the free energy change as a function of angle > between the selected water dipole and the z axis using eABF. In that case, you could constrain the oxygen atom (a real, hard constraint)= using the fixedAtoms feature of NAMD, and measure the angle of the vector = between the oxygen and the two hydrogens. That would match the dipole vecto= r precisely.=20 > It is obvious that the free energy change should be negligible with respe= ct to > the angle because the system is isotropic. It's not that obvious to me. An angle coordinate can have a non-zero Jacobi= an term - generally the probability would be proportional to the sine of th= e angle. You can test this by running a simulation without the ABF bias and= collecting the histogram of the angle. Is it uniform?=20 Best,=20 J=C3=A9r=C3=B4me=20 --=_db91a189-d517-47ce-ade4-13e3fb34f404 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Namho,
We wanted to determine free energy change= upon rotation of a molecule using 'angle' colvar sampled by extended ABF
I don't think you need the extended-syste= m version of ABF for this, standard ABF should work for an angle coordinate= . That said, it will become necessary if you switch to more complicated coo= rdinates, so you can keep it.

So= we tested our methodology on an only-water system which consist of 25= 1 water molecules in 20 X 20 X 20 A sized box.

In the system = the center of mass of a selected water molecule was fixed at the center of = the simulation box using harmonic constraint and was only allowed to rotate= freely.
I don't know how will-defined = the angle will be, since the center of mass is not really fixed, but will f= luctuate around the center of the restraint, giving a noisy version of the = angle.
We were trying to calculate the free ene= rgy change as a function of angle between the selected water dipole and the= z axis using eABF.
In that case, you co= uld constrain the oxygen atom (a real, hard constraint) using the fixedAtom= s feature of NAMD, and measure the angle of the vector between the oxygen a= nd the two hydrogens. That would match the dipole vector precisely.
<= div dir=3D"ltr">
It is obvious that the free energy change should b= e negligible with respect to the angle because the system is isotropic.
It's not that obvious to me. An angle coord= inate can have a non-zero Jacobian term - generally the probability would b= e proportional to the sine of the angle. You can test this by running a sim= ulation without the ABF bias and collecting the histogram of the angle. Is = it uniform?

Best,
J= =C3=A9r=C3=B4me
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Mon, 7 Jun 2021 20:26:58 +0530 (IST) Received: from [47.15.22.22] by webmail.iitd.ac.in with HTTP (HTTP/1.1 POST); Mon, 07 Jun 2021 20:26:58 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit Date: Mon, 07 Jun 2021 20:26:58 +0530 From: Nadira Khatoon To: namd-l@ks.uiuc.edu Subject: namd-l: Protein equilibration User-Agent: Roundcube Webmail/1.4.2 Message-ID: <89332b2f50904aae5d033a95cb514cd7@bioschool.iitd.ac.in> X-Sender: Nadira.Khatoon@bioschool.iitd.ac.in X-Proofpoint-GUID: EhZm536lYoqlE0CbwrUb-BsL8lZCSMEG X-CLX-Response: 1TFkXGxsaEQpMehcaEQpZRBdhfVhhHG5NBVtobhEKWFgXZmAaAUUfGhtkTkw RCnhOF2BBYlBvWkFvfmVSEQp5TBd6S3hvRB5DWkxTZhEKQ0gXBxIdEQpDWRcHGRgRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYTGnEdEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCRVleT 04RCkNOF29CcEcfGRxGc0VbRm8aaUhdWH9IB2hZZhJGcGl5Z29tEQpYXBcfBBoEGBkaBRsaBBsa GgQeEgQbExAbHhofGhEKXlkXchITQk4RCk1cFx0eEQpMWhdoaU1raxEKTEYXb2tra2trEQpCTxd jRUJpAXxeZRJYGREKQ1oXGxoZBBgdBBMEHh8RCkJeFxsRCkJcFxsRCkJLF2NhbFxyTXlYQhkfEQ pCSRdgQWJQb1pBb35lUhEKQkUXbhh7W3BMEkNJWWERCkJOF2BBYlBvWkFvfmVSEQpCTBdmYBoBR R8aG2ROTBEKQmwXYEl7ZElFYmdff2gRCkJAF24aAUlvTEZwHG5TEQpCWBdnc2VzQG5hYUxdYhEK TV4XGxEKWlgXGxEKeUMXZRNpc2dMb20faEgRCllLFxwcHR4RCnBoF2kBX3BYf0J5aUFzEBkaEQp waBdgHnlZbkcTWFNNRhAZGhEKcGgXaUscTGl9QGJAE08QGRoRCnBsF2VmUGZ5ZkJ6SUAYEBkaEQ pwQxdoc31uUwF4XBJtYxAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: EhZm536lYoqlE0CbwrUb-BsL8lZCSMEG X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 suspectscore=0 adultscore=0 spamscore=0 mlxscore=0 malwarescore=0 phishscore=0 clxscore=110 mlxlogscore=365 bulkscore=0 impostorscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106070108 domainage_hfrom=6674 X-Spam-Score: 0 X-Spam-OrigSender: Nadira.Khatoon@bioschool.iitd.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nadira Khatoon Hi, I have to simulate a membrane embedded protein system (267012 atoms). I cannot simulate continuously for longer time due to large size of the system. Can anyone suggest how much time it would take to equilibrate the protein or how can I analyse if after a run my protein has equilibrated or not? From owner-namd-l@halifax.ks.uiuc.edu Sat Jun 12 08:32:19 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15CDWJxv026607; Sat, 12 Jun 2021 08:32:19 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15CDWI1X026606; Sat, 12 Jun 2021 08:32:18 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15CDWIe1026601; Sat, 12 Jun 2021 08:32:18 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15CDWHkQ026600; Sat, 12 Jun 2021 08:32:17 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15CDW8cC026590 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 12 Jun 2021 08:32:08 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15CDU0O6016022 for ; Sat, 12 Jun 2021 13:32:08 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=kevin@skblnw.com Received: from mta-11-4.privateemail.com (mta-11-4.privateemail.com [198.54.127.104]) by mx0b-00007101.pphosted.com with ESMTP id 394k9r3v0u-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 12 Jun 2021 13:32:08 +0000 Received: from mta-11.privateemail.com (localhost [127.0.0.1]) by mta-11.privateemail.com (Postfix) with ESMTP id 04EE380170; Sat, 12 Jun 2021 09:32:07 -0400 (EDT) Received: from APP-06 (unknown [10.50.14.156]) by mta-11.privateemail.com (Postfix) with ESMTPA id DAD2E8016E; Sat, 12 Jun 2021 09:32:06 -0400 (EDT) Date: Sat, 12 Jun 2021 09:32:06 -0400 (EDT) From: Kevin Chan To: yjcoshc Cc: namd-l@ks.uiuc.edu Message-ID: <906680513.2983.1623504726853@privateemail.com> In-Reply-To: <5533ea2f-6e66-fa1d-1773-fb5a147cc305@gmail.com> References: <1333379885.257237.1621949997892@privateemail.com> <5533ea2f-6e66-fa1d-1773-fb5a147cc305@gmail.com> Subject: Re: namd-l: FEP with cudaSOAIntegrate in NAMD 3.0alph9 Content-Type: multipart/alternative; boundary="----=_Part_2982_54717048.1623504726848" X-Priority: 3 Importance: Normal X-Mailer: Open-Xchange Mailer v7.10.4-Rev25 X-Originating-Client: open-xchange-appsuite X-Virus-Scanned: ClamAV using ClamSMTP X-CLX-Response: 1TFkXGRgTEQpMehcaEQpZRBdjXwF5c1pgZ28ZUhEKWFgXY3JfW3xYG2hgZW4 RCnhOF24bTX4cbhN7Ym56EQp5TBdhHEEaQF0aTnlveBEKQ0gXBxsdExEKQ1kXBxgYEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcfHnEfBhgbdwYbGR8GGgYaBhsaGgYbGhpxExAadwYaBhoGGgYHHBoGG gYacRoQGncGGhEKWV4XY2N5EQpJRhdfQ19JdUJFWV5PThEKQ04Xb1hwXEJ4REx9ehNgQFBra2VO fnVLYn1eTn9+SWthcEkRClhcFx8EGgQYGRoFGxoEGxsaBB8aBBseGBAbHhofGhEKXlkXcgFGXFA RCk1cFx4fHhEKTFoXeGlNa2sRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdobl McfHpITxhZaREKQ1oXGxMSBB8eBBsYHQQbGh4RCkJeFxsRCkRJFxsRCkJFF2ZBc19IGGJNYx9rE QpCThduG01+HG4Te2JuehEKQkwXY3JfW3xYG2hgZW4RCkJsF2VlYXN4fWdNfG9ZEQpCQBdpXlMe Q38eTW0bWxEKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF3pDRm5DGEJBXgF6EQpwaBdhfW5tQhh rbxh/YxAZGhEKcGgXZX1Ge3lkGnxaT1oQGRoRCnBoF2RLeh4aSGtwYgVvEBkaEQpwaBdsemVnZk ZlWW4dXhAZGhEKcGgXYkdhXV4dckZ7TB4QGRoRCnB9F21rb3x/XloFQB5ZEBkaEQpwfRdkb0t9G 0FaBR1/bRAZGhEKcH8Xax1rHlN7Z2NLbXoQGxsaEQpwXxdgTGdLbX5HBX1rZRAZGhEKcGwXaVgZ UmBOGH9Pc2gQEx0RCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: ErZvhRnfWP9JjzAAOdT_aHWtdUTcAKZc X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: ErZvhRnfWP9JjzAAOdT_aHWtdUTcAKZc MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 phishscore=0 clxscore=329 priorityscore=0 lowpriorityscore=0 bulkscore=0 adultscore=0 spamscore=0 malwarescore=0 mlxlogscore=999 impostorscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106120095 X-Spam-Score: 0 X-Spam-OrigSender: kevin@skblnw.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kevin Chan ------=_Part_2982_54717048.1623504726848 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Dear Haochuan, I apologize for the late reply. Buried with works. A test case can be found= at https://urldefense.com/v3/__https://github.com/skblnw/namdsntest__;!!DZ= 3fjg!raQUYgqg4Bk9IpqXhAkbIWCEi6-p0ug54Hj1fow03chQgRz6HJt-CiZyPBrB_swSFw$ . Thank you in advance for your time and please let me know if you need more = details. Best, Kevin > On 05/26/2021 7:43 AM yjcoshc wrote: >=20 >=20 >=20 > Hi Kevin, >=20 > Could you share some test input files for testing and debugging? >=20 > Thanks, >=20 > Haochuan Chen >=20 >=20 > On 5/25/21 8:39 AM, Kevin Chan wrote: >=20 > > > Dear Users, > >=20 > > I am trying to speed up an FEP calculation using cudaSOAIntegra= te with NAMD 3.0alpha9 single-node path, however, failed by getting either= =20 > >=20 > > FATAL ERROR: Periodic cell has become too small for original pa= tch grid! > > Possible solutions are to restart from a recent checkpoint, > > increase margin, or disable useFlexibleCell for liquid simulati= on. > >=20 > > or > >=20 > > FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813= ) System unstable or pairlistdist or cutoff too small. > >=20 > > The system has been tested with NAMD2.14 and NAMD3.0alpha9 with= out cudaSOAIntegrate and worked perfectly fine.=20 > >=20 > > So I have tried to tackle the errors by=20 > >=20 > > 1. pairlistdist 13.5 to 16 > > 2. margin 4, 8, 16, 20 > > 3. LangevinPistonDecay 100 to 1000 > >=20 > > None of the combination worked. Sometimes first 1 or 2 windows = (lambda 0 to 0.001) got finished (500k+ steps), but I never got the middle = windows (lambda > 0.1) running. I also tried the alpha8 version and had the= same results. I set stepsPerCycle to 400 and pairlistsPerCycle to 40 all t= he time. The run command is simply "namd3 +p1 +devices 0". > >=20 > > I understand that FEP with CUDA speedup is still in alpha, so a= ny experience shared will be greatly appreciated.=20 > >=20 > > Thanks, > > Kevin > > Zhejiang University=20 > >=20 > > >=20 ------=_Part_2982_54717048.1623504726848 MIME-Version: 1.0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable =20 =20
Dear Haochuan,

I apologize for the late reply. Buried with works. A test case can be fo= und at https://github.com/skblnw/namdsntest.

Thank you in advance for your time and please let me know if you need mo= re details.

Best,
Kevin
On 05/26/2021 7:43 AM yjcoshc <yjcoshc@gmail.com> wrote:


Hi Kevin,

Could you share some test input files for testing and debugging?

Thanks,

Haochuan Chen


On 5/25/21 8:39 AM, Kevin Chan wrote:
Dear Users,

I am trying to speed up an FEP calculation using cudaSOAIntegrate&= nbsp;with NAMD 3.0alpha9 single-node path, however, failed by getting = either 

FATAL ERROR: Periodic cell has become too small for original patch gri= d!=20
Possible solutions are to restart from a recent checkpoint,=20
increase margin, or disable useFlexibleCell for liquid simulation.

or

FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813) Syste= m unstable or pairlistdist or cutoff too small.

The system has been tested with NAMD2.14 and NAMD3.0alpha9 without cudaSOAIntegrate and worked perfectly fine. 

So I have tried to tackle the errors by 

1. pairlistdist 13.5 to 16
2. margin 4, 8, 16, 20
3. LangevinPistonDecay 100 to 1000

None of the combination worked. Sometimes first 1 or 2 windows (lambda= 0 to 0.001) got finished (500k+ steps), but I never got the middle windows= (lambda > 0.1) running. I also tried the alpha8 version and had the sam= e results. I set stepsPerCycle to 400 and pairlistsPerCycle to 40= all the time. The run command is simply "namd3 +p1 +devices 0".

I understand that FEP with CUDA speedup is still in alpha, so any expe= rience shared will be greatly appreciated. 

Thanks,
Kevin
Zhejiang University 
= ------=_Part_2982_54717048.1623504726848-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jun 14 17:00:51 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15EM0pRo027189; Mon, 14 Jun 2021 17:00:51 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15EM0pDj027188; Mon, 14 Jun 2021 17:00:51 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15EM0oxF027184; Mon, 14 Jun 2021 17:00:50 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15EM0oMq027183; Mon, 14 Jun 2021 17:00:50 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15EM0h7O027175 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 14 Jun 2021 17:00:43 -0500 (CDT) Received: from pps.filterd (m0272704.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15ELrn43022290 for ; Mon, 14 Jun 2021 22:00:43 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=max.ebert@me.com; dkim=pass header.s=1a1hai header.d=me.com Received: from st43p00im-zteg10062001.me.com (st43p00im-zteg10062001.me.com [17.58.63.166]) by mx0b-00007101.pphosted.com with ESMTP id 396avbt8fd-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 14 Jun 2021 22:00:42 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=me.com; s=1a1hai; t=1623708041; bh=EuJ/vgalAYCXpuqyhi70yCWV63dzblkclGsVvaXeCqE=; h=From:Content-Type:Mime-Version:Subject:Message-Id:Date:To; b=bVy+DOs5dHypUydJoPU6HygjeXwK7PaAvSoFD6ItHwzit5Hpdb7hd2EoPTWZ92Zn4 U3Y2cfFXZ/bAQf1KkAaS+QCTQh08MEUTzj9ZSz9Q+hJIeir6j0A4f9uR9vBJ+INMpC NwumysY1K1jZwY2QbFjl85rOtAQb//FBS085FXwDnUXiUtIfyJk6NN5fMvutxUo2SV UwY8dOi7F+xsoFCpwqSCkdW5hv71o0mMYHKJ+LgMGTiyHaXMaWZIpr7HZ/1sUBdu8p HTKxrCDawpUomkYXaA1s/KP8DnNvCUrgqMy1N7/Q6bZBE9havnEes4t766XJnMfBQf uJMGl31Ku0jfw== Received: from smtpclient.apple (modemcable037.57-83-70.mc.videotron.ca [70.83.57.37]) by st43p00im-zteg10062001.me.com (Postfix) with ESMTPSA id 1FB406C0651 for ; Mon, 14 Jun 2021 22:00:41 +0000 (UTC) From: Maximilian Ebert Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.100.0.2.22\)) Subject: namd-l: Hydrogen Mass Repartitioning -> NVE energy loss due to rigidBonds Message-Id: Date: Mon, 14 Jun 2021 18:00:40 -0400 To: NAMD list X-Mailer: Apple Mail (2.3654.100.0.2.22) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:6.0.391,18.0.761 definitions=2021-06-14_14:2021-06-14,2021-06-14 signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=0 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1015 mlxscore=0 mlxlogscore=616 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-2009150000 definitions=main-2106140139 X-Proofpoint-GUID: VNZUvH1qG6T4z42Wgkhvv-rfLyIpqNMe X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIaEQpMehcYHRMRCllEF2IdbU9wXVISE2VvEQpYWBdlWFJIQW1aaWV hbhEKeE4XbHBgeUAdYlJpGmIRCnlMF2tIZE9iZllmeUleEQpDSBcHGx4YEQpDWRcHGB4YEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwacRkTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3xkcH9cYhtbbRx+HlAeGH1NQUJcXAdYTGZTY1pbZGdPEQpYXBcfBBoEGBka BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXcgVyc0YRCk1cFxgaHhEKTFoXaGlrTWsRCkxGF29ra2t raxEKQk8XaFBQTgVCZR5lfF0RCkNaFxsdBB8SBBwZBBscHBEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXbHBgeUAdYlJpGmIRCkJJF2xwYHlAHWJSaRpiEQpCRRd6G31JHkFpfH9jGxEKQk4XbHBgeUAdY lJpGmIRCkJMF2VYUkhBbVppZWFuEQpCbBdkRBJGZl1Ye0dpThEKQkAXbHpEQGBIeXt5ZG8RCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdmBV0ZR0VpWxJyTBEKWUsXEx0TGBEKcGgXbhI cWBhSRRtOGVIQGRoRCnBoF2ceE19oR31McB8bEBkaEQpwaBdvQ2UfT2dDeFtCRBAZGhEKcGgXYE tifGcefh8BTHIQGRoRCnBoF2FvTUAFGE99ckxCEBkaEQpwbBdiYWV6TU99G1BITBAZGhEKcEwXb WhlGUFSfXsYRVIQGRoRCnBDF2l/H38ac15ieFhEEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: VNZUvH1qG6T4z42Wgkhvv-rfLyIpqNMe X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 spamscore=0 mlxlogscore=741 impostorscore=0 malwarescore=0 bulkscore=0 phishscore=0 adultscore=0 priorityscore=279 clxscore=180 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106140138 domainage_hfrom=9792 X-Spam-Score: 0 X-Spam-OrigSender: max.ebert@me.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 15EM0i7N027176 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maximilian Ebert I am experimenting with HMR and observed at 2fs time step a constant energy loss in an NVE ensemble when the mass is repartitioned to set the hydrogen mass to 3.024 AMU. The mass comes from the neighboring heavy atom. When I turn off rigidBonds (which I have set to all by default) for the same system the hamiltonian is fluctuating but conserving energy. In contrast, running an NVE ensemble with the same starting coordinates with default mass and 2fs, rigidBonds can be set to all without the loss of energy. Can anyone explain why SHAKE looses energy with non-standard masses in the NVE ensemble? Thanks, Max From owner-namd-l@halifax.ks.uiuc.edu Tue Jun 15 19:25:05 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15G0P5FM011514; Tue, 15 Jun 2021 19:25:05 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15G0P5LY011513; Tue, 15 Jun 2021 19:25:05 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15G0P4kd011509; Tue, 15 Jun 2021 19:25:04 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15G0P4Ku011508; Tue, 15 Jun 2021 19:25:04 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15G0Ooa7011500 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 15 Jun 2021 19:24:50 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15G0DnSR017822 for ; Wed, 16 Jun 2021 00:24:50 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qt1-f174.google.com (mail-qt1-f174.google.com [209.85.160.174]) by mx0b-00007101.pphosted.com with ESMTP id 396c4ha57a-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 16 Jun 2021 00:24:50 +0000 Received: by mail-qt1-f174.google.com with SMTP id z4so546032qts.4 for ; Tue, 15 Jun 2021 17:24:50 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=qm2TYDc5Z0f6T4sgk3tyQ2iGCCO1AS4F+sASPG4dyF4=; b=rlhYz82lYf7XqvGRRb5t0qCX8DSUPL9lTYev6TynjLg9jUBx4amDvpdfEcAa0dMWpH o/A90JsA19mWAJ+epnqvFe0OQ1nuVflEr2SvV6z7uwQlEbk7zXNHL3e4uXgWB+KEmpU2 qYM/Ehb5JnXBFUDCr3rO+78Zte86iJlxh1bkatKgLIwjPnof8AnA6ATbGYx5u4aDhoMc II7XC/uhJiVFP5GN0tvnuHhOcR2mifbCUaa7ROP0sj9vRT3mHYeVyUICTDE01tfe0U78 5K1igMY4vaSlzMd39jSVl1G0stnAZbdiE9QvBBkRdiMy9e7ocYQw/0CoVb6QRMq3ajFV 6r3Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=qm2TYDc5Z0f6T4sgk3tyQ2iGCCO1AS4F+sASPG4dyF4=; b=K9tiuuebwGzJIGIIpaNcyDMEGRNJUJ4If7MT3GhjzUyNtvMr+PBlh0LbHsKmLCGgy2 GgyVSxtc5jxqIxVdngTWxc6Kb23Rbzd0tz5qR/aNwCZDzhWDQpQycwLijtSSt7mrHsSE qek/EJgIfQUNAqzrTZZBDk55UTxm5UfwdfpBztniZPs0/5v4P/tjrUkztqj+Ab8Qx8AS DiAJ4RonRrv/zf21GRHBaBZeoHTbubTOco1CliYHPxH9iEOkYeLxyxtWfIg5EAbvjeoo 80nZBw4P3bPk9g9pAjWQ11YVwvHOdVBpYLm+6rmWBokxEmdWQGU6lCWeH8zl6Igf2dpt PE3w== X-Gm-Message-State: AOAM530zz9u3qwzwXtU4Gf9aUG6EkAAlHJ51MSM5kwuF6JLDVI5CPxKb nlF1tcikTB/B5Kguj29dYG6y6UxaBfJ63w== X-Google-Smtp-Source: ABdhPJy2oasKeSjVvqdDfHGSWxuajP7XPFcKFVBYVX/kuR1ia4/iKyUsuHB7/oN8k1wEROeFKR/hVQ== X-Received: by 2002:ac8:5512:: with SMTP id j18mr2304159qtq.170.1623803089239; Tue, 15 Jun 2021 17:24:49 -0700 (PDT) Received: from [192.168.1.39] ([190.239.201.207]) by smtp.gmail.com with ESMTPSA id z6sm509383qke.24.2021.06.15.17.24.47 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Tue, 15 Jun 2021 17:24:48 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Tue, 15 Jun 2021 19:24:46 -0500 Subject: namd-l: Dual topology FEP From: "Ropon-Palacios G." To: KS UIUC Message-ID: <586BFA83-5E4D-41B1-849C-43EF664F3C4E@gmail.com> Thread-Topic: Dual topology FEP Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3706629888_723978969" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBoSEQpMehcZGx0RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGRoTEQpDWRcHHBgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhJxGx8bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx9pem9af0J8G0RBfURfWGEfS0hdSWYdSEFSQgccWXBzEQpYXBcfBBoEGBka BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3IFX0ZeEQpNXBcZEx4RCkxaF2hpa01NEQpMRhdva2t ra2sRCkJPF2tBU0weElpvTxJsEQpDWhcYGhMEEh8EGxwaBBsdHhEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja 3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXax1AQ0ZMTG1oQxoR CkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdvbXhba1JmXWZ7UhEKWUsXEx4ZExEKcGgXaFJBeWR 8SRJQXUUQGRoRCnBoF24dZRp/bER9ZRwBEBkaEQpwaBdnfEIcbXh9ZlNeaxAZGhEKcGgXY0NcZn 9CGnlTGGgQGRoRCnBoF2hfHk1zengbWngZEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKcEwXZ35Qf U1rUE9PRmIQGRoRCnBDF2cFYB0dHUwcXG5EEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 5CPEpUhV1nkWnurK5abwcL7bkxh-6sZY X-Proofpoint-ORIG-GUID: 5CPEpUhV1nkWnurK5abwcL7bkxh-6sZY X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=208 priorityscore=317 lowpriorityscore=0 adultscore=0 spamscore=0 suspectscore=0 bulkscore=0 impostorscore=0 mlxscore=0 phishscore=0 mlxlogscore=486 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106160000 domainage_hfrom=9439 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3706629888_723978969 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear namd users,=20 =20 I am trying to generate a protein with dual topology, but when the mutator = plugin runs, I get faulty coordinates for the atom that I mutate, example of= the error =20 Created by CHARMM version 36 1 psfgen) ERROR!=C2=A0 Failed to parse autogenerate statement.=C2=A0 Line 40: AUTO AN= GLES DIHE PATCH =20 psfgen) ERROR!=C2=A0 Failed to parse improper statement.=C2=A0 Line 37480: IMPR C=C2=A0= =C2=A0=C2=A0 CA +=C2=A0 N=C2=A0=C2=A0 O=C2=A0=20 =20 =20 reading coordinates from pdb file mtemp-AP1.pdb for segment AP1 psfgen) Warning: failed to set coordinate for atom CB=C2=A0=C2=A0=C2=A0=C2=A0 ALA:10 =C2=A0 AP= 1 psfgen) Warning: failed to set coordinate for atom HB1=C2=A0=C2=A0 ALA:10 =C2=A0 AP1 psfgen) Warning: failed to set coordinate for atom HB2=C2=A0=C2=A0 ALA:10 =C2=A0 AP1 psfgen) Warning: failed to set coordinate for atom HB3=C2=A0=C2=A0 ALA:10 =C2=A0 AP1 =20 =20 help me.=20 =20 Best,=20 =20 Geo.=20 --B_3706629888_723978969 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear namd u= sers,

 

I am trying to generate a protein with dual topology, but when the mutat= or plugin runs, I get faulty coordinates for the atom that I mutate, example= of the error

 

Created by CHARMM version 36 1

=

psfgen) ERROR= !=C2=A0 Failed to parse autogenerate statement.=C2=A0 Line 40: AUTO ANGLES DIHE PATC= H

 

psfgen) ERROR!=C2=A0 Failed to parse improper statement= .=C2=A0 Line 37480: I= MPR C=C2=A0=C2=A0=C2=A0 CA +=C2=A0 N=C2=A0=C2=A0 O=C2=A0

 

&n= bsp;

reading coordinates from pdb file mtemp-AP1.pdb for segment AP1=

psfgen) Warning: failed to set coordinate for atom CB=C2=A0=C2=A0=C2=A0=C2=A0 ALA:10 =C2=A0= AP1

psfgen) Warning: failed to set coordinate for atom HB1=C2=A0=C2=A0 ALA= :10 =C2=A0 AP1

psfgen) Warning: failed to set coordinate for atom HB2=C2=A0=C2= =A0 ALA:10 =C2=A0 AP1

psfgen) Warning: failed to set coordinate for atom = HB3=C2=A0=C2=A0 ALA:10 =C2=A0 AP1

 

 

help me.

 

Best,

=  

Geo.

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I used gcc 9.03 = with following Make.config: ----------Make.config----------CHARMBASE =3D .rootdir/charm-6.10.2include .= rootdir/arch/Linux-x86_64-g++.archCHARMARCH =3D multicore-linux-x86_64-gccC= HARM =3D $(CHARMBASE)/$(CHARMARCH)NAMD_PLATFORM =3D $(NAMD_ARCH)-multicore-= CUDAinclude .rootdir/arch/$(NAMD_ARCH).baseinclude .rootdir/arch/$(NAMD_ARC= H).tclinclude .rootdir/arch/$(NAMD_ARCH).fftwTCLDIR =3D .rootdir/tcl-thread= edFFTDIR =3D .rootdir/fftwinclude .rootdir/arch/$(NAMD_ARCH).cudainclude .r= ootdir/arch/$(NAMD_ARCH).cuda11CUDADIR =3D /opt/nvidia/hpc_sdk/Linux_x86_64= /21.3/cuda/11.0CUDASODIR =3D /opt/nvidia/hpc_sdk/Linux_x86_64/21.3/cuda/11.= 0/lib64LIBCUDARTSO =3DLIBCUFFTSO =3DCUDAGENCODE =3D=C2=A0 -gencode arch=3Dc= ompute_70,code=3Dsm_70CUDADLINKOPTS =3D=C2=A0 -gencode arch=3Dcompute_70,co= de=3Dsm_70CXXOPTS =3D -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.3/math_libs/11.= 0/targets/x86_64-linux/include/ -L/opt/nvidia/hpc_sdk/Linux_x86_64/21.3/mat= h_libs/11.0/targets/x86_64-linux/lib---------------------------------------= -------------------------------- When the compiler linked namd2, it gave following errors for libcufft_stati= c.a: -----------Errors----------------/usr/bin/ld: /opt/nvidia/hpc_sdk/Linux_x86= _64/21.3/math_libs/11.0/targets/x86_64-linux/lib/libcufft_static.a(cbdouble= _32bit_prime_callback_RT_SM35_plus.o): in function `__sti____cudaRegisterAl= l()':cbdouble_32bit_prime_callback_RT_SM35_plus.compute_80.cudafe1.cpp:(.te= xt.startup+0x1d): undefined reference to `__cudaRegisterLinkedBinary_61_cbd= ouble_32bit_prime_callback_RT_SM35_plus_compute_80_cpp1_ii_dc5d5345'/usr/bi= n/ld: /opt/nvidia/hpc_sdk/Linux_x86_64/21.3/math_libs/11.0/targets/x86_64-l= inux/lib/libcufft_static.a(cbdouble_32bit_regular_bluestein_callback_RT_SM3= 5_plus.o): in function `__sti____cudaRegisterAll()':cbdouble_32bit_regular_= bluestein_callback_RT_SM35_plus.compute_80.cudafe1.cpp:(.text.startup+0x1d)= : undefined reference to `__cudaRegisterLinkedBinary_73_cbdouble_32bit_regu= lar_bluestein_callback_RT_SM35_plus_compute_80_cpp1_ii_6a12427e'/usr/bin/ld= : /opt/nvidia/hpc_sdk/Linux_x86_64/21.3/math_libs/11.0/targets/x86_64-linux= /lib/libcufft_static.a(cbdouble_32bit_regular_callback_RT_SM35_plus.o): in = function `__sti____cudaRegisterAll()':........................-------------= ------------ Please suggest and advise! Thanks, Frank ------=_Part_377322_1417805090.1623852378162 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi All,

I tried to build CUDA-11 enabled= NAMD 2.14 on HPE Cray EX (formerly known as Cray Shasta) system= which has NVIDIA V100 GPU. I used gcc 9.03 with following Make.= config:

----------Make.config----------
CHARMBASE =3D .rootdir/c= harm-6.10.2
include .rootdir/arch/Linux-x86_64-g++.arch
CHARMARCH =3D multicore-linux-x86_64-gcc
CHARM =3D $(CHARMBASE)/= $(CHARMARCH)
NAMD_PLATFORM =3D $(NAMD_ARCH)-multicore-CUDA
<= div>include .rootdir/arch/$(NAMD_ARCH).base
include .rootdir/arch= /$(NAMD_ARCH).tcl
include .rootdir/arch/$(NAMD_ARCH).fftw
TCLDIR =3D .rootdir/tcl-threaded
FFTDIR =3D .rootdir/fftw
include .rootdir/arch/$(NAMD_ARCH).cuda
include .rootdir/ar= ch/$(NAMD_ARCH).cuda11
CUDADIR =3D /opt/nvidia/hpc_sdk/Linux_x86_= 64/21.3/cuda/11.0
CUDASODIR =3D /opt/nvidia/hpc_sdk/Linux_x86_64/= 21.3/cuda/11.0/lib64
LIBCUDARTSO =3D
LIBCUFFTSO =3D
CUDAGENCODE =3D  -gencode arch=3Dcompute_70,code=3Dsm_70
<= div>CUDADLINKOPTS =3D  -gencode arch=3Dcompute_70,code=3Dsm_70
CXXOPTS =3D -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.3/math_libs/11.0/targe= ts/x86_64-linux/include/ -L/opt/nvidia/hpc_sdk/Linux_x86_64/21.3/math_libs/= 11.0/targets/x86_64-linux/lib
-----------------------------------= ------------------------------------

When the compiler linked namd2, it gave following erro= rs for libcufft_static.a= :

-----------Errors----------------
/usr/bin/ld: /opt/nvidia/hpc_sdk/L= inux_x86_64/21.3/math_libs/11.0/targets/x86_64-linux/lib/libcufft_static.a(= cbdouble_32bit_prime_callback_RT_SM35_plus.o): in function `__sti____cudaRe= gisterAll()':
cbdouble_32bit_prime_callback_RT_SM35_plus.compute_= 80.cudafe1.cpp:(.text.startup+0x1d): undefined reference to `__cudaRegister= LinkedBinary_61_cbdouble_32bit_prime_callback_RT_SM35_plus_compute_80_cpp1_= ii_dc5d5345'
/usr/bin/ld: /opt/nvidia/hpc_sdk/Linux_x86_64/21.3/m= ath_libs/11.0/targets/x86_64-linux/lib/libcufft_static.a(cbdouble_32bit_reg= ular_bluestein_callback_RT_SM35_plus.o): in function `__sti____cudaRegister= All()':
cbdouble_32bit_regular_bluestein_callback_RT_SM35_plus.co= mpute_80.cudafe1.cpp:(.text.startup+0x1d): undefined reference to `__cudaRe= gisterLinkedBinary_73_cbdouble_32bit_regular_bluestein_callback_RT_SM35_plu= s_compute_80_cpp1_ii_6a12427e'
/usr/bin/ld: /opt/nvidia/hpc_sdk/L= inux_x86_64/21.3/math_libs/11.0/targets/x86_64-linux/lib/libcufft_static.a(= cbdouble_32bit_regular_callback_RT_SM35_plus.o): in function `__sti____cuda= RegisterAll()':
............
............
---= ----------------------

Please suggest and advise!

Thanks,

Frank




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Thu, 17 Jun 2021 16:28:43 +0000 From: "Athreya, Nagendra Bala Murali" To: Giacomo Fiorin , NAMD list Subject: Re: namd-l: Implementing decaying potential (non-linear potential) Thread-Topic: namd-l: Implementing decaying potential (non-linear potential) Thread-Index: AQHW9bIRdbFYHbLmDkm2dT09qBPnTao9esWAgNvFMfs= Date: Thu, 17 Jun 2021 16:28:43 +0000 Message-ID: References: , In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: gmail.com; dkim=none (message not signed) header.d=none;gmail.com; dmarc=none action=none header.from=illinois.edu; x-originating-ip: [128.174.191.9] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: dea1d80f-6381-46aa-12a3-08d931acf955 x-ms-traffictypediagnostic: CH0PR11MB5233: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:10000; x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:CH2PR11MB4293.namprd11.prod.outlook.com;PTR:;CAT:NONE;SFS:(376002)(136003)(366004)(346002)(39860400002)(396003)(26005)(66946007)(64756008)(9686003)(76116006)(8676002)(8936002)(2906002)(55016002)(186003)(66476007)(66556008)(52536014)(7696005)(66446008)(6506007)(19627405001)(38100700002)(122000001)(86362001)(5660300002)(71200400001)(786003)(53546011)(33656002)(478600001)(316002)(110136005)(75432002);DIR:OUT;SFP:1101; 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boundary="_000_CH2PR11MB42933BE045446DB1151FA97FA70E9CH2PR11MB4293namp_" MIME-Version: 1.0 X-OriginatorOrg: illinois.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR11MB4293.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: dea1d80f-6381-46aa-12a3-08d931acf955 X-MS-Exchange-CrossTenant-originalarrivaltime: 17 Jun 2021 16:28:43.5434 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 44467e6f-462c-4ea2-823f-7800de5434e3 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: DUGBOe5ymLth6T68ivApng30a9QcgQpyyW7H6uWC7lziHEYAO/c+wnLcH2ARsLI47aPYL1GWmgu7bGfNcnlP6Q== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH0PR11MB5233 X-Proofpoint-GUID: a9mK2j4s2K3X48UKCN4nX8lg8WVRmMRX X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxsaEQpMehcaEQpZRBdpfBMSeEVgAWkbcBEKWFgXY1wae2NZSHxNZR8 RCnhOF28cGX8cX2hGXGESEQp5TBdsW0dufhNeYnpYHhEKQ0gXBxkYEhEKQ1kXBxsZHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhMacR0QGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFW V5PThEKQ04XXwcbTFp1e0xmbVJ+Qkkcbm8cRHxrW1McTBhbUl9NUHIRClhcFx8EGgQYGRgFGxoE GxoaBB4SBBgYEBseGh8aEQpeWRdza3hQcxEKTVwXGxofEQpMWhd8aWtraxEKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxd6Hn9mb0IfU3JrfREKQ1oXGxoeBB4dBB0ZBB4aEQ pCXhcbEQpEXhcYEQpCRRdvRFBaSBNZaR0dWREKQk4XbxwZfxxfaEZcYRIRCkJMF2NcGntjWUh8T WUfEQpCbBdpYnNmRX5bYX0BchEKQkAXb2lienxNGn1gExIRCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcYEQp5QxdmTVBvUnlwQ1t/RxEKWUsXEhMYGxEKcGcXaUNuUAFZc0cBHlMQGRoRCnBoF2V bZxsFWU8aYGdoEBkaEQpwaBdgHx5/G2VScBNNRhAZGhEKcGgXZmcFeHJGQ0Mec3MQHBoRCnBoF2 5yTmRFZhppU3sYEBkaEQpwaBdoAXBQY09vbh54HBAZGhEKcGwXemwBGHBEX2xoG0AQGRoRCnBMF 21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: u-1fp_QfLGxThc6DE6nVAqy6f2qxugzX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 spamscore=0 clxscore=110 malwarescore=0 adultscore=0 priorityscore=0 suspectscore=0 lowpriorityscore=0 phishscore=0 mlxlogscore=999 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106170104 domainage_hfrom=8921 X-Spam-Score: 0 X-Spam-OrigSender: nathreya@illinois.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Athreya, Nagendra Bala Murali" --_000_CH2PR11MB42933BE045446DB1151FA97FA70E9CH2PR11MB4293namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Giacomo, Sorry for the very late response. I was able to create some grids and run s= ome simulations. Thank you for the help! Nagendra ________________________________ From: Giacomo Fiorin Sent: Thursday, January 28, 2021 2:20 PM To: NAMD list ; Athreya, Nagendra Bala Murali Subject: Re: namd-l: Implementing decaying potential (non-linear potential) Hi Nagendra, GridForces has the ability among others to apply a voltage tha= t depends on the position in space. You'll need to create an OpenDX file for your potential for your decaying v= oltage. One way that I used for this was a Python script that uses the gri= dData module packaged with MDAnalysis. There are certainly other solutions= --_000_CH2PR11MB42933BE045446DB1151FA97FA70E9CH2PR11MB4293namp_-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jun 18 00:29:58 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15I5TwVL015831; Fri, 18 Jun 2021 00:29:58 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15I5Twko015830; Fri, 18 Jun 2021 00:29:58 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15I5Tv0Q015825; Fri, 18 Jun 2021 00:29:57 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15I5Tv7S015824; Fri, 18 Jun 2021 00:29:57 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15I5TlHg015816 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 18 Jun 2021 00:29:48 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15I5EBMJ027201 for ; Fri, 18 Jun 2021 05:29:47 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qt1-f177.google.com (mail-qt1-f177.google.com [209.85.160.177]) by mx0a-00007101.pphosted.com with ESMTP id 397txch7yb-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 18 Jun 2021 05:29:46 +0000 Received: by mail-qt1-f177.google.com with SMTP id o20so6676564qtr.8 for ; Thu, 17 Jun 2021 22:29:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=l5o8rUNJ01ZvrMr7Y3pGjITXPGZrURyOiyV3v2AUzhA=; b=KeDJOKdK8XpX0yVp2k0IeZVggdUaB+3B7UZH2pH/0Z7ObKNN6n+mXys3aSPE/oZ3Y+ nfAdn5sNczWQud9oZlhMtV0b7kc+FGetFkwuaQRgs5yguz2G9MHcsso2i/nt+lOldVJC qiMMt6bZMzKC6IBcon/t3sMH48jnhDN9EtUQFpPe6Cb3RJvjLsqrN8wfyTw7j2WPnGjT 9z7fiZ39bvE4sfEfOdnpWdwOaQuoMB0dIn+A14epvqyxctbWQaHjkeqHRvsE5LP2yrHd o15tsS0cyI2A0zgdmN4B3ilJV0GSlVLBE8U1JcCNDwWOqQP2aBXLkRuQx7hB3VgVzCoU GZVQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=l5o8rUNJ01ZvrMr7Y3pGjITXPGZrURyOiyV3v2AUzhA=; b=rTi0tQWLdHGjtzb58v+UwUVMLxvHHEYVkwe4eZgWhY/LyWbnohHR9BCeGZ0RrXT00Z 5VjrJx50olpitVpsVTlqfi5gaKE9ISjhhUo70oulj4kKKIYMJM3jJ63YjjepyuHjKZIo 3JkpFIJiDMK90knpaVjMDSIXJ7okr93eUHmcwzVjmIOJkQA0jPuj0pJ0jRHfdKJn4kqN Y2VZ1JtoU+OIndTksYfpNUr4p6EAGyo5RXZtbyrBG00Ur18Kq+Nv4WIlRGR8RBmY0ysa FcnYamaOV43g4mu/Yox2ItSlyK2n0SAWYIWiX5urUa8LSuVJLpNTJD42ntb9XB8cRmCO HScQ== X-Gm-Message-State: AOAM530gdPHS7K/FTPmlCotc7D7wnWFzMlCu0qQnSOCMZvEu8V7YxN0I 1yX/vCRf253Cd5OLy1sBjPcjd7xIJWjQTQ== X-Google-Smtp-Source: ABdhPJww+BEV6yPkRsCNhN1jWXKrUK/QAONL7Tua1PC03VDQ9zfxJZI45UbroIwF01ptyA2sfuqZww== X-Received: by 2002:ac8:44ca:: with SMTP id b10mr8903362qto.224.1623994185470; Thu, 17 Jun 2021 22:29:45 -0700 (PDT) Received: from [192.168.1.48] ([190.42.110.98]) by smtp.gmail.com with ESMTPSA id m14sm4774871qti.12.2021.06.17.22.29.44 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Thu, 17 Jun 2021 22:29:45 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 18 Jun 2021 00:29:42 -0500 Subject: namd-l: Jarzynski calculate From: "Ropon-Palacios G." To: KS UIUC Message-ID: <013D1E36-24A5-407C-8E88-B3B8069C6B4A@gmail.com> Thread-Topic: Jarzynski calculate Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3706820984_1830692147" X-Proofpoint-GUID: HpgGyCx4xQsUx2s5HpbOOvKOPLsz3OSS X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwfEQpMehcZHxMRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHGR8TEQpDWRcHHhkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHh9xHx4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYlpNbVNpUh5Se1l/UhhZH2JaSGVlXGFlemZZUBlleXkRClhcFx8EGgQYGRgF GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdza056RxEKTVwXHRkRCkxaF2hpa01NEQpMRhdva2tra2s RCkJPF2tBU0weElpvTxJsEQpDWhcYGhMEEh8EGxwaBBsdHREKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja3sTW H4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXZmxla19pUnJFbUQRCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdpQktafEVBGEMeEhEKWUsXEx4eGxEKcGgXaW5 wBUZDHFpmXGEQGxkdEQpwaBdifBxdQ2NmXFJiZhAZGhEKcGgXYnJwGmRleFNiRBoQGRoRCnBoF2 1NfGlTeX1HQV95EBkaEQpwaBd6QmZDXxxHG3JEexAZGhEKcGwXekdAaxhZeX8eG0gQGRoRCnBMF 2d+UH1Na1BPT0ZiEBkaEQpwQxdtYF9hWB56HR0eGRAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: HpgGyCx4xQsUx2s5HpbOOvKOPLsz3OSS X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 spamscore=0 clxscore=165 malwarescore=0 adultscore=0 priorityscore=359 suspectscore=0 lowpriorityscore=0 phishscore=0 mlxlogscore=616 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106180029 domainage_hfrom=9441 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3706820984_1830692147 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear users, =20 I have calculated the work done by an X puling during SMD and I have repeat= ed the calculation 5 times in total, so I have the following matrix =20 Note: pulling is done along Z. =20 z w1 w2 w3 w4 w5 0 0.22 0.11 0.14 0.33 0.22 1 0.22 0.32 0.35 0.67 0.56 2 0.33 0.24 0.24 0.342 0.23 3 0.242 0.2 0.43 0.343 0.24 =20 My question is this: =20 How do I get the average of the work? =C2=A0 Do I have to average using the rows, or average using the columns? , to = finally rebuild the PMF? =20 This is causing me confusion, please if you could help me. =20 =20 Best.=20 =20 Geo.=20 --B_3706820984_1830692147 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear users,=

 

I = have calculated the work done by an X puling during SMD and I have repeated = the calculation 5 times in total, so I have the following matrix<= /span>

 

Note: pulling = is done along Z.

 

z w1 w2 w3 w4 w5

0 0.22 0.11 0.14 0.33 0.22

1 0.22 0.32 0.35 0.67 0.56

2 0.33= 0.24 0.24 0.342 0.23

3 0.242 0.2 0.43 0.343 0.24

 

My question is this:

 <= /span>

How do I get the= average of the work?

=C2=A0 Do I have to average using the rows, or average using th= e columns? , to finally rebuild the PMF?

 

This is causing me confusion, please i= f you could help me.

 

 

Best.

 

Geo.

--B_3706820984_1830692147-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jun 18 14:20:25 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15IJKPW5028035; Fri, 18 Jun 2021 14:20:25 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15IJKPk1028034; Fri, 18 Jun 2021 14:20:25 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15IJKOGn028029; Fri, 18 Jun 2021 14:20:24 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15IJKO97028028; Fri, 18 Jun 2021 14:20:24 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15IJKCvG028021 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Fri, 18 Jun 2021 12:20:11 -0700 (PDT) Content-Type: multipart/alternative; boundary=Apple-Mail-A4AB2243-481B-4573-BF5D-52389BC0BBC8 Content-Transfer-Encoding: 7bit From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: Jarzynski calculate Date: Fri, 18 Jun 2021 14:20:07 -0500 Message-Id: References: Cc: namd-l@ks.uiuc.edu In-Reply-To: To: Ashkan X-Mailer: iPhone Mail (18B92) X-Proofpoint-GUID: qZL-Ce-NqWOSaTMvC9Mn33yKmTpYvCGg X-CLX-Response: 1TFkXGx0ZEQpMehcZHx8RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHHhkTEQpDWRcHGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGXEZGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdbcGYHaU8HZFt9ZXlLfmdcaRNnRBkZU2FHflpzXGltTREKWFwXHwQaBBgZGAUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdza1pLYhEKTVwXGR4dEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBB sdEhEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmS21YRhhPY0VDQBEKQk4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdv T2RBWkJQbWZrWREKQkAXa31vGF9yXHlncmcRCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdpZ2Q BY29NQlNZbBEKWUsXEx4eGxEKcGcXYxpjR0F/YUZ4GXwQGRoRCnBoF2hgSU9nG0JOWkh5EBkaEQ pwaBdkS19daWxnR1wbWBAZGhEKcGgXYmhDGWxgYkVLTGQQGRoRCnBoF21HElJnHxNYTF94EBkaE QpwaBdlE2J/QH0ZHUFMbhAZGhEKcGwXZ2hDa3MSeRhNYlwQGRoRCnBDF2VeQVlmfFJ7XkdlEBka EQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: qZL-Ce-NqWOSaTMvC9Mn33yKmTpYvCGg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=173 phishscore=0 mlxlogscore=482 impostorscore=0 adultscore=0 lowpriorityscore=0 mlxscore=0 spamscore=0 bulkscore=0 malwarescore=0 priorityscore=355 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106180112 domainage_hfrom=9441 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= --Apple-Mail-A4AB2243-481B-4573-BF5D-52389BC0BBC8 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Them i can average on rows, rigth ?=20 For example for row with of Z O value?=20 Can given example with matrix that i attached ?=20 Enviado desde mi iPhone > El 18 jun. 2021, a la(s) 12:47 p. m., Ashkan e= scribi=C3=B3: >=20 > =EF=BB=BF > ... then simply average over exp(-w) values with equal weights >=20 > On Jun 18, 2021 22:15, Ashkan wrote: > Dear friend, > You have to calculate > exp(-w) >=20 > On Jun 18, 2021 09:59, "Ropon-Palacios G." wrote: > Dear users, >=20 > =20 >=20 > I have calculated the work done by an X puling during SMD and I have repea= ted the calculation 5 times in total, so I have the following matrix >=20 > =20 >=20 > Note: pulling is done along Z. >=20 > =20 >=20 > z w1 w2 w3 w4 w5 >=20 > 0 0.22 0.11 0.14 0.33 0.22 >=20 > 1 0.22 0.32 0.35 0.67 0.56 >=20 > 2 0.33 0.24 0.24 0.342 0.23 >=20 > 3 0.242 0.2 0.43 0.343 0.24 >=20 > =20 >=20 > My question is this: >=20 > =20 >=20 > How do I get the average of the work? >=20 > Do I have to average using the rows, or average using the columns? , to f= inally rebuild the PMF? >=20 > =20 >=20 > This is causing me confusion, please if you could help me. >=20 > =20 >=20 > =20 >=20 > Best. >=20 > =20 >=20 > Geo. >=20 >=20 >=20 --Apple-Mail-A4AB2243-481B-4573-BF5D-52389BC0BBC8 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Them i can average on rows, rigth ? 
For example for row with of Z O value? 
Can given example with matrix that i attached ? 

Enviado desde mi iPhone

El 18 jun. 2021, a la(s) 12:47 p. m., Ashkan <shekaari@= email.kntu.ac.ir> escribi=C3=B3:

=EF=BB=BF
... then simply aver= age over exp(-w) values with equal weights
<= br>
On Jun 18, 2021 22:15, Ashkan <shekaari@ema= il.kntu.ac.ir> wrote:
Dear friend,
You have to calculate
exp(-w)

On Jun 1= 8, 2021 09:59, "Ropon-Palacios G." <biodano.geo@gmail.com> wrote:

Dear= users,

 

I have calculated the work done by an X puling du= ring SMD and I have repeated the calculation 5 times in total, so I have the= following matrix

 <= /p>

Note: pulling is done along Z.

 

z w1 w2 w3 w4 w5

0 0.= 22 0.11 0.14 0.33 0.22

1 0.22 0.= 32 0.35 0.67 0.56

2 0.33 0.24 0.= 24 0.342 0.23

3 0.242 0.2 0.43 0= .343 0.24

 

My question is this:

 

How do I= get the average of the work?

&n= bsp; Do I have to average using the rows, or average using the columns? , to= finally rebuild the PMF?

 =

This is causing me confusion, p= lease if you could help me.

&nbs= p;

 

Best.

&nb= sp;

Geo.

=


= --Apple-Mail-A4AB2243-481B-4573-BF5D-52389BC0BBC8-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jun 21 19:43:13 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15M0hD0f023518; Mon, 21 Jun 2021 19:43:13 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15M0hD6A023517; Mon, 21 Jun 2021 19:43:13 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15M0hCeh023513; Mon, 21 Jun 2021 19:43:12 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15M0hCxI023512; Mon, 21 Jun 2021 19:43:12 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15M0gvxY023502 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000001420d005c55012df" X-Proofpoint-ORIG-GUID: jIkqDOTKGCmVKWzFTuwM5R7NorMt82iT X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0dEQpMehcZGRsRCllEF2hBb0V/U2YSa2tCEQpYWBdlAU1/ZX1MYRN mHREKeE4XY1Nja3sTWH4aX14RCnlMF3pGWl0eaHp8AWdfEQpDSBcHGxsSEQpDWRcHGBoeEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8dcRkcEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0BjQVtuZX5hbWlHfGF9UGx+X11nH3gdZEVYZ14SGEN+EQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc2heS1kRCk1cFxsfEhEKTFoXaGlrTWsRCkxGF29ra2t raxEKQk8XZX5cWVtbR2NTYWwRCkNaFxgaEwQSHwQYGxIEHhMRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXbQVBZ0J+ZGFyaEkRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdlAU1/ZX1MYRNmHREKQmwXaUVbQXJFYUlNbkERCkJAF2xuZGlSTWFgXl5IEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXZmgBWUdzAUwYH2URCllLFxMeHh8RCnBoF2U ZcAFcU05lZU5JEBkaEQpwaBdnU21DTkgFYE1SExAZGhEKcGgXYEdfeQVve2hwT2UQGRoRCnBoF2 lge2BnRH5+cnN7EBkaEQpwaBdkTWxaRlt5WmdzeBAZGhEKcGwXaX5EGAV/G1lkSRsQGRoRCnBMF 21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: jIkqDOTKGCmVKWzFTuwM5R7NorMt82iT X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 impostorscore=0 mlxscore=0 mlxlogscore=555 adultscore=0 bulkscore=0 phishscore=0 clxscore=177 priorityscore=331 suspectscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106220001 domainage_hfrom=9445 X-Spam-Score: 0 X-Spam-OrigSender: ecroitoru1@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ethan Croitoru --0000000000001420d005c55012df Content-Type: text/plain; charset="UTF-8" Hi all, I have inherited a REST2 simulation and am trying to visualize it to make sure there are no abnormalities. I know that I can use show_replicas.vmd to do so, but it is extremely memory intensive, so I was wondering if there are less memory hungry ways of doing so. My PI vaguely remembers something about combining replicas and only viewing the lowest temperature replica, but I cannot find any literature about that. Any advice is appreciated. Thanks for your help, Ethan Croitoru --0000000000001420d005c55012df Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,

I have inherited=C2=A0a REST2 s= imulation and am trying to visualize=C2=A0it to make sure there are no abno= rmalities. I know that I can use show_replicas.vmd to do so, but it is extr= emely memory intensive, so I was wondering if there are less memory hungry = ways of doing so. My PI vaguely=C2=A0remembers something about combining re= plicas and only=C2=A0viewing the lowest temperature replica, but I cannot f= ind any literature about that. Any advice is appreciated.

Thanks for your help,
Ethan Croitoru
--0000000000001420d005c55012df-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jun 23 05:06:37 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15NA6bfC002160; Wed, 23 Jun 2021 05:06:37 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15NA6a3n002159; Wed, 23 Jun 2021 05:06:36 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15NA6a8Q002155; Wed, 23 Jun 2021 05:06:36 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15NA6a9W002154; Wed, 23 Jun 2021 05:06:36 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15NA6Ubi002147 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 23 Jun 2021 05:06:30 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15NA52Rj020633 for ; Wed, 23 Jun 2021 10:06:29 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=jingliang2015@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-wr1-f51.google.com (mail-wr1-f51.google.com [209.85.221.51]) by mx0b-00007101.pphosted.com with ESMTP id 39b0bv40xr-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 23 Jun 2021 10:06:24 +0000 Received: by mail-wr1-f51.google.com with SMTP id h11so1961290wrx.5 for ; Wed, 23 Jun 2021 03:06:24 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=a9+d585FPgEbGOrg12hPvFLcNrmUqa8nwHnmALSNDWo=; b=UoH+BaZP50nf/hDS0O2/WUXq0Yvwt6xX4fhm1aTu5rLsz1nInOkzulbvVQ4nRAJjHP Jz4PMFgkoG5V6wbKN33eB9RyM0Aj2JC7bjStO/JhMYC669XA3RXgv4Idi6wMRLT+VxlI osvv8EDEmgMFVmpjhG8MCslNy088xv3dY+tHZqnVSoyYUmV1i3YH91p5I6FGFGaIDH2Y FeGfftIn67vQN2xMXRVvi7i9y0IIJfT/0I1umyxTLgBM+Zk85onlU8LCwr3oWSmCmkBG +KL13f31Ot4Ld1FxQ8WxgFW9APBEwLHoXzwR7CrQWak89ewe3Yxs1VR2+qnmXKACFkj4 2DUw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=a9+d585FPgEbGOrg12hPvFLcNrmUqa8nwHnmALSNDWo=; b=anfJLuaSTyXGvWeo2jTBdJXAzJw5ZHSqw4DEzlN7QvNTq9mArpv2Ri3VDMEmqrr5ZA x9Xa3GSUJq/hfd3Oo3vxKYmM3zJlP5waEi4CgHvmX2YKCi4zcxZYH0Sk1moZwKBzgorI 9IcMx7UUrk0quV6U3jHCauDfOKJYlrT9TlnE6+S1y+0DElKuF/mrsqEQYuj2YE+oeSR4 c7QMD7RzXf1fnL/ZqqrqaZSpso1NN4vYX33QerO1LS7frKpM5c1O6TVr4py6thNcpfKj vY8qvGZFzpTMtXxzPIRUPBmz4HJ+U47e92KExYK03A61fArF1vteegHGejDGoMdZT3RI lBSA== X-Gm-Message-State: AOAM533EPSCJlgj1nsEhBidFVdWz5vXlG0J+e5UOdcR6ydNCPxd+Y/0u vzcVrEjuepxO7HdmVBiSvt1CR2K6RApmDWZPsY6ZsZBH+Lk= X-Google-Smtp-Source: ABdhPJzv1PgmMmaJhKKtgPRTHhPFecoe+uG25yS1WF/mCI61eBiqclxGTxUH1K1q8rLMm178WefnNgS+VAwDPaVgsok= X-Received: by 2002:adf:f0c1:: with SMTP id x1mr10595673wro.10.1624442782952; Wed, 23 Jun 2021 03:06:22 -0700 (PDT) MIME-Version: 1.0 From: jing liang Date: Wed, 23 Jun 2021 12:06:12 +0200 Message-ID: Subject: namd-l: NAMD on AMD GPU To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000092fd105c56c0fbd" X-Proofpoint-ORIG-GUID: FNngc385JYajThdOgbJrFENR28EVPiAa X-Proofpoint-GUID: FNngc385JYajThdOgbJrFENR28EVPiAa X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 bulkscore=0 phishscore=0 suspectscore=0 mlxlogscore=425 spamscore=0 adultscore=0 malwarescore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106230058 X-Spam-Score: 0 X-Spam-OrigSender: jingliang2015@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, jing liang --000000000000092fd105c56c0fbd Content-Type: text/plain; charset="UTF-8" Hi, I saw a thread on this mailing list about compiling NAMD on AMD GPUs and it said that there was a problem with energy conservation. Is there an update on this? Could the same alpha version be used? http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ thanks. --000000000000092fd105c56c0fbd Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I saw a thread on this mailing list= about compiling NAMD on AMD GPUs and
it said that there was a pr= oblem with energy conservation. Is there an update
on this? Could= the same alpha version be used?


thanks.

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charset="UTF-8" Content-Transfer-Encoding: quoted-printable I fetched the NAMD source code from the link: http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ and followed the BuildInstructions.md. I could build charm++ single node. Then, I tried to build NAMD: cd Linux-x86_64-g++.hip make -j8 but I got the error: In file included from src/ComputePmeCUDAMgr.C:12: src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such file or directory #include do you have any comments about this? El mi=C3=A9, 23 jun 2021 a las 12:08, jing liang (= ) escribi=C3=B3: > Hi, > > I saw a thread on this mailing list about compiling NAMD on AMD GPUs and > it said that there was a problem with energy conservation. Is there an > update > on this? Could the same alpha version be used? > > http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ > > thanks. > > --000000000000bf80f605c588743c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I fetched the NAMD source code from the link:=C2=A0http://www.ks.uiuc.edu/Research/namd/alph= a/2.15_amdhip/=C2=A0
and followed the=C2=A0BuildInstructions.md. I = could build charm++ single node. Then, I tried to build NAMD:
cd Linux-x86_64-g++.hip
make -j8

but I got the error:=C2=A0
In file included from src/ComputePme= CUDAMgr.C:12:
src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No s= uch file or directory
=C2=A0#include <rocfft.h>

=
do you have any comments about this?




=
El mi=C3=A9, 23 jun 2021 a las 12:08,= jing liang (<jingliang2015@g= mail.com>) escribi=C3=B3:
Hi,

I saw a thread on = this mailing list about compiling NAMD on AMD GPUs and
it said th= at there was a problem with energy conservation. Is there an update
on this? Could the same alpha version be used?


thanks.
=
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R-VkbFz2CimbS9lhfT1U2oru1gBLmuFmpDwoZb1u-BHeZop13V649Dw1nyw-CkA$ . The bugs= mentioned about energy=20 conservation are fixed in the master branch there. If rocfft.h can't be=20 found, either there is no ROCm library installed, or AMD changed the=20 directory layout *again*. The NAMD config file looks in /opt/rocm for=20 the rocm installation, however that may not be where it was installed on=20 your system. If this is the case, you'll need to set the --rocm-prefix=20 argument. -Josh On 6/24/21 3:58 PM, jing liang wrote: > I fetched the NAMD source code from the link:=20 > http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/=20 > =20 > > and followed the=C2=A0BuildInstructions.md. I could build charm++ single= =20 > node. Then, I tried to build NAMD: > > cd Linux-x86_64-g++.hip > make -j8 > > but I got the error: > In file included from src/ComputePmeCUDAMgr.C:12: > src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such file or=20 > directory > =C2=A0#include > > do you have any comments about this? > > > > > > El mi=C3=A9, 23 jun 2021 a las 12:08, jing liang ( >) escribi=C3=B3: > > Hi, > > I saw a thread on this mailing list about compiling NAMD on AMD > GPUs and > it said that there was a problem with energy conservation. Is > there an update > on this? Could the same alpha version be used? > > http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ > > > thanks. > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!sVnR-VkbFz2CimbS9lhfT1U2oru1gBLmuFmpDwoZb1u-BHeZop13V64= 9Dw2t8A8EcA$=20 --------------483663FDB8CF2E5E82F9F3B9 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable

One recommendation I would make is to fetch the source from https://gitlab.com/tcbgUIUC/namd. The bugs mentioned about energy conservation are fixed in the master branch there. If rocfft.h can't be found, either there is no ROCm library installed, or AMD changed the directory layout *again*. The NAMD config file looks in /opt/rocm for the rocm installation, however that may not be where it was installed on your system. If this is the case, you'll need to set the --rocm-prefix argument.

-Josh

On 6/24/21 3:58 PM, jing liang wrote:
=20=20=20=20=20=20
I fetched the NAMD source code from the link: <= a href=3D"https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/namd/= alpha/2.15_amdhip/__;!!HXCxUKc!mTSBnVcKgph85ZxeUaK1kWcLQlPdo8R4iwA5HC6v3f6p= CuqWoCXnyRj9ryJ7c7I$" target=3D"_blank" style=3D"font-size:14.6667px" moz-d= o-not-send=3D"true">http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/=  
and followed the BuildInstructions.md. I could build charm++ single node. Then, I tried to build NAMD:

cd Linux-x86_64-g++.hip
make -j8

but I got the error: 
In file included from src/ComputePmeCUDAMgr.C:12:
src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such file or directory
 #include <rocfft.h>

do you have any comments about this?





El mi=C3=A9, 23 jun 2021 a las 12:08, jing liang (<jingliang2015@gmail.com>) escribi=C3=B3:
Hi,

I saw a thread on this mailing list about compiling NAMD on AMD GPUs and
it said that there was a problem with energy conservation. Is there an update
on this? Could the same alpha version be used?


thanks.

--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="00000000000059431905c58f8eef" X-Proofpoint-GUID: 3aDQa9yAQocwITaOsgE6o6SQF_WzXW3_ X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 3aDQa9yAQocwITaOsgE6o6SQF_WzXW3_ X-CLX-Response: 1TFkXGx0YEQpMehcZGBwRCllEF2ltSV5uekVpZBhAEQpYWBd6ell9RkVfGx1 dHBEKeE4XY1Nja3sTWH4aX14RCnlMF2NfHU5/Z04ebmdvEQpDSBcHGR4YEQpDWRcHHh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxhxGRgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XGUtue0sTU2t7RUldY35LZVlNbxxFHHl7bHV9UHJ9GXURClhcFx8EGgQYGRgF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzaVwFYhEKTVwXEhkRCkxaF3tpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XaH1BYENafXNHQRMRCkNaFxgaEwQSHwQbGBIEHh gRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXbmByZGhbTHpvYAURCkJOF2NTY2t7E1h+Gl9eEQpCTBd6ell9RkVfGx1dHBEKQmwXaVxj WE9uYWdJUBMRCkJAF3oYAXBBZFlnHml+EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGxoRCnl DF2VmHEt+QRlFZxhBEQpZSxcTHh4SEQpwaBdkUllMBUxQZ19FTRAZGhEKcGgXaEBvaENZaGRjcx oQGRoRCnBoF2UTHn9nSQFAX015EBkaEQpwaBdiex94el8fY1hOZxAZGhEKcGgXZ19lU0wbYh1Lb UYQGRoRCnB9F2FhXF0ZTAVHXWRAEBkaEQpwfRdkbW1vWUVCBWtAchAZGhEKcH0XbksTXhlDbl0a BXwQHhIRCnB9F2J7XFpfRnIFRlNzEBkaEQpwfRdrehxgUxkYb1BFYBAZGhEKcH0XenN+Zk8eQ3t JR0YQGRoRCnB9F25LehNyRx8bf29mEBkaEQpwfxdrHWseU3tnY0ttehAbGx8RCnBfF2tlXVpMHU l6E19rEBkaEQpwfxdgQlN6bm1YemQBExAbGB4RCnBfF2lNexloXkJkZ1BuEBkaEQpwfxdlWHIYH UkYXkZpfBAbGxwRCnBfF2hPeWVORFtcQ2FzEB4SEQpwfxdtRF9GRW19SHkZbhAbHhkRCnBfF2tG SxN5aGlufBN4EBsbHBEKcH8Xbh9nXX1eQBN4ZHkQGxscEQpwXxdkY2htHn1Qa0xQYBAZGhEKcF8 XZFtPc0FHQ31beXgQGRoRCnB/F2Fmb1saZ2RCSB1bEBsYHBEKcF8XY2ISUEhjeB98Qn0QGxoZEQ pwbBdoGRtoH2JlRkhOQBAZGhEKbX4XGxEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=172 malwarescore=0 bulkscore=0 adultscore=0 mlxlogscore=999 spamscore=0 mlxscore=0 lowpriorityscore=0 impostorscore=0 suspectscore=0 priorityscore=326 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106250023 domainage_hfrom=9448 X-Spam-Score: 0 X-Spam-OrigSender: jingliang2015@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, jing liang --00000000000059431905c58f8eef Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi, rocm is installed in "/proc/rocm" but not rocfft. I guess the rocfft library is this one: https://urldefense.com/v3/__https://github.com/= ROCmSoftwarePlatform/rocFFT__;!!DZ3fjg!tEbDn9ILA1YyF1pGVXOjmIWgeAwIEsR8oHkW= gTaz-tpsKmUR5E9EK1OlJgqEYELSaw$=20 ? I can only install that library in my home because rocm was installed by the sys admin. In this case, changing the argument --rocm-prefix would change the whole location of rocm right? Is there a specific switch for changing the location of the rocfft library only? thanks. El jue, 24 jun 2021 a las 22:21, Josh Vermaas () escribi= =C3=B3: > One recommendation I would make is to fetch the source from > https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!t= EbDn9ILA1YyF1pGVXOjmIWgeAwIEsR8oHkWgTaz-tpsKmUR5E9EK1OlJgrFq5K2fw$ . The bu= gs mentioned about energy > conservation are fixed in the master branch there. If rocfft.h can't be > found, either there is no ROCm library installed, or AMD changed the > directory layout *again*. The NAMD config file looks in /opt/rocm for the > rocm installation, however that may not be where it was installed on your > system. If this is the case, you'll need to set the --rocm-prefix argumen= t. > > -Josh > On 6/24/21 3:58 PM, jing liang wrote: > > I fetched the NAMD source code from the link: > http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ > > > and followed the BuildInstructions.md. I could build charm++ single node. > Then, I tried to build NAMD: > > cd Linux-x86_64-g++.hip > make -j8 > > but I got the error: > In file included from src/ComputePmeCUDAMgr.C:12: > src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such file or > directory > #include > > do you have any comments about this? > > > > > > El mi=C3=A9, 23 jun 2021 a las 12:08, jing liang () > escribi=C3=B3: > >> Hi, >> >> I saw a thread on this mailing list about compiling NAMD on AMD GPUs and >> it said that there was a problem with energy conservation. Is there an >> update >> on this? Could the same alpha version be used? >> >> http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ >> >> >> thanks. >> >> -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > --00000000000059431905c58f8eef Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi,

rocm is installed in "/proc/ro= cm" but not rocfft. I guess the rocfft=C2=A0library is this one:=C2=A0= https://github.com/ROCmSoftwarePlatform/rocFFT ?=C2=A0<= /div>
I can only install that library in my home because rocm was insta= lled by the sys admin. In this case, changing the argument --rocm-prefix
would change the whole location of rocm=C2=A0right? Is there a spec= ific switch for changing the location of the rocfft library only?

thanks.=C2=A0


El jue, 24 jun 2021 a las= 22:21, Josh Vermaas (<vermaasj@msu.= edu>) escribi=C3=B3:
=20=20

One recommendation I would make is to fetch the source from https://gitlab.com/tcbgUIUC/namd. The bugs me= ntioned about energy conservation are fixed in the master branch there. If rocfft.h can't be found, either there is no ROCm library installed, or AMD changed the directory layout *again*. The NAMD config file looks in /opt/rocm for the rocm installation, however that may not be where it was installed on your system. If this is the case, you'll need to set the --rocm-prefix argument.

-Josh

On 6/24/21 3:58 PM, jing liang wrote:
=20=20=20=20=20=20
I fetched the NAMD source code from the link:=C2=A0<= a href=3D"https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/namd/= alpha/2.15_amdhip/__;!!HXCxUKc!mTSBnVcKgph85ZxeUaK1kWcLQlPdo8R4iwA5HC6v3f6p= CuqWoCXnyRj9ryJ7c7I$" style=3D"font-size:14.6667px" target=3D"_blank">http:= //www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/=C2=A0
and followed the=C2=A0BuildInstructions.md. I could build charm++ single node. Then, I tried to build NAMD:

cd Linux-x86_64-g++.hip
make -j8

but I got the error:=C2=A0
In file included from src/ComputePmeCUDAMgr.C:12:
src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such file or directory
=C2=A0#include <rocfft.h>

do you have any comments about this?





El mi=C3=A9, 23 jun 2021 a las 12:08, jing liang (<jingliang2015@gmail.com>) escribi=C3=B3:
Hi,

I saw a thread on this mailing list about compiling NAMD on AMD GPUs and
it said that there was a problem with energy conservation. Is there an update
on this? Could the same alpha version be used?


thanks.

--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
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N4ZHkQGxsYEQpwXxdkY2htHn1Qa0xQYBAeGhEKcGwXemhrYUJtE2Z/cm4QGRoRCnBDF29QZmlpZ EhDUn1+EBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: slUjJqf8em6xMY2-JeBr4qEcBm0XmKYo X-Proofpoint-ORIG-GUID: slUjJqf8em6xMY2-JeBr4qEcBm0XmKYo MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 clxscore=210 priorityscore=0 spamscore=0 malwarescore=0 lowpriorityscore=0 mlxscore=0 bulkscore=0 phishscore=0 impostorscore=0 mlxlogscore=999 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106250076 domainage_hfrom=12469 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Josh Vermaas --------------022B14571391CC1868239A97 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Oooh... Indeed I see that on all of the development platforms I was=20 working on, the rocfft package was installed by default to a reasonable=20 location. For me, the headers I needed were under=20 /opt/rocm/rocfft/include. There is not currently a switch to=20 independently set where rocfft lives, but I've made changes in gitlab to=20 accommodate this: https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/n= amd/-/tree/rocfftprefix__;!!DZ3fjg!ubh99n1khEsCNU0gR4-JsIgfmJYdWm6DvGoW54IO= asVxuW7FSR1Lsnz23fv5xZHtBg$=20 -Josh On 6/25/21 12:27 AM, jing liang wrote: > Hi, > > rocm is installed in "/proc/rocm" but not rocfft. I guess the=20 > rocfft=C2=A0library is this one:=20 > https://urldefense.com/v3/__https://github.com/ROCmSoftwarePlatform/rocFF= T__;!!DZ3fjg!ubh99n1khEsCNU0gR4-JsIgfmJYdWm6DvGoW54IOasVxuW7FSR1Lsnz23fvAgK= x2Zg$=20=20 > =20 > ? > I can only install that library in my home because rocm was installed=20 > by the sys admin. In this case, changing the argument --rocm-prefix > would change the whole location of rocm=C2=A0right? Is there a specific=20 > switch for changing the location of the rocfft library only? > > thanks. > > > El jue, 24 jun 2021 a las 22:21, Josh Vermaas ( >) escribi=C3=B3: > > One recommendation I would make is to fetch the source from > https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3f= jg!ubh99n1khEsCNU0gR4-JsIgfmJYdWm6DvGoW54IOasVxuW7FSR1Lsnz23ftor6Y_gQ$=20 > . > The bugs mentioned about energy conservation are fixed in the > master branch there. If rocfft.h can't be found, either there is > no ROCm library installed, or AMD changed the directory layout > *again*. The NAMD config file looks in /opt/rocm for the rocm > installation, however that may not be where it was installed on > your system. If this is the case, you'll need to set the > --rocm-prefix argument. > > -Josh > > On 6/24/21 3:58 PM, jing liang wrote: >> I fetched the NAMD source code from the link: >> http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ >> >> >> and followed the=C2=A0BuildInstructions.md. I could build charm++ >> single node. Then, I tried to build NAMD: >> >> cd Linux-x86_64-g++.hip >> make -j8 >> >> but I got the error: >> In file included from src/ComputePmeCUDAMgr.C:12: >> src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such >> file or directory >> =C2=A0#include >> >> do you have any comments about this? >> >> >> >> >> >> El mi=C3=A9, 23 jun 2021 a las 12:08, jing liang >> (>) >> escribi=C3=B3: >> >> Hi, >> >> I saw a thread on this mailing list about compiling NAMD on >> AMD GPUs and >> it said that there was a problem with energy conservation. Is >> there an update >> on this? Could the same alpha version be used? >> >> http://www.ks.uiuc.edu/Research/namd/alpha/2.15_amdhip/ >> >> >> thanks. >> > --=20 > Josh Vermaas > > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and M= olecular Biology > Michigan State University > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty= /josh-vermaas/__;!!DZ3fjg!ubh99n1khEsCNU0gR4-JsIgfmJYdWm6DvGoW54IOasVxuW7FS= R1Lsnz23furVWECDA$ > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!ubh99n1khEsCNU0gR4-JsIgfmJYdWm6DvGoW54IOasVxuW7FSR1Lsnz= 23furVWECDA$=20 --------------022B14571391CC1868239A97 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable

Oooh... Indeed I see that on all of the development platforms I was working on, the rocfft package was installed by default to a reasonable location. For me, the headers I needed were under /opt/rocm/rocfft/include. There is not currently a switch to independently set where rocfft lives, but I've made changes in gitlab to accommodate this: https://gitlab.= com/tcbgUIUC/namd/-/tree/rocfftprefix

-Josh

On 6/25/21 12:27 AM, jing liang wrote:
=20=20=20=20=20=20
Hi,

rocm is installed in "/proc/rocm" but not rocfft. I = guess the rocfft library is this one: https://github.com/ROCmSoftwarePlatform/rocFFT
I can only install that library in my home because rocm was installed by the sys admin. In this case, changing the argument --rocm-prefix
would change the whole location of rocm right? Is there a specific switch for changing the location of the rocfft library only?

thanks. 


El jue, 24 jun 2021 a las 22:21, Josh Vermaas (<vermaasj@msu.edu>) escribi=C3=B3:

One recommendation I would make is to fetch the source from https://gitla= b.com/tcbgUIUC/namd. The bugs mentioned about energy conservation are fixed in the master branch there. If rocfft.h can't be found, either there is no ROCm library installed, or AMD changed the directory layout *again*. The NAMD config file looks in /opt/rocm for the rocm installation, however that may not be where it was installed on your system. If this is the case, you'll need to set the --rocm-prefix argument.

-Josh

On 6/24/21 3:58 PM, jing liang wrote:
I fetched the NAMD source code from the link: http://www.ks.uiuc.edu/Rese= arch/namd/alpha/2.15_amdhip/ 
and followed the BuildInstructions.md. I could build charm++ single node. Then, I tried to build NAMD:

cd Linux-x86_64-g++.hip
make -j8

but I got the error: 
In file included from src/ComputePmeCUDAMgr.C:12:
src/CudaPmeSolverUtil.h:11:10: fatal error: rocfft.h: No such file or directory
 #include <rocfft.h>

do you have any comments about this?





El mi=C3=A9, 23 jun 2= 021 a las 12:08, jing liang (<jingliang2015@gmail= .com>) escribi=C3=B3:
Hi,

I saw a thread on this mailing list about compiling NAMD on AMD GPUs and
it said that there was a problem with energy conservation. Is there an update
on this? Could the same alpha version be used?


thanks.

--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https:/=
/prl.natsci.msu.edu/people/faculty/josh-vermaas/
--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="_000_CY4PR1101MB227929574EBB5D01EB2498ADCC069CY4PR1101MB2279_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CY4PR1101MB2279.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 7ea5ca5c-6007-4b51-9c1c-08d938164a6a X-MS-Exchange-CrossTenant-originalarrivaltime: 25 Jun 2021 20:17:43.7842 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 5b11/hKeXivXGZGmoDvMnMg2W3vdPEDo/+NS2nYLqnEFKbPAh5CRSHFPTlCtYofwD4DG0P/eooSM6JC+jn0n0g== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CY4PR1101MB2261 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0dEQpMehcZGhEKWUQXaEdoehIeH0AfGRwRClhYF2RSUFBZQXITHBw bEQp4ThdoYwFMf0V/QkFlQBEKeUwXYFpeTx1GcFkYQV0RCkNIFwceHx8RCkNZFwcZGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGxtxGwYYG3cGGBoaBhoGGgYbHAYacRoQGncGGgYHHxoGGgYaBhoGG nEaEBp3BhoRClleF2hueREKSUYXX0NfSXVCRVleT04RCkNOFxpAaR9ubxxDcFhieUFncHlwX2Rt SGBSZ11EHR5aGxNIEQpYXBcfBBoEGBkYBRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NpExxjEQp NXBcZGBEKTFoXbGlNa2sRCkxGF29ra2tra2sRCkJPF2dgWk97AXp5HmRAEQpDWhceGgQbGh0EGB gaBBMbEQpCXhcbEQpEXhcYEQpCRRdre2EFeUthWGN4SREKQk4XaGMBTH9Ff0JBZUARCkJMF2RSU FBZQXITHBwbEQpCbBdnelpbSWkSc0NTRxEKQkAXaUR7f0hzRHAbfU0RCkJYF2dzZXNAbmFhTF1i EQpNXhcHGxEKWlgXGBEKeUMXYHwZQEkdUGhlY0cRCllLFxsaEhoSEQpwaBdheUMYH0tNfWd5XhA HGRoRCnBoF2dHa1lJQVNIflBHEAcZGhEKcGgXa0JHHm0aWFByXhwQBxkaEQpwaBdofkseQ1Bscl pGXRAHGRoRCnBoF2QBHHkbbR57e1hZEAcZGhEKcGwXaVpAcmd6SXMZeRIQBxkaEQptfhcHGxEKW E0XSxEg X-Proofpoint-GUID: 0jC5DE6iZrHSkMZSZuNGbJxMwn74p19b X-Proofpoint-ORIG-GUID: 0jC5DE6iZrHSkMZSZuNGbJxMwn74p19b X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 clxscore=177 priorityscore=30 spamscore=0 malwarescore=0 lowpriorityscore=0 mlxscore=0 bulkscore=0 phishscore=0 impostorscore=0 mlxlogscore=706 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106250123 domainage_hfrom=10808 X-Spam-Score: 0 X-Spam-OrigSender: sseshan@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Shiv Seshan --_000_CY4PR1101MB227929574EBB5D01EB2498ADCC069CY4PR1101MB2279_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I am a student researcher simulating the dynamics of TIP4P water within sol= vated protein systems. When I used NAMD 2.14 to minimize the energy of a so= lvated system containing the 1UBQ protein (using the appropriate topology, = parameter, PDB, and PSF files), I received the following error message: "FA= TAL ERROR: Must have the same number of LP hosts as lone pairs." However,= when I used an older version of NAMD--NAMD 2.12--to minimize the energy of= the same system (with the same topology and parameter files), the minimiza= tion was successful. Is this a result of a bug in NAMD 2.14? Can I trust = the output of the minimization program I ran on NAMD 2.12? Sincerely, Shiv --_000_CY4PR1101MB227929574EBB5D01EB2498ADCC069CY4PR1101MB2279_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello,

I am a student researcher simulating the dynamics of TIP4P water within sol= vated protein systems. When I used NAMD 2.14 to minimize the energy of a so= lvated system containing the 1UBQ protein (using the appropriate topology, = parameter, PDB, and PSF files), I received the following error message: "FATAL ERROR: Must have the s= ame number of LP hosts as lone pairs."   However, when I use= d an older version of NAMD--NAMD 2.12--to minimize the energy of the same s= ystem (with the same topology and parameter files), the minimization was successful.  Is this a result of a bug in NAMD 2= .14?  Can I trust the output of the minimization program I ran on NAMD= 2.12?  

Sincerely,
Shiv


 
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[51.81.154.37]) by smtp.gmail.com with ESMTPSA id b6sm6572826pgw.67.2021.06.25.19.48.17 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 25 Jun 2021 19:48:18 -0700 (PDT) Subject: Re: namd-l: Potential NAMD Update Bug To: namd-l@ks.uiuc.edu, Shiv Seshan References: From: yjcoshc Message-ID: <01492baa-e777-1731-ad26-b7473d19fbd6@gmail.com> Date: Fri, 25 Jun 2021 21:48:14 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------23E8E1E255D5B7FBE2361301" Content-Language: en-US X-Proofpoint-ORIG-GUID: T4TDD_iJDKs1RzItln4EVwT9I97DEBht X-CLX-Response: 1TFkXGxwSEQpMehcZGRgRCllEF2ZkX1pvRRJLb1hmEQpYWBdmW3x/R0hvHwV PZREKeE4XY1Nja3sTWH4aX14RCkNIFwcYGBoRCkNZFwcfGBEKQ0kXGgQaGhoRCllNF2dmchEKWU kXGnEaEBp3BhseEnEfExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThd+Hn5ub nVDYG5hWRt4UGNeRkQeb3xdfhNjEx1ub2hCXhEKWFwXHwQaBBgZGAUbGgQbGxoEHxoEGx4bEBse Gh8aEQpeWRdzbm5FehEKTVwXGRwaEQpMWhd4aU1NTREKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQp MRhdva2tsa2sRCkJPF20TYBMBYVprbUASEQpDWhcYGhMEEh8EGBsfBBsdExEKQl4XGxEKRF4XGB EKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdkUkIFGlgaX ntDeBEKQk4XY1Nja3sTWH4aX14RCkJMF2ZbfH9HSG8fBU9lEQpCbBdiT2JEGktAG1JfXREKQkAX Yh9bRl55SUcfbmQRCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdrYEx4e2NJa0BwTxEKWUsXEx4 eExEKcGcXa2ZIfHJHaF5ST2AQGRoRCnBoF2dHa1lJQVNIflBHEBkaEQpwaBdiQVx7XxoTTWN5eB AZGhEKcGgXZlpSbGNPexl5Q18QGRoRCnBoF21vaEFuW0NSbFAaEBkaEQpwaBduHmV5QWUdR19bf xAZGhEKcGwXZh5pRRtISE1kaF8QGRoRCnBDF2l9S39+ZQVtRnxPEBoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: T4TDD_iJDKs1RzItln4EVwT9I97DEBht X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 adultscore=0 malwarescore=0 bulkscore=0 spamscore=0 impostorscore=0 clxscore=168 lowpriorityscore=0 phishscore=0 mlxlogscore=999 priorityscore=332 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106260012 domainage_hfrom=9449 X-Spam-Score: 0 X-Spam-OrigSender: yjcoshc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, yjcoshc This is a multi-part message in MIME format. --------------23E8E1E255D5B7FBE2361301 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit Hi Shiv, It might be a bug with the handle of TIP4P water. Could you kindly send me the input files for debugging? Thanks, Haochuan Chen On 6/25/21 3:17 PM, Shiv Seshan wrote: > Hello, > > I am a student researcher simulating the dynamics of TIP4P water > within solvated protein systems. When I used NAMD 2.14 to minimize the > energy of a solvated system containing the 1UBQ protein (using the > appropriate topology, parameter, PDB, and PSF files), I received the > following error message: "FATAL ERROR: Must have the same number of LP > hosts as lone pairs."   However, when I used an older version of > NAMD--NAMD 2.12--to minimize the energy of the same system (with the > same topology and parameter files), the minimization was successful.  > Is this a result of a bug in NAMD 2.14?  Can I trust the output of the > minimization program I ran on NAMD 2.12? > > Sincerely, > Shiv > > --------------23E8E1E255D5B7FBE2361301 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit

Hi Shiv,


It might be a bug with the handle of TIP4P water. Could you kindly send me the input files for debugging?


Thanks,

Haochuan Chen


On 6/25/21 3:17 PM, Shiv Seshan wrote:
Hello,

I am a student researcher simulating the dynamics of TIP4P water within solvated protein systems. When I used NAMD 2.14 to minimize the energy of a solvated system containing the 1UBQ protein (using the appropriate topology, parameter, PDB, and PSF files), I received the following error message: "FATAL ERROR: Must have the same number of LP hosts as lone pairs."   However, when I used an older version of NAMD--NAMD 2.12--to minimize the energy of the same system (with the same topology and parameter files), the minimization was successful.  Is this a result of a bug in NAMD 2.14?  Can I trust the output of the minimization program I ran on NAMD 2.12?  

Sincerely,
Shiv


 
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Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 MIME-Version: 1.0 In-Reply-To: X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 adultscore=0 malwarescore=0 bulkscore=0 spamscore=0 impostorscore=0 clxscore=168 lowpriorityscore=0 phishscore=0 mlxlogscore=999 priorityscore=332 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106260012 domainage_hfrom=9449 X-Spam-Score: 0 X-Spam-OrigSender: yjcoshc@gmail.com X-Spam-Bar: Authentication-Results: relay.mimecast.com; dkim=fail ("body hash did not verify") header.d=gmail.com header.s=20161025 header.b=DMPBVevM; dmarc=fail reason="No valid SPF" header.from=gmail.com (policy=none); spf=none (relay.mimecast.com: domain of owner-namd-l@ks.uiuc.edu has no SPF policy when checking 130.126.120.36) smtp.mailfrom=owner-namd-l@ks.uiuc.edu X-Mimecast-Spam-Score: 1 Content-Type: multipart/alternative; boundary="------------23E8E1E255D5B7FBE2361301" Content-Language: en-US X-CLX-Shades: MLX X-Proofpoint-GUID: HKhSX-qvlxMK4KwqHl4fewsGmN-yLPaN X-Proofpoint-ORIG-GUID: HKhSX-qvlxMK4KwqHl4fewsGmN-yLPaN X-CLX-Response: 1TFkXGB0SEQpMehceEhEKWUQXYX9HR0F4H39dTx4RClhYF2ZbfH9HSG8fBU9 lEQp4ThdjU2NrexNYfhpfXhEKQ0gXBxsbGxEKQ1kXBx4SEQpDXhcbGxEKXloXGxoYHhEKQ0kXGg QaHRgRCllNF2dmchEKWUkXHB5xGwYbGBJ3BhgaGgYaBhoGHRMGGnEaEBp3BhoGGgYaBgccHwYaB hpxGhAadwYaEQpZXhdoY3kRCklGF19DX0l1QkVZXk9OEQpDThdiYUJ5cgdbXEZSZ2EeYV1bYkYe TE9dWW1HZAdTZnpLZBEKWFwXHwQaBBgZGAUbGgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NuUxxvEQp NXBcbHxIRCkxaF3htXWtrEQpFWRdob2sRCkxfF3oFBQUFBQUFBQEFEQpMRhdze2tka2sRCkJPF2 RDEl1sZxlCGH9tEQpDWhcbGRoEGxkaBBgaEgQYGBsRCkJeFxsRCkReFxgRCkJcFxoRCkJFF2RSQ gUaWBpee0N4EQpCThdjU2NrexNYfhpfXhEKQkwXZlt8f0dIbx8FT2URCkJsF2JPYkQaS0AbUl9d EQpCQBdiH1tGXnlJRx9uZBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcbEQp5QxdrYEx4e2N Ja0BwTxEKWUsXEx4fGxEKcGcXa2ZIfHJHaF5ST2AQBxkaEQpwaBdnR2tZSUFTSH5QRxAHGRoRCn BoF2JBXHtfGhNNY3l4EAcZGhEKcGgXZlpSbGNPexl5Q18QBxkaEQpwaBdtb2hBbltDUmxQGhAHG RoRCnBoF24eZXlBZR1HX1t/EAcZGhEKcGwXZh5pRRtISE1kaF8QBxkaEQptfhcHGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=999 suspectscore=0 phishscore=0 lowpriorityscore=0 clxscore=278 priorityscore=48 impostorscore=0 spamscore=0 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280058 domainage_hfrom=9451 X-Spam-Score: 0 X-Spam-OrigSender: owner-namd-l@ks.uiuc.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, yjcoshc --------------23E8E1E255D5B7FBE2361301 Content-Type: text/plain; charset="WINDOWS-1252"; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by halifax.ks.uiuc.edu id 15Q2rSMJ004958 Hi Shiv, It might be a bug with the handle of TIP4P water. Could you kindly send=20 me the input files for debugging? Thanks, Haochuan Chen On 6/25/21 3:17 PM, Shiv Seshan wrote: > Hello, > > I am a student researcher simulating the dynamics of TIP4P water=20 > within solvated protein systems. When I used NAMD 2.14 to minimize the=20 > energy of a solvated system containing the 1UBQ protein (using the=20 > appropriate topology, parameter, PDB, and PSF files), I received the=20 > following error message: "FATAL ERROR: Must have the same number of LP=20 > hosts as lone pairs."=A0 =A0However, when I used an older version of=20 > NAMD--NAMD 2.12--to minimize the energy of the same system (with the=20 > same topology and parameter files), the minimization was successful.=A0= =20 > Is this a result of a bug in NAMD 2.14?=A0 Can I trust the output of the= =20 > minimization program I ran on NAMD 2.12? > > Sincerely, > Shiv > > --------------23E8E1E255D5B7FBE2361301 Content-Type: text/html; charset="windows-1252" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by halifax.ks.uiuc.edu id 15Q2rSMJ004958

Hi Shiv,


It might be a bug with the handle of TIP4P water. Could you kindly send me the input files for debugging?


Thanks,

Haochuan Chen


On 6/25/21 3:17 PM, Shiv Seshan wrote:
Hello,

I am a student researcher simulating the dynamics of TIP4P water within solvated protein systems. When I used NAMD 2.14 to minimize the energy of a solvated system containing the 1UBQ protein (using the appropriate topology, parameter, PDB, and PSF files), I received the following error message: "FATAL ERROR: Must have the same number of LP hosts as lone pairs."=A0 =A0However= , when I used an older version of NAMD--NAMD 2.12--to minimize the energy of the same system (with the same topology and parameter files), the minimization was successful.=A0 Is this a result of a bug in NAMD 2.14?=A0 Can I trust the output of the minimization program I ran on NAMD 2.12?=A0=A0

Sincerely,
Shiv


=A0
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Mon, 28 Jun 2021 08:54:27 +0000 Date: Mon, 28 Jun 2021 08:54:22 +0000 (UTC) From: Prathit Chatterjee To: NAMD Mailing list Message-ID: <2074540803.3663488.1624870462456@mail.yahoo.com> Subject: namd-l: NAMD jobs in SLURM environment, not entering queueing system Content-Type: multipart/alternative; boundary="----=_Part_3663487_392221027.1624870462452" References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18469 YMailNorrin X-CLX-Response: 1TFkXGxsaEQpMehcbGR4RCllEF2R+Y2tAaRJnW25gEQpYWBdlc3pTXk5aGRl nRxEKeE4Xbm1cZlBQTG1jGmMRCnhLF2VzelNeTloZGWdHEQp4TBdoRkZuBU15ZHN5HBEKeUwXaE ZGbgVNeWRzeRwRCkNIFwcYGB0RCkNZFwcbGxwRCkNJFxoEGhoaEQpZTRdnZnIRCllJFxpxGhAad wYTGnEdEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF1pBXEBZBx9TXnx5TFNH cEMaT3N4fnBbeEhMTExPSx1wEQpYXBcfBBoEGBkYBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3N uUGZDEQpNXBcZHRwRCkxaF2hpa2trEQpMRhdva2tva2sRCkJPF2JJH3pcWB9beRseEQpDWhcbGh wEGxoEGB4eBBkdEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdubVxmUFBMbWMaYxEKQkkXbm1cZlBQT G1jGmMRCkJFF2RTaVp+GExJWV5AEQpCThdubVxmUFBMbWMaYxEKQkwXZXN6U15OWhkZZ0cRCkJs F2RyZW4dGmNaUEh8EQpCQBdieV5IYXBCfVtaXBEKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2t EUExlTGdZRxx6EQpwaBdtXV0eZUYZbEt+ZBAZGhEKcGgXYWVuYkxyY1Afa30QGRoRCnBoF2lSWg FzGG0SblxSEBkaEQpwaBduZkdpYmhOR0FCZxAZGhEKcGgXa0tLXEsYbmtBYn8QGRoRCnBsF2RnZ EdZTh9BXXl9EBkaEQpwTBdiQRNQYmtQa09ycBAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: pkvjs-5ytVSfymZi0eYRTZqRbfffea7Z X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: pkvjs-5ytVSfymZi0eYRTZqRbfffea7Z MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 adultscore=0 spamscore=0 impostorscore=0 phishscore=0 clxscore=110 suspectscore=0 mlxlogscore=999 lowpriorityscore=0 bulkscore=0 priorityscore=134 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280061 X-Spam-Score: 0 X-Spam-OrigSender: pc20apr@yahoo.co.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Prathit Chatterjee ------=_Part_3663487_392221027.1624870462452 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Dear Experts, This is regarding GPU job submission with NAMD, compiled specifically for P= ACE CG force field, with CHARMM-GUI, in SLURM environment. Kindly see my submit script below: #!/bin/csh # #SBATCH -J PCCG2000 #SBATCH -N 1 #SBATCH -n 1 #SBATCH -p g3090 # Using a 3090 node #SBATCH --gres=3Dgpu:1=C2=A0 =C2=A0 # Number of GPUs (per node) #SBATCH -o output.log #SBATCH -e output.err # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm-gu= i.org__;!!DZ3fjg!uzul5NRVXaxH6jBb2Q9G5YS_oEiOhHy617xQn-c3N4c6mvGLZWo1Ykiz6O= zuiwzv1w$ ) v3.5 # # The following shell script assumes your NAMD executable is namd2 and that # the NAMD inputs are located in the current directory. # # Only one processor is used below. To parallelize NAMD, use this scheme: # =C2=A0 =C2=A0 charmrun namd2 +p4 input_file.inp > output_file.out # where the "4" in "+p4" is replaced with the actual number of processors y= ou # intend to use. module load compiler/gcc-7.5.0 cuda/11.2=C2=A0 mpi/openmpi-4.0.2-gcc-7 echo "SLURM_NODELIST $SLURM_NODELIST" echo "NUMBER OF CORES $SLURM_NTASKS" set equi_prefix =3D step6.%d_equilibration set prod_prefix =3D step7.1_production set prod_step =C2=A0 =3D step7 # Running equilibration steps set cnt=C2=A0 =C2=A0 =3D 1 set cntmax =3D 6 while ( ${cnt} <=3D ${cntmax} ) =C2=A0 =C2=A0 set step =3D `printf ${equi_prefix} ${cnt}` ##=C2=A0 =C2=A0 /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charm= run /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp= > ${step}.out =C2=A0 =C2=A0 /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 $= {step}.inp > ${step}.out =C2=A0 =C2=A0 @ cnt +=3D 1 end =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D While the jobs are getting submitted, these are not entering the queueing s= ystem, the PIDs of the jobs are invisible with the command "nvidia-smi", bu= t showing with the "top" command inside the gpu node. Any suggestions in rectifying the current discrepancy will be greatly helpf= ul. Thank you and Regards,Prathit ------=_Part_3663487_392221027.1624870462452 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable
Dear Experts,

This i= s regarding GPU job submission with NAMD, compiled specifically for PACE CG= force field, with CHARMM-GUI, in SLURM environment.

Kind= ly see my submit script below:
=

#!/bin/csh

#=

#SBATCH -J PCCG2000<= /p>

#SBATCH -N 1

#SBATCH -n 1

#SBATCH -p g3090 # Using a 3090 node

#SBATCH --gres=3Dgpu:1    # Number of GPUs (per node)

<= p class=3D"ydpe05b1c3ep1" style=3D"margin: 0px; font-stretch: normal; font-= size: 16px; line-height: normal; font-family: Monaco; color: rgb(44, 238, 2= 35);">#SBATCH -o output.log

= #SBATCH -e output.err


# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3= .5

#

# The following shell script assumes your NAMD exec= utable is namd2 and that

# t= he NAMD inputs are located in the current directory.

#

#= Only one processor is used below. To parallelize NAMD, use this scheme:

#     charmrun namd2 +p4 input_file.inp= > output_file.out

# wher= e the "4" in "+p4" is replaced with the actual number of processors you

# intend to use.

module load compiler/gcc-7.5.0 cuda/11.2&nbs= p; mpi/openmpi-4.0.2-gcc-7


echo "SLURM_NODEL= IST $SLURM_NODELIST"

echo= = "NUMBER OF CORES $SLURM_NTASKS"


set equi_prefix =3D step6.= %d_equilibration

s= et prod_prefix =3D step7.1_= production

set prod_step   =3D step7

<= p class=3D"ydpe05b1c3ep2" style=3D"margin: 0px; font-stretch: normal; font-= size: 16px; line-height: normal; font-family: Monaco; color: rgb(242, 242, = 242); min-height: 21px;">


<= span class=3D"ydpe05b1c3es1"># Running equilibration steps

set cnt    =3D 1

set cntmax = =3D 6


while ( ${cnt} <=3D ${cntmax} )

    set step =3D `printf ${equi_prefix} ${cnt}`

##  &= nbsp; /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun= /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp &g= t; ${step}.out

    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out


    @ cnt +=3D 1

end


= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

While th= e jobs are getting submitted, these are not entering the queueing system, t= he PIDs of the jobs are invisible with the command "nvidia-smi", but= showing with the "top" command inside the gpu node.

Any suggestions in rectifying the current discrepancy will be greatly = helpful.

Thank you and Regards,
Prathit

=

<= /div>= ------=_Part_3663487_392221027.1624870462452-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jun 28 04:04:07 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S947hA011315; Mon, 28 Jun 2021 04:04:07 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15S946NH011314; Mon, 28 Jun 2021 04:04:06 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S946c3011310; Mon, 28 Jun 2021 04:04:06 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15S946R9011309; Mon, 28 Jun 2021 04:04:06 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S93xPl011301 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 28 Jun 2021 04:03:59 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15S8x6q6016939 for ; Mon, 28 Jun 2021 09:03:58 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 39du2s294e-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 28 Jun 2021 09:03:58 +0000 Received: from [IPv6:2a02:810c:300:6724:656c:447e:37ba:1ee7] ([IPv6:2a02:810c:300:6724:656c:447e:37ba:1ee7]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 15S93jEN053997 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 28 Jun 2021 11:03:54 +0200 Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system To: namd-l@ks.uiuc.edu, Prathit Chatterjee References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> <2074540803.3663488.1624870462456@mail.yahoo.com> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: Date: Mon, 28 Jun 2021 11:03:46 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 In-Reply-To: <2074540803.3663488.1624870462456@mail.yahoo.com> Content-Type: multipart/alternative; boundary="------------C1D7D3BE4C39F49928229235" Content-Language: de-DE X-Spam-Status: No, hits=-1.599, tests=HELO_NO_DOMAIN=0.164,HTML_FONT_LOW_CONTRAST=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-1.765 X-Spam-Score: (-1.599) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: 1RS1EqMMT53uSUlFqBWF_I3GsYPH0vXO X-Proofpoint-GUID: 1RS1EqMMT53uSUlFqBWF_I3GsYPH0vXO X-CLX-Response: 1TFkXGxIfEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsSHBEKQ1kXBx8aEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxt4eRtvW2dnfh8ZX3l/RmxbaH1sdWMZbVlzemIaXHJlEQpYXBcfBBoEGBkYBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NuUH9wEQpNXBccHREKTFoXeGFNQU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdsX2xmX3BMSxxSSxEKQ1oXGxkbBBgeHAQbGBoEGBgaEQ pCXhcbEQpEXhcYEQpCRRdsHVhyRR8cR0kFbhEKQk4XZBpJbnp6eBpkfVwRCkJMF2BgG1IZHRgaU nIFEQpCbBdma2JkGFlibUh+bBEKQkAXY2BMT2FBHEh+GUcRCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcdEQp5Qxdpe1lIHFAaTUReZhEKcGcXb0N8AWNkcnx7Q0QQGxgRCnBoF2FkW0FTH2N7E01 cEBkaEQpwaBdtXV0eZUYZbEt+ZBAcGhEKcGgXaVJaAXMYbRJuXFIQHBoRCnBoF24BGH5BWkF4YV 9YEBkaEQpwaBduZ1tyeV5haB98ThAZGhEKcH0XYkZoThpPeFlzUk0QGRoRCnB9F2RZWllOSEBNG mVrEB4SEQpwfRdlTEVwH3sTYxxlbxAeEhEKcH8XaRhZR0ltGlxtWWIQGRoRCnBfF2JGaE4aT3hZ c1JNEBkaEQpwfxdtRF9GRW19SHkZbhAbGB8RCnBfF2tGSxN5aGlufBN4EBIZEQpwfxdhZm9bGmd kQkgdWxAbGxgRCnBfF2NiElBIY3gffEJ9EB0fEQpwbBd6H3h5b3hMQ19wRBAZGhEKbX4XGxEKWE 0XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 phishscore=0 adultscore=0 spamscore=0 mlxlogscore=999 priorityscore=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 suspectscore=0 clxscore=185 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280062 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------C1D7D3BE4C39F49928229235 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi =C2=A0=C2=A0=C2=A0 Did you actually use a GPU version of NAMD? =C2=A0=C2=A0=C2=A0 You should see this in the logfile. =C2=A0=C2=A0=C2=A0 If you rely on single node GPU runs the precompiled CUD= A binaries=20 should be sufficient. =C2=A0=C2=A0=C2=A0 And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to th= e namd exec=20 line below for faster execution. Kind regards Ren=C3=A9 On 6/28/2021 10:54 AM, Prathit Chatterjee wrote: > Dear Experts, > > This is regarding GPU job submission with NAMD, compiled specifically=20 > for PACE CG force field, with CHARMM-GUI, in SLURM environment. > > Kindly see my submit script below: > > #!/bin/csh > > # > > #SBATCH -J PCCG2000 > > #SBATCH -N 1 > > #SBATCH -n 1 > > #SBATCH -p g3090 # Using a 3090 node > > #SBATCH --gres=3Dgpu:1# Number of GPUs (per node) > > #SBATCH -o output.log > > #SBATCH -e output.err > > > # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm-= gui.org__;!!DZ3fjg!tVBPMP36gvVp2lW_NjE0cxjrDjBZipk3CQw4snzd1WFkRgur9lon9q8Y= kpiDcegeRA$=20=20 > )=20 > v3.5 > > # > > # The following shell script assumes your NAMD executable is namd2 and=20 > that > > # the NAMD inputs are located in the current directory. > > # > > # Only one processor is used below. To parallelize NAMD, use this scheme: > > # charmrun namd2 +p4 input_file.inp > output_file.out > > # where the "4" in "+p4" is replaced with the actual number of=20 > processors you > > # intend to use. > > module load compiler/gcc-7.5.0cuda/11.2mpi/openmpi-4.0.2-gcc-7 > > > echo"SLURM_NODELIST $SLURM_NODELIST" > > echo"NUMBER OF CORES $SLURM_NTASKS" > > > setequi_prefix =3D step6.%d_equilibration > > setprod_prefix =3D step7.1_production > > setprod_step =3D step7 > > > > # Running equilibration steps > > setcnt=3D 1 > > setcntmax =3D 6 > > > while(${cnt}<=3D${cntmax}) > > setstep=3D `printf ${equi_prefix} ${cnt}` > > ##/home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun=20 > /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2=20 > ${step}.inp > ${step}.out > > /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2=20 > ${step}.inp>${step}.out > > > @ cnt +=3D 1 > > end > > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > While the jobs are getting submitted, these are not entering the=20 > queueing system, the PIDs of the jobs are invisible with the command=20 > "*nvidia-smi*", but showing with the "*top*" command inside the gpu node. > > Any suggestions in rectifying the current discrepancy will be greatly=20 > helpful. > > Thank you and Regards, > Prathit > > --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------C1D7D3BE4C39F49928229235 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi   

    Did you actually use a GPU version of NAMD?

    You should see this in the logfile.

    If you rely on single node GPU runs the precompiled CUDA binaries should be sufficient.

    And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to the namd exec line below for faster execution.

Kind regards

René

On 6/28/2021 10:54 AM, Prathit Chatterjee wrote:
Dear Experts,

This is regarding GPU job submission with NAMD, compiled specifically for PACE CG force field, with CHARMM-GUI, in SLURM environment.

Kindly see my submit script below:

#!/bin/csh

#

#SBATCH -J PCCG2000

#SBATCH -N 1

#SBATCH -n 1

#SBATCH -p g3090 # Using a 3090 node

#SBATCH --gres=gpu:1    # Number of GPUs (per node)

#SBATCH -o output.log

#SBATCH -e output.err


# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.5

#

# The following shell script assumes your NAMD executable is namd2 and that

# the NAMD inputs are located in the current directory.

#

# Only one processor is used below. To parallelize NAMD, use this scheme:

#     charmrun namd2 +p4 input_file.inp > output_file.out

# where the "4" in "+p4" is replaced with the actual number of processors you

# intend to use.

module load compiler/gcc-7.5.0 cuda/11.2  mpi/openmpi-4.0.2-gcc-7


echo "SLURM_NODELIST $SLURM_NODELIST"

echo "NUMBER OF CORES $SLURM_NTASKS"


set equi_prefix = step6.%d_equilibration

set prod_prefix = step7.1_production

set prod_step   = step7



# Running equilibration steps

set cnt    = 1

set cntmax = 6


while ( ${cnt} <= ${cntmax} )

    set step = `printf ${equi_prefix} ${cnt}`

##    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out

    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out


    @ cnt += 1

end


================

While the jobs are getting submitted, these are not entering the queueing system, the PIDs of the jobs are invisible with the command "nvidia-smi", but showing with the "top" command inside the gpu node.

Any suggestions in rectifying the current discrepancy will be greatly helpful.

Thank you and Regards,
Prathit


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
--------------C1D7D3BE4C39F49928229235-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jun 28 04:27:21 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S9RLXF013315; Mon, 28 Jun 2021 04:27:21 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15S9RLcs013314; Mon, 28 Jun 2021 04:27:21 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S9RK5a013310; Mon, 28 Jun 2021 04:27:20 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15S9RK6p013309; Mon, 28 Jun 2021 04:27:20 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S9RA7T013301 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 28 Jun 2021 04:27:10 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 15S9N4mb016540 for ; Mon, 28 Jun 2021 09:27:10 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 39dtks2d2j-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 28 Jun 2021 09:27:09 +0000 Received: from [IPv6:2a02:810c:300:6724:656c:447e:37ba:1ee7] ([IPv6:2a02:810c:300:6724:656c:447e:37ba:1ee7]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 15S9R6w4067498 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 28 Jun 2021 11:27:06 +0200 Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= To: namd-l@ks.uiuc.edu, Prathit Chatterjee References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> <2074540803.3663488.1624870462456@mail.yahoo.com> Message-ID: <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> Date: Mon, 28 Jun 2021 11:27:06 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------B3BA50A554305C9E713541E3" Content-Language: de-DE X-Spam-Status: No, hits=-1.6, tests=HELO_NO_DOMAIN=0.164,HTML_MESSAGE=0.001,NICE_REPLY_A=-1.765 X-Spam-Score: (-1.6) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: Uv7oGGlSWW-NdI_fiL8omO_KhJM3aI0N X-CLX-Shades: MLX X-Proofpoint-GUID: Uv7oGGlSWW-NdI_fiL8omO_KhJM3aI0N X-CLX-Response: 1TFkXGxMbEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp4SxdgYBtSGR0YGlJyBREKeEwXaAFEXFxeW19GfE4RCnlMF25hXE NOaFhHEn5HEQpDSBcHGBsfEQpDWRcHHxoRCkNJFxoEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbH RtxHxoQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19JdUJFWV5PThEKQ04Xf1wdRW1tRnl9fQdkTmN1 TENmEkVHZXVhQmBnGUtjGmQRClhcFx8EGgQYGRgFGxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc25 QW2MRCk1cFxkdGxEKTFoXe2FNQU0RCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTx dsX2xmX3BMSxxSSxEKQ1oXGxkbBBgeHAQbGBoEGBgaEQpCXhcbEQpEXhcYEQpCRRdsHVhyRR8cR 0kFbhEKQk4XZBpJbnp6eBpkfVwRCkJMF2BgG1IZHRgaUnIFEQpCbBdma2JkGFlibUh+bBEKQkAX Y2BMT2FBHEh+GUcRCkJYF2dzZXNAbmFhTF1iEQpaWBcdEQp5Qxdpe1lIHFAaTUReZhEKcGcXbkJ bXGscaX1EQ1sQGhEKcGgXYXxfRVJ4RXtgbAEQGhEKcGgXbUVfRWZnaUMFUhwQGhEKcGgXYWRbQV MfY3sTTVwQHhIRCnBoF2lSWgFzGG0SblxSEB0aEQpwaBduZ1tyeV5haB98ThAeEhEKcH0XYkZoT hpPeFlzUk0QGRoRCnB9F2RZWllOSEBNGmVrEBwaEQpwZxdvQ3wBY2RyfHtDRBAbGBEKcH0XZUxF cB97E2McZW8QHBoRCnB/F2kYWUdJbRpcbVliEBkaEQpwXxdiRmhOGk94WXNSTRAZGhEKcH8XbUR fRkVtfUh5GW4QGxgaEQpwXxdrRksTeWhpbnwTeBASGBEKcH8XYWZvWxpnZEJIHVsQGxsaEQpwXx djYhJQSGN4H3xCfRAdHxEKcGwXeh94eW94TENfcEQQHhIRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 suspectscore=0 clxscore=191 priorityscore=0 bulkscore=0 impostorscore=0 adultscore=0 malwarescore=0 spamscore=0 mlxlogscore=999 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280065 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------B3BA50A554305C9E713541E3 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable I just understood that you have a special=C2=A0 version there. You probably need to (re-)compile your adapted NAMD PACE Source with=20 CUDA support first. On 6/28/2021 11:03 AM, Ren=C3=A9 Hafner TUK wrote: > > Hi > > =C2=A0=C2=A0=C2=A0 Did you actually use a GPU version of NAMD? > > =C2=A0=C2=A0=C2=A0 You should see this in the logfile. > > =C2=A0=C2=A0=C2=A0 If you rely on single node GPU runs the precompiled CU= DA binaries=20 > should be sufficient. > > =C2=A0=C2=A0=C2=A0 And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to t= he namd exec=20 > line below for faster execution. > > Kind regards > > Ren=C3=A9 > > On 6/28/2021 10:54 AM, Prathit Chatterjee wrote: >> Dear Experts, >> >> This is regarding GPU job submission with NAMD, compiled specifically=20 >> for PACE CG force field, with CHARMM-GUI, in SLURM environment. >> >> Kindly see my submit script below: >> >> #!/bin/csh >> >> # >> >> #SBATCH -J PCCG2000 >> >> #SBATCH -N 1 >> >> #SBATCH -n 1 >> >> #SBATCH -p g3090 # Using a 3090 node >> >> #SBATCH --gres=3Dgpu:1# Number of GPUs (per node) >> >> #SBATCH -o output.log >> >> #SBATCH -e output.err >> >> >> # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm= -gui.org__;!!DZ3fjg!pa0EkaSxQCslve1sciRh37NGVdeKOPV35nhbs3ceygrQwtknmpRc98s= HB42SL-UkdQ$=20=20 >> )=20 >> v3.5 >> >> # >> >> # The following shell script assumes your NAMD executable is namd2=20 >> and that >> >> # the NAMD inputs are located in the current directory. >> >> # >> >> # Only one processor is used below. To parallelize NAMD, use this scheme: >> >> # charmrun namd2 +p4 input_file.inp > output_file.out >> >> # where the "4" in "+p4" is replaced with the actual number of=20 >> processors you >> >> # intend to use. >> >> module load compiler/gcc-7.5.0cuda/11.2mpi/openmpi-4.0.2-gcc-7 >> >> >> echo"SLURM_NODELIST $SLURM_NODELIST" >> >> echo"NUMBER OF CORES $SLURM_NTASKS" >> >> >> setequi_prefix =3D step6.%d_equilibration >> >> setprod_prefix =3D step7.1_production >> >> setprod_step =3D step7 >> >> >> >> # Running equilibration steps >> >> setcnt=3D 1 >> >> setcntmax =3D 6 >> >> >> while(${cnt}<=3D${cntmax}) >> >> setstep=3D `printf ${equi_prefix} ${cnt}` >> >> ##/home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun=20 >> /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2=20 >> ${step}.inp > ${step}.out >> >> /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2=20 >> ${step}.inp>${step}.out >> >> >> @ cnt +=3D 1 >> >> end >> >> >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >> >> While the jobs are getting submitted, these are not entering the=20 >> queueing system, the PIDs of the jobs are invisible with the command=20 >> "*nvidia-smi*", but showing with the "*top*" command inside the gpu node. >> >> Any suggestions in rectifying the current discrepancy will be greatly=20 >> helpful. >> >> Thank you and Regards, >> Prathit >> >> > --=20 > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------B3BA50A554305C9E713541E3 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

I just understood that you have a special  version there.

You probably need to (re-)compile your adapted NAMD PACE Source with CUDA support first.

On 6/28/2021 11:03 AM, René Hafner TUK wrote:

Hi   

    Did you actually use a GPU version of NAMD?

    You should see this in the logfile.

    If you rely on single node GPU runs the precompiled CUDA binaries should be sufficient.

    And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to the namd exec line below for faster execution.

Kind regards

René

On 6/28/2021 10:54 AM, Prathit Chatterjee wrote:
Dear Experts,

This is regarding GPU job submission with NAMD, compiled specifically for PACE CG force field, with CHARMM-GUI, in SLURM environment.

Kindly see my submit script below:

#!/bin/csh

#

#SBATCH -J PCCG2000

#SBATCH -N 1

#SBATCH -n 1

#SBATCH -p g3090 # Using a 3090 node

#SBATCH --gres=gpu:1    # Number of GPUs (per node)

#SBATCH -o output.log

#SBATCH -e output.err


# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.5

#

# The following shell script assumes your NAMD executable is namd2 and that

# the NAMD inputs are located in the current directory.

#

# Only one processor is used below. To parallelize NAMD, use this scheme:

#     charmrun namd2 +p4 input_file.inp > output_file.out

# where the "4" in "+p4" is replaced with the actual number of processors you

# intend to use.

module load compiler/gcc-7.5.0 cuda/11.2  mpi/openmpi-4.0.2-gcc-7


echo "SLURM_NODELIST $SLURM_NODELIST"

echo "NUMBER OF CORES $SLURM_NTASKS"


set equi_prefix = step6.%d_equilibration

set prod_prefix = step7.1_production

set prod_step   = step7



# Running equilibration steps

set cnt    = 1

set cntmax = 6


while ( ${cnt} <= ${cntmax} )

    set step = `printf ${equi_prefix} ${cnt}`

##    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out

    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out


    @ cnt += 1

end


================

While the jobs are getting submitted, these are not entering the queueing system, the PIDs of the jobs are invisible with the command "nvidia-smi", but showing with the "top" command inside the gpu node.

Any suggestions in rectifying the current discrepancy will be greatly helpful.

Thank you and Regards,
Prathit


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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Mon, 28 Jun 2021 09:33:44 +0000 Date: Mon, 28 Jun 2021 09:32:05 +0000 (UTC) From: Prathit Chatterjee To: "namd-l@ks.uiuc.edu" , =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= Message-ID: <169301540.3674292.1624872725578@mail.yahoo.com> In-Reply-To: <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> <2074540803.3663488.1624870462456@mail.yahoo.com> <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system Content-Type: text/plain; charset=UTF-8 X-Mailer: WebService/1.1.18469 YMailNorrin X-CLX-Response: 1TFkXExIRCkx6FxsZHhEKWUQXZH5ja0BpEmdbbmARClhYF2VzelNeTloZGWd HEQp4ThdubVxmUFBMbWMaYxEKeEsXZXN6U15OWhkZZ0cRCnhMF2hGRm4FTXlkc3kcEQp5TBdoRk ZuBU15ZHN5HBEKQ0gXBxkcEhEKQ1kXBx8aEQpDSRcaBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGH RJxHxAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdZEmJdY0JDZl1kQmQZSx9F Z31hZX4ZH09gYxxZYlJkchEKWFwXHwQaBBgZGAUbGgQbGxoEHxoEGx4YEBseGh8aEQpeWRdzblB dchEKTVwXHh4SEQpMWhd4aU1raxEKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCk JPF2JJH3pcWB9beRseEQpDWhcbGhwEGxoEGB4bBBIYEQpCXhcbEQpEXhcZEQpCXBcbEQpeThcbE QpCSxdubVxmUFBMbWMaYxEKQkkXbm1cZlBQTG1jGmMRCkJFF2RTaVp+GExJWV5AEQpCThdubVxm UFBMbWMaYxEKQkwXZXN6U15OWhkZZ0cRCkJsF2RyZW4dGmNaUEh8EQpCQBdjYExPYUEcSH4ZRxE KQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2l7WUgcUBpNRF5mEQpwZxdgGUZFe05HGW1cRRAZGh EKcGgXZXlhQB9pRlgYWlwQGRoRCnBoF21TQk5/fUh7ZkJDEBkaEQpwaBdoaQVzU30eWk5CeBAZG hEKcGgXaE4acGEZZHtNaGYQGRoRCnBoF25keW9IexNNTWtOEBkaEQpwbBdkZ2RHWU4fQV15fRAc GhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: s8HwIhiLwNhN3a5oMWKOT35eJI6sHxNX X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: s8HwIhiLwNhN3a5oMWKOT35eJI6sHxNX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 adultscore=0 spamscore=0 impostorscore=0 phishscore=0 clxscore=98 suspectscore=0 mlxlogscore=999 lowpriorityscore=0 bulkscore=0 priorityscore=134 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280066 X-Spam-Score: 0 X-Spam-OrigSender: pc20apr@yahoo.co.in X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 15S9Xn7e015115 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Prathit Chatterjee Hello, Thank you for your suggestions, I shall implement the suggested and again get back to you if needed further. Thanks again for the help, Sincere Regards, Prathit On Monday, 28 June, 2021, 06:29:05 pm GMT+9, René Hafner TUK wrote: I just understood that you have a special  version there. You probably need to (re-)compile your adapted NAMD PACE Source with CUDA support first. On 6/28/2021 11:03 AM, René Hafner TUK wrote: >   Hi        Did you actually use a GPU version of NAMD?     You should see this in the logfile.     If you rely on single node GPU runs the precompiled CUDA binaries should be sufficient.     And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to the namd exec line below for faster execution. Kind regards René On 6/28/2021 10:54 AM, Prathit Chatterjee wrote: >   Dear Experts, This is regarding GPU job submission with NAMD, compiled specifically for PACE CG force field, with CHARMM-GUI, in SLURM environment. Kindly see my submit script below: #!/bin/csh # #SBATCH -J PCCG2000 #SBATCH -N 1 #SBATCH -n 1 #SBATCH -p g3090 # Using a 3090 node #SBATCH --gres=gpu:1    # Number of GPUs (per node) #SBATCH -o output.log #SBATCH -e output.err # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm-gui.org__;!!DZ3fjg!uYrnluqKcx3dqMlahR_VBUlUbKlW2zKbS12HeZNP1gkkUOGxP5FGKyECdYjSdWiuMg$ ) v3.5 # # The following shell script assumes your NAMD executable is namd2 and that # the NAMD inputs are located in the current directory. # # Only one processor is used below. To parallelize NAMD, use this scheme: #     charmrun namd2 +p4 input_file.inp > output_file.out # where the "4" in "+p4" is replaced with the actual number of processors you # intend to use. module load compiler/gcc-7.5.0 cuda/11.2  mpi/openmpi-4.0.2-gcc-7 echo "SLURM_NODELIST $SLURM_NODELIST" echo "NUMBER OF CORES $SLURM_NTASKS" set equi_prefix = step6.%d_equilibration set prod_prefix = step7.1_production set prod_step   = step7 # Running equilibration steps set cnt    = 1 set cntmax = 6 while ( ${cnt} <= ${cntmax} )     set step = `printf ${equi_prefix} ${cnt}` ##    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out     /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out     @ cnt += 1 end ================ While the jobs are getting submitted, these are not entering the queueing system, the PIDs of the jobs are invisible with the command "nvidia-smi", but showing with the "top" command inside the gpu node. Any suggestions in rectifying the current discrepancy will be greatly helpful. Thank you and Regards, Prathit -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany From owner-namd-l@halifax.ks.uiuc.edu Mon Jun 28 04:37:49 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S9bnJJ016266; Mon, 28 Jun 2021 04:37:49 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15S9bnWb016265; Mon, 28 Jun 2021 04:37:49 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S9bmc2016261; Mon, 28 Jun 2021 04:37:48 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15S9bmmJ016259; Mon, 28 Jun 2021 04:37:48 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15S9bdim016196 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=F5x/1NnlYeZZB1hbIXQohJ+a++QcPj9usGvVP4umG1I=; b=FpoxTDdyWJGuyEZB113iOuTKra5qzjybEJ0TXWbyMevGoT4Ft9Odh/xk6YjjmKyZxJ Fv8P+AWAUvvMMBqzMQut/RN7IgLb7c32LDGqRA7dIbrR2hWVf+YXdbURygHEvCt83i/Y 7ZzHljjnbQMZEziEtLpnrBCA0GkgfyXRe+e756c83KLimf8czhnLJ7Q5Py+v3k/Vwxqd wiRoRTXSZ2KY76/vMMyfmqESjSpdJn4NUEtX530r7hqdra2aYtYbtOKS+sSPUGRXE6h6 6WQbVQRTUZG8ybTR0RYBboR+mdkT23R8Qg8AfQ30wNiUUMjQmt654gk0FvXcjyayQ+ZT 5cfw== X-Gm-Message-State: AOAM530e6VKBkjy8POyOLYgBHmq/r01gZIHGY9lNJc/W60gbBpbY2LdM KqA+qAmUgw6bnFHAj4srY4J/4lwdeW3xwvB+1Vs1iRKLcZQ= X-Google-Smtp-Source: ABdhPJyyr4OFSIAcuwSwe2zNP5UqNVFTCnJ6ZubMZ76rD9utQeO5CaEmYl9k0/GkuuoyaT0f5MHfCQTOwAyGHpQbj1k= X-Received: by 2002:a19:f805:: with SMTP id a5mr17403748lff.558.1624873056915; Mon, 28 Jun 2021 02:37:36 -0700 (PDT) References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> <2074540803.3663488.1624870462456@mail.yahoo.com> <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> In-Reply-To: <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> From: Natalia Ostrowska Date: Mon, 28 Jun 2021 11:37:25 +0200 Message-ID: Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= Content-Type: multipart/alternative; boundary="0000000000005ce50005c5d03dbe" X-Proofpoint-ORIG-GUID: X9z6w5ZJ4ViSMrdOB-Js6rAAjNHGMJYh X-CLX-Shades: MLX X-Proofpoint-GUID: X9z6w5ZJ4ViSMrdOB-Js6rAAjNHGMJYh X-CLX-Response: 1TFkXGxIaEQpMehcbGBoRCllEF21fHUlIHGdCR0JiEQpYWBdte3J+Z2VZQmh nRREKeE4XYxNfR2R6Y3tEbmwRCnlMF2xQSRMBT2RmRh9mEQpDSBcHGRoTEQpDWRcHHxoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBpxGRMQGncGGBoGGhEKWV4XaGN5EQpJRhdfQ19Jd UJFWV5PThEKQ04XchNQHF0fcGAefEN5Z1hOZWgHYFkcWGtrQGRibWdgc0IRClhcFx8EGgQYGRgF GxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc25QUBMRCk1cFxgeGREKTFoXeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQQfHh EKQl4XGxEKRF4XGBEKQkUXZ2UfHhlISBloeWERCkJOF2MTX0dkemN7RG5sEQpCTBdte3J+Z2VZQ mhnRREKQmwXZBtoQEZ/TVscSGERCkJAF2NgTE9hQRxIfhlHEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXHxEKeUMXaXtZSBxQGk1EXmYRCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdjU0JBZU1EW0B yehAZGhEKcGgXYnBmWlgeYUNMYE4QGRoRCnBoF2gFZkESa2NYeVJrEBkaEQpwaBdsGRMSRGFIXW h6WBAZGhEKcGgXa2hIR0YTeWVHWnMQGRoRCnB9F2JGaE4aT3hZc1JNEBkaEQpwfRdsbH5Ben5CB WFzXRAZGhEKcH0XYWFsQmF4e1oTEhwQGRoRCnB/F2kYWUdJbRpcbVliEBkaEQpwXxdiRmhOGk94 WXNSTRAZGhEKcH8XbURfRkVtfUh5GW4QGxgYEQpwXxdrRksTeWhpbnwTeBASGREKcH8XYWZvWxp nZEJIHVsQGxsaEQpwXxdjYhJQSGN4H3xCfRAdHxEKcGwXaWR6f0weQxhpThIQGRoRCm1+FxsRCl hNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 suspectscore=0 clxscore=180 priorityscore=120 bulkscore=0 impostorscore=0 adultscore=0 malwarescore=0 spamscore=0 mlxlogscore=999 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280066 X-Spam-Score: 0 X-Spam-OrigSender: n.ostrowska@cent.uw.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Natalia Ostrowska --0000000000005ce50005c5d03dbe Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Maybe slurm wants namd to be located somwhere else? I mean not in your home folder. Ask your IT department, they will probably want to install it themselves Natalia Ostrowska Univeristy of Warsaw, Poland Centre of New Technologies Biomolecular Machines Laboratory pon., 28 cze 2021 o 11:28 Ren=C3=A9 Hafner TUK napisa=C5=82(a): > I just understood that you have a special version there. > > You probably need to (re-)compile your adapted NAMD PACE Source with CUDA > support first. > On 6/28/2021 11:03 AM, Ren=C3=A9 Hafner TUK wrote: > > Hi > > Did you actually use a GPU version of NAMD? > > You should see this in the logfile. > > If you rely on single node GPU runs the precompiled CUDA binaries > should be sufficient. > > And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to the namd exec > line below for faster execution. > > Kind regards > > Ren=C3=A9 > On 6/28/2021 10:54 AM, Prathit Chatterjee wrote: > > Dear Experts, > > This is regarding GPU job submission with NAMD, compiled specifically for > PACE CG force field, with CHARMM-GUI, in SLURM environment. > > Kindly see my submit script below: > > #!/bin/csh > > # > > #SBATCH -J PCCG2000 > > #SBATCH -N 1 > > #SBATCH -n 1 > > #SBATCH -p g3090 # Using a 3090 node > > #SBATCH --gres=3Dgpu:1 # Number of GPUs (per node) > > #SBATCH -o output.log > > #SBATCH -e output.err > > > # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm-= gui.org__;!!DZ3fjg!pAlGyttSNy3GVSp-Q8_JUfsaQ0V3m9_3AsRIvN969W8iwUNVPMwD8cW2= b_z0sNBiyA$=20 > ) > v3.5 > > # > > # The following shell script assumes your NAMD executable is namd2 and th= at > > # the NAMD inputs are located in the current directory. > > # > > # Only one processor is used below. To parallelize NAMD, use this scheme: > > # charmrun namd2 +p4 input_file.inp > output_file.out > > # where the "4" in "+p4" is replaced with the actual number of processors > you > > # intend to use. > > module load compiler/gcc-7.5.0 cuda/11.2 mpi/openmpi-4.0.2-gcc-7 > > > echo "SLURM_NODELIST $SLURM_NODELIST" > > echo "NUMBER OF CORES $SLURM_NTASKS" > > > set equi_prefix =3D step6.%d_equilibration > > set prod_prefix =3D step7.1_production > > set prod_step =3D step7 > > > > # Running equilibration steps > > set cnt =3D 1 > > set cntmax =3D 6 > > > while ( ${cnt} <=3D ${cntmax} ) > > set step =3D `printf ${equi_prefix} ${cnt}` > > ## /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun > /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > > ${step}.out > > /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step} > .inp > ${step}.out > > > @ cnt +=3D 1 > > end > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > While the jobs are getting submitted, these are not entering the queueing > system, the PIDs of the jobs are invisible with the command "*nvidia-smi*= ", > but showing with the "*top*" command inside the gpu node. > > Any suggestions in rectifying the current discrepancy will be greatly > helpful. > > Thank you and Regards, > Prathit > > > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --0000000000005ce50005c5d03dbe Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Maybe slurm wants namd to be located somwhere else? I mean= not in your home folder. Ask your IT department, they will probably want t= o install it themselves


Natalia Ostrowska
Univeristy of Warsaw, Poland
Centre of New Technologies
Biomolecular Machines Laboratory


pon., 28 cze 20= 21 o 11:28=C2=A0Ren=C3=A9 Hafner TUK <hamburge@physik.uni-kl.de> napisa=C5=82(a):
=20 =20 =20

I just understood that you have a special=C2=A0 version there.

You probably need to (re-)compile your adapted NAMD PACE Source with CUDA support first.

On 6/28/2021 11:03 AM, Ren=C3=A9 Hafner TUK wrote:
=20

Hi =C2=A0=C2=A0

=C2=A0=C2=A0=C2=A0 Did you actually use a GPU version of NAMD?

=C2=A0=C2=A0=C2=A0 You should see this in the logfile.

=C2=A0=C2=A0=C2=A0 If you rely on single node GPU runs the precomp= iled CUDA binaries should be sufficient.

=C2=A0=C2=A0=C2=A0 And do add `+p${SLURM_NTASKS_PER_NODE} +idlepol= l` to the namd exec line below for faster execution.

Kind regards

Ren=C3=A9

On 6/28/2021 10:54 AM, Prathit Chatterjee wrote:
=20
Dear Experts,

This is regarding GPU job submission with NAMD, compiled specifically for PACE CG force field, with CHARMM-GUI, in SLURM environment.

Kindly see my submit script below:

#!/bin/csh<= /span>

#

#SBATCH -J = PCCG2000

#SBATCH -N = 1

#SBATCH -n = 1

#SBATCH -p = g3090 # Using a 3090 node

#SBATCH --g= res=3Dgpu:1=C2=A0 =C2=A0 # Number of GPUs (per node)

#SBATCH -o = output.log

#SBATCH -e = output.err

=

# Generated= by CHARMM-GUI (http://www.charmm-gui.org) v3.5

#

# The follo= wing shell script assumes your NAMD executable is namd2 and that

# the NAMD = inputs are located in the current directory.

#

# Only one = processor is used below. To parallelize NAMD, use this scheme:

# =C2= =A0 =C2=A0 charmrun namd2 +p4 input_file.inp > output_file.out

# where the= "4" in "+p4" is replaced with the actual number of processors you<= /p>

# intend to= use.

module load compiler/gcc-7.5.0 cuda/11.2=C2=A0 mpi/openmpi-4.0.2-gcc-7

=

echo "SLURM_NODELIST $SLURM_NODELIST"

echo "NUMBER OF CORES $SLURM_NTASKS"

=

s= et equi_prefix =3D step6.%d_equilibration

s= et prod_prefix =3D step7.1_production

s= et prod_step =C2=A0 =3D step7

=

=

# Running e= quilibration steps

s= et cnt=C2=A0 =C2=A0 =3D 1

s= et cntmax =3D 6

=

while <= /span>( ${cnt} <=3D ${cntmax} )

= =C2=A0 =C2=A0 set step =3D `pr= intf ${equi_prefix} ${cnt}`

##=C2= =A0 =C2=A0 /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/cha= rmrun /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out

=C2=A0 =C2=A0 /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_6= 4-g++/namd2 ${step}.inp > ${step}.out<= /span>

=

=C2=A0 =C2=A0 @ cnt +=3D 1=

end<= /p>


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=

While the jobs are getting submitted, these are not entering the queueing system, the PIDs of the jobs are invisible with the command "nvidia= -smi", but showing with the "top" command inside the = gpu node.

Any suggestions in rectifying the current discrepancy will be greatly helpful.

Thank you and Regards,
Prathit


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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charset="UTF-8" Hi, I am starting a constant ph md on a ph activated lipopeptide (lp) insertion into a lipid bilayer. Lp has 9 titrable residues. My questions are as follows: 1) I have applied a cter patch during psf generation. Since there is also a cter patch present in charmm 36 cph ff, will this also be included as a titrable part? 2) As lp inserts into the bilayer it's environment will change. How do I for that in cphmd? Thanks in advance. Diship Srivastava JRF IIT(ISM) Dhanbad India --000000000000b9221005c5d31a87 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,=C2=A0
I am starting a constant ph md= on a ph activated lipopeptide (lp) insertion into a lipid bilayer. Lp has = 9 titrable residues. My questions are as follows:=C2=A0
1) I have applied a cter patch during psf generation. Since there is al= so a cter patch present in charmm 36 cph ff, will this also be included as = a titrable part?=C2=A0
2) As lp inserts into the bil= ayer it's=C2=A0 environment will change. How do I for that in cphmd?=C2= =A0


Thanks in advance.=C2=A0

Diship Srivastava
JRF
IIT(ISM) Dhanbad
India
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([2601:184:497f:c640:fa40:cd4c:bad9:9bf2]) by smtp.gmail.com with ESMTPSA id z22sm4031481qki.42.2021.06.28.13.07.40 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Mon, 28 Jun 2021 13:07:40 -0700 (PDT) Subject: Re: namd-l: Constant ph md To: namd-l@ks.uiuc.edu, Diship Srivastava References: From: Brian Radak Message-ID: <5fb70f7b-0440-a80a-d663-c28be1cb0fa9@gmail.com> Date: Mon, 28 Jun 2021 16:07:39 -0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Content-Language: en-US X-Proofpoint-ORIG-GUID: t0OSe7RmYQYCdsjByuovDUw49Nw2pap8 X-Proofpoint-GUID: t0OSe7RmYQYCdsjByuovDUw49Nw2pap8 X-CLX-Response: 1TFkXGxIcEQpMehcZGBsRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGRwdEQpDWRcHHh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBxxHh8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XXhpleU8deEdze3NpTllAaFNfRVxuf10eE2RdGFpLWhIRClhcFx8EGgQYGRgF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc24TaUURCk1cFx0eEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdvb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbHRwRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaxMaYU5fXlgYHWURCkJOF2NTY2t7E1h+Gl9eEQpCTBdpSUgaS35pRht4cxEKQmwX YR4ZeFpubGdjX2IRCkJAF24eTxh6T2RmQgUSEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXbE1IWkxjfFlDRh4RCllLFxMeHxsRCnBoF2tkcmNOHUVpemJNEBkaEQpwaBdrSFMYHUtlQW 8YWRAZGhEKcGgXblpnaEBHQk1Lc04QGRoRCnBoF2ZmHAVOfnBjUGBNEBkaEQpwaBdkGVBdbERAW R1sZBAZGhEKcGwXbh1mexJLGngSXG0QGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 phishscore=0 adultscore=0 spamscore=0 mlxlogscore=999 priorityscore=321 impostorscore=0 lowpriorityscore=0 bulkscore=0 suspectscore=0 clxscore=186 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2106280129 domainage_hfrom=9451 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak C-termini and N-termini titrations are implemented, but not parameterized. You would have to build the residues and find/compute reference values yourself. The syntax is explained in the developer's manual, but I'm not sure this ever got posted on the website (contact me off-line if you are interested in a copy). Unfortunately membrane simulations are an unsolved problem for constant-pH MD in NAMD since they frequently produce massive PMF artifacts. There are some post-hoc corrections (described in the paper), but they can be cumbersome and may not work well for large systems with many titratable residues. HTH, BKR On 6/28/21 9:02 AM, Diship Srivastava wrote: > Hi, > I am starting a constant ph md on a ph activated lipopeptide (lp) > insertion into a lipid bilayer. Lp has 9 titrable residues. My > questions are as follows: > 1) I have applied a cter patch during psf generation. Since there is > also a cter patch present in charmm 36 cph ff, will this also be > included as a titrable part? > 2) As lp inserts into the bilayer it's environment will change. How do > I for that in cphmd? > > > Thanks in advance. > > Diship Srivastava > JRF > IIT(ISM) Dhanbad > India From owner-namd-l@halifax.ks.uiuc.edu Wed Jun 30 10:49:00 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15UFmxQ5029188; Wed, 30 Jun 2021 10:49:00 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15UFmxNd029187; Wed, 30 Jun 2021 10:48:59 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15UFmxO0029183; Wed, 30 Jun 2021 10:48:59 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 15UFmxd2029182; Wed, 30 Jun 2021 10:48:59 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 15UFmo8t029173 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Hello, I am Sandeep Dash, a graduate student at Binghamton University pursuing my degree in Computational Chemistry. I use NAMD for my classical simulations and I am writing this mail to check if there is a version of NAMD available for the Apple M1 chip yet. Please let me know. Thank you in advance Sandeep --0000000000007a1c2705c5fda80c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,

I am Sandeep Dash, a graduate st= udent at Binghamton University pursuing my degree in Computational Chemistr= y. I use NAMD for my classical simulations and I am writing this mail to ch= eck if there is a version of NAMD available for the Apple M1 chip yet.

Please let me know.

Thank you= in advance
Sandeep
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boundary="_000_SN6PR11MB2878AD6A09EB2D604F3909D8B0009SN6PR11MB2878namp_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SN6PR11MB2878.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 69413acc-561e-48b0-7e03-08d93c31c0bc X-MS-Exchange-CrossTenant-originalarrivaltime: 01 Jul 2021 01:44:23.3768 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: Xs+H1DSmv7XneL0bkss2MSpgcoLyYZOFfY6HeuA6AmHSDBJExZMv2AafEAr7MgSKN5fbVYx6htiJP6uMVO9tvw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SA0PR11MB4559 X-CLX-Response: 1TFkXGRwaEQpMehcZGhEKWUQXbm18a3l5fExCYHkRClhYF2dCHxpIUmhAGEZ CEQp4ThdoYwFMf0V/QkFlQBEKeUwXem9rRXAYExtSbFkRCkNIFwcZHBEKQ1kXBxsTHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXHBhxGwYbGBl3BhgaGgYaBhoGExIGGnEaEBp3BhoGGgYaBhoGGgYac RoQGncGGhEKWV4XaG55EQpJRhdfQ19JdUJFWV5PThEKQ04XH3hoa1lDHhJQG0lcWUN9GxJzf1tu eBpnGRxpQWJ4ZXgRClhcFx8EGgQYGRgFGxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzb1lhfBEKTVw XGxMdEQpMWhdoaU1raxEKTEYXb2tra2traxEKQk8Xel5zQRJPG2kcRnMRCkNaFx4aBBsaHQQTGA QbGBkRCkJeFxsRCkReFxgRCkJFF25uUB5sYRhhcx8fEQpCThdoYwFMf0V/QkFlQBEKQkwXZ0IfG khSaEAYRkIRCkJsF2RiZgFncxNTRU9SEQpCQBdsG2BebAESemNeRREKQlgXZ3Nlc0BuYWFMXWIR Ck1eFwcbEQpaWBcYEQp5Qxdta3prelJ8cktMaREKWUsXGxoSGx4RCnBoF2B9RF9pXkBaT1tFEAc ZGhEKcGgXZHIdaEgZTUhLaU0QBxkaEQpwaBdrSHxyen5sY3xNSRAHGRoRCnBoF2R5RxJfUhxHEl 4ZEAcZGhEKcGgXaXNef3h8QH9Me2wQBxkaEQpwbBdmTX1na1tjSX5HSRAHGRoRCm1+FwcbEQpYT RdLESA= X-Proofpoint-GUID: 5RBAsi48z1cvsiW18YUqDR0M36CkHROR X-Proofpoint-ORIG-GUID: 5RBAsi48z1cvsiW18YUqDR0M36CkHROR X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=360 suspectscore=0 bulkscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 mlxscore=0 mlxlogscore=883 malwarescore=0 spamscore=0 phishscore=0 priorityscore=30 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107010010 domainage_hfrom=10814 X-Spam-Score: 0 X-Spam-OrigSender: royi@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ishaan Roy --_000_SN6PR11MB2878AD6A09EB2D604F3909D8B0009SN6PR11MB2878namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, I am running an ABF simulation on a membrane protein to find the binding fr= ee energy. In one of the systems, when running ABF on the tilt angle colvar= , the protein flips over almost 180 degrees within the membrane. However, i= n other systems, the protein stays within a smell tilt angle range in the m= embrane when running the ABF on it. The tilt colvar currently has an upper = and lower limit of 1 and -1. Could this problem be a result of the ABF coun= tering interactions that would normally keep the protein in a natural orien= tation? If so, then to what values should the upper and lower limit be chan= ged? Thanks, Ishaan --_000_SN6PR11MB2878AD6A09EB2D604F3909D8B0009SN6PR11MB2878namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

 

I am running an ABF simulation on a membrane protein= to find the binding free energy. In one of the systems, when running ABF o= n the tilt angle colvar, the protein flips over almost 180 degrees within t= he membrane. However, in other systems, the protein stays within a smell tilt angle range in the membrane when run= ning the ABF on it. The tilt colvar currently has an upper and lower limit = of 1 and -1. Could this problem be a result of the ABF countering interacti= ons that would normally keep the protein in a natural orientation? If so, then to what values should the up= per and lower limit be changed?

 

Thanks,

Ishaan

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boundary="000000000000dfdd5105c6061ae9" X-Proofpoint-GUID: glb0k1itcmZm7OY4DU4hC-LzOp88sdC0 X-CLX-Response: 1TFkXGxwfEQpMehcZHhwRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGBkbEQpDWRcHGxsbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4fcRgdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF01GSBpBG0NeSUdwRx1lcx5ufx5CaQdmUGVaEhJZTmkaEQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc29ZeVARCk1cFxgfGREKTFoXaXhpa01rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGx0TEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9YeGARCkJs F2FfelMZQ0Qaeht+EQpCQBdoeW1HWX0SS0toaREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxg RCnlDF2drBUdNZn9AG19OEQpZSxcTHh8eEQpwaBdpc15/eHxAf0x7bBAHGxIRCnBoF2xcaHxhZV AcY1oeEBkaEQpwaBdnR3xASH9tGlJjXBAZGhEKcGgXZ2NCWGZbcBhgWk0QGRoRCnBoF21eS2x5Z 1Bga21nEBkaEQpwbBdmH3tYXGIFS1hkHxAZGhEKcEwXbWhlGUFSfXsYRVIQGhEKbX4XGxEKWE0X SxEg X-Proofpoint-ORIG-GUID: glb0k1itcmZm7OY4DU4hC-LzOp88sdC0 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=165 suspectscore=0 lowpriorityscore=0 mlxscore=0 malwarescore=0 adultscore=0 mlxlogscore=999 phishscore=0 bulkscore=0 spamscore=0 impostorscore=0 priorityscore=346 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107010011 domainage_hfrom=9454 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000dfdd5105c6061ae9 Content-Type: text/plain; charset="UTF-8" Hi Ishaan, ABF or other adaptive biasing methods will try to overcome all free energy barriers, including those preventing flipping. So flipping is to be expected at some point, the question is whether the mechanism is realistic and the associated energy as well. That depends on how big the protein is, whether it's atomistic or CG, and a variety of other factors that are specific to your project. The upper limit and lower limit that you are using are the natural boundaries of the tilt colvar: it makes sense to define a PMF in that range. You didn't specify whether you also have walls at those locations, but even if you did they would have no effect. Giacomo On Wed, Jun 30, 2021 at 9:45 PM Ishaan Roy wrote: > Hi, > > > > I am running an ABF simulation on a membrane protein to find the binding > free energy. In one of the systems, when running ABF on the tilt angle > colvar, the protein flips over almost 180 degrees within the membrane. > However, in other systems, the protein stays within a smell tilt angle > range in the membrane when running the ABF on it. The tilt colvar currently > has an upper and lower limit of 1 and -1. Could this problem be a result of > the ABF countering interactions that would normally keep the protein in a > natural orientation? If so, then to what values should the upper and lower > limit be changed? > > > > Thanks, > > Ishaan > --000000000000dfdd5105c6061ae9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Ishaan, ABF or other adaptive biasing methods will try = to overcome all free energy barriers, including those preventing flipping.= =C2=A0 So flipping is to be expected at some point, the question is whether= the mechanism is realistic and the associated energy as well.=C2=A0 That d= epends on how big the protein is, whether it's atomistic or CG, and a v= ariety of other factors that are specific to your project.

The upper limit and lower limit that you are using are the natural bound= aries of the tilt colvar: it makes sense to define a PMF in that range.=C2= =A0 You didn't specify whether you also have walls at those locations, = but even if you did they would have no effect.

Gia= como

On Wed, Jun 30, 2021 at 9:45 PM Ishaan Roy <royi@uchicago.edu> wrote:

Hi,

=C2=A0

I am running an ABF simulation on a membrane protein= to find the binding free energy. In one of the systems, when running ABF o= n the tilt angle colvar, the protein flips over almost 180 degrees within t= he membrane. However, in other systems, the protein stays within a smell tilt angle range in the membrane when run= ning the ABF on it. The tilt colvar currently has an upper and lower limit = of 1 and -1. Could this problem be a result of the ABF countering interacti= ons that would normally keep the protein in a natural orientation? If so, then to what values should the up= per and lower limit be changed?

=C2=A0

Thanks,

Ishaan

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Thu, 1 Jul 2021 11:45:46 +0000 Date: Thu, 1 Jul 2021 11:45:44 +0000 (UTC) From: Prathit Chatterjee To: "namd-l@ks.uiuc.edu" , =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= , Natalia Ostrowska Message-ID: <1908450501.4730684.1625139944317@mail.yahoo.com> In-Reply-To: References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> <2074540803.3663488.1624870462456@mail.yahoo.com> <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system Content-Type: multipart/alternative; boundary="----=_Part_4730683_356989286.1625139944310" X-Mailer: WebService/1.1.18469 YMailNorrin X-CLX-Response: 1TFkXGRkaEQpMehcbHx4RCllEF2R+Y2tAaRJnW25gEQpYWBdlc3pTXk5aGRl nRxEKeE4Xbm1cZlBQTG1jGmMRCnhLF2VzelNeTloZGWdHEQp4TBdoRkZuBU15ZHN5HBEKeUwXaE ZGbgVNeWRzeRwRCkNIFwcZGhIRCkNZFwcZHxEKQ0kXGgQaGhoRCllNF2dmchEKWUkXHBpxGwYbG xN3BhgaGgYaBhoGGxoaBhkacRsQGncGGgYaBhoGBxwaBhoGGnEaEBp3BhoRClleF2xseREKSUYX X0NfSXVCRVleT04RCkNOF09iQlxkT21iHU1MbG5ZWEcHREd4WWFue0BCYkRnGh4eEQpYXBcfBBo EGBkYBRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc28aAWMRCk1cFxkfGxEKTFoXeGlNa2sRCkVZF2 9rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiSR96XFgfW3kbHhEKQ1oXGxocBBsaB BgeGwQSGBEKQl4XGxEKRF4XHhEKQlwXGxEKXk4XGxEKQksXbm1cZlBQTG1jGmMRCkJJF25tXGZQ UExtYxpjEQpCRRdkU2lafhhMSVleQBEKQk4Xbm1cZlBQTG1jGmMRCkJMF2VzelNeTloZGWdHEQp CbBdkcmVuHRpjWlBIfBEKQkAXY2BMT2FBHEh+GUcRCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qx dpe1lIHFAaTUReZhEKcGgXYkZTT05lX2xlQ2cQGRoRCnBoF20dQFx8b3theBJlEBkaEQpwaBdrZ kJcYR9SbXp6SRAZGhEKcGgXY0ZzSF1TZ1hDaGcQGRoRCnBoF2RCXVlrAX1MUHByEBkaEQpwbBdk Z2RHWU4fQV15fRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: eHhvNeGH7gfFDsrm-nmRsKDQjhHnM044 X-Proofpoint-ORIG-GUID: eHhvNeGH7gfFDsrm-nmRsKDQjhHnM044 X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=330 suspectscore=0 bulkscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 mlxscore=0 mlxlogscore=999 malwarescore=0 spamscore=0 phishscore=0 priorityscore=154 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107010076 X-Spam-Score: 0 X-Spam-OrigSender: pc20apr@yahoo.co.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Prathit Chatterjee ------=_Part_4730683_356989286.1625139944310 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Dear Experts, Just for your information, and for getting proper suggestions, I am sharing= with you a few more details.I tried to play around, apart from compiling N= AMD with CUDA, as follows... I am pasting a part of my submission script as follows: module load compiler/gcc-7.5.0 cuda/11.2 =C2=A0mpi/openmpi-4.0.2-gcc-7 echo "SLURM_NODELIST $SLURM_NODELIST" echo "NUMBER OF CORES $SLURM_NTASKS" echo "CUDA_VISIBLE_DEVICES=3D$SLURM_NODELIST" export PATH=3D/home2/Prathit/apps/NAMD_PACE_source/Linux-x86_64-g++:${PATH} ............/home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 +p= ${SLURM_NTASKS_PER_NODE} +idlepoll ${prod_step}_run.inp > ${outputname}.out Nevertheless, the error remians... The job is visible in my submitted jobs list as follows: (base) [Prathit@master]~/APP/PACE-CG/APP-Gamma_1000/charmm-gui-2444606374/n= amd>sq Thu Jul=C2=A0 1 20:11:40 2021 =C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 JOBID PARTITION =C2=A0 =C2= =A0 NAME =C2=A0 =C2=A0 USER=C2=A0 =C2=A0 STATE =C2=A0 =C2=A0 =C2=A0 TIME TI= ME_LIMI=C2=A0 NODES NODELIST(REASON) =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0326924 =C2=A0 =C2=A0 =C2=A0 = gpu PCCG1000=C2=A0 Prathit=C2=A0 RUNNING=C2=A0 =C2=A0 2:03:10 3-00:00:00=C2= =A0 =C2=A0 =C2=A0 1 gpu1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 326891 =C2=A0 =C2=A0 g3090 2000-A= PP=C2=A0 Prathit=C2=A0 RUNNING=C2=A0 =C2=A0 5:54:45 3-00:00:00=C2=A0 =C2=A0= =C2=A0 1 gpu6 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 326890 =C2=A0 =C2=A0 g3090 1500-A= PP=C2=A0 Prathit=C2=A0 RUNNING=C2=A0 =C2=A0 5:57:55 3-00:00:00=C2=A0 =C2=A0= =C2=A0 1 gpu6 -------- Also, it is visible to be running with the "top" command, after logging int= o the gpu: =C2=A0 =C2=A0PID USER=C2=A0 =C2=A0 =C2=A0 PR=C2=A0 NI=C2=A0 =C2=A0 VIRT=C2= =A0 =C2=A0 RES=C2=A0 =C2=A0 SHR S=C2=A0 %CPU %MEM =C2=A0 =C2=A0 TIME+ COMMA= ND=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A036566 exay=C2=A0 =C2=A0 =C2=A0 20 =C2=A0 0 =C2=A0 18.9g =C2=A0 2.3g 3= 07624 S 120.9=C2=A0 1.5 =C2=A0 6368:00 python =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A049595 junsu =C2=A0 =C2=A0 20 =C2=A0 0 =C2=A0 27.2g =C2=A0 3.4g 323256= R 100.7=C2=A0 2.1 =C2=A0 2162:55 python =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A049633 junsu =C2=A0 =C2=A0 20 =C2=A0 0 =C2=A0 19.9g =C2=A0 3.5g 323120= R 100.3=C2=A0 2.2 =C2=A0 2010:20 python =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A065081 Prathit =C2=A0 20 =C2=A0 0 3514556 =C2=A0 1.7g =C2=A0 5600 R 10= 0.3=C2=A0 1.1 127:02.83 namd2=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A049453 junsu =C2=A0 =C2=A0 20 =C2=A0 0 =C2=A0 27.2g =C2=A0 2.3g 323252= R 100.0=C2=A0 1.5 =C2=A0 1908:17 python =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A049502 junsu =C2=A0 =C2=A0 20 =C2=A0 0 =C2=A0 30.9g =C2=A0 2.2g 323248= R 100.0=C2=A0 1.4 =C2=A0 2008:01 python=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 -------- Yet, the job is not visible in queue as follows (with nvidia-smi command): +--------------------------------------------------------------------------= ---+ | Processes:=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 | |=C2=A0 GPU =C2=A0 GI =C2=A0 CI=C2=A0 =C2=A0 =C2=A0 =C2=A0 PID =C2=A0 Type = =C2=A0 Process name=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 GPU Memory | |=C2=A0 =C2=A0 =C2=A0 =C2=A0 ID =C2=A0 ID =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Usage= =C2=A0 =C2=A0 =C2=A0 | |=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D| |=C2=A0 =C2=A0 0 =C2=A0 N/A=C2=A0 N/A =C2=A0 =C2=A0 36566=C2=A0 =C2=A0 =C2= =A0 C =C2=A0 python =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 9351MiB | |=C2=A0 =C2=A0 1 =C2=A0 N/A=C2=A0 N/A =C2=A0 =C2=A0 49453=C2=A0 =C2=A0 =C2= =A0 C =C2=A0 ...nvs/conda_lgbm/bin/python =C2=A0 =C2=A0 2413MiB | |=C2=A0 =C2=A0 2 =C2=A0 N/A=C2=A0 N/A =C2=A0 =C2=A0 49502=C2=A0 =C2=A0 =C2= =A0 C =C2=A0 ...nvs/conda_lgbm/bin/python =C2=A0 =C2=A0 2135MiB | |=C2=A0 =C2=A0 4 =C2=A0 N/A=C2=A0 N/A =C2=A0 =C2=A0 49595=C2=A0 =C2=A0 =C2= =A0 C =C2=A0 ...nvs/conda_lgbm/bin/python =C2=A0 =C2=A0 2939MiB | |=C2=A0 =C2=A0 5 =C2=A0 N/A=C2=A0 N/A =C2=A0 =C2=A0 49633=C2=A0 =C2=A0 =C2= =A0 C =C2=A0 ...nvs/conda_lgbm/bin/python =C2=A0 =C2=A0 2541MiB | +--------------------------------------------------------------------------= ---+ Also, as a consequence, the job is too slow. Any further suggestions as to how I can run a job with compiled NAMD_PACE i= n a proper queueing system, will be greatly helpful. Any inconvenience on my behalf is deeply regretted, Sincerely, Prathit On Monday, 28 June, 2021, 07:12:32 pm GMT+9, Natalia Ostrowska <= n.ostrowska@cent.uw.edu.pl> wrote:=20=20 =20 Maybe slurm wants namd to be located somwhere else? I mean not in your hom= e folder. Ask your IT department, they will probably want to install it the= mselves Natalia Ostrowska Univeristy of Warsaw, Poland Centre of New Technologies Biomolecular Machines Laboratory pon., 28 cze 2021 o 11:28=C2=A0Ren=C3=A9 Hafner TUK napisa=C5=82(a): =20=20 I just understood that you have a special=C2=A0 version there. =20 You probably need to (re-)compile your adapted NAMD PACE Source with CUDA s= upport first. =20 On 6/28/2021 11:03 AM, Ren=C3=A9 Hafner TUK wrote: =20=20 =20 Hi =C2=A0=C2=A0=20 =20 =20 =C2=A0=C2=A0=C2=A0 Did you actually use a GPU version of NAMD? =20 =C2=A0=C2=A0=C2=A0 You should see this in the logfile. =20 =C2=A0=C2=A0=C2=A0 If you rely on single node GPU runs the precompiled CUDA= binaries should be sufficient. =20 =C2=A0=C2=A0=C2=A0 And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to the= namd exec line below for faster execution. =20 =20 Kind regards =20 Ren=C3=A9 =20 On 6/28/2021 10:54 AM, Prathit Chatterjee wrote: =20=20 Dear Experts,=20 This is regarding GPU job submission with NAMD, compiled specifically for= PACE CG force field, with CHARMM-GUI, in SLURM environment.=20 Kindly see my submit script below:=20 =20=20=20=20 #!/bin/csh =20 # =20 #SBATCH -J PCCG2000 =20 #SBATCH -N 1 =20 #SBATCH -n 1 =20 #SBATCH -p g3090 # Using a 3090 node =20 #SBATCH --gres=3Dgpu:1=C2=A0 =C2=A0 # Number of GPUs (per node) =20 #SBATCH -o output.log =20 #SBATCH -e output.err =20 =20 =20 # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm-gu= i.org__;!!DZ3fjg!oP3UdBWr9sYssqXLXHy2-lpGaTgBYd1jUKC2ADPNzTw1tWb7L4mbLssGr3= 0d2ZeNzw$ ) v3.5 =20 # =20 # The following shell script assumes your NAMD executable is namd2 and that =20 # the NAMD inputs are located in the current directory. =20 # =20 # Only one processor is used below. To parallelize NAMD, use this scheme: =20 # =C2=A0 =C2=A0 charmrun namd2 +p4 input_file.inp > output_file.out =20 # where the "4" in "+p4" is replaced with the actual number of processors y= ou =20 # intend to use. =20 module load compiler/gcc-7.5.0 cuda/11.2=C2=A0 mpi/openmpi-4.0.2-gcc-7 =20 =20 =20 echo "SLURM_NODELIST $SLURM_NODELIST" =20 echo "NUMBER OF CORES $SLURM_NTASKS" =20 =20 =20 set equi_prefix =3D step6.%d_equilibration =20 set prod_prefix =3D step7.1_production =20 set prod_step =C2=A0 =3D step7 =20 =20 =20 =20 =20 # Running equilibration steps =20 set cnt=C2=A0 =C2=A0 =3D 1 =20 set cntmax =3D 6 =20 =20 =20 while ( ${cnt} <=3D ${cntmax} ) =20 =C2=A0 =C2=A0 set step =3D `printf ${equi_prefix} ${cnt}` =20 ##=C2=A0 =C2=A0 /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charm= run/home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp = > ${step}.out =20 =C2=A0 =C2=A0 /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 $= {step}.inp > ${step}.out =20 =20 =20 =C2=A0 =C2=A0 @ cnt +=3D 1 =20 end =20=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 While the jobs are getting submitted, these are not entering the queueing= system, the PIDs of the jobs are invisible with the command "nvidia-smi", = but showing with the "top" command inside the gpu node.=20 Any suggestions in rectifying the current discrepancy will be greatly hel= pful.=20 Thank you and Regards, Prathit=20 =20=20 =20=20=20 --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany=20 --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany=20 =20=20= ------=_Part_4730683_356989286.1625139944310 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
D= ear Experts,

Just for your information, and for getting proper sugge= stions, I am sharing with you a few more details.
I tried to play around, apart from compili= ng NAMD with CUDA, as follows...

I am pasting a part of my submission script as= follows:

module load compiler/gcc-7.5.0= cuda/11.2  mpi/openmpi-4.0.2-gcc-7echo = "SLURM_NODELIST $SLURM_NODELIST"
<= span style=3D"color: rgb(0, 0, 0);">echo "NUMBER OF CORES $SLURM_NTASKS"
echo "CUDA_VISIBLE_DEVICES=3D$SLURM_NODELIST"
export PATH=3D/home2/Prat= hit/apps/NAMD_PACE_source/Linux-x86_64-g++:${PATH}
....
....
.....
/home2/Prathit/= apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 +p${SLURM_NTASKS_PER_NODE} +id= lepoll ${prod_step}_run.inp > ${outputname}.out

Nevertheless, the error remian= s...

The job is visible in my submitt= ed jobs list as follows:

(base) [Prathit@master]~/APP/PACE-CG/APP-G= amma_1000/charmm-gui-2444606374/namd>sq


Thu Jul  1 20:11:40 2021
         &n= bsp;   JOBID PARTITION     NAME     USER  &nb= sp; STATE       TIME TIME_LIMI  NODES NODELIST(REASON)<= /span>

          &n= bsp; 326924       gpu PCCG1000  Prathit  R= UNNING    2:03:10 3-00:00:00      1 gpu1
&n= bsp;           326891     g3090 2000-APP=   Prathit  RUNNING    5:54:45 3-00:00:00    &= nbsp; 1 gpu6
            326890   &nb= sp; g3090 1500-APP  Prathit  RUNNING    5:57:55 3-00:00= :00      1 gpu6
--------

Also, it is visible to be run= ning with the "top" command, after logging into the gpu:

  &n= bsp;PID USER      PR  NI    VIRT   = RES    SHR S  %CPU %MEM     TIME+ COMMAND  &= nbsp;                    =                     &nbs= p;                     &n= bsp;                
 36566= exay      20   0   18.9g   2.3g 307624 S 120= .9  1.5   6368:00 python            = ;                     &nb= sp;                     &= nbsp;                    =        
 49595 junsu     20   0=   27.2g   3.4g 323256 R 100.7  2.1   2162:55 python &n= bsp;                     =                      = ;                     &nb= sp;                   = ;49633 junsu     20   0   19.9g   3.5g 323120 R 10= 0.3  2.2   2010:20 python           &nbs= p;                     &n= bsp;                     =                      = ;        
 65081 Prathit   20   0 = 3514556   1.7g   5600 R 100.3  1.1 127:02.83 namd2 =                     &nbs= p;                     &n= bsp;                     =                    

&n= bsp;49453 junsu     20   0   27.2g   2.3g 323252 R= 100.0  1.5   1908:17 python           &= nbsp;                    =                     &nbs= p;                     &n= bsp;        
<= span style=3D"color: rgb(0, 0, 0);"> 49502 junsu     20 &nbs= p; 0   30.9g   2.2g 323248 R 100.0  1.4   2008:01 pytho= n             

--------
Yet, the job is not visible in queue as follows (w= ith nvidia-smi command):

+-----------------------------------------= ------------------------------------+

| Processes:      &= nbsp;                    =                     &nbs= p;                 |
|  GPU=   GI   CI        PID   Type   Proc= ess name                  GPU = Memory |
|        ID   ID       =                      = ;                     &nb= sp; Usage      |
|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D|
|    0 &n= bsp; N/A  N/A     36566      C   python =                      = ;     9351MiB |
|    1   N/A  N/A   &= nbsp; 49453      C   ...nvs/conda_lgbm/bin/python  = ;   2413MiB |
|    2   N/A  N/A     4= 9502      C   ...nvs/conda_lgbm/bin/python    = ; 2135MiB |
|    4   N/A  N/A     49595&nb= sp;     C   ...nvs/conda_lgbm/bin/python     2939M= iB |
|    5   N/A  N/A     49633  &nb= sp;   C   ...nvs/conda_lgbm/bin/python     2541MiB |

+-------------------------------------------------------------------------= ----+

Also, as a conse= quence, the job is too slow.
<= br style=3D"color: rgb(0, 0, 0);">
Any further suggestions as t= o how I can run a job with compiled NAMD_PACE in a proper queueing system, = will be greatly helpful.

Any inco= nvenience on my behalf is deeply regretted,
Sincerely,
Prathit
=20
=20
On Monday, 28 June, 2021, 07:12:32 pm GMT+9, Natalia Os= trowska <n.ostrowska@cent.uw.edu.pl> wrote:


Maybe = slurm wants namd to be located somwhere else? I mean not in your home folde= r. Ask your IT department, they will probably want to install it themselves=


Natalia Ost= rowska
Univeristy of Warsaw, Poland
Centre of New Technologies
Biomolecular Machines Laboratory

=

pon., 28 cze 2021 o 11:28 Ren= =C3=A9 Hafner TUK <hamburge@physik.uni-kl.de> napisa=C5= =82(a):
=20 =20 =20

I just understood that you have a special  version there.

You probably need to (re-)compile your adapted NAMD PACE Source with CUDA support first.

On 6/28/2021 11:03 AM, Ren=C3=A9 Hafner TUK wrote:
=20

Hi   

    Did you actually use a GPU version of NAMD?

    You should see this in the logfile.

    If you rely on single node GPU runs the precomp= iled CUDA binaries should be sufficient.

    And do add `+p${SLURM_NTASKS_PER_NODE} +idlepol= l` to the namd exec line below for faster execution.

Kind regards

Ren=C3=A9

On 6/28/2021 10:54 AM, Prathit Chatterjee wrote:
=20
Dear Experts,

This is regarding GPU job submission with NAMD, compiled specifically for PACE CG force field, with CHARMM-GUI, in SLURM environment.

Kindly see my submit script below:

#!/bin/csh=

#

#SBATCH -J= PCCG2000

#SBATCH -N= 1

#SBATCH -n= 1

#SBATCH -p= g3090 # Using a 3090 node

#SBATCH --= gres=3Dgpu:1    # Number of GPUs (per node)

#SBATCH -o= output.log

#SBATCH -e= output.err


# Generate= d by CHARMM-GUI (http://www.charmm-gui.org) v3.5

#

# The foll= owing shell script assumes your NAMD executable is namd2 and that

# the NAMD= inputs are located in the current directory.

#

# Only one= processor is used below. To parallelize NAMD, use this scheme:

# &n= bsp;   charmrun namd2 +p4 input_file.inp > output_file.out

# where th= e "4" in "+p4" is replaced with the actual number of processors you<= /p>

# intend t= o use.

module load compiler/gcc<= span style=3D"color:rgb(251,0,255);">-7.5.0 cuda/= 11.2  mpi/openmpi-4.0.2-gcc-7


echo <= /span>"SLURM_NODELIST = $SLURM_NODELIST"

echo <= /span>"NUMBER OF CORES $SLURM_NTASKS"


set equi_prefix =3D step6.%d_equilibration

set prod_prefix =3D step7.1_production

set prod_step   =3D step7



# Running = equilibration steps

set cnt    =3D 1

set cntmax =3D 6


while ( ${cnt} <=3D<= span style=3D"color:rgb(242,242,242);"> ${cntmax} )

    set step =3D `printf ${equi_prefix} ${cnt}`

##&n= bsp;   /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/ch= armrun /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out

    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86= _64-g++/namd2 ${step}.inp > ${step}= .out


    @ cnt +=3D 1

end=


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=

While the jobs are getting submitted, these are not entering the queueing system, the PIDs of the jobs are invisible with the command "nvidia-smi<= /b>", but showing with the "top" command inside the gpu node.

Any suggestions in rectifying the current discrepancy will be greatly helpful.

Thank you and Regards,
Prathit


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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Thu, 1 Jul 2021 15:42:40 +0000 Date: Thu, 1 Jul 2021 15:41:31 +0000 (UTC) From: Prathit Chatterjee To: "namd-l@ks.uiuc.edu" , =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= , Natalia Ostrowska , "Vermaas, Josh" Message-ID: <2132017751.4778961.1625154091008@mail.yahoo.com> In-Reply-To: <60376EC4-7538-4BAB-9CCF-7296CE483A52@msu.edu> References: <2074540803.3663488.1624870462456.ref@mail.yahoo.com> <2074540803.3663488.1624870462456@mail.yahoo.com> <07201c05-bcd5-5022-f62b-917eab6aaa91@physik.uni-kl.de> <1908450501.4730684.1625139944317@mail.yahoo.com> <60376EC4-7538-4BAB-9CCF-7296CE483A52@msu.edu> Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system Content-Type: text/plain; charset=UTF-8 X-Mailer: WebService/1.1.18469 YMailNorrin X-CLX-Shades: MLX X-Proofpoint-GUID: q8xym4MjDrnlU6q_Lkd-TMulrCUdK8bp X-CLX-Response: 1TFkXHhoSEQpMehcbHxMRCllEF2R+Y2tAaRJnW25gEQpYWBdlc3pTXk5aGRl nRxEKeE4Xbm1cZlBQTG1jGmMRCnhLF2VzelNeTloZGWdHEQp4TBdoRkZuBU15ZHN5HBEKeUwXaE ZGbgVNeWRzeRwRCkNIFwcYGhgRCkNZFwcZHREKQ0kXGgQaGhoRCllNF2dmchEKWUkXGBtxGAYYG ncGGBoaBhsaGkIdBhoGGxoaBh4ScRgQGncGGgYaBhoGBxwaBhoGGnEaEBp3BhoRClleF2xseREK SUYXX0NfSXVCRVleT04RCkNOF1sSUlNHHmdAblhERn8cW3VmQU4HfmdfRlhpf05hEkhaEQpYXBc fBBoEGBkYBRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc28eSWURCk1cFxgZHREKTFoXaXhpTWtrEQ pFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYkkfelxYH1t5Gx4RCkNaFxsaH AQbGgQYHhoEGx4ZEQpCXhcbEQpEXhcfEQpCXBcbEQpeThcbEQpCSxdubVxmUFBMbWMaYxEKQkkX bm1cZlBQTG1jGmMRCkJFF2RTaVp+GExJWV5AEQpCThdubVxmUFBMbWMaYxEKQkwXZXN6U15OWhk ZZ0cRCkJsF2RyZW4dGmNaUEh8EQpCQBdjYExPYUEcSH4ZRxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFx sRClpYFxkRCnlDF2l7WUgcUBpNRF5mEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXbWtcHUdpQkl/Z lkQGRoRCnBoF2RIZlJnTlBFHFNnEBkaEQpwaBdueURvWEhwcmhFchAZGhEKcGgXbmN5S0dgUk1a WGwQGRoRCnBoF2kSYFh9ZBNsTRxkEBkaEQpwfRdnXW5PUxNzQnJMARAZGhEKcH8XZVhyGB1JGF5 GaXwQGxoaEQpwXxdmf2NsfU9nfnJfZhAZGhEKcGwXZGdkR1lOH0FdeX0QHBoRCm1+FxsRClhNF0 sRIA== X-Proofpoint-ORIG-GUID: q8xym4MjDrnlU6q_Lkd-TMulrCUdK8bp MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 clxscore=408 bulkscore=0 priorityscore=159 mlxlogscore=999 impostorscore=0 malwarescore=0 suspectscore=0 lowpriorityscore=0 phishscore=0 spamscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107010094 X-Spam-Score: 0 X-Spam-OrigSender: pc20apr@yahoo.co.in X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 161FgjKI025033 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Prathit Chatterjee Dear Dr. Vermaas and Dr. Hafner, Thank you for the feedback. NAMD PACE cannot be compiled with CUDA currently, I enquired the CHARMM-GUI team. Therefore, the NAMD startup is not yielding similar message (as mentioned in your previous email), as follows: Charm++: standalone mode (not using charmrun) Converse/Charm++ Commit ID: v6.5.0-beta1-293-gd148fb7 CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (40-way SMP). Charm++> cpu topology info is gathered in 0.001 seconds. Info: NAMD 2.9 for Linux-x86_64-multicore Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: for updates, documentation, and support information. Info: Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 60500 for multicore-linux64 Info: Built Tue May 25 19:00:30 KST 2021 by Prathit on master Info: 1 NAMD  2.9  Linux-x86_64-multicore  1    gpu1  Prathit Info: Running on 1 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.00398183 s Info: 34.4961 MB of memory in use based on /proc/self/stat Info: Configuration file is step7_run.inp Info: Working in the current directory /home2/Prathit/APP/PACE-CG/APP-Gamma_1000/charmm-gui-2444606374/namd TCL: Suspending until startup complete. Instead, I have to try whether with multiple processes, I am able to run the required simulations. Thanks a lot anyways. Kindly let me know if you have any more related information. Sincere Regards, Prathit On Thursday, 1 July, 2021, 09:55:36 pm GMT+9, Vermaas, Josh wrote: Is the binary under  /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 compiled with CUDA support enabled or not? On a GPU build of NAMD, you should get output like this at the very beginning of NAMD startup:   Charm++> cpu topology info is gathered in 0.001 seconds. Info: Built with CUDA version 10010 Did not find +devices i,j,k,... argument, using all Pe 0 physical rank 0 binding to CUDA device 0 on PRL-VERMAAS-WS1: 'NVIDIA Quadro RTX 8000'  Mem: 48567MB   Rev: 7.5  PCI: 0:81:0 Info: NAMD 2.14 for Linux-x86_64-multicore-CUDA   Note the “Info:†lines. The first says that the NAMD build was compiled with CUDA 10.1. The second “Info†line says that this is a multicore (one node) build with CUDA support. What do those lines say for you when NAMD starts?   -Josh   From: on behalf of Prathit Chatterjee Reply-To: "namd-l@ks.uiuc.edu" , Prathit Chatterjee Date: Thursday, July 1, 2021 at 7:54 AMTo: "namd-l@ks.uiuc.edu" , René Hafner TUK , Natalia Ostrowska Subject: Re: namd-l: NAMD jobs in SLURM environment, not entering queueing system   Dear Experts, Just for your information, and for getting proper suggestions, I am sharing with you a few more details. I tried to play around, apart from compiling NAMD with CUDA, as follows...   I am pasting a part of my submission script as follows:   module load compiler/gcc-7.5.0 cuda/11.2  mpi/openmpi-4.0.2-gcc-7 echo "SLURM_NODELIST $SLURM_NODELIST" echo "NUMBER OF CORES $SLURM_NTASKS" echo "CUDA_VISIBLE_DEVICES=$SLURM_NODELIST" export PATH=/home2/Prathit/apps/NAMD_PACE_source/Linux-x86_64-g++:${PATH} ... ... .... /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 +p${SLURM_NTASKS_PER_NODE} +idlepoll ${prod_step}_run.inp > ${outputname}.out   Nevertheless, the error remians... The job is visible in my submitted jobs list as follows: (base) [Prathit@master]~/APP/PACE-CG/APP-Gamma_1000/charmm-gui-2444606374/namd>sq Thu Jul  1 20:11:40 2021              JOBID PARTITION     NAME     USER    STATE       TIME TIME_LIMI  NODES NODELIST(REASON)             326924       gpu PCCG1000  Prathit  RUNNING    2:03:10 3-00:00:00      1 gpu1             326891     g3090 2000-APP  Prathit  RUNNING    5:54:45 3-00:00:00      1 gpu6             326890     g3090 1500-APP  Prathit  RUNNING    5:57:55 3-00:00:00      1 gpu6 -------- Also, it is visible to be running with the "top" command, after logging into the gpu:    PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                     36566 exay      20   0   18.9g   2.3g 307624 S 120.9  1.5   6368:00 python                                                                                      49595 junsu     20   0   27.2g   3.4g 323256 R 100.7  2.1   2162:55 python                                                                                      49633 junsu     20   0   19.9g   3.5g 323120 R 100.3  2.2   2010:20 python                                                                                      65081 Prathit   20   0 3514556   1.7g   5600 R 100.3  1.1 127:02.83 namd2                                                                                       49453 junsu     20   0   27.2g   2.3g 323252 R 100.0  1.5   1908:17 python                                                                                      49502 junsu     20   0   30.9g   2.2g 323248 R 100.0  1.4   2008:01 python              -------- Yet, the job is not visible in queue as follows (with nvidia-smi command): +-----------------------------------------------------------------------------+ | Processes:                                                                  | |  GPU   GI   CI        PID   Type   Process name                  GPU Memory | |        ID   ID                                                   Usage      | |=======================================================| |    0   N/A  N/A     36566      C   python                           9351MiB | |    1   N/A  N/A     49453      C   ...nvs/conda_lgbm/bin/python     2413MiB | |    2   N/A  N/A     49502      C   ...nvs/conda_lgbm/bin/python     2135MiB | |    4   N/A  N/A     49595      C   ...nvs/conda_lgbm/bin/python     2939MiB | |    5   N/A  N/A     49633      C   ...nvs/conda_lgbm/bin/python     2541MiB | +-----------------------------------------------------------------------------+   Also, as a consequence, the job is too slow.   Any further suggestions as to how I can run a job with compiled NAMD_PACE in a proper queueing system, will be greatly helpful. Any inconvenience on my behalf is deeply regretted, Sincerely, Prathit On Monday, 28 June, 2021, 07:12:32 pm GMT+9, Natalia Ostrowska wrote:     Maybe slurm wants namd to be located somwhere else? I mean not in your home folder. Ask your IT department, they will probably want to install it themselves Natalia OstrowskaUniveristy of Warsaw, PolandCentre of New TechnologiesBiomolecular Machines Laboratory     pon., 28 cze 2021 o 11:28 René Hafner TUK napisał(a): >   >   > I just understood that you have a special  version there. > > You probably need to (re-)compile your adapted NAMD PACE Source with CUDA support first. > >   > On 6/28/2021 11:03 AM, René Hafner TUK wrote: > > >>   >> Hi    >> >>     Did you actually use a GPU version of NAMD? >> >>     You should see this in the logfile. >> >>     If you rely on single node GPU runs the precompiled CUDA binaries should be sufficient. >> >>     And do add `+p${SLURM_NTASKS_PER_NODE} +idlepoll` to the namd exec line below for faster execution. >> >> Kind regards >> >> René >> >>   >> On 6/28/2021 10:54 AM, Prathit Chatterjee wrote: >> >> >>>   >>>   >>>   >>> Dear Experts, >>> >>> >>>   >>>    >>> >>> >>>   >>> This is regarding GPU job submission with NAMD, compiled specifically for PACE CG force field, with CHARMM-GUI, in SLURM environment. >>> >>> >>>   >>>    >>> >>> >>>   >>> Kindly see my submit script below: >>> >>> >>>   >>>    >>> >>> >>>   >>>   >>> #!/bin/csh >>> >>> # >>> >>> #SBATCH -J PCCG2000 >>> >>> #SBATCH -N 1 >>> >>> #SBATCH -n 1 >>> >>> #SBATCH -p g3090 # Using a 3090 node >>> >>> #SBATCH --gres=gpu:1    # Number of GPUs (per node) >>> >>> #SBATCH -o output.log >>> >>> #SBATCH -e output.err >>> >>>    >>> >>> # Generated by CHARMM-GUI (https://urldefense.com/v3/__http://www.charmm-gui.org__;!!DZ3fjg!uotXwdn_atHouQnAZvtrBd5MzD78SRFnRy7FFtJz79ZzSrKhaTqJTavLSXrSmgMiKA$ ) v3.5 >>> >>> # >>> >>> # The following shell script assumes your NAMD executable is namd2 and that >>> >>> # the NAMD inputs are located in the current directory. >>> >>> # >>> >>> # Only one processor is used below. To parallelize NAMD, use this scheme: >>> >>> #     charmrun namd2 +p4 input_file.inp > output_file.out >>> >>> # where the "4" in "+p4" is replaced with the actual number of processors you >>> >>> # intend to use. >>> >>> module load compiler/gcc-7.5.0 cuda/11.2  mpi/openmpi-4.0.2-gcc-7 >>> >>>    >>> >>> echo "SLURM_NODELIST $SLURM_NODELIST" >>> >>> echo "NUMBER OF CORES $SLURM_NTASKS" >>> >>>    >>> >>> set equi_prefix = step6.%d_equilibration >>> >>> set prod_prefix = step7.1_production >>> >>> set prod_step   = step7 >>> >>>    >>> >>>    >>> >>> # Running equilibration steps >>> >>> set cnt    = 1 >>> >>> set cntmax = 6 >>> >>>    >>> >>> while ( ${cnt} <= ${cntmax} ) >>> >>>     set step = `printf ${equi_prefix} ${cnt}` >>> >>> ##    /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/charmrun /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out >>> >>>     /home2/Prathit/apps/NAMD_PACE_Source/Linux-x86_64-g++/namd2 ${step}.inp > ${step}.out >>> >>>    >>> >>>     @ cnt +=  1 >>> >>> end >>> >>> >>>    >>> >>> >>>   >>> ================ >>> >>> >>>   >>>    >>> >>> >>>   >>> While the jobs are getting submitted, these are not entering the queueing system, the PIDs of the jobs are invisible with the command "nvidia-smi", but showing with the "top" command inside the gpu node. >>> >>> >>>   >>>    >>> >>> >>>   >>> Any suggestions in rectifying the current discrepancy will be greatly helpful. >>> >>> >>>   >>>    >>> >>> >>>   >>> Thank you and Regards, >>> >>> >>>   >>> Prathit >>> >>> >>>   >>>    >>> >>> >>>   >>>    >>> >>> >>> >> -- --Dipl.-Phys. René HafnerTU KaiserslauternGermany > -- --Dipl.-Phys. René HafnerTU KaiserslauternGermany > From owner-namd-l@halifax.ks.uiuc.edu Tue Jul 6 22:05:07 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 167357Sp011456; Tue, 6 Jul 2021 22:05:07 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 167357JF011455; Tue, 6 Jul 2021 22:05:07 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 167356TN011451; Tue, 6 Jul 2021 22:05:06 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 167356Mo011450; Tue, 6 Jul 2021 22:05:06 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16734r4O011437 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 6 Jul 2021 22:04:54 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16732EZk002496 for ; Wed, 7 Jul 2021 03:04:53 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=zebamir85@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-io1-f44.google.com (mail-io1-f44.google.com [209.85.166.44]) by mx0b-00007101.pphosted.com with ESMTP id 39mjc66bms-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 07 Jul 2021 03:04:53 +0000 Received: by mail-io1-f44.google.com with SMTP id b15so1239326iow.4 for ; Tue, 06 Jul 2021 20:04:53 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=JKfA4UZUgcji4el2uibHJR3sLkxcoon4IY7rDw/3TKM=; b=fjlmARdE1tPNTZmR8a350iJqB4kmZMZXUBEHULvNl6tPpGMAmB7v2onOqzpNmiPYf6 Etd15jFFXt/rpDqo0MWxnuoB65nJXIXZ2evtiyKZcS5yhpSmKYbIEi66GVgGNJ8x9DUS fEdhsYkIasW8IWPUfTsbTLydzdkCDMczhx0OaR3+DRRcrGT7l70UC/KoHSGzgxiHD5eO RMsPA60e/wZrmeCW0XI2w5ZoNw8W8QtDHlcL8NLmXyYMZfMD4ONkQxbO3Liigq/9G9iq 0Vum3u/ZPMQQktaatY7Whelk2DGN+AO6Go/Go83aRMLNaJsRnv5a9xWu0VubKYzg0mmB 0kbQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=JKfA4UZUgcji4el2uibHJR3sLkxcoon4IY7rDw/3TKM=; b=crdhtLETXJNa3XsIpV7EwkrfGgzMBHeNK35vWG8tX5wqWih7ySGlBBuTw24tM/dsdP EX4JR7EWgOxgr7PE3YM2+JgnpupGEo0luDRfv9/xXR/YiwJ1mCVtiP/gmW98VvhAq+WO odNN+TqflpWELt3WGfIGi29eLMSU7oWdqfg1b4+ESZOGNL5qY5ZNdesFp7W+uVapxQD9 +tcImucwixMs5MVx1NG3M29y3I7+fH7eIkUyhQVpakyj3lfHuA76r/Y4YP0t44mVZzvl 3MOk40HoLdubnfDzGdy6IJ4VKbnk2gE8QVOa8gJCCshU9EgoEJc3qK3QHqGL/IJ58RAT 1WpA== X-Gm-Message-State: AOAM530RAkO14cfHsIqGP1PhTMXICAb0raQLAbyjGk0oj9ehi1s99QOr K7R5EoJN8Cag/FYhgry8tTXp3KMo+K/fplXTlj0Yzi0Ldz1sug== X-Google-Smtp-Source: ABdhPJy6vXWZ0DEcD66AKNWQCuaRvFnyEY27JpKCUp8nv57MdcsLSqPEpvMqBIWWWtF/iFncAYnUmPMtO/Knh8uXLkY= X-Received: by 2002:a02:880f:: with SMTP id r15mr15720065jai.36.1625627092405; Tue, 06 Jul 2021 20:04:52 -0700 (PDT) MIME-Version: 1.0 From: Amir Zeb Date: Wed, 7 Jul 2021 12:04:42 +0900 Message-ID: Subject: namd-l: Simulation of protein-lipid complex by NAMD with OPLS3e ff? To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="00000000000061509b05c67fcdf5" X-CLX-Shades: MLX X-Proofpoint-GUID: 1WO06T3StRMIQBY6Tx2zEh-_ae9s4cPs X-CLX-Response: 1TFkXGBgcEQpMehcZHx4RCllEF3prYB9EQ0wbfEtPEQpYWBdoWUcSGQF8ZXJ HQREKeE4XY1Nja3sTWH4aX14RCnlMF2FLBR17fENHZGdHEQpDSBcHHhkRCkNZFwcYHx0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsccRgGGx93BhIcBhkaQh8GGgYeHQYeEnEYEBp3BhoGGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XG31lGhx+GXleeGdje2hzHH5S GFBvQgd1S08TWR5JelkRClhcFx8EGgQYGRgFGxoEGxsaBB8aBBseGBAbHhofGhEKXlkXc21YH10 RCk1cFxMeEQpMWhdpaGlNa2sRCkxGF29ra2traxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHw QbHBwEHh4RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXa0RzbhsYGWREX2gRCkJOF2NTY2t7E1h+Gl9eEQpCTBdoWUcSGQF8ZXJHQREKQmwXbnoY cHxFfGJ/G2kRCkJAF2tTb2Bha21yQnBFEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUM XbXNJZnBpZGlQbhwRCllLFxMeHBoRCnBoF25zHUtMHHwbBUxoEBoRCnBoF29JY19SQWR/GkFjEB oRCnBoF2BmAUR/HE0aTwVIEBoRCnBoF219Q2xDQxJNRXJEEBoRCnBoF2ZMaEQbaWVnWUxBEBoRC nBsF2ZFWGgabl1OcG1EEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 1WO06T3StRMIQBY6Tx2zEh-_ae9s4cPs X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=561 bulkscore=0 mlxscore=0 malwarescore=0 spamscore=0 adultscore=0 clxscore=226 impostorscore=0 phishscore=0 lowpriorityscore=0 priorityscore=354 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107070014 domainage_hfrom=9460 X-Spam-Score: 0 X-Spam-OrigSender: zebamir85@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Amir Zeb --00000000000061509b05c67fcdf5 Content-Type: text/plain; charset="UTF-8" Hello NAMD team, I want to simulate a protein in the lipid membrane but I will apply negative lateral pressure to the membrane during the simulation, which is possible in NAMD. But I want to simulate this system with OPLS3e or OPLS4 ff parameters. Is this kindly possible to plug in OPLS3e or OPLS4 ff to NAMD? If yes, how can I do this? Kind regards! Amir --00000000000061509b05c67fcdf5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello NAMD team,

I want to simulate a p= rotein in the lipid membrane=C2=A0but I will apply negative lateral pressur= e to the membrane during the simulation, which is possible in NAMD. But I w= ant to simulate this system with OPLS3e or OPLS4 ff=C2=A0parameters. Is thi= s kindly possible to plug in OPLS3e or OPLS4 ff to NAMD? If yes, how can I = do this?

Kind regards!

Am= ir
--00000000000061509b05c67fcdf5-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 7 09:32:16 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 167EWGKg020717; Wed, 7 Jul 2021 09:32:16 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 167EWG8k020716; Wed, 7 Jul 2021 09:32:16 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 167EWF4r020712; Wed, 7 Jul 2021 09:32:15 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 167EWFrS020711; Wed, 7 Jul 2021 09:32:15 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 167EVv9L020700 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello Ishaan, the list should be copied in. I agree that a full protein flip is very unlikely to occur under normal equilibrium sampling. However, you are using an enhanced sampling method precisely with the purpose of *making such rare events occur more frequently*. When ABF or similar methods are used properly (i.e. along collective variables that can quickly exchange the supplied external energy with the rest of the system), you can observe the structural details of the mechanism and compute the free-energy cost associated with such rare events. The methodology and technical details are explained in the literature and in the code documentation, respectively. For example, you could start from the latter, which contains references to the former: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvarbias_abf__;Iw!!DZ3fjg!uVUdY8aJ-Q4GC2_4-KK= TetJC6_m4HYM1-fxUqer2HmI2Z7uiWTx2xlwlFOanL0H6lg$=20 After reading those, please narrow your questions down to specific details, preferably technical ones that traditionally find little space in the scientific literature (and for which a question to the mailing list is most suitable). Giacomo On Tue, Jul 6, 2021 at 8:39 PM Ishaan Roy wrote: > Hi Giacomo, > > > > Thank you for the response. We have considered what you said and agree > that if there were no other natural constraints on the molecule then the > flipping should be expected. However, in our case, the lipids in the > membrane would prevent the protein from ever flipping in reality, so the > mechanism does not seem realistic as you put it. It seems extremely > unnatural. Does this still mean the flipping should occur in the simulati= on > to find the free energy? If not, are there any changes you could recommen= d? > > > > Thank you, > > Ishaan > > > > *From: *Giacomo Fiorin > *Sent: *Wednesday, June 30, 2021 8:53 PM > *To: *NAMD list ; Ishaan Roy > *Subject: *Re: namd-l: Membrane Protein Flipping in ABF > > > > Hi Ishaan, ABF or other adaptive biasing methods will try to overcome all > free energy barriers, including those preventing flipping. So flipping is > to be expected at some point, the question is whether the mechanism is > realistic and the associated energy as well. That depends on how big the > protein is, whether it's atomistic or CG, and a variety of other factors > that are specific to your project. > > > > The upper limit and lower limit that you are using are the natural > boundaries of the tilt colvar: it makes sense to define a PMF in that > range. You didn't specify whether you also have walls at those locations, > but even if you did they would have no effect. > > > > Giacomo > > > > On Wed, Jun 30, 2021 at 9:45 PM Ishaan Roy wrote: > > Hi, > > > > I am running an ABF simulation on a membrane protein to find the binding > free energy. In one of the systems, when running ABF on the tilt angle > colvar, the protein flips over almost 180 degrees within the membrane. > However, in other systems, the protein stays within a smell tilt angle > range in the membrane when running the ABF on it. The tilt colvar current= ly > has an upper and lower limit of 1 and -1. Could this problem be a result = of > the ABF countering interactions that would normally keep the protein in a > natural orientation? If so, then to what values should the upper and lower > limit be changed? > > > > Thanks, > > Ishaan > > > --0000000000007e09bb05c68966df Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello Ishaan, the list should be copied in.

=
I agree that a full protein flip is very unlikely to occur under norma= l equilibrium sampling.=C2=A0 However, you are using an enhanced sampling m= ethod precisely with the purpose of making such rare events occur more f= requently.=C2=A0 When ABF or similar methods are used properly (i.e. al= ong collective variables that can quickly exchange the supplied external en= ergy with the rest of the system), you can observe the structural details o= f the mechanism and compute the free-energy cost associated with such rare = events.

The methodology and technical details are = explained in the literature and in the code documentation, respectively.=C2= =A0 For example, you could start from the latter, which contains references= to the former:=C2=A0https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.ht= ml#sec:colvarbias_abf=C2=A0

After reading thos= e, please narrow your questions down to specific details, preferably techni= cal ones that traditionally find little space in the scientific literature = (and for which a question to the mailing list is most suitable).
=
Giacomo

On Tue, Jul 6, 2021 at 8:39 PM Ishaan Roy <= ;royi@uchicago.edu> wrote:
<= /div>

Hi Giacomo,

=C2=A0

Thank you for the response. We have considered what = you said and agree that if there were no other natural constraints on the m= olecule then the flipping should be expected. However, in our case, the lip= ids in the membrane would prevent the protein from ever flipping in reality, so the mechanism does not seem = realistic as you put it. It seems extremely unnatural. Does this still mean= the flipping should occur in the simulation to find the free energy? If no= t, are there any changes you could recommend?

=C2=A0

Thank you,

Ishaan

=C2=A0

From: Giacomo Fiorin=
Sent: Wednesday, June 30, 2021 8:53 PM
To: NAMD lis= t; Ishaan Roy
Subject: Re: namd-l: Membrane Protein Flipping in ABF

=C2=A0

Hi Ishaan, ABF or other adaptive biasing methods wil= l try to overcome all free energy barriers, including those preventing flip= ping.=C2=A0 So flipping is to be expected at some point, the question is wh= ether the mechanism is realistic and the associated energy as well.=C2=A0 That depends on how big the protein is, w= hether it's atomistic or CG, and a variety of other factors that are sp= ecific to your project.

=C2=A0

The upper limit and lower limit that you are using a= re the natural boundaries of the tilt colvar: it makes sense to define a PM= F in that range.=C2=A0 You didn't specify whether you also have walls a= t those locations, but even if you did they would have no effect.

=C2=A0

Giacomo

=C2=A0

On Wed, Jun 30, 2021 at 9:45 PM Ishaan Roy <royi@uchicago.edu>= wrote:

Hi,

=C2=A0

I am running an ABF simulation on a membrane protein= to find the binding free energy. In one of the systems, when running ABF o= n the tilt angle colvar, the protein flips over almost 180 degrees within the membrane. However, in other systems, the protein st= ays within a smell tilt angle range in the membrane when running the ABF on= it. The tilt colvar currently has an upper and lower limit of 1 and -1. Co= uld this problem be a result of the ABF countering interactions that would normally keep the protein in a = natural orientation? If so, then to what values should the upper and lower = limit be changed?

=C2=A0

Thanks,

Ishaan

=C2=A0

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boundary="000000000000fc218505c6a11963" X-Proofpoint-ORIG-GUID: 1ddkT8FT9FZIHb3tCdTABhBQ7HbiAtCF X-CLX-Response: 1TFkXGxIeEQpMehcZGR4RCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHGBkZEQpDWRcHGxISEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwecR4ZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxtOTkF+Emx+E2xwY2JIGV5pTn5raEJoex1iSENrXmlsEQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc2JlGkgRCk1cFxgaGREKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHBwEGxIaEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hacBhJH2Z4HkBeEQpCT hdjU2NrexNYfhpfXhEKQkwXbB9eWVpuTGFgW0ERCkJsF29CaX9uTltSGXgaEQpCQBdsWHBNR21p axtARREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF28Ffn9sTWRvU2NAEQpZSxcTHhw bEQpwaBdmRnxGHn8FfkdlfRAZGhEKcGgXYWlrGVhfG15lZhIQGRoRCnBoF2l+bmFkfn1rf2MdEB kaEQpwaBdteE5AWmlEf1tAHBAZGhEKcGgXaWxaWml6R3NbYmEQGRoRCnBsF2d4c3NCR1xbfUZLE BkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: 1ddkT8FT9FZIHb3tCdTABhBQ7HbiAtCF X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 bulkscore=0 adultscore=0 spamscore=0 clxscore=184 mlxscore=0 phishscore=0 lowpriorityscore=0 mlxlogscore=416 malwarescore=0 impostorscore=0 priorityscore=334 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107080096 domainage_hfrom=9461 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000fc218505c6a11963 Content-Type: text/plain; charset="UTF-8" Dear Colleagues, In one of our papers, we have run MD simulations for 60 ns. The RMSDs were found reasonable stable but one reviewer asked to see what is the difference of Binding Energy among original seeded (best docked) structure and at some time intervals eg. at 20 ns or 30ns etc. We have successfully extracted frames at different time intervals but really have no idea how to calculate binding free energy for a frame without changing specific docked structure? We docked protein-ligand with autodock vina, prepared MD input with VMD and ran through NAMD. Any helpful suggestions will be highly encouraging? Best Regards, Dr. Shabbir --000000000000fc218505c6a11963 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
In one of our papers, we h= ave run MD simulations for 60 ns. The RMSDs were found reasonable stable bu= t one reviewer asked to see what is the difference of Binding Energy among = original seeded (best docked) structure and at some time intervals eg. at 2= 0 ns or 30ns etc.
We have successfully extracted frames at differ= ent time intervals but really have no idea how to calculate binding free en= ergy for a frame without changing specific docked structure?

=
We docked protein-ligand with autodock vina, prepared MD input w= ith VMD and ran through NAMD.
Any helpful suggestions will be hig= hly encouraging?
Best Regards,
Dr. Shabbir

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boundary="000000000000ca812905c6a20cc9" X-Proofpoint-GUID: 3FngXmcLnLp8zxtStLSSjUgQupUyoWAC X-CLX-Response: 1TFkXGxwZEQpMehcZHx4RCllEF2tpHmZvE1gFHxt/EQpYWBdtZAFsR3hcZmh SaBEKeE4XY1Nja3sTWH4aX14RCnlMF2FjZGhBRRtJQk1sEQpDSBcHHxscEQpDWRcHGx4bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ZcR8YEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxlsRE1yR0lmRGZaElBSXnleZnl5QH9Ne19af1NFfWtpEQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc2J6Gm0RCk1cFxseGREKTFoXeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGw QeHxEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRd6H38ceV1efFgcGhEKQk4XY1Nja3sTWH4aX14RCkJMF21kAWxHeFxmaFJoEQpCbBdi aXxGZ1BPbmkcBREKQkAXa1NQRmVyelgdQVMRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxduZxh6HF0FGmhdAREKWUsXEx4cGxEKcGcXY01JG3JeR0loZ1AQGRoRCnBoF2BtYBxkAWZAXF p5EBkaEQpwaBdib05DQE1FBR1/GhAZGhEKcGgXbXx8AUEfRUBQTk8QGRoRCnBoF214TkBaaUR/W 0AcEB0aEQpwaBdpbFpaaXpHc1tiYRAdGhEKcGwXZmweExkYbVhiU1kQGRoRCm1+FxsRClhNF0sR IA== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 3FngXmcLnLp8zxtStLSSjUgQupUyoWAC X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 mlxlogscore=622 clxscore=163 lowpriorityscore=0 priorityscore=354 malwarescore=0 phishscore=0 spamscore=0 adultscore=0 bulkscore=0 impostorscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107080101 domainage_hfrom=9461 X-Spam-Score: 0 X-Spam-OrigSender: pratik.narain@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Pratik Narain Srivastava --000000000000ca812905c6a20cc9 Content-Type: text/plain; charset="UTF-8" I assume you plan to do MMPBSA for binding free energy calculation. You can use the Cafe plugin for VMD. It requires a dcd file with your required number of frames and the psf file. So the starting pose of your ligand really shouldn't matter. You can also calculate non bonding interaction energies using the namd energy plugin. The documentation is self explanatory and very simple to follow. On Fri, 9 Jul, 2021, 12:20 am Mi Yang, wrote: > Dear Colleagues, > In one of our papers, we have run MD simulations for 60 ns. The RMSDs were > found reasonable stable but one reviewer asked to see what is the > difference of Binding Energy among original seeded (best docked) structure > and at some time intervals eg. at 20 ns or 30ns etc. > We have successfully extracted frames at different time intervals but > really have no idea how to calculate binding free energy for a frame > without changing specific docked structure? > > We docked protein-ligand with autodock vina, prepared MD input with VMD > and ran through NAMD. > Any helpful suggestions will be highly encouraging? > Best Regards, > Dr. Shabbir > > --000000000000ca812905c6a20cc9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I assume you plan to do MMPBSA for binding free energy ca= lculation. You can use the Cafe plugin for VMD. It requires a dcd file with= your required number of frames and the psf file. So the starting pose of y= our ligand really shouldn't matter.

You can also calculate non bonding interaction energies using the= namd energy plugin. The documentation is self=C2=A0explanatory and very si= mple to follow.

On Fri, 9 Jul, 2021, 12:20 am Mi Yang, <drmiyang2019@gmail.com> wrote:
Dear Colleagues,
In one of our papers, we have run MD simulations for 60 ns. The RMS= Ds were found reasonable stable but one reviewer asked to see what is the d= ifference of Binding Energy among original seeded (best docked) structure a= nd at some time intervals eg. at 20 ns or 30ns etc.
We have succe= ssfully extracted frames at different time intervals but really have no ide= a how to calculate binding free energy for a frame without changing specifi= c docked structure?

We docked protein-ligand with = autodock vina, prepared MD input with VMD and ran through NAMD.
A= ny helpful suggestions will be highly encouraging?
Best Regards,<= /div>
Dr. Shabbir

--000000000000ca812905c6a20cc9-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jul 9 18:50:02 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 169No1qZ028886; Fri, 9 Jul 2021 18:50:01 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 169No1iC028884; Fri, 9 Jul 2021 18:50:01 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 169No1ao028880; Fri, 9 Jul 2021 18:50:01 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 169No079028879; Fri, 9 Jul 2021 18:50:00 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 169Nnj7f028870 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 9 Jul 2021 18:49:46 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 169NnaLg001883 for ; Fri, 9 Jul 2021 23:49:45 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-pg1-f175.google.com (mail-pg1-f175.google.com [209.85.215.175]) by mx0a-00007101.pphosted.com with ESMTP id 39p4sr2r93-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 09 Jul 2021 23:49:44 +0000 Received: by mail-pg1-f175.google.com with SMTP id t9so11516768pgn.4 for ; Fri, 09 Jul 2021 16:49:44 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:message-id:thread-topic :mime-version; bh=8XyWDMXY6LZOu/MB2CVcSq4Evq1TxHJr8eN0HmxGmjs=; b=dh1KOsAH2btVQwxpaDejARWm7Dot1g1LnF0uM8gjn0bR8VmwBKP6b725gm3nwVHLHk anhq+On2o6GDtLw9DtJcuSGuuHAdqHhDMjpMCFMyBAH2l2E7ULv9NuZbsI9uHPDnUi4K i+7iCK80ezkuTTsQpr+elxmqfRHssSano+CCzCgfPtuwo2n/pds9+7LhcvCXsicLzZji aPPQbAxAHDCtmFvKIx2Kgwc09xKBD/DQhPAWunBnY/cXWF0V36tVJJNT0Gb6VoSlJtV1 6GjZs3eb0fPd1es64zWewnnfzyG7rHv6TlHreojuYnCvb6jqhHBgPocjXpRG4ZzFcMZx D9VA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:message-id :thread-topic:mime-version; bh=8XyWDMXY6LZOu/MB2CVcSq4Evq1TxHJr8eN0HmxGmjs=; b=P/OnKwdMc+zHUE/9OonpJavYIJblrHqDOm8EQ6upbCmNjIvjmVwZF82n6JMQjSyHQo Jr9ztE+iM5sRKUwKIpgqoCMbTkEo3jP2YMRhDAZqEgkhMjh2y+3KX/mHAlpNOLLorvNO vTRoJnUbI64KAiOmZEizUUS0IMSTXZ0KnBu1Owod6JZwQEG0ZYt6dFzps7/X/p6nXAg4 uOL2I10qMZaWbn3HGOQVQiUL/r+xwaD59yCBIZbNIHMwNIwP22b/wDk3GOYHut6f0fXz Dn/7FZzPcBP385ZJeZwjHFueSw3WBqqNiFKuTR4HSW1EpdCiVolodaIzTiGc/zMCnimF XMgA== X-Gm-Message-State: AOAM532/oO4j7YwJr3mDqK5rQt6PlQbdvB/EsSUiJvnEtNZaAAny5C+s SXC5GDk/+RhWML0PPxOmIoZiODN3/YaGfQ== X-Google-Smtp-Source: ABdhPJzMdxafFowswqNXDE5Zogb6AkosytcnH0IVjllSI5jf8fYq2UDp9NzjF9BzPaLZmLieEEA05g== X-Received: by 2002:a63:4302:: with SMTP id q2mr40510399pga.428.1625874583882; Fri, 09 Jul 2021 16:49:43 -0700 (PDT) Received: from [192.168.1.48] ([190.43.78.113]) by smtp.gmail.com with ESMTPSA id u9sm13913332pjm.34.2021.07.09.16.49.42 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Fri, 09 Jul 2021 16:49:43 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Fri, 09 Jul 2021 18:49:40 -0500 Subject: namd-l: Temperature accelerated MD with Colvar or TclForces From: "Ropon-Palacios G." To: KS UIUC Message-ID: <61C3CD27-8678-424C-A3C6-FA7306AC1AC9@gmail.com> Thread-Topic: Temperature accelerated MD with Colvar or TclForces Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3708701382_1845234131" X-CLX-Response: 1TFkXGxwZEQpMehcZHxMRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHxsSEQpDWRcHGxwSEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ZcR8YEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2sHRgdkaHx4ZHlGbVxdfxJhSUNZHW5wSUJ5a29zE2hOEQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc2JFfxoRCk1cFxsTEhEKTFoXbGlrTU0RCkxGF29ra2t raxEKQk8XbRNgEwFhWmttQBIRCkNaFxgaEwQSHwQYGx8EGx0fEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2Nre xNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF2NpWW96Tx1yR09/EQpCQBdsTUJofU98Rlp9fxEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2NOZ04TH218cn1oEQpZSxcTHhwYEQpwaBd kG2lvU35Da0dkeRAZGhEKcGgXYkhcHWFPH0dQeBMQGRoRCnBoF2lucAVGQxxaZlxhEBsZHxEKcG gXaQFvfmh4QhN5ZFAQGRoRCnBoF2JibEBBWn19Wl5fEBkaEQpwbBd6R0BrGFl5fx4bSBAZGhEKc EwXZ35QfU1rUE9PRmIQGRoRCnBDF2JsZWEdH2hNZmhfEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: A-l-NBVRNSlGvwU8Kcis7DZchSAEY9Bd X-Proofpoint-ORIG-GUID: A-l-NBVRNSlGvwU8Kcis7DZchSAEY9Bd X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=163 suspectscore=0 phishscore=0 priorityscore=359 lowpriorityscore=0 bulkscore=0 mlxscore=0 adultscore=0 impostorscore=0 spamscore=0 mlxlogscore=416 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107090124 domainage_hfrom=9462 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3708701382_1845234131 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear users, I have implemented in TclForces Temperature accelerated MD using COM as colvar, but I want to use more sophisticated colvar, such as number of contacts and alpha helix orientations, how could I do this, either in a colvar or tclforces module please. Best, Geo. --B_3708701382_1845234131 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear users,=

 

I = have implemented in TclForces Temperature accelerated MD using COM as colvar= , but I want to use more sophisticated colvar, such as number of contacts an= d alpha helix orientations, how could I do this, either in a colvar or tclfo= rces module please.

 

Best,

 

Geo.

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A" Date: Tue, 13 Jul 2021 18:11:10 +0430 Message-ID: Subject: namd-l: question about free energy calculation through FEP method in NAMD To: NAMD Content-Type: multipart/alternative; boundary="0000000000009e68d805c70165aa" X-CLX-Shades: MLX X-Proofpoint-GUID: RNrKqUrRMVUHYa_7zF3c8x62NuQEgqg- X-Proofpoint-ORIG-GUID: RNrKqUrRMVUHYa_7zF3c8x62NuQEgqg- X-CLX-Response: 1TFkXGx0YEQpMehcZGxkRCllEF2xoH2xzXEYbehoYEQpYWBdvWU9DRXNFZUt SXREKeE4XY1Nja3sTWH4aX14RCnlMF2Ede2NlWE1OekBhEQpDSBcHGBoaEQpDWRcHGB8bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8YcRweEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3hkWGFbf1h4Z3x/YnNLdR1QbBlJElIcGGRfe29NW00HEQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc2NQU14RCk1cFxMbEQpMWhdsaU1NTREKTEYXb2tra2t rEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGAQbHRIRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZx0fSRhOWURgW1IRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdvWU9DRXNFZUtSXREKQmwXbF9OYB9hbWABARgRCkJAF2ByHEZIbHxrRhxcEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXbU1gX0d/TxMeZUERCllLFxMeHBwRCnBoF2Z QS15/QHNJfxlMEBkaEQpwaBdhYU9rHhh6GWN6ZBAZGhEKcGgXb2lue01NYHNDBRwQGRoRCnBoF3 p+RWB4GhlBQRIBEBkaEQpwaBdgRV5hHkxSH1ptRxAZGhEKcGwXax18ZRJ9GVNEcE4QGRoRCm1+F xsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=490 suspectscore=0 adultscore=0 phishscore=0 priorityscore=313 impostorscore=0 lowpriorityscore=0 malwarescore=0 clxscore=172 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107130087 domainage_hfrom=9466 X-Spam-Score: 0 X-Spam-OrigSender: matabay2010@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "M. A" --0000000000009e68d805c70165aa Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear all, I want to calculate the free energy (=CE=94G) between a ligand and protein through FEP method in NAMD. In my structure, the ligand is located on the surface of the protein, not inside the protein, lt means a part of the ligand that is closed to the protein surface has interaction with protein, and the other part of the ligand which is in contact with water molecules, has interaction with these molecules. So, when I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both) while I need to eliminate the only interaction between the ligand and protein. How can I specify that it eliminates just the interaction between the ligand and protein and does not consider the interaction of ligand and water molecules. I appreciate your help. best, Maryam =D9=91 --=20 Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology --0000000000009e68d805c70165aa Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear all,

I want to calculat= e the free energy (=CE=94G= ) between a ligand and protein through FEP method in NAMD.=C2=A0 In = my structure, the ligand is located on the surface of the protein, not insi= de the protein, lt means a part of the ligand that is closed to the protein= surface has interaction with protein, and the other part of the ligand whi= ch is in contact with water molecules, has interaction with these molecules= . So, when I change the B column of atoms of ligand to -1 (in solvate.fep f= ile), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms= in contact with protein and water molecules both) while I need to eliminat= e the only interaction between the ligand and protein. How can I specify th= at it eliminates just the interaction between the ligand and protein and do= es not consider the interaction of ligand and water molecules.=C2=A0
<= div>I appreciate your help.

best,
Ma= ryam
=D9=91


-- <= br>
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology

--0000000000009e68d805c70165aa-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 01:35:42 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16E6ZgVo002484; Wed, 14 Jul 2021 01:35:42 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16E6ZgRR002483; Wed, 14 Jul 2021 01:35:42 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16E6Zfsc002479; Wed, 14 Jul 2021 01:35:41 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16E6ZfqE002478; Wed, 14 Jul 2021 01:35:41 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16E6ZXFU002471 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 14 Jul 2021 01:35:33 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16E6Z3Gp007093 for ; Wed, 14 Jul 2021 06:35:32 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=matabay2010@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qt1-f177.google.com (mail-qt1-f177.google.com [209.85.160.177]) by mx0b-00007101.pphosted.com with ESMTP id 39rvnshvcp-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 14 Jul 2021 06:35:32 +0000 Received: by mail-qt1-f177.google.com with SMTP id x24so1126527qts.11 for ; Tue, 13 Jul 2021 23:35:32 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=0NlOB4W09w8qpnksl6wT0zyJX6lRPG4BCWETDokwo3Y=; b=cl9d7vSa9YOSgQGAHJNoY4QeAzY6+zbzMDftyNfgTEXSCzl0pO8Lnrcb1H0KObphJ+ bMPFO9t4J9hBzTaGtorzlwHLg1GXPgN3Mh58k8ptQrLFkLSNAK3vVRafyzJp2wRVIwN0 97n8dVtfkjgRpvoloYJ6K29A2pcjuLfLRBP0ftnDNkunfsfncTvDzTPlM1TGPqcuTntA ZPa2tarSGtBvvBW4RpfF69eIkAcf8BzT7+D8CzVKXSJyplF/lvfkvON6v9shLxMh8bIa 0jYYspPiC7xG8AeVjKPnP82lH4gqVFa9R6IbSUJnv0vnNoU7NNO8UgM1wu4VFaEBK2RV N2Zg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=0NlOB4W09w8qpnksl6wT0zyJX6lRPG4BCWETDokwo3Y=; b=OPbMURyoK7fI8Ev7x6Y7DjcDfINJY0ME7N+nU86Zxe+AEplM2Qvc92hJpL7peUFS/G DXCFktcALAfVbLxI7sJYIU00w3LQkltSOy7P6Edzx9KQxouiLIoZwm3h8O03qdLLg1UB V2x0NN4fjFbxCAcUXFnjtqkbq8wp0/H1lckRH4dNWPyO36u0pb7ceYOk7GyDEm3/HY9p 45TL8NwYDIf1qdirBYtiX1mD2tUn62U1J9QR0zX+B0MyH8nnL5kPcAfP7M1MA1hcR0PV 52eHDCMClLWvj+06c4lK9Dgk/5FOCTLdYu0x9UyiHfiYabAFC0YZV/afnc1xapJnq0mA 87aQ== X-Gm-Message-State: AOAM531hdxFZIqp5MiDEFGO2m4LQsN3AopmD/Iz1VwtGJnAMbEBQiOte EzZXmZ54YsBJEX8iexHppTfoaiVltm0k9/d/ffpk4xsp/wBdSg== X-Google-Smtp-Source: ABdhPJw4mvIiGoDaZn8ey2TOVe8ZPCvR948rQ8Z45zfCAELzIEqD3L0RNvD7EF8O3scmx0zk4b0e2XAfJDxC/IcUUeg= X-Received: by 2002:a05:622a:1a1a:: with SMTP id f26mr7787994qtb.381.1626244531385; Tue, 13 Jul 2021 23:35:31 -0700 (PDT) MIME-Version: 1.0 From: "M. A" Date: Wed, 14 Jul 2021 11:05:05 +0430 Message-ID: Subject: namd-l: question about free energy calculation through FEP method in NAMD To: NAMD , =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= Content-Type: multipart/alternative; boundary="0000000000009c777005c70f8f86" X-Proofpoint-ORIG-GUID: WU3_0EtYkYpE75pQ4_xEHQ4hbHLpEbZA X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIfEQpMehcZHBoRCllEF2xoH2xzXEYbehoYEQpYWBdvWU9DRXNFZUt SXREKeE4XY1Nja3sTWH4aX14RCnlMF2Ede2NlWE1OekBhEQpDSBcHGxgTEQpDWRcHGB4TEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF31/GXUab15zQXNabx0fWnsedVJvYnseQkhiZlpvSHBrEQpYXBcfBBoEGBkY BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NgaVp6EQpNXBcZGhEKTFoXbGlNTWsRCkxGF29ra2t raxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHBoEGx0dEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2cdH0kYTllEYFtSEQpCT hdjU2NrexNYfhpfXhEKQkwXb1lPQ0VzRWVLUl0RCkJsF2xfTmAfYW1gAQEYEQpCQBdgchxGSGx8 a0YcXBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF21NYF9Hf08THmVBEQpZSxcTHhw dEQpwaBdvaW57TU1gc0MFHBAZGhEKcGgXaEtjT1wTSR1FbX8QGRoRCnBoF3p+RWB4GhlBQRIBEB kaEQpwaBdkeHJTeEYYZUwYUhAZGhEKcGgXYEVeYR5MUh9abUcQHhIRCnBsF2sdfGUSfRlTRHBOE BkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: WU3_0EtYkYpE75pQ4_xEHQ4hbHLpEbZA X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 malwarescore=0 priorityscore=360 bulkscore=0 mlxscore=0 lowpriorityscore=0 clxscore=185 impostorscore=0 spamscore=0 mlxlogscore=557 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140041 domainage_hfrom=9467 X-Spam-Score: 0 X-Spam-OrigSender: matabay2010@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "M. A" --0000000000009c777005c70f8f86 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear J=C3=A9r=C3=B4me, Hi Do you have any suggestions to solve this problem? I want to calculate the free energy (=CE=94G) between a ligand and protein through FEP method in NAMD. In my structure, the ligand is located on the surface of the protein, not inside the protein, lt means a part of the ligand that is closed to the protein surface has interaction with protein, and the other part of the ligand which is in contact with water molecules, has interaction with these molecules. So, when I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both) while I need to eliminate the only interaction between the ligand and protein. How can I specify that it eliminates just the interaction between the ligand and protein and does not consider the interaction of ligand and water molecules. I appreciate all your help. best regards Maryam --=20 Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology --0000000000009c777005c70f8f86 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear J=C3=A9r=C3=B4me,
Hi

Do you have any suggestions to solve this problem?
I want to calculate the free energy (=CE=94G) between a ligand and protein through FEP method in NAMD.=C2=A0 In my struc= ture, the ligand is located on the surface of the protein, not inside the p= rotein, lt means a part of the ligand that is closed to the protein surface= has interaction with protein, and the other part of the ligand which is in= contact with water molecules, has interaction with these molecules. So, wh= en I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both)=20 while I need to eliminate the only interaction between the ligand and prote= in. How can I specify that it eliminates just the interaction between the l= igand and protein and does not consider the interaction of ligand and water= molecules.=C2=A0
I appreciate all your help.

best regards
Maryam

--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology

--0000000000009c777005c70f8f86-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 05:31:27 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EAVR1c007110; Wed, 14 Jul 2021 05:31:27 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EAVRR1007109; Wed, 14 Jul 2021 05:31:27 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EAVQNW007105; Wed, 14 Jul 2021 05:31:26 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EAVQit007104; Wed, 14 Jul 2021 05:31:26 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EAVEgt007096 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 14 Jul 2021 05:31:15 -0500 (CDT) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16EANXwM030699 for ; Wed, 14 Jul 2021 10:31:14 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0b-00007101.pphosted.com with ESMTP id 39rvr32p2v-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 14 Jul 2021 10:31:13 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 20FEF1E4056C; Wed, 14 Jul 2021 12:31:12 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id DjtYgtaUIwqT; Wed, 14 Jul 2021 12:31:07 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 540781E4057C; Wed, 14 Jul 2021 12:31:07 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id u8WgAD7pxn68; Wed, 14 Jul 2021 12:31:07 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id D5FB71E4056C; Wed, 14 Jul 2021 12:31:06 +0200 (CEST) Date: Wed, 14 Jul 2021 12:31:05 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: "M." Cc: NAMD list Message-ID: <1875177069.1358506.1626258665470.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: namd-l: Re: question about free energy calculation through FEP method in NAMD MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_e065902b-ac9d-4277-9c29-76bfba4bf328" X-Originating-IP: [82.120.142.252] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC90 (Linux)/8.8.15_GA_4026) Thread-Topic: question about free energy calculation through FEP method in NAMD Thread-Index: rcvGrLpz6mfGbYsMb4SW2EICiBe5MA== X-Proofpoint-ORIG-GUID: jq82NauIq887K6YljGeVy98FzOr_DwlO X-CLX-Shades: MLX X-Proofpoint-GUID: jq82NauIq887K6YljGeVy98FzOr_DwlO X-CLX-Response: 1TFkXGxwSEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxwfEQpDWRcHGBwaEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ScR8SEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0BbEhhkS19jWxISHWEcc0ZAbU98UxMSbFBlWHVuXUZlEQpYXBcfBBoEGBkYBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NgbW1kEQpNXBcfGREKTFoXbG1rTU0RCkxGF2xraxEKQk8 XaEBFSBgYfGtbehkRCkNaFxsTGQQeEwQYGR4EGBgbEQpCXhcbEQpESRcbEQpCRRdkWFxcTX5SSR tlSREKQk4XZU9+EkNpZlkcAWkRCkJMF3oSZ2lgWXlGQU9lEQpCbBdhEhJPT0xNf08eBREKQkAXZ E1YS2l4HWVbYxkRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdtTWBfR39PEx5lQREK cGcXZmAYWUZOWRMdWX8QHhIRCnBoF2sFc0lBWmJjY1htEBkaEQpwaBdoTwVnGGRHZ3kYWhAZGhE KcGgXaV5NXlxLWn5BbUMQGRoRCnBoF3ocbRNvRmxaTl99EBkaEQpwaBdhWnNvSWV9a2xEeRAZGh EKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 priorityscore=0 adultscore=0 phishscore=0 impostorscore=0 mlxlogscore=873 malwarescore=0 suspectscore=0 bulkscore=0 clxscore=168 spamscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140067 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_e065902b-ac9d-4277-9c29-76bfba4bf328 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Maryam,=20 ----- On 14 Juil 21, at 8:35, M. wrote:=20 > Dear J=C3=A9r=C3=B4me, > Hi > Do you have any suggestions to solve this problem? > I want to calculate the free energy ( =CE=94G ) between a ligand and prot= ein through > FEP method in NAMD. In my structure, the ligand is located on the surface= of > the protein, not inside the protein, lt means a part of the ligand that i= s > closed to the protein surface has interaction with protein, and the other= part > of the ligand which is in contact with water molecules, has interaction w= ith > these molecules. So, when I change the B column of atoms of ligand to -1 = (in > solvate.fep file), the energy (VdW and Elc) turns off for all atoms of li= gand > (all atoms in contact with protein and water molecules both) while I need= to > eliminate the only interaction between the ligand and protein. Not really. In the double decoupling scheme you need to remove interactions= with the solvent as well. Here, you could say that half of the binding sit= e is made of water.=20 The other branch of double decoupling will let you compare this with the fr= ee energy of interaction of the ligand with pure water.=20 > How can I specify that it eliminates just the interaction between the lig= and and > protein and does not consider the interaction of ligand and water molecul= es. That is not implemented, but I don't think it is necessary.=20 Best,=20 J=C3=A9r=C3=B4me=20 --=_e065902b-ac9d-4277-9c29-76bfba4bf328 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Maryam,

----- On 14 Juil 21, at 8:35, M. &l= t;matabay2010@gmail.com> wrote:
Dear J=C3=A9r=C3=B4me,
Hi

Do you= have any suggestions to solve this problem?
I want to c= alculate the free energy (= =CE=94G) between a ligand and protein through FEP method in NAMD.  In my struc= ture, the ligand is located on the surface of the protein, not inside the p= rotein, lt means a part of the ligand that is closed to the protein surface= has interaction with protein, and the other part of the ligand which is in= contact with water molecules, has interaction with these molecules. So, wh= en I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both)=20 while I need to eliminate the only interaction between the ligand and prote= in.
Not really. In the double decouplin= g scheme you need to remove interactions with the solvent as well. Here, yo= u could say that half of the binding site is made of water.

The other branch of double decoupling will l= et you compare this with the free energy of interaction of the ligand with = pure water.
How can I specify that it eliminates just the i= nteraction between the ligand and protein and does not consider the interac= tion of ligand and water molecules. 
That is not implemented, but I don't think it is necessary.
Best,
J=C3=A9r=C3=B4me
--=_e065902b-ac9d-4277-9c29-76bfba4bf328-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 05:42:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EAgKJV008929; Wed, 14 Jul 2021 05:42:20 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EAgKqj008928; Wed, 14 Jul 2021 05:42:20 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EAgJY8008924; Wed, 14 Jul 2021 05:42:19 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EAgJZB008923; Wed, 14 Jul 2021 05:42:19 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EAg8YO008915 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 14 Jul 2021 05:42:09 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16EAYjK8004521 for ; Wed, 14 Jul 2021 10:42:08 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=shekaari@email.kntu.ac.ir; dkim=pass header.s=zimbraemail.kntu.ac.ir header.d=email.kntu.ac.ir Received: from mail.kntu.ac.ir (mail.kntu.ac.ir [94.184.176.111]) by mx0a-00007101.pphosted.com with ESMTP id 39ru56km3t-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 14 Jul 2021 10:42:07 +0000 Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 771611C42C9; Wed, 14 Jul 2021 15:12:03 +0430 (+0430) Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id u27_zFRUBkWN; Wed, 14 Jul 2021 15:12:03 +0430 (+0430) Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id E3FE61C42CB; Wed, 14 Jul 2021 15:12:02 +0430 (+0430) DKIM-Filter: OpenDKIM Filter v2.10.3 mail.kntu.ac.ir E3FE61C42CB DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=email.kntu.ac.ir; s=zimbraemail.kntu.ac.ir; t=1626259322; bh=PhyKE96aiPyxyVb9zhQ6VO9tb7vhKbm6HiMsInK4fY4=; h=Date:From:To:Message-ID:MIME-Version; b=EZIUWUvi5C4n6nJK9giP2KPHHes20r17wCr/gc3q1TXLhsT98NGzZ7bLx/vUgKP3r zYdfhzldlehDnVtkHjo3fLGPpq/SiiUsm1eScxGLZVOGWNWbEiWkPJMuSeX2NLhZds 0KVXxcpvzuvLPaJxIk4S+WOGjYugSkTQ10ZnwmA+3y66L+BOS+23f84xjmx/hrbAvq MVnFoprK0vJ2gtKRxymUXuWRaVloPaKHlh1jef0czJgz+BP5CfpyItj6+fZ/lFVj1S 6ih4UytpR8TzAQBpl3zvggZTxY2BMD3Sie2IK5eME3qQftbCkuhQOMRhcg25L+0yFE uzq4hgP0u6geg== X-Virus-Scanned: amavisd-new at Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id hQcOlUsxm9_q; Wed, 14 Jul 2021 15:12:02 +0430 (+0430) Received: from strga.kntu.ac.ir (strga.kntu.ac.ir [172.27.1.221]) by mail.kntu.ac.ir (Postfix) with ESMTP id 8E5CE1C42C9; Wed, 14 Jul 2021 15:12:02 +0430 (+0430) Date: Wed, 14 Jul 2021 15:12:02 +0430 (IRDT) From: Ashkan Shekaari To: namd-l , "M. A" Message-ID: <2120569504.4747180.1626259322780.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: References: Subject: Re: namd-l: question about free energy calculation through FEP method in NAMD Content-Type: multipart/alternative; boundary="=_21164c71-4b22-461f-aafc-3ced77d4b475" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC76 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: question about free energy calculation through FEP method in NAMD Thread-Index: gMmE0l+/XVsms6nEXsjCXT1EFgZ0Wg== X-CLX-Shades: MLX X-Proofpoint-GUID: 6pQ70YnQwgKNBd74rVte2T-rVBgAPbUu X-Proofpoint-ORIG-GUID: 6pQ70YnQwgKNBd74rVte2T-rVBgAPbUu X-CLX-Response: 1TFkXGxwSEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBx4SEQpDWRcHGx4TEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ScRgTEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFxxaex0ac0R7XU1hZGhOHR5YfF5PGH4HWHxoTWt6SH9fEQpYXBcfBBoEGBkYBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXc2Bte0gRCk1cFxgZHhEKTFoXeGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGx sRCkJeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXY R0eZmtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8 a3gRCkJAF21Ff3Jvb2Z7c3BpEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXbEdQSQV lb19uZUARCllLFwcZEQpwZxdjGmNHQX9hRngZfBAZGhEKcGgXZlJJHGETRnsYQxIQGRoRCnBoF2 liGRgcRWxhGx4fEBkaEQpwaBdoWUFCW21/bGxvZBAZGhEKcGgXYmdIZ0tub0wdWlAQGRoRCnBoF 2VBSFppclN5bHlCEBkaEQpwfRdjc3tNBV0dAXhBcBAZGhEKcGcXZmAYWUZOWRMdWX8QHBoRCnBn F2lDblABWXNHAR5TEBkaEQpwZxdlQk1mexwcR1oaTBAZGhEKcH0XaRplTlxIE2BHeUYQGRoRCnB /F29EYVASE38bHBJ+EB8aEQpwXxdiGBoYH3hHTHt7exAbGxwRCnBsF29gf215TEFEa05OEBkaEQ ptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=576 suspectscore=0 adultscore=0 phishscore=0 priorityscore=0 impostorscore=0 lowpriorityscore=0 malwarescore=0 clxscore=168 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140067 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_21164c71-4b22-461f-aafc-3ced77d4b475 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Maryam,=20 Give it a try using=20 1- SMD and then the Jarzynski's equality=20 or=20 2- replica-exchange umbrella sampling.=20 Both are implemented in NAMD.=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!sqBe6JihE0aFs8dIlpjvF3p5aILDvQuzCcsnkUAAgrEyl9Gst96rqy7n= fCWBxxkPQA$ ]=20 From: "M. A" =20 To: "namd-l" , "J=C3=A9r=C3=B4me H=C3=A9nin" =20 Sent: Wednesday, July 14, 2021 11:05:05 AM=20 Subject: namd-l: question about free energy calculation through FEP method = in NAMD=20 Dear J=C3=A9r=C3=B4me,=20 Hi=20 Do you have any suggestions to solve this problem?=20 I want to calculate the free energy ( =CE=94G ) between a ligand and protei= n through FEP method in NAMD. In my structure, the ligand is located on the= surface of the protein, not inside the protein, lt means a part of the lig= and that is closed to the protein surface has interaction with protein, and= the other part of the ligand which is in contact with water molecules, has= interaction with these molecules. So, when I change the B column of atoms = of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off f= or all atoms of ligand (all atoms in contact with protein and water molecul= es both) while I need to eliminate the only interaction between the ligand = and protein. How can I specify that it eliminates just the interaction betw= een the ligand and protein and does not consider the interaction of ligand = and water molecules.=20 I appreciate all your help.=20 best regards=20 Maryam=20 --=20 Maryam Atabay=20 Ph.D in Nano Computational Chemistry=20 Department of Physics, Sharif University of Technology=20 --=_21164c71-4b22-461f-aafc-3ced77d4b475 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Hi Maryam,
Give it a try using
1- SMD and then the Jarzynski's equality
or
2- = replica-exchange umbrella sampling.
Both are implemented in NAMD.=

---
,Best
=
=
=
<= div dir=3D"ltr">
Ashkan Shekaari
PhD Candidate in Solid State Physics=
Depart= ment of Physics
K. N. Toosi Univer= sity of Technology, Tehran, 15875-4416, Iran
=


From: "M. A" <matabay2010@gmail.com>
To: "namd= -l" <namd-l@ks.uiuc.edu>, "J=C3=A9r=C3=B4me H=C3=A9nin" <jerome.he= nin@ibpc.fr>
Sent: Wednesday, July 14, 2021 11:05:05 AM
= Subject: namd-l: question about free energy calculation through FEP met= hod in NAMD

Dear J=C3=A9r=C3=B4me,
Hi

Do yo= u have any suggestions to solve this problem?
I want to = calculate the free energy (=CE=94G) between a ligand and protein through FEP method in NAMD.  In my struc= ture, the ligand is located on the surface of the protein, not inside the p= rotein, lt means a part of the ligand that is closed to the protein surface= has interaction with protein, and the other part of the ligand which is in= contact with water molecules, has interaction with these molecules. So, wh= en I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both)=20 while I need to eliminate the only interaction between the ligand and prote= in. How can I specify that it eliminates just the interaction between the l= igand and protein and does not consider the interaction of ligand and water= molecules. 
I appreciate all your help.

best = regards
Maryam

--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology


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boundary="=_8dd34c33-ce53-4934-9c63-40596c63c4c6" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC76 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: question about free energy calculation through FEP method in NAMD Thread-Index: gMmE0l+/XVsms6nEXsjCXT1EFgZ0WiBE0m7s X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwTEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxsZHREKQ1kXBxseExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseE3EZGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThddXQdvSXgSRRh/axllc2YbX1x5eHJtW3AZGHwbeEd5bREKWFwXHwQaBBgZGAUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3NgbXIcEQpNXBcdGhEKTFoXe2lNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGx sRCkJeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXY R0eZmtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8 a3gRCkJAF21Ff3Jvb2Z7c3BpEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHxEKeUMXbEdQSQV lb19uZUARCllLFwcZEQpwZxdjGmNHQX9hRngZfBAeEhEKcGgXb1xbQG5eRURkX24QGhEKcGgXaW IZGBxFbGEbHh8QGRoRCnBoF2hZQUJbbX9sbG9kEB4SEQpwaBdiZ0hnS25vTB1aUBAZGhEKcGgXZ UFIWmlyU3lseUIQHhIRCnB9F2Nze00FXR0BeEFwEBkaEQpwZxdpQ25QAVlzRwEeUxAeEhEKcGcX ZmAYWUZOWRMdWX8QHRoRCnB9F2VtWnpFeVtfX25uEBkaEQpwZxdlQk1mexwcR1oaTBAeEhEKcH0 XaRplTlxIE2BHeUYQGRoRCnB9F2VtWF8fH2lBbwV6EBkaEQpwfxdvRGFQEhN/GxwSfhAfHxEKcF 8XYhgaGB94R0x7e3sQGxscEQpwfxdhZm9bGmdkQkgdWxAbGhMRCnBfF2NiElBIY3gffEJ9EBwSE QpwbBdvYH9teUxBRGtOThAeEhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: ww-EcR8o2UA3OYL1uvSRXGqZ32V1RmSG X-Proofpoint-GUID: ww-EcR8o2UA3OYL1uvSRXGqZ32V1RmSG MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 bulkscore=0 clxscore=169 impostorscore=0 lowpriorityscore=0 suspectscore=0 mlxscore=0 adultscore=0 malwarescore=0 phishscore=0 mlxlogscore=608 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140068 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_8dd34c33-ce53-4934-9c63-40596c63c4c6 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable One more thing,=20 Because the ligand is presumably much smaller than your protein of interest= ,=20 you may have to use QMMM.=20 Good luck with your calculations ...=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!t5MpHIp-EC7S9EzJNG0W5y1kmPlRQM9sKfdsCwEUeGLHd1D9Jyh6vuKF= o7DwYt8nfg$ ]=20 From: "shekaari" =20 To: "namd-l" , "M." =20 Sent: Wednesday, July 14, 2021 3:12:02 PM=20 Subject: Re: namd-l: question about free energy calculation through FEP met= hod in NAMD=20 Hi Maryam,=20 Give it a try using=20 1- SMD and then the Jarzynski's equality=20 or=20 2- replica-exchange umbrella sampling.=20 Both are implemented in NAMD.=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!sqBe6JihE0aFs8dIlpjvF3p5aILDvQuzCcsnkUAAgrEyl9Gst96rqy7n= fCWBxxkPQA$ ]=20 From: "M. A" =20 To: "namd-l" , "J=C3=A9r=C3=B4me H=C3=A9nin" =20 Sent: Wednesday, July 14, 2021 11:05:05 AM=20 Subject: namd-l: question about free energy calculation through FEP method = in NAMD=20 Dear J=C3=A9r=C3=B4me,=20 Hi=20 Do you have any suggestions to solve this problem?=20 I want to calculate the free energy ( =CE=94G ) between a ligand and protei= n through FEP method in NAMD. In my structure, the ligand is located on the= surface of the protein, not inside the protein, lt means a part of the lig= and that is closed to the protein surface has interaction with protein, and= the other part of the ligand which is in contact with water molecules, has= interaction with these molecules. So, when I change the B column of atoms = of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off f= or all atoms of ligand (all atoms in contact with protein and water molecul= es both) while I need to eliminate the only interaction between the ligand = and protein. How can I specify that it eliminates just the interaction betw= een the ligand and protein and does not consider the interaction of ligand = and water molecules.=20 I appreciate all your help.=20 best regards=20 Maryam=20 --=20 Maryam Atabay=20 Ph.D in Nano Computational Chemistry=20 Department of Physics, Sharif University of Technology=20 --=_8dd34c33-ce53-4934-9c63-40596c63c4c6 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
One more thing,
Because the ligan= d is presumably much smaller than your protein of interest,
you m= ay have to use QMMM.
Good luck with your calculations ...

---
,Best
<= /div>
<= div dir=3D"ltr">
Ashkan ShekaariPhD Candidate in Solid State Physics=
H= i Maryam,
Give it a try using
1- SMD and then the Jarzy= nski's equality
or
2- replica-exchange umbrella samplin= g.
Both are implemented in NAMD.

---
,Best
=
<= div dir=3D"ltr">
Ashkan Shekaari=
PhD Candidate in Solid State Phys= ics
Dep= artment of Physics
K. N. Toosi Uni= versity of Technology, Tehran, 15875-4416, Iran
=


From: "M. A" <matabay2010@gmail.com>
To: "namd-l" = <namd-l@ks.uiuc.edu>, "J=C3=A9r=C3=B4me H=C3=A9nin" <jerome.henin@= ibpc.fr>
Sent: Wednesday, July 14, 2021 11:05:05 AM
Subj= ect: namd-l: question about free energy calculation through FEP method = in NAMD

Dear J=C3=A9r=C3=B4me,
Hi

Do you have any suggestions to solve this problem?
I want to calculate the free energy (=CE=94G) between a ligand and protein through FEP method in NAMD.  In my struc= ture, the ligand is located on the surface of the protein, not inside the p= rotein, lt means a part of the ligand that is closed to the protein surface= has interaction with protein, and the other part of the ligand which is in= contact with water molecules, has interaction with these molecules. So, wh= en I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both)=20 while I need to eliminate the only interaction between the ligand and prote= in. How can I specify that it eliminates just the interaction between the l= igand and protein and does not consider the interaction of ligand and water= molecules. 
I appreciate all your help.

best = regards
Maryam

--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology


= --=_8dd34c33-ce53-4934-9c63-40596c63c4c6-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 06:17:27 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBHRU7012714; Wed, 14 Jul 2021 06:17:27 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBHR41012713; Wed, 14 Jul 2021 06:17:27 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBHQA2012709; Wed, 14 Jul 2021 06:17:26 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBHQnh012708; Wed, 14 Jul 2021 06:17:26 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBHBSe012701 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000dd641e05c7137e85" X-CLX-Shades: MLX X-Proofpoint-GUID: CKwaeUeKrVCt9FepH9GBd_XsP7UaagLq X-Proofpoint-ORIG-GUID: CKwaeUeKrVCt9FepH9GBd_XsP7UaagLq X-CLX-Response: 1TFkXGx4cEQpMehcZHhkRCllEF2wBb2EbHU5zfmZYEQpYWBdnUE1sT1Macxp fTxEKeE4XY1Nja3sTWH4aX14RCnlMF2FwYm16W0hDekNtEQpDSBcbGh8RCkNZFwcYHhoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGBxxGx0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XaWFdS09/T2FYfGleE2xPWmITbWhOdXJZeh1/S0tNZlsRClhcFx8EGgQYGRgF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzYG1SeREKTVwXGxwaEQpMWhdoaU1rTREKTEYXb2tra2t rEQpCTxdtE2ATAWFaa21AEhEKQ1oXGBoTBBIfBBgbHwQbHRgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXYh1LeltkTGJgZmURCkJOF2NTY2t7E 1h+Gl9eEQpCTBdnUE1sT1MacxpfTxEKQmwXaU14QAV6eR8eW2sRCkJAF3prTkQcBXxnYE5lEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaX9mfmFNYnlbcngRCllLFxMeHB0RCnBoF2t EWG9neEJtf3JbEBkaEQpwaBdkf2Bpb2VmUh4FYhAZGhEKcGgXZgVnUH5Cch18cxMQGRoRCnBoF2 EBUhMYf3xYBVtvEBkaEQpwaBdiTmZFXXBgU0VMaBAZGhEKcGwXaXpOE0VjfmgZTm0QGRoRCm1+F xsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=278 suspectscore=0 adultscore=0 phishscore=0 priorityscore=343 impostorscore=0 lowpriorityscore=0 malwarescore=0 clxscore=146 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140070 domainage_hfrom=9467 X-Spam-Score: 0 X-Spam-OrigSender: kapoornancy25@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nancy Singh --000000000000dd641e05c7137e85 Content-Type: text/plain; charset="UTF-8" Hii, I have done the protein-ligand simulations with namd for 10ns. But the problem is after 5ns protein and ligand complex starts to move out of the box. I have already put wrapALL, wrapNearest and wrapWater as ON but still the complex is coming out of the box. Is there something wrong with simulations or it is natural for protein to move from one periodic cell to another? and How can I tackle this if I want to make th animation of my trajectory? Thank You Regards, Nancy --000000000000dd641e05c7137e85 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hii,
I have done the protein-ligand simulations with n= amd for 10ns. But the problem is after 5ns protein and ligand complex start= s to move out of the box. I have already put=C2=A0 wrapALL, wrapNearest and= wrapWater as ON but still the complex is coming out of the box. Is there s= omething wrong with simulations or it is natural for protein to move from o= ne periodic=C2=A0cell to another?
and How can I tackle this if I = want to make th animation=C2=A0of my trajectory?

T= hank You

Regards,
Nancy
--000000000000dd641e05c7137e85-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 06:27:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBRjON014524; Wed, 14 Jul 2021 06:27:45 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBRjFU014523; Wed, 14 Jul 2021 06:27:45 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBRiGn014519; Wed, 14 Jul 2021 06:27:44 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBRiZP014518; Wed, 14 Jul 2021 06:27:44 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBRYZc014511 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 14 Jul 2021 06:27:34 -0500 (CDT) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16EBJfRW025933 for ; Wed, 14 Jul 2021 11:27:33 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 39rvr32xp8-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 14 Jul 2021 11:27:33 +0000 Received: from [IPv6:2a02:810c:300:6724:2cbc:422a:2750:579b] ([IPv6:2a02:810c:300:6724:2cbc:422a:2750:579b]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 16EBROS0171113 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Wed, 14 Jul 2021 13:27:29 +0200 Subject: Re: namd-l: Protein-ligand complex is coming out of the water box To: namd-l@ks.uiuc.edu, Nancy Singh References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: Date: Wed, 14 Jul 2021 13:27:23 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: de-DE X-Spam-Status: No, hits=-0.367, tests=HELO_NO_DOMAIN=0.001,NICE_REPLY_A=-0.368 X-Spam-Score: (-0.367) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: GYKWi4FngFOOh80LsLC6DerLO-LXLpIU X-CLX-Shades: MLX X-Proofpoint-GUID: GYKWi4FngFOOh80LsLC6DerLO-LXLpIU X-CLX-Response: 1TFkXGxwfEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsdGBEKQ1kXBx4eEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4fcR8eEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF21zYX1DHmxETWxlZUISGmZZZmkcbk9YZmUHZnJmWmN/EQpYXBcfBBoEGBkYBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NgbR1rEQpNXBcZGRwRCkxaF3hhTUFNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2Yff0FteBlhWnhbEQpCWBdnc2VzQG5hYUxdYhEKWlgX GREKeUMXaHheS2lfc0Z5HBsRCnBoF2wfaFh7T1tgQElkEBkaEQpwaBdgQ355Rn16f29aGhAZGhE KcGgXax5YHFJYSUAZbHgQGRoRCnBoF216W1JDE2lJRE5IEBkaEQpwaBdiTmZFXXBgU0VMaBAZGh EKcH0XaHwcXkRoUk8aXksQGRoRCnB/F2sdax5Te2djS216EBsbExEKcF8XZGRLQRh/XklmU1sQG RoRCnBsF3ofeHlveExDX3BEEBkaEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 priorityscore=0 adultscore=0 phishscore=0 impostorscore=0 mlxlogscore=955 malwarescore=0 suspectscore=0 bulkscore=0 clxscore=165 spamscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140071 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 16EBRYZb014512 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Hi Nancy,     its not unexpected that it might move and might cross borders, but with wrapAll on the atoms should be wrapped back (resulting in long bonds).     Check the logfile if all those parameters got parsed correctly.     You can wrap the trajectory around the protein using the very fast implementation qwrap https://urldefense.com/v3/__https://github.com/jhenin/qwrap__;!!DZ3fjg!rMKLQ9m3-wylw4U29SWTjXOuaeNcLtUghl30P_YydcBTvP44NBMJuV0HgFHXvepQDQ$ . Regards René On 7/14/2021 1:16 PM, Nancy Singh wrote: > Hii, > I have done the protein-ligand simulations with namd for 10ns. But the > problem is after 5ns protein and ligand complex starts to move out of > the box. I have already put  wrapALL, wrapNearest and wrapWater as ON > but still the complex is coming out of the box. Is there something > wrong with simulations or it is natural for protein to move from one > periodic cell to another? > and How can I tackle this if I want to make th animation of my trajectory? > > Thank You > > Regards, > Nancy -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 06:30:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBUagg015873; Wed, 14 Jul 2021 06:30:36 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBUaPh015871; Wed, 14 Jul 2021 06:30:36 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBUZKv015860; Wed, 14 Jul 2021 06:30:35 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBUZvd015857; Wed, 14 Jul 2021 06:30:35 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBUSqw015763 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="=_ca4fe797-2444-4fe7-8b72-e1a3d0e9b9f6" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC76 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: Protein-ligand complex is coming out of the water box Thread-Index: De0aogzkxsHKfa1ZD00ItB1CO5s9vA== X-Proofpoint-ORIG-GUID: tgQFOa9w73PBG4mnDRIpELwzCcHdtg8I X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwTEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxkbEQpDWRcHHh4RCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHhNxGRoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XXk17bGVLE10dGXpobR5HRG54Y1pvZl1QaUliTl5NEmMRClhcFx8EGgQYGRgFGxoE GxoaBB4SBBgZEBseGh8aEQpeWRdzYG0TXxEKTVwXGx0aEQpMWhd4aU1NTREKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2IFaENATFpARXJOEQpDWhcTHgQbEh4EGx0cBBsbGx EKQl4XGxEKRF4XGBEKQlwXGxEKQksXeh5tW0t8R19iBXoRCkJJF2hfemFGAWJAQU95EQpCRRdhH R5ma3JBUhkZeBEKQk4XaF96YUYBYkBBT3kRCkJMF20TQUFaQURDE314EQpCbBdhZBlnXUIZRXxr eBEKQkAXZh9/QW14GWFaeFsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdoeF5LaV9 zRnkcGxEKWUsXBxkRCnBnF2MaY0dBf2FGeBl8EB4SEQpwaBdlSE5mXgVjQVJkGBAaEQpwaBdoWU FCW21/bGxvZBAeEhEKcGgXZU1IfXl5Y2xQbGAQGhEKcGgXemljbR9AQWR+WmkQGhEKcGgXZUFIW mlyU3lseUIQHhIRCnB9F2Nze00FXR0BeEFwEBkaEQpwZxdlWwFCeXNpekJvGRAaEQpwZxdpQ25Q AVlzRwEeUxAeEhEKcH0XaRplTlxIE2BHeUYQGRoRCnB/F29EYVASE38bHBJ+EBwcEQpwXxdiGBo YH3hHTHt7exAbGxwRCnBsF29gf215TEFEa05OEB4SEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: tgQFOa9w73PBG4mnDRIpELwzCcHdtg8I MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 priorityscore=0 malwarescore=0 adultscore=0 lowpriorityscore=0 clxscore=169 impostorscore=0 suspectscore=0 phishscore=0 bulkscore=0 mlxlogscore=629 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140071 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_ca4fe797-2444-4fe7-8b72-e1a3d0e9b9f6 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear researcher,=20 As I mentioned before, ligand is very small, then:=20 * timestep becomes very important, you presumably have to use timesteps= less than 1=20 * taking into account quantum mechanical considerations becomes very im= portant depending on the problem=20 * periodic interactions become very important, use boxes with > 20 Angs= trom padding, or use spherical BCs for being more safe.=20 I have also seen people having exactly the same issue using GROMACS; theref= ore, it has nothing to do with the computational code you are working with.= =20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!uTJZNZx1FuisMA2jYpHB7jK77HOf3qCyEKrIRXnBocvFN3I072JPsBm7= qb8Y4pPMmg$ ]=20 From: "Nancy Singh" =20 To: "namd-l" =20 Sent: Wednesday, July 14, 2021 3:46:58 PM=20 Subject: namd-l: Protein-ligand complex is coming out of the water box=20 Hii,=20 I have done the protein-ligand simulations with namd for 10ns. But the prob= lem is after 5ns protein and ligand complex starts to move out of the box. = I have already put wrapALL, wrapNearest and wrapWater as ON but still the c= omplex is coming out of the box. Is there something wrong with simulations = or it is natural for protein to move from one periodic cell to another?=20 and How can I tackle this if I want to make th animation of my trajectory?= =20 Thank You=20 Regards,=20 Nancy=20 --=_ca4fe797-2444-4fe7-8b72-e1a3d0e9b9f6 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear researcher,
As I mentioned b= efore, ligand is very small, then: 
  • timestep becomes very= important, you presumably have to use timesteps less than 1
  • taking= into account quantum mechanical considerations becomes very important depe= nding on the problem
  • periodic interactions become very important, u= se boxes with > 20 Angstrom padding, or use spherical BCs for being more= safe.
I have also seen people having exactly the same issue = using GROMACS; therefore, it has nothing to do with the computational code = you are working with.

=
---
,Best
<= /div>
<= div dir=3D"ltr">
Ashkan Shekaari
PhD Candidate in= Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran<= a href=3D"mailto:shekaari@email.kntu.ac.ir" rel=3D"nofollow noopener norefe= rrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noo= pener noreferrer" style=3D"color:rgb( 17 , 85 , 204 )" target=3D"_blank">
<= /div>


From: "Nancy Singh" <kapoornancy25@gmai= l.com>
To: "namd-l" <namd-l@ks.uiuc.edu>
Sent: Wednesday, July 14, 2021 3:46:58 PM
Subject: namd-l: Protein-lig= and complex is coming out of the water box

Hii,
I have done the prot= ein-ligand simulations with namd for 10ns. But the problem is after 5ns pro= tein and ligand complex starts to move out of the box. I have already put&n= bsp; wrapALL, wrapNearest and wrapWater as ON but still the complex is comi= ng out of the box. Is there something wrong with simulations or it is natur= al for protein to move from one periodic cell to another?
an= d How can I tackle this if I want to make th animation of my trajector= y?

Thank You

Regards,
Nancy

= --=_ca4fe797-2444-4fe7-8b72-e1a3d0e9b9f6-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 06:47:04 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBl49i018123; Wed, 14 Jul 2021 06:47:04 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBl4vn018122; Wed, 14 Jul 2021 06:47:04 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBl3vx018117; Wed, 14 Jul 2021 06:47:03 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EBl36g018116; Wed, 14 Jul 2021 06:47:03 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EBkpTD018105 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000ea23ab05c713e8ef" X-Proofpoint-ORIG-GUID: _Nm2I5f5BocgBMzpOL-dBKaV52Wb7eeN X-CLX-Shades: MLX X-CLX-Response: 1TFkXExoRCkx6FxkfGBEKWUQXbAFvYRsdTnN+ZlgRClhYF2dQTWxPUxpzGl9 PEQp4ThdjU2NrexNYfhpfXhEKeUwXYXBibXpbSEN6Q20RCkNIFxMSEQpDWRcHGxsSEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGHRpxHhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZX k9OEQpDThd1ZEcYYx9MH2hFSU1oZ1BaZWYHTmhhS3wfGH1IHU9PZBEKWFwXHwQaBBgZGAUbGgQb GxoEHxoEGx4YEBseGh8aEQpeWRdzYGJkbREKTVwXGBIZEQpMWhdpaGlNa2sRCkxGF29ra2traxE KQk8XYmdbH1AZU2B7HBMRCkNaFxgaEwQSHwQYGxoEGx0cEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2IdS3pbZExiYGZlEQpCThdjU2NrexNYf hpfXhEKQkwXZ1BNbE9TGnMaX08RCkJsF2lNeEAFenkfHltrEQpCQBd6bBlzfHtmT0F/SREKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF3pJHXpBGR9CRERFEQpZSxcTHhwdEQpwaBd6aFk YaVJ4WXBZfhAaEQpwaBdhUB9jTWhSBURoexAaEQpwaBdmW01DQmB+AWAcXhAaEQpwaBdlb19tHF Nye2d+chAaEQpwaBdteW97SGEBYB9BQhAaEQpwbBdpek4TRWN+aBlObRAYGBEKbX4XGxEKWE0XS xEg X-Proofpoint-GUID: _Nm2I5f5BocgBMzpOL-dBKaV52Wb7eeN X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 malwarescore=0 priorityscore=352 bulkscore=0 mlxscore=0 lowpriorityscore=0 clxscore=90 impostorscore=0 spamscore=0 mlxlogscore=629 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140072 domainage_hfrom=9467 X-Spam-Score: 0 X-Spam-OrigSender: kapoornancy25@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nancy Singh --000000000000ea23ab05c713e8ef Content-Type: text/plain; charset="UTF-8" Hii, I am a little confused about the space partitioning parameters switchdist, cutoff and pairlistdist. I have read the manual and know that cutoff indicates the distance beyond which electrostatic and Van der waals interactions are cutoff. I want to know if there are any particular criteria for selecting values for these parameters? and also if these parameters can affect our simulations or how the protein residues are interacting during simulations? Thank you Regards, Nancy --000000000000ea23ab05c713e8ef Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hii,

I am a little confused about the s= pace partitioning parameters switchdist, cutoff and pairlistdist.
I have read the manual and know that cutoff indicates the=C2=A0 distance b= eyond which electrostatic and Van der waals interactions are cutoff. I want= to know if there are any particular criteria for selecting values for thes= e parameters? and also if these parameters can affect=C2=A0our=C2=A0simulat= ions or how the protein residues are interacting during simulations?
<= div>
Thank you

Regards,
Na= ncy=C2=A0
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Larger cutoffs generally improve accuracy, but cost more non-bonded evaluations per timestep which lowers performance. CHARMM force fields are parameterized with 10, 12, and some number greater than 12 (usually I use 14) for the switchdistance, cutoff, and pairlist distance. AMBER, depending on the biopolymer, is something like 7 or 8, 10, 12. I'm less familiar with the numbers other force fields recommend, but the infamous reviewer #2 will (should?) complain if you don't follow the strictures dictated by the force field you pick. -Josh On 7/14/21 7:45 AM, Nancy Singh wrote: > Hii, > > I am a little confused about the space partitioning parameters > switchdist, cutoff and pairlistdist. > I have read the manual and know that cutoff indicates the distance > beyond which electrostatic and Van der waals interactions are cutoff. > I want to know if there are any particular criteria for selecting > values for these parameters? and also if these parameters can > affect our simulations or how the protein residues are interacting > during simulations? > > Thank you > > Regards, > Nancy -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!pbRK3c9EtT20A9z7imo1EFKu_J7luEqxBFFlDF7yV6AVWegxQ6NNHWXApXnwBnETjQ$ From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 13:42:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EIgawc025883; 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boundary="000000000000e0e33f05c719b652" X-Proofpoint-ORIG-GUID: 03XjSSj_0BrFPHbQ6OTmv_vKZobqLtu- X-CLX-Response: 1TFkXGxIfEQpMehcZGxkRCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHGR4cEQpDWRcHGxkTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxoZckB5eUB1GmhYbHpiSHscZX5HXHVcYXBFSFtmXl8HEQpYXBcfBBoEGBkY BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc2BkeVkRCk1cFx8aGBEKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHwQbHBwEHhsRCkJeFxsRCkReFxgRCkJcFxsRCl 5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaFpwGEkfZngeQF4RCkJOF 2NTY2t7E1h+Gl9eEQpCTBdsH15ZWm5MYWBbQREKQmwXb0Jpf25OW1IZeBoRCkJAF2AcZB1jGEVF R09jEQpCWBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXZFJNfEJha3hZEl0RCllLFxMeHB0RCnBoF2l PeVBbUGFbQ0BhEBkaEQpwaBdnZhhMYlhCaGBOYBAZGhEKcGgXbUhZRUcaT2BJEhsQGRoRCnBoF2 Ieb1IbaGUTXVITEBkaEQpwaBdhfUJyeUdAXXlIGRAZGhEKcGwXZ3hzc0JHXFt9RksQGRoRCm1+F xoRClhNF0sRIA== X-CLX-Shades: MLX X-Proofpoint-GUID: 03XjSSj_0BrFPHbQ6OTmv_vKZobqLtu- X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 phishscore=0 adultscore=0 mlxscore=0 bulkscore=0 mlxlogscore=999 clxscore=185 impostorscore=0 priorityscore=313 suspectscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140111 domainage_hfrom=9467 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000e0e33f05c719b652 Content-Type: text/plain; charset="UTF-8" Dear Colleagues, We have calculated MM/GBSA energy using MolAICal and NAMD. Its final value is coming positive even for nicely bounded poses after MD. Any idea what parameters can be adjusted in MD inputs. All inputs are given below: =======MolAICal out with MM/GBSA energy======= Total run 1010 frames from complex.log. Average BOND: 952.4267987128711 Average ANGLE: 2593.3628327722813 Average DIHED: 2935.6501275247506 Average IMPRP: 161.37262722772294 Average ELECT: -5463.052478217821 Average VDW: -1274.3825897029692 ############################### Total run 1010 frames from protein.log. Average BOND: 952.4267987128711 Average ANGLE: 2593.3628327722813 Average DIHED: 2935.6501275247506 Average IMPRP: 161.37262722772294 Average ELECT: -5463.052478217821 Average VDW: -1274.3825897029692 ############################### Total run 1010 frames from ligand.log. Average BOND: 952.4267987128711 Average ANGLE: 2593.3628327722813 Average DIHED: 2935.6501275247506 Average IMPRP: 161.37262722772294 Average ELECT: -5463.052478217821 Average VDW: -1274.3825897029692 ############################### delta E(internal): -6642.812386237626 delta E(electrostatic) + deltaG(sol): 5463.052478217821 delta E(VDW) + deltaG(sol): 1274.3825897029692 delta G binding: 94.62268168316405 PS E:\ac\004-MMGBSA> =====Input for MM calculations with NAMD===== # ----------input----- coordinates ionized.pdb structure ionized.psf paratypecharmm on parameters ./par_all36m_prot.prm parameters ./par_all36_na.prm parameters ./toppar_water_ions.str parameters ./par_all35_ethers.prm parameters ./par_all36_carb.prm parameters ./par_all36_lipid.prm parameters ./par_all36_cgenff.prm parameters ./par_hbond.inp parameters ./lig.prm parameters ./ligand.str #bincoordinates minimized.restart.coor #binvelocities minimized.restart.vel # ----------output------ set output output outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 1000 xstFreq 1000 binaryoutput yes binaryrestart yes outputEnergies 1000 restartfreq 1000 # ---------Basic dynamics------- exclude scaled1-4 1-4scaling 1 COMmotion no dielectric 1.0 # --------Simulation space partitioning---- switching on switchdist 9 cutoff 10 pairlistdist 11 MARGIN 3 # --------Multiple time stepping---- firsttimestep 0 timestep 1 stepspercycle 1 rigidbonds all rigidTolerance 1e-08 # -------Temperature control---- set temperature 300 temperature $temperature; # initial temperature # -------Langevin Dynamics------ langevin on; # do langevin dynamics langevinDamping 1; # damping coefficient (gamma) of 1/ps langevinTemp $temperature; # bath temperature # =============================================== PME on PMEGridSizeX 100 PMEGridSizeY 100 PMEGridSizeZ 100 # doesnt work with just pme useGroupPressure yes # with grouppressure, works better, holes still there LangevinPiston on LangevinPistonTarget 1.02 LangevinPistonPeriod 150 LangevinPistonDecay 90 LangevinPistonTemp $temperature # with langevin piston, works!!! But slower. # =============================================== # Periodic Boundary conditions cellBasisVector1 63.62900114059448 0 0 cellBasisVector2 0 71.53299903869629 0 cellBasisVector3 0 0 69.11299800872803 cellOrigin 25.233444213867188 7.527408123016357 21.83285140991211 wrapWater on ;# wrap water to central cell wrapAll on ;# wrap other molecules too wrapNearest off # ---------Scripting minimize 10000 ;# lower potential energy for 10000 steps reinitvels $temperature ;# since minimization zeros velocities run 6000000; # END =============Input for GBSA calculations after MM in NAMD======= ############################################################# ## JOB DESCRIPTION ## ############################################################# # Eq. of KcsA # embedded in POPC membrane, ions and water. # Protein released. PME, Constant Pressure/Area. ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure complex.psf coordinates complex.pdb outputName complex set temperature 310 # Continuing a job from the restart files if {0} { set inputname LRRK2-VB12-out1 binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem $inputname.restart.xsc } firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all36_prot.prm parameters par_all36_cgenff.prm parameters ligand.str parameters toppar_water_ions.str # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! temperature $temperature # Periodic Boundary Conditions # NOTE: Do not set the periodic cell basis if you have also # specified an .xsc restart file! if {0} { cellBasisVector1 98. 0. 0. cellBasisVector2 0. 98. 0. cellBasisVector3 0. 0. 96. cellOrigin -0.0390621498227 -0.0503903478384 0.05063835904 } # wrapWater on wrapAll on ### gbsa GBIS on solventDielectric 78.5 ionConcentration 0.3 alphaCutoff 15 sasa on surfaceTension 0.0072 # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 16. switching on switchdist 15. pairlistdist 18 # Integrator Parameters timestep 1 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 #PME (for full-system periodic electrostatics) if {0} { PME yes PMEGridSizeX 81 PMEGridSizeY 81 PMEGridSizeZ 90 } # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature # Constant Pressure Control (variable volume) if {0} { useGroupPressure yes ;# needed for 2fs steps useFlexibleCell no ;# no for water box, yes for membrane useConstantArea no ;# no for water box, yes for membrane langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 50. langevinPistonTemp $temperature } #restartfreq 10000 ;# 1000steps = every 2ps #dcdfreq 10000 #xstFreq 10000 #outputEnergies 10000 #outputPressure 10000 # Fixed Atoms Constraint (set PDB beta-column to 1) if {0} { fixedAtoms on fixedAtomsFile nottails.fix.pdb fixedAtomsCol B fixedAtomsForces on } ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Put here any custom parameters that are specific to # this job (e.g., SMD, TclForces, etc...) #eFieldOn yes #eField 0 0 -0.155 ############################################################# ## EXECUTION SCRIPT ## ############################################################# set ts 0 coorfile open dcd complex.dcd while {[coorfile read] != -1 } { firstTimestep $ts run 0 incr ts 1 } coorfile close Best regards, Dr.Shabbir --000000000000e0e33f05c719b652 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
We have calculated MM/GBSA= energy using MolAICal and NAMD. Its final value is coming positive even fo= r nicely bounded poses after MD. Any idea what parameters can be adjusted i= n MD inputs. All inputs are given below:

=3D= =3D=3D=3D=3D=3D=3DMolAICal out with MM/GBSA energy=3D=3D=3D=3D=3D=3D=3D
=
Total run 1010 frames from complex.log.
Average BOND: 952.426= 7987128711
Average ANGLE: 2593.3628327722813
Average DIHED: 2935.6501= 275247506
Average IMPRP: 161.37262722772294
Average ELECT: -5463.0524= 78217821
Average VDW: -1274.3825897029692
###########################= ####

Total run 1010 frames from protein.log.
Average BOND: 952.42= 67987128711
Average ANGLE: 2593.3628327722813
Average DIHED: 2935.650= 1275247506
Average IMPRP: 161.37262722772294
Average ELECT: -5463.052= 478217821
Average VDW: -1274.3825897029692
##########################= #####

Total run 1010 frames from ligand.log.
Average BOND: 952.42= 67987128711
Average ANGLE: 2593.3628327722813
Average DIHED: 2935.650= 1275247506
Average IMPRP: 161.37262722772294
Average ELECT: -5463.052= 478217821
Average VDW: -1274.3825897029692
##########################= #####

delta E(internal): -6642.812386237626
delta E(electrostatic= ) + deltaG(sol): 5463.052478217821
delta E(VDW) + deltaG(sol): 1274.3825= 897029692
delta G binding: 94.62268168316405
PS E:\ac\004-MMGBSA><= /div>

=3D=3D=3D=3D=3DInput for MM calculations with NAMD= =3D=3D=3D=3D=3D
# ----------input-----

coordinates =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ionized.pdb
structure =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ionized.psf
paratypecharmm =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0on
parameters ./par_all36m_prot.prm
parameter= s ./par_all36_na.prm
parameters ./toppar_water_ions.str
parameters ./= par_all35_ethers.prm
parameters ./par_all36_carb.prm
parameters ./par= _all36_lipid.prm
parameters ./par_all36_cgenff.prm
parameters ./par_h= bond.inp
parameters ./lig.prm
parameters ./ligand.str
#bincoordina= tes =C2=A0 =C2=A0 =C2=A0 =C2=A0 minimized.restart.coor
#binvelocities = =C2=A0 =C2=A0 =C2=A0 =C2=A0 minimized.restart.vel

# ----------output= ------

set output =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0ou= tput

outputname =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$out= put
dcdfile =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ${ou= tput}.dcd
xstFile =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 ${output}.xst
dcdfreq =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 1000
xstFreq =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 1000
binaryoutput =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0yesbinaryrestart =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 yes
outputEnergies = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01000
restartfreq =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 1000


# ---------Basic dynamics-------
ex= clude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scaled1-4
= 1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01
COMmotion = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 no
dielectric =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0

# --------Simulation sp= ace partitioning----
switching =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 on
switchdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A09<= br>cutoff =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A010<= br>pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A011
MARGIN =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A03

# -----= ---Multiple time stepping----
firsttimestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0
timestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A01
stepspercycle =C2=A0 1
rigidbonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0all
rigidTolerance =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A01e-08

# -------Temperature control----
set temperature =C2=A0 = =C2=A0 =C2=A0 =C2=A0 300
temperature =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 $temperature; =C2=A0# initial temperature

# -------Langevin D= ynamics------
langevin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0on; =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0# do langevin dynamicslangevinDamping =C2=A0 =C2=A0 =C2=A0 =C2=A0 1; =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0# damping coefficient (gamma) of 1/ps
langevinTe= mp =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature; =C2=A0 # bath tem= perature

# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D

PME on
PMEGridSizeX 100
PMEGridSizeY 100
PMEGridS= izeZ 100

# doesnt work with just pme

useGroupPressure yes
=
# with grouppressure, works better, holes still there

LangevinPi= ston =C2=A0 on
LangevinPistonTarget 1.02
LangevinPistonPeriod 150
= LangevinPistonDecay =C2=A090
LangevinPistonTemp =C2=A0$temperature
# with langevin piston, works!!! But slower.

# =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

# Periodic Boundary= conditions
cellBasisVector1 63.62900114059448 0 0
cellBasisVector2 0= 71.53299903869629 0
cellBasisVector3 0 0 69.11299800872803
cellOrigi= n 25.233444213867188 7.527408123016357 21.83285140991211
wrapWater =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0;# wrap water to central cell
wrapAll =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 on =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0;# wra= p other molecules too
wrapNearest =C2=A0 =C2=A0 =C2=A0 =C2=A0 off
# ---------Scripting
minimize =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 10000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ;# lower potential energy for 10000 steps=
reinitvels =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature =C2=A0;# sinc= e minimization zeros velocities
run 6000000;

# END
=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DInput for GBSA calculations after MM in= NAMD=3D=3D=3D=3D=3D=3D=3D
##################################= ###########################
## JOB DESCRIPTION =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ##
###########################= ##################################

# Eq. of KcsA
# embedded in PO= PC membrane, ions and water.
# Protein released. PME, Constant Pressure/= Area.

#############################################################<= br>## ADJUSTABLE PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 #= #
#############################################################

s= tructure =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0complex.psf
coordinates =C2= =A0 =C2=A0 =C2=A0 =C2=A0complex.pdb
outputName =C2=A0 =C2=A0 =C2=A0 =C2= =A0 complex

set temperature =C2=A0 =C2=A0310

# Continuing a j= ob from the restart files
if {0} {
set inputname =C2=A0 =C2=A0 =C2=A0= LRRK2-VB12-out1
binCoordinates =C2=A0 =C2=A0 $inputname.restart.coor
= binVelocities =C2=A0 =C2=A0 =C2=A0$inputname.restart.vel =C2=A0;# remove th= e "temperature" entry if you use this!
extendedSystem =C2=A0 = $inputname.restart.xsc
}

firsttimestep =C2=A0 =C2=A0 =C2=A00
=

#############################################################
##= SIMULATION PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ##
##= ###########################################################

# Input<= br>paraTypeCharmm =C2=A0 =C2=A0 =C2=A0on
parameters =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0par_all36_prot.prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0par_all36_cgenff.prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= ligand.str
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_water_ion= s.str

# NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file!
=C2=A0temperature =C2=A0 =C2= =A0 =C2=A0 =C2=A0 $temperature
=C2=A0

# Periodic Boundary Conditi= ons
# NOTE: Do not set the periodic cell basis if you have also
# sp= ecified an .xsc restart file!
if {0} {
cellBasisVector1 =C2=A0 =C2= =A098. =C2=A0 =C2=A00. =C2=A0 0.
cellBasisVector2 =C2=A0 =C2=A0 0. =C2= =A0 98. =C2=A0 0.
cellBasisVector3 =C2=A0 =C2=A0 0. =C2=A0 =C2=A00. =C2= =A096.
cellOrigin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0-0.0390621498227 -0.= 0503903478384 0.05063835904
}
# wrapWater =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 on
wrapAll =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on

#= ## gbsa
GBIS on
solventDielectric 78.5
ionConcentration 0.3
alp= haCutoff 15


sasa on
surfaceTension =C2=A00.0072


# = Force-Field Parameters
exclude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= scaled1-4
1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
cutoff = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A016.
switching =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 on
switchdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A015.
pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A018


# Integrato= r Parameters
timestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0;= # 2fs/step
rigidBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0all =C2=A0;# nee= ded for 2fs steps
nonbondedFreq =C2=A0 =C2=A0 =C2=A0 2
fullElectFrequ= ency =C2=A04 =C2=A0
stepspercycle =C2=A0 =C2=A0 =C2=A0 20


#PM= E (for full-system periodic electrostatics)
if {0} {
PME =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 yes
PMEGridSizeX =C2=A0 = =C2=A0 =C2=A0 81
PMEGridSizeY =C2=A0 =C2=A0 =C2=A0 81
PMEGridSizeZ = =C2=A0 =C2=A0 =C2=A0 90
}


# Constant Temperature Control
l= angevin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on =C2=A0 =C2=A0;# do lang= evin dynamics
langevinDamping =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 ;# damping c= oefficient (gamma) of 5/ps
langevinTemp =C2=A0 =C2=A0 =C2=A0 =C2=A0$temp= erature

# Constant Pressure Control (variable volume)
if {0} {useGroupPressure =C2=A0 =C2=A0 =C2=A0yes ;# needed for 2fs steps
useFle= xibleCell =C2=A0 =C2=A0 =C2=A0 no =C2=A0;# no for water box, yes for membra= ne
useConstantArea =C2=A0 =C2=A0 =C2=A0 no =C2=A0;# no for water box, ye= s for membrane

langevinPiston =C2=A0 =C2=A0 =C2=A0 =C2=A0on
lange= vinPistonTarget =C2=A01.01325 ;# =C2=A0in bar -> 1 atm
langevinPiston= Period =C2=A0200.
langevinPistonDecay =C2=A0 50.
langevinPistonTemp = =C2=A0 =C2=A0$temperature
}


#restartfreq =C2=A0 =C2=A0 =C2=A0= =C2=A010000 =C2=A0 =C2=A0 ;# 1000steps =3D every 2ps
#dcdfreq =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A010000
#xstFreq =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A010000
#outputEnergies =C2=A0 =C2=A0 =C2=A010000
#= outputPressure =C2=A0 =C2=A0 =C2=A010000


# Fixed Atoms Constrain= t (set PDB beta-column to 1)
if {0} {
fixedAtoms =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0on
fixedAtomsFile =C2=A0 =C2=A0 =C2=A0nottails.fix.pdb
= fixedAtomsCol =C2=A0 =C2=A0 =C2=A0 B
fixedAtomsForces =C2=A0 =C2=A0on}

#############################################################
= ## EXTRA PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0##
###########################################################= ##

# Put here any custom parameters that are specific to
# this = job (e.g., SMD, TclForces, etc...)

#eFieldOn yes
#eField 0 0 -0.1= 55


#############################################################=
## EXECUTION SCRIPT =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0##
####################################################= #########


set ts 0

coorfile open dcd complex.dcd

w= hile {[coorfile read] !=3D -1 } {
=C2=A0 =C2=A0 firstTimestep $ts
=C2= =A0 =C2=A0 run 0
=C2=A0 =C2=A0 incr ts 1
}
coorfile close


Best regards,
Dr.Shabbir

--000000000000e0e33f05c719b652-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 14 14:41:35 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EJfZuN028487; Wed, 14 Jul 2021 14:41:35 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EJfZbg028486; Wed, 14 Jul 2021 14:41:35 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EJfYSA028482; Wed, 14 Jul 2021 14:41:34 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16EJfYLq028481; Wed, 14 Jul 2021 14:41:34 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16EJfOBA028473 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 14 Jul 2021 14:41:25 -0500 (CDT) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16EJdLX2007248 for ; Wed, 14 Jul 2021 19:41:24 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=matabay2010@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qk1-f169.google.com (mail-qk1-f169.google.com [209.85.222.169]) by mx0b-00007101.pphosted.com with ESMTP id 39rvr36mqs-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 14 Jul 2021 19:41:24 +0000 Received: by mail-qk1-f169.google.com with SMTP id r125so2832725qkf.1 for ; Wed, 14 Jul 2021 12:41:24 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=Z/9DLm5/B4zTpImE5sGcqtJSY+tpbABechjzJC/twkk=; b=NcdmfEqRWGKY2/0W3+9egI+f1QQwHKyck0+pPlXiGzaXON19siiuLE0nMD6zUDZ79e dLsIdEf6TwDfbAewX0BjebfKPi3sJRzeYY+Czy984af1K5XPq9MHmAlVCCa5hjImATeZ i2dibd6Hr9oUoe7Jdrc3RPw0h3z8F1qXKk3m7K7SV7fgpytuhejMDfnHLyatYpj761Yp M3vStb8TJlN1yYow/7LtTzNuwQoiMJSzrCjZjMa+JedltgZURO6dvGW+tQfDtfXMdAeU Y4VCiLZgNlildMihCpFejT4YfY4sadNJO/ZX4tR2uK+HxiE098TyNQxQMpG6ye4wO3l9 DK5g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=Z/9DLm5/B4zTpImE5sGcqtJSY+tpbABechjzJC/twkk=; b=afMAYjgMU7V/YBt4lS49fUJezoDNvytYCiNJs5U6RKM66QCsF21ZmBMw0+3b95eUju T/zJrvf7hSsGOdfYUtgu02wRNz1rBdZK15jcxh0PTufXNpcMa6xbPhV2BmtNtjMjhZ8R bzwjz4HjB3+ovjBWf/r/pzr4J8OagMGBNaFmZjCEgGsIBVdLphoiDdPZtfjCruDLLQ87 EA3pqGDt5DbG0JzyqcCYNEE+VZ5qv0OxbspyX6CLy0pwIJucxpNBKf5dPfA8m5rAvvN1 buSMVhCdW8BScB2aGfB6Dez17K1ykpc3l11cmeRABsBfCcQiewgUK1i9swjMzlY9XPOw Lcjg== X-Gm-Message-State: AOAM5307wEWVgoNeNzUU8dddYcxrjkIzukWWouBzp0N0+bnxToVgYKmc 5yOp0R+Cxa2W2kTkauDNvkbggTYCiuU9VZBHwM0= X-Google-Smtp-Source: ABdhPJzRVnCLXqK2hsfRhgzaFjRnrOqbZPYlQnQgivQliiQF7KqtIQ2/tD6U5YDxlO9TFys9xAC4Cmw7/izVHEHjF4Y= X-Received: by 2002:a37:41c3:: with SMTP id o186mr9861060qka.197.1626291683597; Wed, 14 Jul 2021 12:41:23 -0700 (PDT) References: <2120569504.4747180.1626259322780.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: <2120569504.4747180.1626259322780.JavaMail.zimbra@email.kntu.ac.ir> From: "M. A" Date: Thu, 15 Jul 2021 00:10:56 +0430 Message-ID: Subject: Re: namd-l: question about free energy calculation through FEP method in NAMD To: Ashkan Shekaari Cc: NAMD Content-Type: multipart/alternative; boundary="0000000000001a209105c71a8a2e" X-Proofpoint-ORIG-GUID: 5i82_UElcAiI-TIn8Byjyx0_TWVswHBu X-CLX-Shades: MLX X-Proofpoint-GUID: 5i82_UElcAiI-TIn8Byjyx0_TWVswHBu X-CLX-Response: 1TFkXGxIcEQpMehcZHBsRCllEF2xoH2xzXEYbehoYEQpYWBdvWU9DRXNFZUt SXREKeE4XY1Nja3sTWH4aX14RCnlMF2Ede2NlWE1OekBhEQpDSBcHHh4YEQpDWRcHGx8ZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwccR4fEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx9DEhh1f29GSWtDYwd+Y0QSaFNAU1IadX59fFldYmhfEQpYXBcfBBoEGBkY BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NgZWAFEQpNXBcbExoRCkxaF3hpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGB gEGxwTEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2cdH0kYTllEYFtSEQpCThdjU2NrexNYfhpfXhEKQkwXb1lPQ0VzRWVLUl0RCkJs F2xfTmAfYW1gAQEYEQpCQBdtRX9yb29me3NwaREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4 RCnlDF2xHUEkFZW9fbmVAEQpZSxcTHhwdEQpwZxdjGmNHQX9hRngZfBAaEQpwaBdvaW57TU1gc0 MFHBAaEQpwaBdtQB4TfxNObXwbUhAaEQpwaBdiWl1vSWNnbRxZbBAaEQpwaBdgRV5hHkxSH1ptR xAaEQpwaBdiZlhSYxpGUkFIexAaEQpwfRdjc3tNBV0dAXhBcBAaEQpwZxdpQ25QAVlzRwEeUxAa EQpwZxdlQk1mexwcR1oaTBAaEQpwfRdpGmVOXEgTYEd5RhAaEQpwfxdvRGFQEhN/GxwSfhATHxE KcF8XYhgaGB94R0x7e3sQGxgYEQpwbBdrHXxlEn0ZU0RwThAaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 priorityscore=361 adultscore=0 phishscore=0 impostorscore=0 mlxlogscore=860 malwarescore=0 suspectscore=0 bulkscore=0 clxscore=186 spamscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107140116 domainage_hfrom=9467 X-Spam-Score: 0 X-Spam-OrigSender: matabay2010@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "M. A" --0000000000001a209105c71a8a2e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Ashkan, Hi Thank you for your help. Both methods you recommended are time-consuming and I have no enough time and in addition, the FEP method worked for my other simulations except for the problem that I mentioned I didn't have any problems with. bests, Maryam On Wed, Jul 14, 2021 at 3:12 PM Ashkan Shekaari wrote: > Hi Maryam, > Give it a try using > 1- SMD and then the Jarzynski's equality > or > 2- replica-exchange umbrella sampling. > Both are implemented in NAMD. > > --- > ,Best > Ashkan Shekaari > PhD Candidate in Solid State Physics > Department of Physics > K. N. Toosi University of Technology, Tehran, 15875-4416, Iran > > > > ------------------------------ > *From: *"M. A" > *To: *"namd-l" , "J=C3=A9r=C3=B4me H=C3=A9nin" > *Sent: *Wednesday, July 14, 2021 11:05:05 AM > *Subject: *namd-l: question about free energy calculation through FEP > method in NAMD > > Dear J=C3=A9r=C3=B4me, > Hi > > Do you have any suggestions to solve this problem? > I want to calculate the free energy (=CE=94G) between a ligand and protein > through FEP method in NAMD. In my structure, the ligand is located on the > surface of the protein, not inside the protein, lt means a part of the > ligand that is closed to the protein surface has interaction with protein, > and the other part of the ligand which is in contact with water molecules, > has interaction with these molecules. So, when I change the B column of > atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) tur= ns > off for all atoms of ligand (all atoms in contact with protein and water > molecules both) while I need to eliminate the only interaction between the > ligand and protein. How can I specify that it eliminates just the > interaction between the ligand and protein and does not consider the > interaction of ligand and water molecules. > I appreciate all your help. > > best regards > Maryam > > -- > Maryam Atabay > Ph.D in Nano Computational Chemistry > Department of Physics, Sharif University of Technology > > > --=20 Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology --0000000000001a209105c71a8a2e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear Ashkan,
Hi
Thank you for you= r help. Both methods you recommended are time-consuming and I have no enoug= h time and in addition, the FEP method worked for my other simulations exce= pt for the problem that I mentioned I didn't have any problems with.

bests,
Maryam

On Wed, Jul 14= , 2021 at 3:12 PM Ashkan Shekaari <shekaari@email.kntu.ac.ir> wrote:
Hi Maryam,
= Give it a try using
1- SMD and then the Jarzynski's equality<= /div>
or
2- replica-exchange umbrella sampling.
Bot= h are implemented in NAMD.

---
,Best
<= /div>
Ashkan Shekaari=
PhD Candidate in Solid State Phys= ics
Department of Physics
K. N.= Toosi University of Technology,=C2=A0Tehran,=C2=A015875-4416, Iran
<= /div>

<= /div>
From: "M= . A" <ma= tabay2010@gmail.com>
To: "namd-l" <namd-l@ks.uiuc.edu>, &= quot;J=C3=A9r=C3=B4me H=C3=A9nin" <jerome.henin@ibpc.fr>
Sent: Wedn= esday, July 14, 2021 11:05:05 AM
Subject: namd-l: question about = free energy calculation through FEP method in NAMD

=
Dear J=C3=A9r=C3=B4me,
Hi

Do you have any suggestions to solve this problem?
I w= ant to calculate the free energy (=CE=94G) between a ligand and protein through FEP method in NAMD.=C2=A0 In my struc= ture, the ligand is located on the surface of the protein, not inside the p= rotein, lt means a part of the ligand that is closed to the protein surface= has interaction with protein, and the other part of the ligand which is in= contact with water molecules, has interaction with these molecules. So, wh= en I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both)=20 while I need to eliminate the only interaction between the ligand and prote= in. How can I specify that it eliminates just the interaction between the l= igand and protein and does not consider the interaction of ligand and water= molecules.=C2=A0
I appreciate all your help.

best = regards
Maryam

--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology




--
Maryam Atabay
Ph.D in Nano Computational Chemistry
D= epartment of Physics, Sharif University of Technology

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From: "Ropon-Palacios G." To: KS UIUC Message-ID: <6D39D2ED-AC58-4EF7-8DE8-57C301EB1835@gmail.com> Thread-Topic: wrap is On to Diffusion phenomena ? 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Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3709215928_1800592388 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: 7bit Dear NAMD Users, I really have a problem, which does not let me sleep. During the diffusion process (where I want to observe the input of an ion to a channel), I have been using the wrapAll and wrapWater on options in the config file, at the end of the simulation I have been able to see that there is really the input of ions, but Many authors say that you have to "unwrap" the trajectory, when doing diffusion analysis, then, I have done it, using pbc both only for the ions and for the whole system and in both cases it is not seen that the ion penetrates, so I thought about extending the dynamics, but what happens is that when I extend the dynamics, the structure with which I start is the one that is inside the channel, so all this causes me enormous confusion. Please, could you tell me in which cases wrapAll or wrapWater can be used in a dynamic. Greetings, Geo. --B_3709215928_1800592388 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear NAMD U= sers,

 

I really have a problem, which does not let me sleep. During the diffusio= n process (where I want to observe the input of an ion to a channel), I have= been using the wrapAll and wrapWater on options in the config file, at the = end of the simulation I have been able to see that there is really the input= of ions, but Many authors say that you have to "unwrap" the traje= ctory, when doing diffusion analysis, then, I have done it, using pbc both o= nly for the ions and for the whole system and in both cases it is not seen t= hat the ion penetrates, so I thought about extending the dynamics, but what = happens is that when I extend the dynamics, the structure with which I start= is the one that is inside the channel, so all this causes me enormous confu= sion.

Please, could you tell me in which cases wrapAll or wrapWater can be used i= n a dynamic.

 

Greetings,

 

Geo.

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boundary="00000000000004659105c73b6161" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxkfEQpMehcZGR8RCllEF2ZbAUJEbk8cW09oEQpYWBdmHxN7GV8bWkV vWBEKeE4XY1Nja3sTWH4aX14RCnlMF2hGWEhJcEZLQAFBEQpDSBcHGRgZEQpDWRcHGBgcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxsfcRsZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF39STEdwSBpwYAdlfBtja3NybmJkckJJZFhLYWl5Hk5ZEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NgXUYaEQpNXBcbExMRCkxaF2xpTWtNEQpMRhdva2t ra2sRCkJPF2V+XFlbW0djU2FsEQpDWhcYGhMEEh8EGBsSBB4TEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2x/QVJDbmMTZFAeEQpCThdjU2Nre xNYfhpfXhEKQkwXZh8TexlfG1pFb1gRCkJsF2MSTlpBX0xsWhwaEQpCQBdrUl8ZUGMcfntyRhEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2xYT25wZBNcYR5hEQpZSxcTHhwTEQpwaBd nHW1kTwFkbEhGUBAZGhEKcGgXYlhOWUB9TRhYQkkQGRoRCnBoF2RETltwW1pcYn9DEBkaEQpwaB dsb1NBYFBwbR9nRBAZGhEKcGgXaGt7QUMYRwFYGlMQGRoRCnBsF216GXtGbFJtTWRmEBkaEQptf hcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: UxfmZb0ZJ-OV1IAYXDHNXhcNraKCS4ds X-Proofpoint-GUID: UxfmZb0ZJ-OV1IAYXDHNXhcNraKCS4ds X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 mlxscore=0 clxscore=135 bulkscore=0 mlxlogscore=717 impostorscore=0 malwarescore=0 priorityscore=335 adultscore=0 lowpriorityscore=0 spamscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107160065 domainage_hfrom=9469 X-Spam-Score: 0 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --00000000000004659105c73b6161 Content-Type: text/plain; charset="UTF-8" Hi, I have protein containing 28 mino acid residues. The protein has 4 leucine residues which forms 2 leucine zipper structures and whole protein adopting alpha helix config with several salt bridges between different residues. I started with a structure similar to this ( made by Avogadro) and I was able to get proper psf file. During equilibration with protein in water box whole protein loses its alpha helix config ( I measured the alpha helix content using alpha helix colvar) resulting in an open ended structure with less than 20% alpha helix content which was around 75 % in the initial structure. My question is what constraint do I apply to protein such that I get accurate description of it during equilibration and production run? Also on applying these constraints will it affect the PES of the system? Diship Srivastava JRF IIT (ISM) Dhanbad India --00000000000004659105c73b6161 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,=C2=A0
I have protein containing 28 m= ino acid residues. The protein has 4 leucine residues which forms 2 leucine= zipper structures and whole protein adopting alpha helix config with sever= al salt bridges between different residues. I started with a structure simi= lar to this ( made by Avogadro) and I was able to get proper psf=C2=A0 file= . During equilibration with protein in water box whole protein loses its al= pha helix config ( I measured the alpha helix content using alpha helix col= var) resulting in an open ended structure with less than 20% alpha helix co= ntent which was around 75 % in the initial structure.
=C2=A0
My question is what constraint do I apply t= o protein such that I get accurate description of it during equilibration a= nd production run? Also on applying these constraints will it affect the PE= S of the system?=C2=A0

D= iship Srivastava
JRF
IIT (ISM= ) Dhanbad
India
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boundary="=_40f23088-f0d0-4d20-9872-e2f6e32fb2fa" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC73 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: Constraints required for alpha helix secondary structure Thread-Index: L38RGJAFxafK2l2KBXT/XHUkhG/kHQ== X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxkfHREKQ1kXBxsTHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscE3EeEhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThcYQ2ViEnAfUBhyXBIYZB4YQ1NlRBtbGGNQHxNocmhyZREKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzYBtlQhEKTVwXGBgZEQpMWhd8aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2IFaENATFpARXJOEQpDWhcTHgQbEh4EGx0cBB sbGxEKQl4XGxEKRF4XGBEKQlwXGxEKQksXeh5tW0t8R19iBXoRCkJJF2hfemFGAWJAQU95EQpCR RdhHR5ma3JBUhkZeBEKQk4XaF96YUYBYkBBT3kRCkJMF20TQUFaQURDE314EQpCbBdhZBlnXUIZ RXxreBEKQkAXa35wXWZfWUtET1IRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBceEQp5QxdpU3J cElpcG0tuQhEKWUsXBxkRCnBnF2MaY0dBf2FGeBl8EBkaEQpwaBduZn8ZU1h8Yx5sWBAZGhEKcG gXY2IfS3l6E2l9WBoQHR8RCnBoF2BPYXBbWHx4RUFtEBkaEQpwaBdrTmtTARsSf2hvfBAZGhEKc GgXY11JYmJkfRxAGhsQGRoRCnB9F2Nze00FXR0BeEFwEBkaEQpwZxdpQ25QAVlzRwEeUxAZGhEK cH0XaRplTlxIE2BHeUYQGRoRCnB/F29EYVASE38bHBJ+EBMaEQpwXxdiGBoYH3hHTHt7exAbGx0 RCnBsF29gf215TEFEa05OEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 2iOH8Z5z2Xv82N42iyOn1q2Iz59BXBXO X-Proofpoint-GUID: 2iOH8Z5z2Xv82N42iyOn1q2Iz59BXBXO MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 mlxscore=0 clxscore=189 bulkscore=0 mlxlogscore=999 impostorscore=0 malwarescore=0 priorityscore=0 adultscore=0 lowpriorityscore=0 spamscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107160099 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_40f23088-f0d0-4d20-9872-e2f6e32fb2fa Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear Diship,=20 Did you neutralize the whole system electrostatically?=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!tLapbJpVcCmriGdRUlfwNjwDLXw3knztLNwJHTlfU4gIgFv5vpJXXmFZ= EwcZjnxBgQ$ ]=20 From: "Diship Srivastava" =20 To: "namd-l" =20 Sent: Friday, July 16, 2021 3:21:56 PM=20 Subject: namd-l: Constraints required for alpha helix secondary structure=20 Hi,=20 I have protein containing 28 mino acid residues. The protein has 4 leucine = residues which forms 2 leucine zipper structures and whole protein adopting= alpha helix config with several salt bridges between different residues. I= started with a structure similar to this ( made by Avogadro) and I was abl= e to get proper psf file. During equilibration with protein in water box wh= ole protein loses its alpha helix config ( I measured the alpha helix conte= nt using alpha helix colvar) resulting in an open ended structure with less= than 20% alpha helix content which was around 75 % in the initial structur= e.=20 My question is what constraint do I apply to protein such that I get accura= te description of it during equilibration and production run? Also on apply= ing these constraints will it affect the PES of the system?=20 Diship Srivastava=20 JRF=20 IIT (ISM) Dhanbad=20 India=20 --=_40f23088-f0d0-4d20-9872-e2f6e32fb2fa Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear Diship,

Did you neutralize the whole system electrostatically?=

---
,Best
=
=
=
<= div dir=3D"ltr">
Ashkan Shekaari
PhD Candidate in Solid State Physics=
Depart= ment of Physics
K. N. Toosi Univer= sity of Technology, Tehran, 15875-4416, Iran
=


From: "Diship Srivastava" <dishipsrivastava@gmail.com>To: "namd-l" <namd-l@ks.uiuc.edu>
Sent: Friday, Ju= ly 16, 2021 3:21:56 PM
Subject: namd-l: Constraints required for = alpha helix secondary structure

Hi, 
I have prote= in containing 28 mino acid residues. The protein has 4 leucine residues whi= ch forms 2 leucine zipper structures and whole protein adopting alpha helix= config with several salt bridges between different residues. I started wit= h a structure similar to this ( made by Avogadro) and I was able to get pro= per psf  file. During equilibration with protein in water box whole pr= otein loses its alpha helix config ( I measured the alpha helix content usi= ng alpha helix colvar) resulting in an open ended structure with less than = 20% alpha helix content which was around 75 % in the initial structure.
 
My question is what const= raint do I apply to protein such that I get accurate description of it duri= ng equilibration and production run? Also on applying these constraints wil= l it affect the PES of the system? 

<= div dir=3D"auto">Diship Srivastava
JRF
IIT (ISM) Dhanbad
India

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boundary="00000000000064545605c73ffc52" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: Ot7wGY8weztp1XqtFiIdtRe6XsgDNCjR X-Proofpoint-GUID: Ot7wGY8weztp1XqtFiIdtRe6XsgDNCjR X-CLX-Response: 1TFkXGxkfEQpMehcZGRMRCllEF2ZbAUJEbk8cW09oEQpYWBdmHxN7GV8bWkV vWBEKeE4XY1Nja3sTWH4aX14RCnlMF2hGWEhJcEZLQAFBEQpDSBcHGBIdEQpDWRcHGxMcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxsfcRsZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2VeHV1tcxJdT1BeWhtyW15sQ2NOXnhPHHJZTW5kaUB4EQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc2AbSwURCk1cFxkaExEKTFoXeGlNa2sRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdlflxZW1tHY1NhbBEKQ1oXGBoTBBIfBBgbEg QfGxEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdsf0FSQ25jE2RQHhEKQk4XY1Nja3sTWH4aX14RCkJMF2YfE3sZXxtaRW9YEQpCbBdj Ek5aQV9MbFocGhEKQkAXa35wXWZfWUtET1IRCkJYF2dzZXNAbmFhTF1iEQpaWBceEQp5QxdpU3J cElpcG0tuQhEKWUsXEx4cExEKcGcXYxpjR0F/YUZ4GXwQHBoRCnBoF2RIf05GRG5/GRlaEBkaEQ pwaBdnSEkeYEZtY3liTBAZGhEKcGgXYmZYUmMaRlJBSHsQGRoRCnBoF2R6BUFOH0dgcHJ9EBkaE QpwaBdsb1NBYFBwbR9nRBAcGhEKcH0XY3N7TQVdHQF4QXAQGRoRCnBnF2lDblABWXNHAR5TEBwa EQpwfRdpGmVOXEgTYEd5RhAZGhEKcH8Xb0RhUBITfxscEn4QExIRCnBfF2IYGhgfeEdMe3t7EBs bHREKcGwXbXoZe0ZsUm1NZGYQHBoRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 lowpriorityscore=0 spamscore=0 impostorscore=0 priorityscore=339 mlxscore=0 suspectscore=0 phishscore=0 clxscore=135 malwarescore=0 bulkscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107160100 domainage_hfrom=9469 X-Spam-Score: 0 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --00000000000064545605c73ffc52 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Yeah, I neutalized the whole system using NaCl through vmd's solvate plugin On Fri, 16 Jul 2021, 21:38 Ashkan Shekaari, wrote: > Dear Diship, > > Did you neutralize the whole system electrostatically? > > --- > ,Best > Ashkan Shekaari > PhD Candidate in Solid State Physics > Department of Physics > K. N. Toosi University of Technology, Tehran, 15875-4416, Iran > > > > ------------------------------ > *From: *"Diship Srivastava" > *To: *"namd-l" > *Sent: *Friday, July 16, 2021 3:21:56 PM > *Subject: *namd-l: Constraints required for alpha helix secondary > structure > > Hi, > I have protein containing 28 mino acid residues. The protein has 4 leucine > residues which forms 2 leucine zipper structures and whole protein adopti= ng > alpha helix config with several salt bridges between different residues. I > started with a structure similar to this ( made by Avogadro) and I was ab= le > to get proper psf file. During equilibration with protein in water box > whole protein loses its alpha helix config ( I measured the alpha helix > content using alpha helix colvar) resulting in an open ended structure wi= th > less than 20% alpha helix content which was around 75 % in the initial > structure. > > My question is what constraint do I apply to protein such that I get > accurate description of it during equilibration and production run? Also = on > applying these constraints will it affect the PES of the system? > > Diship Srivastava > JRF > IIT (ISM) Dhanbad > India > > --00000000000064545605c73ffc52 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Yeah, I neutalized the whole system using NaCl through vm= d's solvate plugin

On Fri, 16 Jul 2021, 21:38 Ashkan Shekaari, <shekaari@email.kntu.ac.ir> w= rote:
Dear=C2=A0<= span style=3D"color:#000000;font-family:'Segoe UI','Lucida Sans= ',sans-serif;font-size:14.16px;font-style:normal;font-variant-ligatures= :normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text= -align:start;text-indent:0px;text-transform:none;white-space:normal;word-sp= acing:0px;background-color:#fdfcfb;text-decoration-style:initial;text-decor= ation-color:initial;display:inline!important;float:none">Diship,
Did you neutralize the whole system electrostatic= ally?

---
,= Best
<= /div>
=
<= div dir=3D"rtl" style=3D"text-align:left">
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics=
K. N. Toosi University of Technology,=C2= =A0Tehran,=C2=A015875-4416, Iran
=


From: "Diship Srivastava&quo= t; <dishipsrivastava@gmail.com>
To: "namd= -l" <namd-l@ks.uiuc.edu>
Sent: Friday, July 16, 20= 21 3:21:56 PM
Subject: namd-l: Constraints required for alpha hel= ix secondary structure

Hi,= =C2=A0
I have protein containing 28 mino acid residues. Th= e protein has 4 leucine residues which forms 2 leucine zipper structures an= d whole protein adopting alpha helix config with several salt bridges betwe= en different residues. I started with a structure similar to this ( made by= Avogadro) and I was able to get proper psf=C2=A0 file. During equilibratio= n with protein in water box whole protein loses its alpha helix config ( I = measured the alpha helix content using alpha helix colvar) resulting in an = open ended structure with less than 20% alpha helix content which was aroun= d 75 % in the initial structure.
=C2=A0
My question is what constraint do I apply to protein such that I= get accurate description of it during equilibration and production run? Al= so on applying these constraints will it affect the PES of the system?=C2= =A0

Diship Srivastava
JRF
IIT (ISM) Dhanbad
India

--00000000000064545605c73ffc52-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jul 16 14:39:16 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16GJdGI2008511; Fri, 16 Jul 2021 14:39:16 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16GJdG51008510; Fri, 16 Jul 2021 14:39:16 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16GJdFr1008506; Fri, 16 Jul 2021 14:39:15 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16GJdFu9008505; Fri, 16 Jul 2021 14:39:15 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16GJd5JT008497 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000005fa5b305c742bd6f" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: L2tQMXfMOQXn5M4KXxmRauYH59vV4Fnl X-Proofpoint-GUID: L2tQMXfMOQXn5M4KXxmRauYH59vV4Fnl X-CLX-Response: 1TFkXGRIfEQpMehcTGhEKWUQXYRN9HWdieUtofGwRClhYF2IeRmdrHgUaHRk fEQp4Thdhcx9tSF5IRF4bXxEKeUwXb31Fa3gTG2kBRVsRCkNIFwceHxMRCkNZFwcfHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXHB1xGwYbGR53BhgaGgYdEkAGGgYbGhoGGnEaEBp3BhoGGgYaBgccG gYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdmGF57Z3JMZ2V7ckQfZx5h clJHeEtfc2IfE1x8HmxERhEKWFwXHwQaBBgZGQUbGgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3NgHn5 QEQpNXBcYGhsRCkxaF3tpTWtrEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk 8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGx0ZEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbE QpCSxdhcx9tSF5IRF4bXxEKQkkXYXMfbUheSEReG18RCkJFF2R7HGABfmBSGElPEQpCThdhcx9t SF5IRF4bXxEKQkwXYh5GZ2seBRodGR8RCkJsF2t5GxtPYWBtHkNwEQpCQBdnYmF9ZWR9bnpERBE KQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcYEQp5QxdrYURnZXpGT0RnZhEKWUsXGxgeHxwRCn BoF2RgEnxnXGRfaF9ZEAcZGhEKcGgXbn1AYwFEZkJZYmkQBxkaEQpwaBdkRE5bcFtaXGJ/QxAbE hEKcGgXbx58RnNnbV14Tk8QBxkaEQpwaBdsb1NBYFBwbR9nRBAZGhEKcGwXbnJhT3taQ3hTTh4Q BxkaEQptfhcHGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 lowpriorityscore=0 spamscore=0 impostorscore=0 priorityscore=90 mlxscore=0 suspectscore=0 phishscore=0 clxscore=385 malwarescore=0 bulkscore=0 mlxlogscore=982 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107160121 domainage_hfrom=12456 X-Spam-Score: 0 X-Spam-OrigSender: sdash2@binghamton.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Sandeep Dash --0000000000005fa5b305c742bd6f Content-Type: text/plain; charset="UTF-8" Hello Diship, I think you can try putting in constraints on the heavy atoms in the backbone (C,N,O) during the minimization and equilibration and see how it goes. If the secondary structure stays nearly alpha helix, then you can proceed with an unconstrained production run. Also, apart from net neutrality of the whole system, you may check if each of the residues has the proper charge, as it involves the salt bridges. On Fri, Jul 16, 2021 at 6:57 AM Diship Srivastava < dishipsrivastava@gmail.com> wrote: > Hi, > I have protein containing 28 mino acid residues. The protein has 4 leucine > residues which forms 2 leucine zipper structures and whole protein adopting > alpha helix config with several salt bridges between different residues. I > started with a structure similar to this ( made by Avogadro) and I was able > to get proper psf file. During equilibration with protein in water box > whole protein loses its alpha helix config ( I measured the alpha helix > content using alpha helix colvar) resulting in an open ended structure with > less than 20% alpha helix content which was around 75 % in the initial > structure. > > My question is what constraint do I apply to protein such that I get > accurate description of it during equilibration and production run? Also on > applying these constraints will it affect the PES of the system? > > Diship Srivastava > JRF > IIT (ISM) Dhanbad > India > --0000000000005fa5b305c742bd6f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
=C2=A0Hello Diship,

I think you can try= putting=C2=A0in constraints on the heavy atoms in the backbone (C,N,O) dur= ing the minimization and equilibration and see how it goes. If the secondar= y structure stays nearly alpha helix, then you can proceed with an unconstr= ained production run. Also, apart from net=C2=A0neutrality of the whole sys= tem, you may check if each of the residues has the proper charge, as it inv= olves the salt bridges.

On Fri, Jul 16, 2021 at 6:57 AM Diship Srivas= tava <dishipsrivastava@gma= il.com> wrote:
Hi,=C2=A0
I have protein containin= g 28 mino acid residues. The protein has 4 leucine residues which forms 2 l= eucine zipper structures and whole protein adopting alpha helix config with= several salt bridges between different residues. I started with a structur= e similar to this ( made by Avogadro) and I was able to get proper psf=C2= =A0 file. During equilibration with protein in water box whole protein lose= s its alpha helix config ( I measured the alpha helix content using alpha h= elix colvar) resulting in an open ended structure with less than 20% alpha = helix content which was around 75 % in the initial structure.
=C2=A0
My question is what constraint do I= apply to protein such that I get accurate description of it during equilib= ration and production run? Also on applying these constraints will it affec= t the PES of the system?=C2=A0

Diship Srivastava
JRF
= IIT (ISM) Dhanbad
India
--0000000000005fa5b305c742bd6f-- From owner-namd-l@halifax.ks.uiuc.edu Tue Jul 20 18:06:38 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16KN6cpu013025; Tue, 20 Jul 2021 18:06:38 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16KN6cI8013024; Tue, 20 Jul 2021 18:06:38 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16KN6bLM013020; Tue, 20 Jul 2021 18:06:37 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16KN6bPQ013019; Tue, 20 Jul 2021 18:06:37 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16KN6Svk013011 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 20 Jul 2021 18:06:29 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16KN4hJN023477 for ; Tue, 20 Jul 2021 23:06:28 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=rlwoltz@ucdavis.edu; dkim=pass header.d=ucdavis.edu header.s=google Received: from mail-lf1-f43.google.com (mail-lf1-f43.google.com [209.85.167.43]) by mx0a-00007101.pphosted.com with ESMTP id 39vyywx3j9-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Tue, 20 Jul 2021 23:06:27 +0000 Received: by mail-lf1-f43.google.com with SMTP id u13so363630lfs.11 for ; Tue, 20 Jul 2021 16:06:27 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=ucdavis.edu; s=google; h=mime-version:from:date:message-id:subject:to; bh=gM1ASEjMH1NtQrFDs+/KkxOEm3pSrtYIRHeUJ4Ayx7g=; b=s4IrFBsYcGqrO5Ts0jaNhv5RpCjXDt6V44RGnxvG7AYdpFSkyrGQuM6xYylwQb7Mfk Eu/VB99RRM0O/VvQxK5Cy0tt4avprHm2LtccISJO8DgQjvXjAwyarSKXMJiqcd+q5s7b tUWgcDVg060OyJ4mH991PS6HcqdgM9iCag8eQ= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=gM1ASEjMH1NtQrFDs+/KkxOEm3pSrtYIRHeUJ4Ayx7g=; b=EaMjBLUB4tSLSOW7dLxe2ZE5iyAQq99fkhDzZdXKaRe19LEu13jvsO+PqVTsx+0hAh 4A0/B1b2cYPksYPdk4u6B0qqZWnkCYr3C4e4RuGiZ+CSZsyjzJMFrQB12B/e7qVP/mWE BRBju8Olx/7Yu17VU+pEN9mSsBdTgztQu8Hhy2uIscn/+5CgKktAHYT/tSdNNjo0XHkv t20vEZ1+BUyDe0oOAk82qqKgG7nJBGLeQcp4b7YsTFOJvM0/Akv+jIUKokpB/CvqGkL4 MGNJnJEeR/w6DeXbe1zAxhNNUfKlL0RynpEJHmDeGTGeJn7WGwF+3xPl3Ugs8Yzkt6SA Gwtg== X-Gm-Message-State: AOAM531dRj/K+RiAShIUocA6B4yisLVdR/FX2FvIA9fhjU8lIlyK5Ai/ zLFQZzQqLLacY3I8V3bn2OPhZXocY4Y4w4/9xGob1H0V1YBM X-Google-Smtp-Source: ABdhPJx1/3iEJzJ5vwlxXjagZ8Olc7qVsXsUrVaA7Dgkf4+g2ekOavCik4C4u+mKYB/mJ8KRUye/1lVaV3h6Blo1H9A= X-Received: by 2002:a19:e201:: with SMTP id z1mr23289810lfg.176.1626822385124; Tue, 20 Jul 2021 16:06:25 -0700 (PDT) From: Ryan Woltz Date: Tue, 20 Jul 2021 16:06:14 -0700 Message-ID: Subject: namd-l: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="00000000000060f1e505c7961ab9" X-Proofpoint-GUID: kqUYeZ-C80CNPQBkvXDZbFpJ4ioBEpVz X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0eEQpMehcbHBgRCllEF25BW1sfQnx4RWYFEQpYWBdnaUQcbhpbYHt uYREKeE4XYm5hExJ7aW17SHwRCnlMF2hcXn9LZn8dc15oEQpDSBcHHh0aEQpDWRcHGxISEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ecRkeEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0Fbf3NPcAdpEhppZHp7aEFccm5wSGxaYB5DRWhvWnxQEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc2Z6X3oRCk1cFxkSHBEKTFoXaWhpTU1rEQpMRhdva2t ra2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB4ZEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdibmETEntpbXtIfBEKQkkXYm5hExJ7aW17SHwRCkJFF2NaekJlHXJ5Y1AFEQpCThdibmETE ntpbXtIfBEKQkwXZ2lEHG4aW2B7bmERCkJsF2xGQXoZclhfHG9lEQpCQBdrHF9lSUdGRGsFfREK QlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF2h/XkZyE0FZc0duEQpwaBdvGlxQYH5QThtGGBAaEQp waBd6GU9LAV1pRF9lRRAaEQpwaBdraFp9E2FQfBNyTxAaEQpwaBdiHHB9WRl/c1wbWRAaEQpwaB draBJPQ3ltGF0SaBAaEQpwfRdgQVpwUhsceWJvZxAaEQpwfRdmUHsZHBNmYk1MUhAaEQpwfxdlG XlmXkdpG2RPcxASHxEKcF8XZlBAYGUTWGJtYngQGhEKcH8XbAV6QxpAR1sTGGMQEhoRCnBfF29e TRxsBU9AUFtdEBoRCnBsF2hZfHxEfkFlU19vEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: kqUYeZ-C80CNPQBkvXDZbFpJ4ioBEpVz MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 spamscore=0 suspectscore=0 phishscore=0 clxscore=174 impostorscore=0 mlxscore=0 mlxlogscore=999 adultscore=0 bulkscore=0 malwarescore=0 priorityscore=162 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107200143 X-Spam-Score: 0 X-Spam-OrigSender: rlwoltz@ucdavis.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ryan Woltz --00000000000060f1e505c7961ab9 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear community, I have a 300k atom membrane embedded channel system that is stable on NAMD2.14 but wanted to upgrade to take advantage of the increased speed. I downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on EXPANSE if that matters. I've had several errors which I fixed a few but not sure how it affects my system, I don't expect they did but I'll state them as I go along just in case. Almost all errors relate to cudasoaintegrate. My system is set up as follows. Minimize, equilibrate system (step6.1-6.6), slowly release restraints on protein to prevent large RMSD jumps (Step7.1-7.13), production (step7.14). 1. My first attempt was to use NAMD3 to continue a NAMD2.14 run that was in production for 30ns. This failed immediately with error: OPENING EXTENDED SYSTEM TRAJECTORY FILE FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, 0, 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, line 4263 on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202 >From what I gathered from posts you cannot continue a NAMD2 simulation with NAMD3. Or more specifically the post said I cannot continue a simulation that did not previously include cudasoaintegrate turned on.B.I then tried starting it from scratch by separating the minimize step and the equilibration steps (6.1-6.6) but the cudasoaintegrate turned on is not compatible with reassigntemp or reassignfreq. 1. I then turned off cudasoaintegrate for steps 6.1-6.6 and then turned it on for steps 7.1 and beyond as the steps with protein restraints on the = CA atoms which are slowly released in steps 7.1-7.13 do not require reassignment. I used suggested options such as 1) margin 8 2) outputEnergies/outputTiming=3D 400 3) pairlistpercycle =3D 4 4) stepsper= cycle =3D 40. Simulation fails quickly with atoms moving too fast. 2. I then readjusted outputEnergies/outputTiming to 5000 (charmm-gui default). However, step7.1 fails after 105000 steps due to fatal error Periodic cell has become too small for original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation.. 3. I played with the margins 0-20 and once I no longer got the atoms escaping error I then got the allocated memory exceeded, too many atoms = in a patch error. 4. Finally I also took out pairlistpercycle and stepspercycle as noted on NAMD3 website that these are obsolete. Now the error of ERROR: Atoms moving too fast at timestep 135902; simulation has become unstable (0 at= oms on pe 0). FATAL ERROR: SequencerCUDA: Atoms moving too fast I was able to collect bits and pieces from the forums but mostly it is on NAMD2 or on NAMD3 but the errors were similar but not the same. From error E) I don=E2=80=99t think I=E2=80=99m running out of RAM since I have 93GB a= llocated and it runs fine on NAMD2. I=E2=80=99ve gotten most of my information from Nvidia=E2=80=99s website an= d NAMD3 website and adjusted .inp files based on these sites. https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up= -to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!vaZ6nZprVW7FtNybFJ2= f4Z7QkVPOwCod_rfu8WA6vXXFQnLc4HlkmtDZP-EgY2gPrg$=20 I have a suspicion that the reason things are failing after equilibration is because I=E2=80=99m turning on cudasoaintegrate after dynamics has start= ed. However, I don=E2=80=99t know how to equilibrate with cudasoaintegrate on a= nd reassignTemp/reassingFreq. I=E2=80=99ve worked a year to get this system st= able so don=E2=80=99t want to play around too much with options I=E2=80=99m unfamil= iar with. Again system is stable with NAMD2 and most of the errors I get is failure due to the cudasoaintegrate option on. If any of these steps or errors could be fixed even if there was an option to do steps6.1-7.13 without cudasoaintegrate on and turn it on for the production I=E2=80=99d be happy.= I=E2=80=99m also wondering if cudasoaintegrate doesn=E2=80=99t like restraints on the p= rotein as I=E2=80=99ve been told by others that use very early versions. Any suggestions on how to fix any of these errors? Do I just need to keep playing with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ stepspercycle parameters until it works? Thank you, Ryan --00000000000060f1e505c7961ab9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

Dear comm= unity,


=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0I have a 300k atom membrane embedded chann= el system that is stable on NAMD2.14 but wanted to upgrade to take advantag= e of the increased speed.=C2=A0 I downloaded NAMD3.0 alpha9. I'm also u= sing the V100 GPUs on EXPANSE if that matters. I've had several errors = which I fixed a few but not sure how it affects my system, I don't expe= ct they did but I'll state them as I go along just in case. Almost all = errors relate to cudasoaintegrate.


=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0My s= ystem is set up as follows. Minimize, equilibrate system (step6.1-6.6), slo= wly release restraints on protein to prevent large RMSD jumps (Step7.1-7.13= ), production (step7.14).=C2=A0


  1. My first attempt was to use NAMD3 to = continue a NAMD2.14 run that was in production for 30ns. This failed immedi= ately with error:

OPENING EXTENDED SYSTEM TRAJECTO= RY FILE
FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussra= nd_x, n, 0, 1) in file src/SequencerCUDAKernel.cu, function langevinVelocit= iesBBK2, line 4263
=C2=A0on Pe 0 (exp-12-57 device 0 pci 0:af:0): status= value 202
From what I g= athered from posts you cannot continue a NAMD2 simulation with NAMD3. Or mo= re specifically the post said I cannot continue a simulation that did not p= reviously include cudasoaintegrate turned on.B.I then tried starting it from scratch by separating the= minimize step and the equilibration steps (6.1-6.6) but the cudasoaintegra= te turned on is not compatible with reassigntemp or reassignfreq.=C2=A0
  1. I then turned off cudasoaintegrate for steps 6.1-6.6 and then turned it on= for steps 7.1 and beyond as the steps with protein restraints on the CA at= oms which are slowly released in steps 7.1-7.13 do not require reassignment= . I used suggested options such as 1) margin 8 2) outputEnergies/outputTimi= ng=3D 400 3) pairlistpercycle =3D 4 4) stepspercycle =3D 40. Simulation fai= ls quickly with atoms moving too fast.

  2. I= then readjusted outputEnergies/outputTiming to 5000 (charmm-gui default). = However, step7.1 fails after 105000 steps due to fatal error Periodic cell = has become too small for original patch grid! Possible solutions are to res= tart from a recent checkpoint, increase margin, or disable useFlexibleCell = for liquid simulation..=C2=A0

  3. I played w= ith the margins 0-20 and once I no longer got the atoms escaping error I th= en got the allocated memory exceeded, too many atoms in a patch error.

  4. Finally I also took out pairlistpercycle and= stepspercycle as noted on NAMD3 website that these are obsolete. Now the e= rror of = ERROR: Atoms moving too fast at timestep 135902; simulation has become unst= able (0 atoms on pe 0).

    FATAL ERROR: SequencerCUDA: Atoms moving = too fast

I wa= s able to collect bits and pieces from the forums but mostly it is on NAMD2= or on NAMD3 but the errors were similar but not the same. From error E) I = don=E2=80=99t think I=E2=80=99m running out of RAM since I have 93GB alloca= ted and it runs fine on NAMD2.


I=E2=80=99ve gotten most of my information from Nvidia= =E2=80=99s website and NAMD3 website and adjusted .inp files based on these= sites.


https://www.ks.uiuc.= edu/Research/namd/alpha/3.0alpha/

https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd= -v3-and-a100-gpu/


I have a suspicion that the reason things are failing after equil= ibration is because I=E2=80=99m turning on cudasoaintegrate after dynamics = has started. However, I don=E2=80=99t know how to equilibrate with cudasoai= ntegrate on and reassignTemp/reassingFreq. I=E2=80=99ve worked a year to ge= t this system stable so don=E2=80=99t want to play around too much with opt= ions I=E2=80=99m unfamiliar with. Again system is stable with NAMD2 and mos= t of the errors I get is failure due to the cudasoaintegrate option on. If = any of these steps or errors could be fixed even if there was an option to = do steps6.1-7.13 without cudasoaintegrate on and turn it on for the product= ion I=E2=80=99d be happy. I=E2=80=99m also wondering if cudasoaintegrate do= esn=E2=80=99t like restraints on the protein as I=E2=80=99ve been told by o= thers that use very early versions.


Any suggestions on how to fix any of these errors? = Do I just need to keep playing with margin/ outputenergy/ outputtimeing/ pa= irlistpercycle/ stepspercycle parameters until it works?


Thank you,


Ryan

--00000000000060f1e505c7961ab9-- From owner-namd-l@halifax.ks.uiuc.edu Tue Jul 20 18:15:02 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16KNF2h4014843; Tue, 20 Jul 2021 18:15:02 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16KNF1KB014842; Tue, 20 Jul 2021 18:15:01 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16KNF1Rx014837; Tue, 20 Jul 2021 18:15:01 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16KNF1mS014836; Tue, 20 Jul 2021 18:15:01 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16KNEkis014826 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 20 Jul 2021 18:14:47 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16KNDvh2007233 for ; Tue, 20 Jul 2021 23:14:45 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=rlwoltz@ucdavis.edu; dkim=pass header.s=google header.d=ucdavis.edu Received: from mail-lf1-f47.google.com (mail-lf1-f47.google.com [209.85.167.47]) by mx0a-00007101.pphosted.com with ESMTP id 39vyytp464-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Tue, 20 Jul 2021 23:14:44 +0000 Received: by mail-lf1-f47.google.com with SMTP id q16so430078lfa.5 for ; Tue, 20 Jul 2021 16:14:44 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=ucdavis.edu; s=google; h=mime-version:from:date:message-id:subject:to; bh=/hkRZTX6XJJfXCjwbmr8wO7thNbQSdoGQAJJp4Ff7gg=; b=XNvpoGZpxjqdIKt7spaFwk4PTEivRLsrF+swmR305zs982F6R75LY+9cJLhnOaEmZ3 964Ft0hF5SCZZxW3A/9j+yEGlddzXs212KcECk6krq485bkCV/H61Q5O8A+Lkkni/xgw 8Z3e68P03EIUXhjQEvhRAFDXcBepyO2TrBT4M= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=/hkRZTX6XJJfXCjwbmr8wO7thNbQSdoGQAJJp4Ff7gg=; b=NB/60lLqdTeOl6rIiyby2tZiXE3BETHa3lYKTw3MyiTcN6JxZ/t3YM8ZZKdylHKY3y QN3ILskKSWFWhUq2Yw6z13Hp3gK0MXxBohSaaCXU9rRVQ3Z4HgO9xXJuDJyQIqQ8JZUf 6JBVNJJwBZxCd6JrN86FyMt0QYDV5X2OMuotcBkkTxPcLUsg70gh28OGAKiD9eutQRZj XF/f+/bRvyyPWX514xokfm4DCZ0Gg7OnmpxLTImN8AUTktxzcYNw2oUJp742nFHxv5v3 XUgsyd+ev5IUvLmeGeuatYGwfdZ7Yrnx51ZSRe7AU85E2VsTG9UXUg5kIXieQFENOlUc pxrQ== X-Gm-Message-State: AOAM5320t0OBnOB/pLBRPYAHXX5jmBUbpQuZuAhQpbmT4/3OLajrxMyA ibY6hEXncScNTKNvznXXRf5Xy2+gYgpFGY8aEkdLFy5WR0y7 X-Google-Smtp-Source: ABdhPJxDcOEUzw59tgCZlTDTJ3EtF9kR0EV/Hdh5Q6BFbFPKS55RPQSCK6vQ2/VJ+pLzCv4/50jYr74jTwh7W0t1igE= X-Received: by 2002:a05:6512:3444:: with SMTP id j4mr24540549lfr.147.1626822882145; Tue, 20 Jul 2021 16:14:42 -0700 (PDT) From: Ryan Woltz Date: Tue, 20 Jul 2021 16:14:31 -0700 Message-ID: Subject: namd-l: Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000000115bc05c7963808" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: k_H88th9aMYy2TCfjeDqNB8XysEAir9I X-CLX-Response: 1TFkXGxITEQpMehcbHxsRCllEF25BW1sfQnx4RWYFEQpYWBdnaUQcbhpbYHt uYREKeE4XYm5hExJ7aW17SHwRCnlMF2hcXn9LZn8dc15oEQpDSBcHHhIcEQpDWRcHHh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBNxHhIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XQXViEhJeQhNLZ3NTGH5pTEBPbltkaBJyU1lva0NYE2MRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdzZnoYaxEKTVwXHh4YEQpMWhdsaU1NaxEKTEYXb2tra2t rEQpCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQQeHREKQl4XGxEKQlwXGxEKXk4XGxEKQk sXYm5hExJ7aW17SHwRCkJJF2JuYRMSe2lte0h8EQpCRRdjWnpCZR1yeWNQBREKQk4XYm5hExJ7a W17SHwRCkJMF2dpRBxuGltge25hEQpCbBdsRkF6GXJYXxxvZREKQkAXZBNNeH5/R0RHUlMRCkJY F2dzZXNAbmFhTF1iEQpaWBceEQp5QxdsWmYeW0FAeQUdTREKcGgXbxpcUGB+UE4bRhgQGhEKcGg XZXNjGk5sek5HbEIQGRoRCnBoF2toWn0TYVB8E3JPEBoRCnBoF2IccH1ZGX9zXBtZEBoRCnBoF2 toEk9DeW0YXRJoEBoRCnB9F2BBWnBSGxx5Ym9nEBoRCnB9F2ZQexkcE2ZiTUxSEBkaEQpwfRdrX HtPS0YcWFNzRxAZGhEKcH8XZRl5Zl5HaRtkT3MQBxsSEQpwXxdmUEBgZRNYYm1ieBAaEQpwfxds BXpDGkBHWxMYYxAcHBEKcF8Xb15NHGwFT0BQW10QGRoRCnB/F29EYVASE38bHBJ+EBwcEQpwXxd ubkdnQBJhe198ARAZGhEKcGwXaFl8fER+QWVTX28QGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: k_H88th9aMYy2TCfjeDqNB8XysEAir9I MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 priorityscore=151 lowpriorityscore=0 mlxlogscore=999 spamscore=0 suspectscore=0 malwarescore=0 adultscore=0 phishscore=0 bulkscore=0 impostorscore=0 clxscore=189 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107200145 X-Spam-Score: 0 X-Spam-OrigSender: rlwoltz@ucdavis.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ryan Woltz --0000000000000115bc05c7963808 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear community, I have a 300k atom membrane embedded channel system that is stable on NAMD2.14 but wanted to upgrade to take advantage of the increased speed. I downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on EXPANSE if that matters. I've had several errors which I fixed a few but not sure how it affects my system, I don't expect they did but I'll state them as I go along just in case. Almost all errors relate to cudasoaintegrate. My system is set up as follows. Minimize, equilibrate system (step6.1-6.6), slowly release restraints on protein to prevent large RMSD jumps (Step7.1-7.13), production (step7.14). 1. My first attempt was to use NAMD3 to continue a NAMD2.14 run that was in production for 30ns. This failed immediately with error: OPENING EXTENDED SYSTEM TRAJECTORY FILE FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, 0, 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, line 4263 on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202 >From what I gathered from posts you cannot continue a NAMD2 simulation with NAMD3. Or more specifically the post said I cannot continue a simulation that did not previously include cudasoaintegrate turned on. Working with NAMD3 from beginning: 1. I then tried starting it from scratch by separating the minimize step and the equilibration steps (6.1-6.6) but the cudasoaintegrate turned on is not compatible with reassigntemp or reassignfreq. 2. I then turned off cudasoaintegrate for steps 6.1-6.6 and then turned it on for steps 7.1 and beyond as the steps with protein restraints on t= he CA atoms which are slowly released in steps 7.1-7.13 do not require reassignment. I used suggested options such as 1) margin 8 2) outputEnergies/outputTiming=3D 400 3) pairlistpercycle =3D 4 4) stepsper= cycle =3D 40. Simulation fails quickly with atoms moving too fast. 3. I then readjusted outputEnergies/outputTiming to 5000 (charmm-gui default). However, step7.1 fails after 105000 steps due to fatal error Periodic cell has become too small for original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation.. 4. I played with the margins 0-20 and once I no longer got the atoms escaping error I then got the allocated memory exceeded, too many atoms = in a patch error. 5. Finally I also took out pairlistpercycle and stepspercycle as noted on NAMD3 website that these are obsolete. Now the error of ERROR: Atoms moving too fast at timestep 135902; simulation has become unstable (0 at= oms on pe 0). FATAL ERROR: SequencerCUDA: Atoms moving too fast I was able to collect bits and pieces from the forums but mostly it is on NAMD2 or on NAMD3 but the errors were similar but not the same. From error E) I don=E2=80=99t think I=E2=80=99m running out of RAM since I have 93GB a= llocated and it runs fine on NAMD2. I=E2=80=99ve gotten most of my information from Nvidia=E2=80=99s website an= d NAMD3 website and adjusted .inp files based on these sites. https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up= -to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!vYzmDPKUph4SSFqEco-= Zik5G2d8jAy4sSMUXSJNjpiIRmc_eGEhoPYi1DYgw47POAA$=20 I have a suspicion that the reason things are failing after equilibration is because I=E2=80=99m turning on cudasoaintegrate after dynamics has start= ed. However, I don=E2=80=99t know how to equilibrate with cudasoaintegrate on a= nd reassignTemp/reassingFreq. I=E2=80=99ve worked a year to get this system st= able so don=E2=80=99t want to play around too much with options I=E2=80=99m unfamil= iar with. Again system is stable with NAMD2 and most of the errors I get is failure due to the cudasoaintegrate option on. If any of these steps or errors could be fixed even if there was an option to do steps6.1-7.13 without cudasoaintegrate on and turn it on for the production I=E2=80=99d be happy.= I=E2=80=99m also wondering if cudasoaintegrate doesn=E2=80=99t like restraints on the p= rotein as I=E2=80=99ve been told by others that use very early versions. Any suggestions on how to fix any of these errors? Do I just need to keep playing with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ stepspercycle parameters until it works? Attachments https://urldefense.com/v3/__https://drive.google.com/drive/folders/1NgNWLrD= FQLdcB77I0U9U_sGD2KVEoJ_X?usp=3Dsharing__;!!DZ3fjg!vYzmDPKUph4SSFqEco-Zik5G= 2d8jAy4sSMUXSJNjpiIRmc_eGEhoPYi1DYhaurOdNQ$=20 Thank you, Ryan --0000000000000115bc05c7963808 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

Dear comm= unity,


=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0I have a 300k atom membrane embedded chann= el system that is stable on NAMD2.14 but wanted to upgrade to take advantag= e of the increased speed.=C2=A0 I downloaded NAMD3.0 alpha9. I'm also u= sing the V100 GPUs on EXPANSE if that matters. I've had several errors = which I fixed a few but not sure how it affects my system, I don't expe= ct they did but I'll state them as I go along just in case. Almost all = errors relate to cudasoaintegrate.


=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0My s= ystem is set up as follows. Minimize, equilibrate system (step6.1-6.6), slo= wly release restraints on protein to prevent large RMSD jumps (Step7.1-7.13= ), production (step7.14).=C2=A0


  1. My first attempt was to use NAMD3 to = continue a NAMD2.14 run that was in production for 30ns. This failed immedi= ately with error:

OPENING EXTENDED SYSTEM TRAJECTO= RY FILE
FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussra= nd_x, n, 0, 1) in file src/SequencerCUDAKernel.cu, function langevinVelocit= iesBBK2, line 4263
=C2=A0on Pe 0 (exp-12-57 device 0 pci 0:af:0): status= value 202
From what I g= athered from posts you cannot continue a NAMD2 simulation with NAMD3. Or mo= re specifically the post said I cannot continue a simulation that did not p= reviously include cudasoaintegrate turned on.

Working with NAMD3 from beginning:
  1. I then tried starting it from scratch by separating the minimize st= ep and the equilibration steps (6.1-6.6) but the cudasoaintegrate turned on is not compatible with reassigntemp or reassig= nfreq.=C2=A0
  2. I then turned off cudasoaintegrate for s= teps 6.1-6.6 and then turned it on for steps 7.1 and beyond as the steps wi= th protein restraints on the CA atoms which are slowly released in steps 7.= 1-7.13 do not require reassignment. I used suggested options such as 1) mar= gin 8 2) outputEnergies/outputTiming=3D 400 3) pairlistpercycle =3D 4 4) st= epspercycle =3D 40. Simulation fails quickly with atoms moving too fast.
  3. I then readjusted outputEnergies/outputTiming = to 5000 (charmm-gui default). However, step7.1 fails after 105000 steps due= to fatal error Periodic cell has become too small for original patch grid!= Possible solutions are to restart from a recent checkpoint, increase margi= n, or disable useFlexibleCell for liquid simulation..=C2=A0

  4. =
  5. I played with the margins 0-20 and once I no longer got= the atoms escaping error I then got the allocated memory exceeded, too man= y atoms in a patch error.

  6. Finally I also= took out pairlistpercycle and stepspercycle as noted on NAMD3 website that= these are obsolete. Now the error of ERROR: Atoms moving too fast at timestep 1359= 02; simulation has become unstable (0 atoms on pe 0).

    FATAL ERROR= : SequencerCUDA: Atoms moving too fast

I was able to collect bits and pieces from the fo= rums but mostly it is on NAMD2 or on NAMD3 but the errors were similar but = not the same. From error E) I don=E2=80=99t think I=E2=80=99m running out o= f RAM since I have 93GB allocated and it runs fine on NAMD2.


=

= I=E2=80=99ve gotten most o= f my information from Nvidia=E2=80=99s website and NAMD3 website and adjust= ed .inp files based on these sites.


https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/

https://developer.nvidia.com/blog/delivering-u= p-to-9x-throughput-with-namd-v3-and-a100-gpu/


I have a suspicion that the reason th= ings are failing after equilibration is because I=E2=80=99m turning on cuda= soaintegrate after dynamics has started. However, I don=E2=80=99t know how = to equilibrate with cudasoaintegrate on and reassignTemp/reassingFreq. I=E2= =80=99ve worked a year to get this system stable so don=E2=80=99t want to p= lay around too much with options I=E2=80=99m unfamiliar with. Again system = is stable with NAMD2 and most of the errors I get is failure due to the cud= asoaintegrate option on. If any of these steps or errors could be fixed eve= n if there was an option to do steps6.1-7.13 without cudasoaintegrate on an= d turn it on for the production I=E2=80=99d be happy. I=E2=80=99m also wond= ering if cudasoaintegrate doesn=E2=80=99t like restraints on the protein as= I=E2=80=99ve been told by others that use very early versions.

<= br>

Any suggestions on how = to fix any of these errors? Do I just need to keep playing with margin/ out= putenergy/ outputtimeing/ pairlistpercycle/ stepspercycle parameters until = it works?


Attachments

https://drive.goo= gle.com/drive/folders/1NgNWLrDFQLdcB77I0U9U_sGD2KVEoJ_X?usp=3Dsharing

Thank you,


Ryan

=
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Thread-Topic: namd-l: Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. 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boundary="_000_21F183D703E442EDBA48659C976C3953msuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 690abe9d-5667-44ab-1286-08d94c57c350 X-MS-Exchange-CrossTenant-originalarrivaltime: 21 Jul 2021 14:56:47.1051 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: TJW+yLrhqbITXd98OOwvgRX7UrXud6Mug60lBYoiGqhri28PpoNG2uUx8EblBI7O5Q0Cd1xDAwnsWvhIlOjfyg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB4247 X-Proofpoint-GUID: RgznsxgFG_ZsNPrgr4RzQSVbTF-H6n6f X-CLX-Response: 1TFkXGBgaEQpMehcZGhEKWUQXaXtSfmRsGVBgYWQRClhYF29hWBMaS10bQ0F lEQp4Thdob0xmAXJmZEtdEhEKeUwXYGVTYE0dTx5nGFwRCkNIFwcYHBMRCkNZFwcbHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhgaGnEbExIQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04XeE1QRFlSTWxtdXBZZHpYTVgeeFB7eXxIfmwHYhxEHEwRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXc2ZOWmcRCk1cFx4YHxEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2tra2xraxEKQk8XZ2BaT3sBenkeZEARCkNaFx4aBBsaHQQYGB oEHh0RCkJeFxsRCkReFxkRCkJFF2hta2B5EktAWh59EQpCThdob0xmAXJmZEtdEhEKQkwXb2FYE xpLXRtDQWURCkJsF2F5HB8SXHtPWmlCEQpCQBdpXxhgGktzcmcbHxEKQlgXZ3Nlc0BuYWFMXWIR ClpYFx4RCnlDF29weGRhGG5mHRNfEQpZSxcbGB4THxEKcGcXbUdha01jGUxTaW4QGRoRCnBoF2l jW1NIUnxkbFp4EBkaEQpwaBdtZRwST1lSHF9gYxAZGhEKcGgXbB9AYGReYEcaXmMQGRoRCnBoF2 5cZGxlbmgcEl94EBkaEQpwaBdnclsfegVYZRxgHBAZGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnB9F 2dlUBpGTltTUBlFEBkaEQpwfRdjQ35sU0lCRR9DcBAZGhEKcH0XYx5nWHJ7HlJtQwUQGRoRCnB/ F2UZeWZeR2kbZE9zEBkaEQpwXxdmUEBgZRNYYm1ieBAZGhEKcH8XbAV6QxpAR1sTGGMQEhgRCnB fF2RkTF1fR1lcSAVjEBkaEQpwfxdvRGFQEhN/GxwSfhATHhEKcF8Xbm5HZ0ASYXtffAEQGRoRCn BsF2d4GkBiGEkafnlNEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: RgznsxgFG_ZsNPrgr4RzQSVbTF-H6n6f MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 clxscore=220 priorityscore=30 impostorscore=0 phishscore=0 malwarescore=0 adultscore=0 mlxlogscore=999 bulkscore=0 lowpriorityscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107210086 domainage_hfrom=12495 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_21F183D703E442EDBA48659C976C3953msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Ryan, In my experience, NAMD3.0a9 can restart from 2.14 inputs, and I=E2=80=99ve = done it for membrane systems. However, I=E2=80=99ll admit that I don=E2=80= =99t use CHARMM-GUI=E2=80=99s recommended scheme for equilibrating the memb= rane, which I think is too conservative. There isn=E2=80=99t anything obvio= usly wrong with your input deck. One thing I=E2=80=99d check is the interme= diate structures, particularly near the indices that NAMD is barfing on. On= e thing I *have* noticed is that minimization with 3.0a9 is broken, with or= without CUDASOAIntegrate. In some cases, it is possible to end up with ver= y unphysical structures, and the structures rattle themselves apart once dy= namics starts. Otherwise, you may have an inadvertent ring piercing, which = will also cause dynamics to blow up. -Josh From: on behalf of Ryan Woltz Reply-To: "namd-l@ks.uiuc.edu" , Ryan Woltz Date: Tuesday, July 20, 2021 at 7:18 PM To: "namd-l@ks.uiuc.edu" Subject: namd-l: Please ignore previous poor formatted: difficulty converti= ng namd2 channel system to namd3 Atom velocity too fast, box too small erro= rs. Dear community, I have a 300k atom membrane embedded channel system that is stable on= NAMD2.14 but wanted to upgrade to take advantage of the increased speed. = I downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on EXPANSE if tha= t matters. I've had several errors which I fixed a few but not sure how it = affects my system, I don't expect they did but I'll state them as I go alon= g just in case. Almost all errors relate to cudasoaintegrate. My system is set up as follows. Minimize, equilibrate system (step6= .1-6.6), slowly release restraints on protein to prevent large RMSD jumps (= Step7.1-7.13), production (step7.14). A. My first attempt was to use NAMD3 to continue a NAMD2.14 run that was= in production for 30ns. This failed immediately with error: OPENING EXTENDED SYSTEM TRAJECTORY FILE FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, 0,= 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, li= ne 4263 on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202 >From what I gathered from posts you cannot continue a NAMD2 simulation with= NAMD3. Or more specifically the post said I cannot continue a simulation t= hat did not previously include cudasoaintegrate turned on. Working with NAMD3 from beginning: 1. I then tried starting it from scratch by separating the minimize step= and the equilibration steps (6.1-6.6) but the cudasoaintegrate turned on i= s not compatible with reassigntemp or reassignfreq. 2. I then turned off cudasoaintegrate for steps 6.1-6.6 and then turned = it on for steps 7.1 and beyond as the steps with protein restraints on the = CA atoms which are slowly released in steps 7.1-7.13 do not require reassig= nment. I used suggested options such as 1) margin 8 2) outputEnergies/outpu= tTiming=3D 400 3) pairlistpercycle =3D 4 4) stepspercycle =3D 40. Simulatio= n fails quickly with atoms moving too fast. C. I then readjusted outputEnergies/outputTiming to 5000 (charmm-gui defa= ult). However, step7.1 fails after 105000 steps due to fatal error Periodic= cell has become too small for original patch grid! Possible solutions are = to restart from a recent checkpoint, increase margin, or disable useFlexibl= eCell for liquid simulation.. D. I played with the margins 0-20 and once I no longer got the atoms esca= ping error I then got the allocated memory exceeded, too many atoms in a pa= tch error. E. Finally I also took out pairlistpercycle and stepspercycle as noted o= n NAMD3 website that these are obsolete. Now the error of ERROR: Atoms movi= ng too fast at timestep 135902; simulation has become unstable (0 atoms on = pe 0). FATAL ERROR: SequencerCUDA: Atoms moving too fast I was able to collect bits and pieces from the forums but mostly it is on N= AMD2 or on NAMD3 but the errors were similar but not the same. From error E= ) I don=E2=80=99t think I=E2=80=99m running out of RAM since I have 93GB al= located and it runs fine on NAMD2. I=E2=80=99ve gotten most of my information from Nvidia=E2=80=99s website an= d NAMD3 website and adjusted .inp files based on these sites. https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up= -to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!pzNFZMqbqHgZlePLlsM= KpMe7xJFUG2HT_z4yBeOrGyjMpR2ybbN8byC8sBwKqoM20g$ I have a suspicion that the reason things are failing after equilibration i= s because I=E2=80=99m turning on cudasoaintegrate after dynamics has starte= d. However, I don=E2=80=99t know how to equilibrate with cudasoaintegrate o= n and reassignTemp/reassingFreq. I=E2=80=99ve worked a year to get this sys= tem stable so don=E2=80=99t want to play around too much with options I=E2= =80=99m unfamiliar with. Again system is stable with NAMD2 and most of the = errors I get is failure due to the cudasoaintegrate option on. If any of th= ese steps or errors could be fixed even if there was an option to do steps6= .1-7.13 without cudasoaintegrate on and turn it on for the production I=E2= =80=99d be happy. I=E2=80=99m also wondering if cudasoaintegrate doesn=E2= =80=99t like restraints on the protein as I=E2=80=99ve been told by others = that use very early versions. Any suggestions on how to fix any of these errors? Do I just need to keep p= laying with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ stepsper= cycle parameters until it works? Attachments https://urldefense.com/v3/__https://drive.google.com/drive/folders/1NgNWLrD= FQLdcB77I0U9U_sGD2KVEoJ_X?usp=3Dsharing__;!!DZ3fjg!pzNFZMqbqHgZlePLlsMKpMe7= xJFUG2HT_z4yBeOrGyjMpR2ybbN8byC8sBwdL14RcA$ Thank you, Ryan --_000_21F183D703E442EDBA48659C976C3953msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: Content-Transfer-Encoding: base64 PGh0bWwgeG1sbnM6bz0idXJuOnNjaGVtYXMtbWljcm9zb2Z0LWNvbTpvZmZpY2U6b2ZmaWNlIiB4 bWxuczp3PSJ1cm46c2NoZW1hcy1taWNyb3NvZnQtY29tOm9mZmljZTp3b3JkIiB4bWxuczptPSJo dHRwOi8vc2NoZW1hcy5taWNyb3NvZnQuY29tL29mZmljZS8yMDA0LzEyL29tbWwiIHhtbG5zPSJo dHRwOi8vd3d3LnczLm9yZy9UUi9SRUMtaHRtbDQwIj4NCjxoZWFkPg0KPG1ldGEgaHR0cC1lcXVp dj0iQ29udGVudC1UeXBlIiBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9dXRmLTgiPg0KPG1l dGEgbmFtZT0iR2VuZXJhdG9yIiBjb250ZW50PSJNaWNyb3NvZnQgV29yZCAxNSAoZmlsdGVyZWQg bWVkaXVtKSI+DQo8c3R5bGU+PCEtLQ0KLyogRm9udCBEZWZpbml0aW9ucyAqLw0KQGZvbnQtZmFj ZQ0KCXtmb250LWZhbWlseToiQ2FtYnJpYSBNYXRoIjsNCglwYW5vc2UtMToyIDQgNSAzIDUgNCA2 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([fe80::b89e:393:28df:9867%7]) with mapi id 15.20.4331.034; Wed, 21 Jul 2021 20:18:31 +0000 From: "Renfro, Michael" To: "namd-l@ks.uiuc.edu" Subject: namd-l: NAMD download form unavailable? Thread-Topic: NAMD download form unavailable? 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boundary="_000_BN7PR07MB4388349424DCE463C8160F38A2E39BN7PR07MB4388namp_" MIME-Version: 1.0 X-OriginatorOrg: TNTECH.EDU X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BN7PR07MB4388.namprd07.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: d96d1af0-ce64-4cf6-4613-08d94c84b5a5 X-MS-Exchange-CrossTenant-originalarrivaltime: 21 Jul 2021 20:18:31.5897 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 66fecaf8-3dc0-4d2c-b8b8-eff0ddea46f0 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: +LJkMtXpDo1tfOp/RARU1Clb2H5wAjrTbbSFLFk+1qlL0MicTstxRcdSNv5jq9RWHrSoVKYWDzIKwHWBgWtK+A== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BN6PR07MB3092 X-CLX-Shades: MLX X-Proofpoint-GUID: IYJ_pkjIBBL567HFLw9WcCc4GDUSETYr X-CLX-Response: 1TFkXGB4dEQpMehcaEQpZRBdiS1IaAUdLTHldbhEKWFgXbVxYX2RYbW5ccGA RCnhOF2NYU05/WGMafQVfEQp5TBdka3hhbBl6f1BYTREKQ0gXBxkSHBEKQ1kXBxIYEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGBgdcRkdHhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdjc2B1WkFAY2hoZh8cHWJsZl0TfUlpSR5tbn95b35zWBEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdzZkN9GhEKTVwXGR8TEQpMWhdsaU1NTREKTEYXb2tra2t raxEKQk8XbXJpXm5PTBNSHxwRCkNaFx4aBBsaHQQYHh4EGxgYEQpCXhcbEQpEXhcYEQpCRRdpGW JCf0ZyW31gExEKQk4XY1hTTn9YYxp9BV8RCkJMF21cWF9kWG1uXHBgEQpCbBdnThMZemYdRlgFG REKQkAXbHJABU1LZUZjHUURCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdleGtdW2daZlJjcBEK cGgXZloFY1NTS0x9YhkQGRoRCnBoF3p7BQVtRhhuQn1YEBkaEQpwaBdrRmlmW0hgZk9HHxAZGhE KcGgXY0YFb35acB0BY2YQGRoRCnBoF2ETWBgZHmh4AXxiEBkaEQpwfRdrUmtsR1teWBhTXhAZGh EKcH8XZRl5Zl5HaRtkT3MQHxwRCnBfF2x+AQEYG0dheUl/EBkaEQpwbBdneGdGR0ZnZk8FRxAZG hEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: IYJ_pkjIBBL567HFLw9WcCc4GDUSETYr X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 suspectscore=0 clxscore=247 phishscore=0 spamscore=0 malwarescore=0 priorityscore=0 mlxlogscore=681 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107210121 X-Spam-Score: 0 X-Spam-OrigSender: Renfro@tntech.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Renfro, Michael" --_000_BN7PR07MB4388349424DCE463C8160F38A2E39BN7PR07MB4388namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Just checking with others: I'm unable to get to https://www.ks.uiuc.edu/Dev= elopment/Download/download.cgi?PackageName=3DNAMD from two different locati= ons. I get a Gateway Timeout at the moment, might have seen some other HTTP= 500 errors earlier in the day. Is this happening to everyone? -- Mike Renfro, PhD / HPC Systems Administrator, Information Technology Servi= ces 931 372-3601 / Tennessee Tech University --_000_BN7PR07MB4388349424DCE463C8160F38A2E39BN7PR07MB4388namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Just checking with others: I'm unable to get to https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=3DNAM= D from two different locations. I get a Gateway Timeout at the moment, = might have seen some other HTTP 500 errors earlier in the day. Is this happ= ening to everyone?

 

--

Mike Renfro, PhD  /= HPC Systems Administrator, Information Technology Services
931 372-3601      / Tennessee Tech University

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boundary="000000000000982c7a05c7b026aa" X-Proofpoint-GUID: Ut5PPG23l-P8vZtOwKoyJ6DwGgqOaz42 X-CLX-Response: 1TFkXGxkSEQpMehcZGRwRCllEF3prYB9EQ0wbfEtPEQpYWBdoWUcSGQF8ZXJ HQREKeE4XY1Nja3sTWH4aX14RCnlMF2FLBR17fENHZGdHEQpDSBcHHhkeEQpDWRcHHhsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGxJxGx4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xf14fenptGBlGB3oSXHBeZV1hRVNgHG5dbU1bZUtQHhgRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdzZlhpehEKTVwXGR4cEQpMWhdsaU1raxEKTEYXb2tra2t rEQpCTxd6UHhka1pSclpGRhEKQ1oXGBoTBBIfBBscHAQeHxEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdrRHNuGxgZZERfaBEKQk4XY1Nja3sTW H4aX14RCkJMF2hZRxIZAXxlckdBEQpCbBduehhwfEV8Yn8baREKQkAXaBtoYn0FWH5af3gRCkJY F2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdvXUNgc1ATWWZLbREKWUsXEx4dHxEKcGcXYE9fRWZden8 fRRoQGRoRCnBoF29vE08bZH5MZEB7EBkaEQpwaBdtel1+XE9QbUZfZBAZGhEKcGgXYWUFGkxaeW RiRRMQGRoRCnBoF2JAc0BfTUxjbUMdEBkaEQpwaBdjf09Eb1JfbmZFbxAZGhEKcGwXZkVYaBpuX U5wbUQQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: Ut5PPG23l-P8vZtOwKoyJ6DwGgqOaz42 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 lowpriorityscore=0 clxscore=138 impostorscore=0 adultscore=0 mlxscore=0 phishscore=0 priorityscore=336 spamscore=0 malwarescore=0 bulkscore=0 mlxlogscore=905 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107220036 domainage_hfrom=9475 X-Spam-Score: 0 X-Spam-OrigSender: zebamir85@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Amir Zeb --000000000000982c7a05c7b026aa Content-Type: text/plain; charset="UTF-8" Dear NAMD users, I want to simulate protein-popc complex while applying surface tension to the membrane only. I minimized my system for 40,000 steps of minimization. When I subject the minimized system to simulation without assigning surface tension, it runs smoothly. But when I apply surface tension (even 5 dyn/cm), the simulation crashes immediately after the minimization step (let say 5000 or 20000 whatever minimization I use). I tried a number of options e.g. timestep increase and decrease, Temperature increase and decrease, surface tension value increase and decrease and several others, but couldn't find the solution. The error message and confi my config file is given here. Kindly guide me if possible. Thanks! ENERGY: 5000 19885.2122 16807.7101 10747.2198 81.3473 -700796.1791 73517.3579 0.0000 0.0000 136165.4787 -443591.8531 311.4674 -579757.3318 -444166.6838 311.4674 3188.3368 297.2494 1420037.6825 3188.3368 297.2494 ERROR: Atom 140395 velocity is -2211.21 -27266.4 25447 (limit is 20000, atom 2054 of 2872 on patch 45 pe 2) ERROR: Atom 140403 velocity is 160465 76709.9 -72614.6 (limit is 20000, atom 2062 of 2872 on patch 45 pe 2) ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 45 pe 2). ERROR: Atom 143592 velocity is -5558.3 -10113.8 -16964.4 (limit is 20000, atom 1948 of 2190 on patch 62 pe 7) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 62 pe 7). ENERGY: 5100 154229.9852 143179.4387 14400.4069 1361.8310 -645727.1251 1769540.7398 0.0000 0.0000 18635435.6060 20072420.8824 42627.0377 1436985.2765 6399910.8948 871.4869 1050248.7237 482934.9381 1919091.2003 25085.8492 19233.1721 WRITING COORDINATES TO DCD FILE bmdrc_mscl.dcd AT STEP 5100 FATAL ERROR: Exiting prematurely; see error messages above. [Partition 0][Node 0] End of program Configuration file: # NAMD Config file - autogenerated by NAMDgui plugin # Author: Amir Zeb, amirzeb@bmdrc.org # input #set input simulation.namd #coordinates ${input}.coor #velocities ${input}.vel #extendedSystem ${input}.xsc coordinates minimized.pdb structure minimized.psf parameters par_all27_prot_lipid_na.inp parameters param.prm paratypecharmm on # output set output simul_traj outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 100 xstFreq 100 binaryoutput no binaryrestart no outputEnergies 100 restartfreq 1000 fixedAtoms off # Basic dynamics exclude scaled1-4 1-4scaling 1 COMmotion no dielectric 1.0 # Simulation space partitioning switching on switchdist 9 cutoff 10 pairlistdist 12 # Multiple timestepping firsttimestep 0 timestep 0.5 stepspercycle 20 #rigidBonds all nonbondedFreq 2 fullElectFrequency 2 # Temperature control set temperature 310 temperature $temperature; # initial temperature ##################################################################################################### # -------Langevin Dynamics------ langevin on; # do langevin dynamics langevinDamping 1; # damping coefficient (gamma) of 1/ps langevinTemp $temperature; # bath temperature #temperature increment #reassignTemp 100 #reassignIncr 5 #reassignHold 310 #reassignFreq 1000 # =============================================== PME on PMEGridSpacing 1.0 wrapWater on ;# wrap water to central cell wrapAll on ;# wrap other molecules too wrapNearest off margin 10 cellBasisVector1 115.976 0 0 cellBasisVector2 0 114.77 0 cellBasisVector3 0 0 106.685 cellOrigin 1.6169999999999973 -0.0019999999999988916 -10.3205 ################################################################################## useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE) useFlexibleCell yes; # yes for an anisotropic system like membrane useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B # with grouppressure, works better, holes still there LangevinPiston on LangevinPistonTarget 1.01325 LangevinPistonPeriod 200 LangevinPistonDecay 100 LangevinPistonTemp $temperature SurfaceTensionTarget 5.0 ExcludeFromPressure on ExcludeFromPressureFile except-tension.ref ExcludeFromPressureCol B #LangevinHydrogen off ;# don't couple langevin bath to hydrogen # with langevin piston, works!!! But slower. # =============================================== # =============================================== # ---------Scripting minimize 5000 ;# lower potential energy for 1000 steps reinitvels $temperature ;# since minimization zeros velocities run 5000; Your cooperation will highly be appreciated! Kind regards! Amir --000000000000982c7a05c7b026aa Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD users,
I want to simulate protein-popc complex while applying surface = tension to the membrane only.
I minimized my system for 40,000 st= eps of minimization. When I subject the minimized system to simulation with= out assigning surface tension, it runs smoothly. But when I apply surface t= ension (even 5 dyn/cm), the simulation=C2=A0crashes immediately after the m= inimization step (let say 5000 or 20000 whatever minimization I use). I tri= ed a number of options e.g. timestep increase and decrease, Temperature inc= rease and decrease, surface tension value increase and decrease and several= others, but couldn't find the solution. The error message and confi my= config file is given here. Kindly guide me if possible.

Thanks!

ENERGY:=C2=A0 =C2=A0 5000=C2= =A0 =C2=A0 =C2=A019885.2122=C2=A0 =C2=A0 =C2=A016807.7101=C2=A0 =C2=A0 =C2= =A010747.2198=C2=A0 =C2=A0 =C2=A0 =C2=A0 81.3473=C2=A0 =C2=A0 =C2=A0 =C2=A0= -700796.1791=C2=A0 =C2=A0 =C2=A073517.3579=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A00.0000=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00.0000=C2=A0 =C2=A0 136165.4787= =C2=A0 =C2=A0 =C2=A0 =C2=A0 -443591.8531=C2=A0 =C2=A0 =C2=A0 =C2=A0311.4674= =C2=A0 =C2=A0-579757.3318=C2=A0 =C2=A0-444166.6838=C2=A0 =C2=A0 =C2=A0 =C2= =A0311.4674=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A03188.3368=C2=A0 =C2=A0 = =C2=A0 =C2=A0297.2494=C2=A0 =C2=A01420037.6825=C2=A0 =C2=A0 =C2=A0 3188.336= 8=C2=A0 =C2=A0 =C2=A0 =C2=A0297.2494

ERROR: Atom 1= 40395 velocity is -2211.21 -27266.4 25447 (limit is 20000, atom 2054 of 287= 2 on patch 45 pe 2)
ERROR: Atom 140403 velocity is 160465 76709.9= -72614.6 (limit is 20000, atom 2062 of 2872 on patch 45 pe 2)
ER= ROR: Atoms moving too fast; simulation has become unstable (2 atoms on patc= h 45 pe 2).
ERROR: Atom 143592 velocity is -5558.3 -10113.8 -1696= 4.4 (limit is 20000, atom 1948 of 2190 on patch 62 pe 7)
ERROR: A= toms moving too fast; simulation has become unstable (1 atoms on patch 62 p= e 7).
ENERGY:=C2=A0 =C2=A0 5100=C2=A0 =C2=A0 154229.9852=C2=A0 = =C2=A0 143179.4387=C2=A0 =C2=A0 =C2=A014400.4069=C2=A0 =C2=A0 =C2=A0 1361.8= 310=C2=A0 =C2=A0 =C2=A0 =C2=A0 -645727.1251=C2=A0 =C2=A01769540.7398=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A00.0000=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00.0000= =C2=A0 18635435.6060=C2=A0 =C2=A0 =C2=A0 =C2=A020072420.8824=C2=A0 =C2=A0 = =C2=A042627.0377=C2=A0 =C2=A01436985.2765=C2=A0 =C2=A06399910.8948=C2=A0 = =C2=A0 =C2=A0 =C2=A0871.4869=C2=A0 =C2=A0 =C2=A0 =C2=A0 1050248.7237=C2=A0 = =C2=A0 482934.9381=C2=A0 =C2=A01919091.2003=C2=A0 =C2=A0 =C2=A025085.8492= =C2=A0 =C2=A0 =C2=A019233.1721

WRITING COORDINATES= TO DCD FILE bmdrc_mscl.dcd AT STEP 5100
FATAL ERROR: Exiting pre= maturely; see error messages above.
[Partition 0][Node 0] End of = program

Configuration file:

# NAMD Config file - autogenerated by NAMDgui plugin
# Author: Amir Zeb,=C2=A0 amirzeb@bm= drc.org

# input

#set = input=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0simulation.namd=
#coordinates=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0${in= put}.coor
#velocities=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 ${input}.vel
#extendedSystem=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 ${input}.xsc


coordinates=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0minimized.pdb
struct= ure=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0minimized.psf
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 par_all27= _prot_lipid_na.inp
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 param.prm
paratypecharmm=C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 on


# output
set o= utput=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 simul_traj
= outputname=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 $output
dcdfile=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0${ou= tput}.dcd
xstFile=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0${output}.xst
dcdfreq=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0100
xstFreq=C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0100

bina= ryoutput=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 no
binaryrestar= t=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0no
outputEnergies=C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 100
restartfreq=C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A01000

fixedAtoms=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 off

# Ba= sic dynamics
exclude=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0scaled1-4
1-4scaling=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 1
COMmotion=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0no
dielectric=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 1.0

# Simulation space partit= ioning
switching=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0on
switchdist=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 9
cutoff=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 10
pairlistdist=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 12

# Multiple timestepping
firsttime= step=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00
timestep=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.5
stepspercycle= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020
#rigidBonds=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 all
nonbondedFreq=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A02
fullElectFrequency=C2=A0 =C2= =A0 =C2=A0 2

# Temperature control

<= /div>
set temperature=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0310
te= mperature=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature;=C2= =A0 # initial temperature
#######################################= ##############################################################
# = -------Langevin Dynamics------
langevin=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on;=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 # do langevin dynamics
langevinDamping=C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A01;=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 # damping c= oefficient (gamma) of 1/ps
langevinTemp=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 $temperature;=C2=A0 =C2=A0# bath temperature
#temperature increment
#reassignTemp=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 100
#reassignIncr=C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 5
#reassignHold=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 310
#reassignFreq=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 1000

# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

PME=C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on
PMEGr= idSpacing=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
wrapWater=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 ;# wrap water to central cell
wrapAll=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on=C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 ;# wrap other molecules too
wrapNearest=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 off
margin=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A010

cellBasisVector1 115.976 0 0
cellBasisVector2 0 114.77 0
cellBasisVector3 0 0 106.685
cellOrigin=C2=A0 1.61699999999999= 73 -0.0019999999999988916 -10.3205
##############################= ####################################################

useGroupPressure yes; # use a hydrogen-group based pseudo-molecular vira= l to calcualte pressure and
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0# has less fluctuation, is needed for rigid = bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for an anisot= ropic system like membrane
useConstantRatio no; # keeps the ratio= of the unit cell in the x-y plane constant A=3DB

= # with grouppressure, works better, holes still there

<= div>LangevinPiston=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on
Lan= gevinPistonTarget=C2=A0 =C2=A0 =C2=A01.01325
LangevinPistonPeriod= =C2=A0 =C2=A0 =C2=A0200
LangevinPistonDecay=C2=A0 =C2=A0 =C2=A0 1= 00
LangevinPistonTemp=C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature
SurfaceTensionTarget=C2=A0 =C2=A0 =C2=A05.0
ExcludeFromPres= sure=C2=A0 =C2=A0 =C2=A0 on
ExcludeFromPressureFile=C2=A0 except-= tension.ref
ExcludeFromPressureCol=C2=A0 =C2=A0B
#Lange= vinHydrogen=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0off=C2=A0 =C2=A0 ;# don't = couple langevin bath to hydrogen


# with langevin piston, works!!! But slower.

# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D
# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D


# ---------Scripting
minimize=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A05000= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ;# lower potential energy for 1000 steps=
reinitvels=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0$tempe= rature=C2=A0 ;# since minimization zeros velocities
run 5000;

Your cooperation will highly be appreciated!

Kind regards!

Amir
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boundary="=_a25e6a95-309a-4b97-bb4d-51c2d2078a23" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC73 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: Request for help on error fixing Thread-Index: qYwgTmgiHfsM62nAUPl27foy4kVS7w== X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBx4cHBEKQ1kXBxIeEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ZcR8YEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF097SWhTZEFYHW1uUnxvRBtoS15dY0RJWRlCf0VAb0l/EQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NmX2sBEQpNXBcbHRMRCkxaF3xpTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYgVoQ0BMWkBFck4RCkNaFxMeBBsSHgQbHRwEGx sbEQpCXhcbEQpEXhcYEQpCXBcbEQpCSxd6Hm1bS3xHX2IFehEKQkkXaF96YUYBYkBBT3kRCkJFF 2EdHmZrckFSGRl4EQpCThdoX3phRgFiQEFPeREKQkwXbRNBQVpBREMTfXgRCkJsF2FkGWddQhlF fGt4EQpCQBdtBXNIH2NIHWt4axEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF25SUhN ofRtiH21zEQpZSxcHGREKcGcXYxpjR0F/YUZ4GXwQGRoRCnBoF2VITmZeBWNBUmQYEBkaEQpwaB dpYhkYHEVsYRseHxAZGhEKcGgXaFlBQlttf2xsb2QQGRoRCnBoF2JnSGdLbm9MHVpQEBkaEQpwa BdlQUhaaXJTeWx5QhAZGhEKcH0XY3N7TQVdHQF4QXAQGRoRCnBnF25iRRt4GXJQYEhIEBkaEQpw ZxdpQ25QAVlzRwEeUxAaEQpwZxdgT19FZl16fx9FGhAeEhEKcH0XaRplTlxIE2BHeUYQGRoRCnB /F29EYVASE38bHBJ+EB4aEQpwXxdiGBoYH3hHTHt7exAbGxIRCnBsF29gf215TEFEa05OEBkaEQ ptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: eQcByNkr7GDxVEn1BatwIncs3hUojEcU X-Proofpoint-ORIG-GUID: eQcByNkr7GDxVEn1BatwIncs3hUojEcU MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 clxscore=163 suspectscore=0 lowpriorityscore=0 impostorscore=0 mlxlogscore=999 priorityscore=0 bulkscore=0 spamscore=0 malwarescore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107220062 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_a25e6a95-309a-4b97-bb4d-51c2d2078a23 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear researcher,=20 Use=20 margin 3=20 in your input file.=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!oNI5q7K-dorKOfWpI4bqyF4uqRzAa8xptI7RYPnxXoexPzA_yZToMwLv= kymJ2YyPhw$ ]=20 From: "Amir Zeb" =20 To: "namd-l" =20 Sent: Thursday, July 22, 2021 10:40:49 AM=20 Subject: namd-l: Request for help on error fixing=20 Dear NAMD users,=20 I want to simulate protein-popc complex while applying surface tension to t= he membrane only.=20 I minimized my system for 40,000 steps of minimization. When I subject the = minimized system to simulation without assigning surface tension, it runs s= moothly. But when I apply surface tension (even 5 dyn/cm), the simulation c= rashes immediately after the minimization step (let say 5000 or 20000 whate= ver minimization I use). I tried a number of options e.g. timestep increase= and decrease, Temperature increase and decrease, surface tension value inc= rease and decrease and several others, but couldn't find the solution. The = error message and confi my config file is given here. Kindly guide me if po= ssible.=20 Thanks!=20 ENERGY: 5000 19885.2122 16807.7101 10747.2198 81.3473 -700796.1791 73517.35= 79 0.0000 0.0000 136165.4787 -443591.8531 311.4674 -579757.3318 -444166.683= 8 311.4674 3188.3368 297.2494 1420037.6825 3188.3368 297.2494=20 ERROR: Atom 140395 velocity is -2211.21 -27266.4 25447 (limit is 20000, ato= m 2054 of 2872 on patch 45 pe 2)=20 ERROR: Atom 140403 velocity is 160465 76709.9 -72614.6 (limit is 20000, ato= m 2062 of 2872 on patch 45 pe 2)=20 ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on pa= tch 45 pe 2).=20 ERROR: Atom 143592 velocity is -5558.3 -10113.8 -16964.4 (limit is 20000, a= tom 1948 of 2190 on patch 62 pe 7)=20 ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on pa= tch 62 pe 7).=20 ENERGY: 5100 154229.9852 143179.4387 14400.4069 1361.8310 -645727.1251 1769= 540.7398 0.0000 0.0000 18635435.6060 20072420.8824 42627.0377 1436985.2765 = 6399910.8948 871.4869 1050248.7237 482934.9381 1919091.2003 25085.8492 1923= 3.1721=20 WRITING COORDINATES TO DCD FILE bmdrc_mscl.dcd AT STEP 5100=20 FATAL ERROR: Exiting prematurely; see error messages above.=20 [Partition 0][Node 0] End of program=20 Configuration file:=20 # NAMD Config file - autogenerated by NAMDgui plugin=20 # Author: Amir Zeb, [ mailto:amirzeb@bmdrc.org | amirzeb@bmdrc.org ]=20 # input=20 #set input simulation.namd=20 #coordinates ${input}.coor=20 #velocities ${input}.vel=20 #extendedSystem ${input}.xsc=20 coordinates minimized.pdb=20 structure minimized.psf=20 parameters par_all27_prot_lipid_na.inp=20 parameters param.prm=20 paratypecharmm on=20 # output=20 set output simul_traj=20 outputname $output=20 dcdfile ${output}.dcd=20 xstFile ${output}.xst=20 dcdfreq 100=20 xstFreq 100=20 binaryoutput no=20 binaryrestart no=20 outputEnergies 100=20 restartfreq 1000=20 fixedAtoms off=20 # Basic dynamics=20 exclude scaled1-4=20 1-4scaling 1=20 COMmotion no=20 dielectric 1.0=20 # Simulation space partitioning=20 switching on=20 switchdist 9=20 cutoff 10=20 pairlistdist 12=20 # Multiple timestepping=20 firsttimestep 0=20 timestep 0.5=20 stepspercycle 20=20 #rigidBonds all=20 nonbondedFreq 2=20 fullElectFrequency 2=20 # Temperature control=20 set temperature 310=20 temperature $temperature; # initial temperature=20 ###########################################################################= ##########################=20 # -------Langevin Dynamics------=20 langevin on; # do langevin dynamics=20 langevinDamping 1; # damping coefficient (gamma) of 1/ps=20 langevinTemp $temperature; # bath temperature=20 #temperature increment=20 #reassignTemp 100=20 #reassignIncr 5=20 #reassignHold 310=20 #reassignFreq 1000=20 # =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 PME on=20 PMEGridSpacing 1.0=20 wrapWater on ;# wrap water to central cell=20 wrapAll on ;# wrap other molecules too=20 wrapNearest off=20 margin 10=20 cellBasisVector1 115.976 0 0=20 cellBasisVector2 0 114.77 0=20 cellBasisVector3 0 0 106.685=20 cellOrigin 1.6169999999999973 -0.0019999999999988916 -10.3205=20 ###########################################################################= #######=20 useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral t= o calcualte pressure and=20 # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)=20 useFlexibleCell yes; # yes for an anisotropic system like membrane=20 useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane co= nstant A=3DB=20 # with grouppressure, works better, holes still there=20 LangevinPiston on=20 LangevinPistonTarget 1.01325=20 LangevinPistonPeriod 200=20 LangevinPistonDecay 100=20 LangevinPistonTemp $temperature=20 SurfaceTensionTarget 5.0=20 ExcludeFromPressure on=20 ExcludeFromPressureFile except-tension.ref=20 ExcludeFromPressureCol B=20 #LangevinHydrogen off ;# don't couple langevin bath to hydrogen=20 # with langevin piston, works!!! But slower.=20 # =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 # =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 # ---------Scripting=20 minimize 5000 ;# lower potential energy for 1000 steps=20 reinitvels $temperature ;# since minimization zeros velocities=20 run 5000;=20 Your cooperation will highly be appreciated!=20 Kind regards!=20 Amir=20 --=_a25e6a95-309a-4b97-bb4d-51c2d2078a23 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear researcher,
Use
<= strong>margin    3   
in yo= ur input file.

---
,Best
<= div dir=3D"ltr">
Ashka= n Shekaari
PhD Candidate in Solid = State Physics
Department of Physics
K. N.= Toosi University of Technology, Tehran, 15875-4416, Iran
<= /div>


From: "Amir Zeb" <zebamir85@gmail.com>
= To: "namd-l" <namd-l@ks.uiuc.edu>
Sent: Thursday, Ju= ly 22, 2021 10:40:49 AM
Subject: namd-l: Request for help on erro= r fixing

Dear NAMD users,
I wa= nt to simulate protein-popc complex while applying surface tension to the m= embrane only.
I minimized my system for 40,000 steps of minimizat= ion. When I subject the minimized system to simulation without assigning su= rface tension, it runs smoothly. But when I apply surface tension (even 5 d= yn/cm), the simulation crashes immediately after the minimization step= (let say 5000 or 20000 whatever minimization I use). I tried a number of o= ptions e.g. timestep increase and decrease, Temperature increase and decrea= se, surface tension value increase and decrease and several others, but cou= ldn't find the solution. The error message and confi my config file is give= n here. Kindly guide me if possible.

Thanks!

ENERGY:    5000     19885.2122    &nb= sp;16807.7101     10747.2198        81.3= 473        -700796.1791     73517.3579&n= bsp;        0.0000         0.0= 000    136165.4787        -443591.8531  =      311.4674   -579757.3318   -444166.6= 838       311.4674          &n= bsp;3188.3368       297.2494   1420037.6825&n= bsp;     3188.3368       297.2494

ERROR: Atom 140395 velocity is -2211.21 -27266.4 25447 (limit is 20000, = atom 2054 of 2872 on patch 45 pe 2)
ERROR: Atom 140403 velocity i= s 160465 76709.9 -72614.6 (limit is 20000, atom 2062 of 2872 on patch 45 pe= 2)
ERROR: Atoms moving too fast; simulation has become unstable = (2 atoms on patch 45 pe 2).
ERROR: Atom 143592 velocity is -5558.= 3 -10113.8 -16964.4 (limit is 20000, atom 1948 of 2190 on patch 62 pe 7)
ERROR: Atoms moving too fast; simulation has become unstable (1 ato= ms on patch 62 pe 7).
ENERGY:    5100    1542= 29.9852    143179.4387     14400.4069   =   1361.8310        -645727.1251   17695= 40.7398         0.0000        =  0.0000  18635435.6060       20072420.8824&nb= sp;    42627.0377   1436985.2765   6399910.89= 48       871.4869        1050248.72= 37    482934.9381   1919091.2003     250= 85.8492     19233.1721

WRITING COORDINATES TO = DCD FILE bmdrc_mscl.dcd AT STEP 5100
FATAL ERROR: Exiting prematu= rely; see error messages above.
[Partition 0][Node 0] End of prog= ram

Configuration file:

# NAMD Confi= g file - autogenerated by NAMDgui plugin
# Author: Amir Zeb, = ; amirzeb@bmdrc.org

# input

#set input               simulati= on.namd
#coordinates            &nb= sp;${input}.coor
#velocities          &n= bsp;   ${input}.vel
#extendedSystem      &nbs= p;   ${input}.xsc


coordinates      &n= bsp;      minimized.pdb
structure    &nb= sp;          minimized.psf
parameters&nb= sp;             par_all27_prot_lipid_na.inp
parameters              param.p= rm
paratypecharmm          on

<= br>
# output
set output          &nb= sp;   simul_traj
outputname         = ;     $output
dcdfile         =        ${output}.dcd
xstFile    &n= bsp;            ${output}.xst
dcdfr= eq                 100
xstFreq                 100=

binaryoutput            no
binaryrestart           no
o= utputEnergies          100
restartfreq&n= bsp;            1000

fixedAtoms=               off

# Basic = dynamics
exclude              =    scaled1-4
1-4scaling        &nbs= p;     1
COMmotion          &n= bsp;    no
dielectric         =     1.0

# Simulation space partitioning
= switching               on
switchdist              9
cu= toff                  10
=
pairlistdist            12

# Multiple timestepping
firsttimestep       =    0
timestep           =     0.5
stepspercycle         = ;  20
#rigidBonds            &= nbsp; all
nonbondedFreq           2=
fullElectFrequency      2

# Tempera= ture control

set temperature         = ;310
temperature             $= temperature;  # initial temperature
########################= ###########################################################################= ##
# -------Langevin Dynamics------
langevin  &nbs= p;             on;       =     # do langevin dynamics
langevinDamping   = ;      1;              # = damping coefficient (gamma) of 1/ps
langevinTemp    &nb= sp;       $temperature;   # bath temperature
=
#temperature increment
#reassignTemp     =       100
#reassignIncr       = ;     5
#reassignHold         =   310
#reassignFreq           = ; 1000

# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

PME            =         on
PMEGridSpacing     =    1.0
wrapWater          &nb= sp;   on              ;# wrap water= to central cell
wrapAll           =     on              ;# wrap o= ther molecules too
wrapNearest          =   off
margin             =    10

cellBasisVector1 115.976 0 0
cellB= asisVector2 0 114.77 0
cellBasisVector3 0 0 106.685
cel= lOrigin  1.6169999999999973 -0.0019999999999988916 -10.3205
= ###########################################################################= #######

useGroupPressure yes; # use a hydrogen-group based ps= eudo-molecular viral to calcualte pressure and
    &nbs= p;                     &n= bsp;            # has less fluctuation, is ne= eded for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # ye= s for an anisotropic system like membrane
useConstantRatio no; # = keeps the ratio of the unit cell in the x-y plane constant A=3DB

<= div># with grouppressure, works better, holes still there

Lan= gevinPiston           on
LangevinPi= stonTarget     1.01325
LangevinPistonPeriod  =    200
LangevinPistonDecay      100
LangevinPistonTemp       $temperature
S= urfaceTensionTarget     5.0
ExcludeFromPressure&nb= sp;     on
ExcludeFromPressureFile  except-tension= .ref
ExcludeFromPressureCol   B
#LangevinHydr= ogen         off    ;# don't couple lang= evin bath to hydrogen



# with langevin piston, works!!= ! But slower.

# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D
# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D


# ---------Scripting
minimize               5000 =         ;# lower potential energy for 1000 steps
=
reinitvels             $temperature=   ;# since minimization zeros velocities
run 5000;

Your cooperation will highly be appreciated!

Kind = regards!

Amir

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Dear Namd user  I am using  Meta dynamic = using Path collective variables .I would  like to know how to set = ; lowerBoundary u= pperBoundary  and width 1.0<= /div>
It would be highly appreciable if someone suggest the method of assigning values=
With High Regards<= /b>
S.VIDHYA SANKAR=
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Thread-Topic: NAMD download form unavailable? 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boundary="_000_BN7PR07MB4388CEE5B8CE6A3DF1F99BCAA2E49BN7PR07MB4388namp_" X-OriginatorOrg: TNTECH.EDU X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BN7PR07MB4388.namprd07.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: bc6afbbb-7cf7-43c9-5120-08d94d14bc3b X-MS-Exchange-CrossTenant-originalarrivaltime: 22 Jul 2021 13:29:30.1115 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 66fecaf8-3dc0-4d2c-b8b8-eff0ddea46f0 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: bmxYbiaaYsby88cTs46i1t4gKDGFAKcIBevZ3zCS+shOvkUErLN7oUpP0Xw22a93Y7azMzteb1SxNMWwAxhEWw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BN8PR07MB7169 X-Proofpoint-GUID: bfo7VdvvS8AZJaJ-JO8zQqf64YAkvXN0 X-CLX-Response: 1TFkXHh0RCkx6FxsZHhEKWUQXYktSGgFHS0x5XW4RClhYF21cWF9kWG1uXHB gEQp4ThdjWFNOf1hjGn0FXxEKeUwXZGt4YWwZen9QWE0RCkNIFwcYGRMRCkNZFwcbEhgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYYHXETHxAfGncGGBoGGhEKWV4XaGN5EQpJRhdfQ19Jd UJFWV5PThEKQ04XSExFHXxOXFx5EmtwYEtgB2BlElB7W0wcHnNrQVxyZBoRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc2ZSTnIRCk1cFxIdEQpMWhdoaU1NTREKTEYXb2tra2x raxEKQk8XbXJpXm5PTBNSHxwRCkNaFx4aBBsaHQQTHgQbGR0RCkJeFxsRCkReFxgRCkJFF2kZYk J/RnJbfWATEQpCThdjWFNOf1hjGn0FXxEKQkwXbVxYX2RYbW5ccGARCkJsF2dOExl6Zh1GWAUZE QpCQBdsYGQBX3lCW0d5ThEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnlDF2hmbk1TYV94 aBkBEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXYmtIYhlLfl9AHlMQGRoRCnBoF2tGaWZbSGBmT0c fEBkaEQpwaBdpTnIZSGBHTnlMWRAZGhEKcGgXaHMeTUhHcmBEeQUQGx4aEQpwaBd6QGZLa199GX pTchAZGhEKcGcXaUNuUAFZc0cBHlMQHBoRCnB9F3pnWGNpSHwSWmZoEBkaEQpwfRdlU10TGBtvY QUbUhAZGhEKcH8XZRl5Zl5HaRtkT3MQGxoSEQpwXxdsfgEBGBtHYXlJfxAeEhEKcH8XbFpgZRN/ Z2RgEkQQGx8YEQpwXxdgfl96UxpnHWVCZBAbHxsRCnBsF2d4Z0ZHRmdmTwVHEBkaEQptfhcbEQp YTRdLESA= X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: bfo7VdvvS8AZJaJ-JO8zQqf64YAkvXN0 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 clxscore=47 priorityscore=134 impostorscore=0 phishscore=0 malwarescore=0 adultscore=0 mlxlogscore=999 bulkscore=0 lowpriorityscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107220090 X-Spam-Score: 0 X-Spam-OrigSender: Renfro@tntech.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Renfro, Michael" --_000_BN7PR07MB4388CEE5B8CE6A3DF1F99BCAA2E49BN7PR07MB4388namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: Quoted-printable Whatever the root cause was, it's now back to normal. From: owner-namd-l@ks.uiuc.edu on behalf of Renf= ro, Michael Date: Wednesday, July 21, 2021 at 4:01 PM To: namd-l@ks.uiuc.edu Subject: namd-l: NAMD download form unavailable? Just checking with others: I'm unable to get to https://www.ks.uiuc.edu/Dev= elopment/Download/download.cgi?PackageName=3DNAMD from two different locations. I get a Gatewa= y Timeout at the moment, might have seen some other HTTP 500 errors earlier= in the day. Is this happening to everyone? -- Mike Renfro, PhD / HPC Systems Administrator, Information Technology Servi= ces 931 372-3601 / Tennessee Tech University --_000_BN7PR07MB4388CEE5B8CE6A3DF1F99BCAA2E49BN7PR07MB4388namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: Quoted-printable

Whatever the root cause was, it's now back to normal= .

 

From: owner-namd-l@ks.uiu= c.edu <owner-namd-l@ks.uiuc.edu> on behalf of Renfro, Michael <Ren= fro@tntech.edu>
Date: Wednesday, July 21, 2021 at 4:01 PM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>
Subject: namd-l: NAMD download form unavailable?

Just checking with others: I'm unable to get to https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=3DNAM= D from two different locations. I get a Gateway Timeout at the moment, = might have seen some other HTTP 500 errors earlier in the day. Is this happ= ening to everyone?

 

--

Mike Renfro, PhD  /= HPC Systems Administrator, Information Technology Services
931 372-3601      / Tennessee Tech University

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boundary="000000000000e1191f05c7b64871" X-CLX-Shades: MLX X-Proofpoint-GUID: E9xWMaEKYrvGxAMzCYzKdzRMGA8zums4 X-CLX-Response: 1TFkXGxIaEQpMehcZHxkRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGRMZEQpDWRcHExkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBpxHRIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XbxNSfWdLb2FzWFxtUmtnUGlzUGFOUHhnbWsSUF9HWR4RClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc2ZSTh4RCk1cFxscHREKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRsRCkJeFxsRCkReFxoRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4 YBEKQmwXYV96UxlDRBp6G34RCkJAF2JfYlIfb2waHRwcEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxE KWlgXGREKeUMXZk5MRGNoZVJwYGQRCllLFxMeHR8RCnBoF3pMe299W0JLWVhkEBkaEQpwaBdsZ2 ZSRB0Zfl9eaRAZGhEKcGgXZV4BSEJrfkF4Hn4QGRoRCnBoF2ldEn1NYl5ickJZEBkaEQpwaBdrQ ltdWAVfGlBAfRAZGhEKcH0XemBOfUtoQxpNXGIQGRoRCnB9F2tjREFvY2hwTR5zEBkaEQpwfxdi TgUBcEReaUR7ZRAbGhMRCnBfF2IaX1BMRgFGHBpSEBkaEQpwbBdmH3tYXGIFS1hkHxAZGhEKcEw XZgVhHEcdRmF5Q38QHhIRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: E9xWMaEKYrvGxAMzCYzKdzRMGA8zums4 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 adultscore=0 impostorscore=0 suspectscore=0 clxscore=180 phishscore=0 spamscore=0 malwarescore=0 priorityscore=353 mlxlogscore=593 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107220090 domainage_hfrom=9475 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000e1191f05c7b64871 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello Vidhya, from the documentation about how to define a colvar: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvar__;Iw!!DZ3fjg!rYlTVJ26R1Gsy_zx4gIdginc6gg= IUOc396LIQTaUXBZ-h1pM68XB29R_u16zkzMdnw$=20 You can read specifically about the grid parameters that you're referring to: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvar_grid_params__;Iw!!DZ3fjg!rYlTVJ26R1Gsy_z= x4gIdginc6ggIUOc396LIQTaUXBZ-h1pM68XB29R_u17tGGFSJw$=20 In particular, "width 1" is the default, so you can safely leave it out. Set lowerBoundary and upperBoundary as the widest interval of possible values of the variable. Giacomo On Thu, Jul 22, 2021 at 9:21 AM Vidhya Sankar < vidhyasankar7928@remove_yahoo.com> wrote: > Dear Namd user I am using Meta dynamic using Path collective variables > .I would like to know how to set * lowerBoundary upperBoundary > and width 1.0* > *It would be highly **appreciable** if someone suggest the method of > assigning values* > *With High Regards* > *S.VIDHYA SANKAR* > --000000000000e1191f05c7b64871 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello Vidhya, from the documentation about how to define a= colvar:
You can read specifically about the grid = parameters that you're referring to:
In particular, "width 1" is the default, so = you can safely leave it out.=C2=A0 Set lowerBoundary and upperBoundary as t= he widest interval of possible values of the variable.

=
Giacomo

On Thu, Jul 22, 2021 at 9:21 AM Vidhya Sankar <vidhyasanka= r7928@remove_yahoo.com> wrote:
Dea= r Namd user=C2=A0 I am using=C2=A0 Meta dynamic using Path collective varia= bles .I would=C2=A0 like to know how to set=C2=A0=C2=A0lowe= rBoundary=C2=A0upperBoundary=C2=A0 and=C2=A0width 1.0
It would be highly <= /b>appreciable=C2=A0if someone suggest the method of assigning values
With High Regards
S.VIDHYA SANKAR
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charset="UTF-8" Respected NAMD users, I got this error after implementing the namd command in power shell for md simulation: Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str LINE=*set nat ?NATC* FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str LINE=*set nat ?NATC* Kindly suggest a solution. -- *Regards,Dr.Anupama Tiwari* --000000000000b0f5da05c7f32730 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Respected NAMD users,

I got this error = after implementing the namd command in power shell for md simulation:

Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETE= RS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_wate= r_ions.str
LINE=3D*set nat ?NATC*
FATAL ERROR: UNKNOWN PARAMETER IN C= HARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*
<= /div>

Kindly suggest a solution.
--
<= span style=3D"color:rgb(102,51,255);background-color:rgb(255,255,255)">Rega= rds,
Dr.Anupama Tiw= ari

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boundary="=_117388c3-1d4f-48e5-b118-aa1986f0d802" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC73 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: namd-I: Request for help in error fixing Thread-Index: uVmZRV7FZaMV5knMXBn7fe2Qu3llZQ== X-CLX-Response: 1TFkXGx0cEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxsTHBEKQ1kXBx0eEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF2JbR0ccXVhNTx16X0JufEFlcktmfkJZZUJEf05LXB5GEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NnU2F9EQpNXBcZGRsRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYgVoQ0BMWkBFck4RCkNaFxMeBBsSHgQbHRwEGx sbEQpCXhcbEQpEXhcYEQpCXBcbEQpCSxd6Hm1bS3xHX2IFehEKQkkXaF96YUYBYkBBT3kRCkJFF 2EdHmZrckFSGRl4EQpCThdoX3phRgFiQEFPeREKQkwXbRNBQVpBREMTfXgRCkJsF2FkGWddQhlF fGt4EQpCQBdofGFNX2hra2ZYThEKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF2ZpZ1Bba0JiSUx yEQpZSxcHGREKcGcXYxpjR0F/YUZ4GXwQGRoRCnBoF2IFZEtDYmRveUgfEBkaEQpwaBdpYhkYHE VsYRseHxAZGhEKcGgXaFlBQlttf2xsb2QQGRoRCnBoF2JnSGdLbm9MHVpQEBkaEQpwaBdlQUhaa XJTeWx5QhAZGhEKcH0XY3N7TQVdHQF4QXAQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwfRdpGmVO XEgTYEd5RhAZGhEKcH8Xb0RhUBITfxscEn4QBxsfEQpwXxdiGBoYH3hHTHt7exAbGxgRCnBsF29 gf215TEFEa05OEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: Hqmm6wrge7PuhDVkOXaLThsOhnUdav4l X-Proofpoint-ORIG-GUID: Hqmm6wrge7PuhDVkOXaLThsOhnUdav4l MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 adultscore=0 priorityscore=0 lowpriorityscore=0 phishscore=0 clxscore=176 malwarescore=0 bulkscore=0 mlxlogscore=786 impostorscore=0 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107250109 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_117388c3-1d4f-48e5-b118-aa1986f0d802 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear friend,=20 Use the file "toppar_water_ions_namd.str".=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!rCftT8jHBHCpw_o7BB1VpTDHtZ6tTalz0zN-Rmd0y-yw6GTZRVzN_Yms= QnHwMu0PpQ$ ]=20 From: "Dr. Anupama Tiwari" =20 To: "namd-l" =20 Sent: Sunday, July 25, 2021 6:37:10 PM=20 Subject: namd-l: namd-I: Request for help in error fixing=20 Respected NAMD users,=20 I got this error after implementing the namd command in power shell for md = simulation:=20 Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS=20 FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions= .str=20 LINE=3D*set nat ?NATC*=20 FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions= .str=20 LINE=3D*set nat ?NATC*=20 Kindly suggest a solution.=20 --=20 Regards,=20 Dr.Anupama Tiwari=20 --=_117388c3-1d4f-48e5-b118-aa1986f0d802 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear friend,
Use the file "toppar= _water_ions_namd.str".

<= div dir=3D"ltr">
---
,Best
<= /div>
<= div dir=3D"ltr">
Ashkan Shekaari
PhD Candidate in= Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran<= a href=3D"mailto:shekaari@email.kntu.ac.ir" rel=3D"nofollow noopener norefe= rrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noo= pener noreferrer" style=3D"color:rgb( 17 , 85 , 204 )" target=3D"_blank">
<= /div>


From: "Dr. Anupama Tiwari" <anoopama.ti= wari@gmail.com>
To: "namd-l" <namd-l@ks.uiuc.edu>
= Sent: Sunday, July 25, 2021 6:37:10 PM
Subject: namd-l: namd-= I: Request for help in error fixing

Respected NAMD users,
I got = this error after implementing the namd command in power shell for md simula= tion:

Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETE= RS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_wate= r_ions.str
LINE=3D*set nat ?NATC*
FATAL ERROR: UNKNOWN PARAMETER IN C= HARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*
<= /div>

Kindly suggest a solution.
--
Regards,
Dr.Anup= ama Tiwari

<= /div>= --=_117388c3-1d4f-48e5-b118-aa1986f0d802-- From owner-namd-l@halifax.ks.uiuc.edu Sun Jul 25 14:13:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16PJDaS0026020; Sun, 25 Jul 2021 14:13:36 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16PJDZLJ026019; Sun, 25 Jul 2021 14:13:35 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16PJDZZm026015; Sun, 25 Jul 2021 14:13:35 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16PJDZU0026014; Sun, 25 Jul 2021 14:13:35 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16PJDLoO026006 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sun, 25 Jul 2021 14:13:22 -0500 (CDT) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16PJ4XrF014755 for ; Sun, 25 Jul 2021 19:13:21 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=hosseinizeynab93@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-il1-f181.google.com (mail-il1-f181.google.com [209.85.166.181]) by mx0b-00007101.pphosted.com with ESMTP id 3a090bqpus-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Sun, 25 Jul 2021 19:13:21 +0000 Received: by mail-il1-f181.google.com with SMTP id z3so6779637ile.12 for ; Sun, 25 Jul 2021 12:13:21 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=Eijd3wwtC+yVA8OfIAVyFeb8e8dtUFXfqgj2YAU2pxY=; b=KW5+mIfI+ERefyxrfiPvU2O9HauHkRojfOANiDWSS6JaFEI6aGvJXDFltEmvctcunV DV4jnOW7EWjD8hr/fpWlyYPVDY7Aw5n88FZAOMWb+zwGH05zgCe6+Qv3GoQY2mziwiGT iK5xChUPhjAY0WjRp3xwOAEWT7LfpHgzqIdkrM4cw7+3df43wBWqAbEHsDxBi8cFUk6p Y8psFY6NRtVENjkzBu4+Nagz9qA9TTf3nPLko1LZd6uSXjGdM1dYK1UYLEZUXjJ8h6Ia VKmiDylq/A7WQ95J9I7y3C7j2Rg23CuQoGldlGlc8HDOGtH996WlzxPVWaeio2jXVE1a o0Ug== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=Eijd3wwtC+yVA8OfIAVyFeb8e8dtUFXfqgj2YAU2pxY=; b=LQ2JRZqBhhQFGvnlskJPXKTjESkQgbCPxLm5A58onDuDIsxkxdhL/aO6ljIJBGpg04 KM67c9MHIQ0i43Hyn1XsOD4xffYmCIktGRRr4mpY8udIDr4F0+uBttsrZmuxExOV+jbY 3HMaFw0lbMRrUnF8YIB/GO7pHY/UwyymmZNk0l3Q4pKzRVhF/I9CaUjgJXEh7EVqqLas nimRPCVmyn1zfiZ7mBZhEVyAhohtMayA+9EJkrCFSZFZpqCSBH54L3K+sWfhsKHfbMGs ZzgBqNi1RxkjL5ax6NXg7qOTmKGpU1Ro93lAuEsZhbejPr5368CG5YmtgrNVXFbSNyVj WuBA== X-Gm-Message-State: AOAM531rwfh69L9t5Z/ue0Hf1sIYa0qRCWcCAF0mQBdknUXnsGmcvH8n 4kBca+1IuT89HTnJPjB2uycPTrEe66iKiwlIWO/ki8uNqMfCRQ== X-Google-Smtp-Source: ABdhPJwdj687TR5HII1R3QROoABV8XVW5JqQePFOF18uHwLmOltjkycqy6OaHO3x6Le083QpT5EE3C8Yo9MlVh5iwp0= X-Received: by 2002:a05:6e02:16c7:: with SMTP id 7mr10969185ilx.269.1627240400544; Sun, 25 Jul 2021 12:13:20 -0700 (PDT) From: zeynab hosseini Date: Sun, 25 Jul 2021 15:07:42 -0400 Message-ID: Subject: namd-l: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? To: NAMD list Content-Type: multipart/alternative; boundary="00000000000009e97e05c7f76e22" X-Proofpoint-ORIG-GUID: jaIuAuh1tqtOgJBzkLCmZxu6rawkRnOE X-Proofpoint-GUID: jaIuAuh1tqtOgJBzkLCmZxu6rawkRnOE X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIYEQpMehcZHhMRCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHGR8aEQpDWRcHGxgZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwYcR4bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0BLY19rX0IbXlteZU1gaFBBZmlHcFJfHFhLXUF4RGVvEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NnG1JZEQpNXBcbHhkRCkxaF2xpa01NEQpMRhdva2t ra2sRCkJPF21tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBBsSGxEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdvfE8bb15FX3IYGBEKQk4XY1Nja 3sTWH4aX14RCkJMF2h6e2BucFJzcFpfEQpCbBdvUAV/T2FmGU9FchEKQkAXZh1cG2Z7WnxceUAR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdmGkhrTGteHRhOcxEKWUsXEx4dEhEKcGg Xa2NMQURobhhIf1wQGRoRCnBoF21CXx9MfWN5HXJhEBkaEQpwaBduZx5ZcBMaHEBoRhAZGhEKcG gXaxh8HR9dGnpwBVIQGRoRCnBoF2taGhNEWkRFHUhwEBkaEQpwfRdlQWFpbXJaY3xwbhAZGhEKc H0XbHNjG2ZefRJjQHAQGRoRCnB/F2RtE3x9c2B7UE8ZEB4SEQpwbBdsUh1baWZsXnJIYRAZGhEK cEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 suspectscore=0 priorityscore=349 adultscore=0 mlxscore=0 spamscore=0 lowpriorityscore=0 clxscore=182 mlxlogscore=999 malwarescore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107250136 domainage_hfrom=9478 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --00000000000009e97e05c7f76e22 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear all, I have the intention to perform molecular dynamics (MD) simulation of carbon nanotubes (CNT) using the Drude polarizable force field implemented in NAMD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CNT in= puts for NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation (using non-polarizable FF) for this system. But as soon as I=E2=80=8C use t= hese inputs (.pdb & .psf files) to produce Drude-Prepper inputs for MD simulation of polarizable force field, I=E2=80=8C receive a message mention= ing CHARMM was terminated abnormally with the following error. It seems that the residue TUBE is not recognized. My question is how it is recognized before (when performing MD with non-polarizable force field), but when it comes to polarizable FF the TUBE residue is not recognized? CHARMM was terminated abnormally. Please check the output or report this failure to the CHARMM-GUI developers. Output Excerpt from step2_drude.out: Comparing "NONE" and "CNEU". IF test evaluated as false. Skipping command CHARMM> if @cterpatch .eq. CT1 if @cname .eq. GLY set cterpatch CT1G Parameter: CTERPATCH -> "NONE" Parameter: CNAME -> "TUBE" Comparing "NONE" and "CT1". IF test evaluated as false. Skipping command CHARMM> if @cterpatch .eq. CT2 if @cname .eq. GLY set cterpatch CT2G Parameter: CTERPATCH -> "NONE" Parameter: CNAME -> "TUBE" Comparing "NONE" and "CT2". IF test evaluated as false. Skipping command CHARMM> CHARMM> set gene =3D 0 Parameter: GENE <- "0" CHARMM> if @type eq protein then Parameter: TYPE -> "ELSE" Comparing "ELSE" and "PROTEIN". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if @type eq rna then !UMB: explicitly for rna Parameter: TYPE -> "ELSE" Comparing "ELSE" and "RNA". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if @type eq dna then !UMB: explicitly for dna Parameter: TYPE -> "ELSE" Comparing "ELSE" and "DNA". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if @type eq carb then Parameter: TYPE -> "ELSE" Comparing "ELSE" and "CARB". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if gene .eq. 0 then Comparing "0" and "0". IF test evaluated as true. Performing command CHARMM> ! default generate if not protein or water CHARMM> generate @segname first none last none setup warn drude dmass 0.4 ! show Parameter: SEGNAME -> "NM" Drude polarizability will be setup for SEGID: NM mass of Drudes particles =3D 0.4000 ***** ERROR in GENIC ***** Residue 'TUBE ' was not found. /---------\ / \ / \ / \ ! XXXX XXXX ! ! XXXX XXXX ! ! XXX XXX ! ! X ! --\ XXX /-- ! ! XXX ! ! ! ! ! ! ! I I I I I ! ! I I I I ! \ / -- -- \---/ XXX XXX XXXX XXXX XXXXX XXXXX XXX XXX XXX XXX XXXXX XXX XXX XXX XXX XXX XXX XXXXX XXXXX XXXX XXXX XXX XXX Execution terminated due to the detection of a fatal error. ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL 1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 2.11 SECONDS CPU TIME: 2.11 SECONDS All the Best, Zeynab --00000000000009e97e05c7f76e22 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear all,

I have the intention to perform molecular dynamics = (MD) simulation of carbon nanotubes (CNT) using the Drude polarizable force= field implemented in NAMD. I=E2=80=8Cnitially, I used CHARMM-GUI to produc= e a solvated CNT inputs for NAMD using Nanomaterial Modeler in CHARMM-GUI. = I can run the MD simulation (using non-polarizable FF) for this system. But= as soon as I=E2=80=8C use these inputs (.pdb & .psf files) to produce = Drude-Prepper inputs for MD simulation of polarizable force field, I=E2=80= =8C receive a message mentioning CHARMM was terminated abnormally with the = following error. It seems that the residue TUBE is not recognized. My quest= ion is how it is recognized before (when performing MD with non-polarizable= force field), but when it comes to polarizable FF the TUBE residue is not = recognized?

CHARMM was te= rminated abnormally.=C2=A0
Please check the output or=C2=A0report=C2=A0this failure to the CHARMM-GUI developer= s.
Output Excerpt from=C2=A0s= tep2_drude.out:
 Comp=
aring "NONE" and "CNEU".
 IF test evaluated as false.  Skipping command
=20=20
 CHARMM>       if @cterpatch .eq. CT1  if @cname .eq. GLY set cterpatch =
CT1G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT1".
 IF test evaluated as false.  Skipping command
=20=20
 CHARMM>       if @cterpatch .eq. CT2  if @cname .eq. GLY set cterpatch =
CT2G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT2".
 IF test evaluated as false.  Skipping command
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       set gene =3D 0
 Parameter: GENE <- "0"
=20=20
 CHARMM>       if @type eq protein then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "PROTEIN".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if @type eq rna then  !UMB: explicitly for rna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "RNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if @type eq dna then     !UMB: explicitly for dna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "DNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if @type eq carb then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "CARB".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if gene .eq. 0 then
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
=20=20
 CHARMM>          ! default generate if not protein or water
=20=20
 CHARMM>          generate @segname first none last none setup warn drud=
e dmass 0.4 ! show
 Parameter: SEGNAME -> "NM"
 Drude polarizability will be setup for SEGID: NM      mass of Drudes parti=
cles =3D    0.4000

 ***** ERROR in GENIC ***** Residue 'TUBE  ' was not found.


=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
                            /---------\=20=20=20=20=20=20=20=20=20=20=20
                           /           \=20=20=20=20=20=20=20=20=20=20
                          /             \=20=20=20=20=20=20=20=20=20
                         /               \=20=20=20=20=20=20=20=20
                         !  XXXX   XXXX  !=20=20=20=20=20=20=20=20
                         !  XXXX   XXXX  !=20=20=20=20=20=20=20=20
                         !  XXX     XXX  !=20=20=20=20=20=20=20=20
                         !       X       !=20=20=20=20=20=20=20=20
                          --\   XXX   /--=20=20=20=20=20=20=20=20=20
                           ! !  XXX  ! !=20=20=20=20=20=20=20=20=20=20
                           ! !       ! !=20=20=20=20=20=20=20=20=20=20
                           ! I I I I I !=20=20=20=20=20=20=20=20=20=20
                           !  I I I I  !=20=20=20=20=20=20=20=20=20=20
                            \         /=20=20=20=20=20=20=20=20=20=20=20
                             --     --=20=20=20=20=20=20=20=20=20=20=20=20
                               \---/=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20
                        XXX             XXX=20=20=20=20=20=20=20
                       XXXX             XXXX=20=20=20=20=20=20
                       XXXXX           XXXXX=20=20=20=20=20=20
                          XXX         XXX=20=20=20=20=20=20=20=20=20
                            XXX     XXX=20=20=20=20=20=20=20=20=20=20=20
                               XXXXX=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20
                              XXX XXX=20=20=20=20=20=20=20=20=20=20=20=20=20
                            XXX     XXX=20=20=20=20=20=20=20=20=20=20=20
                          XXX         XXX=20=20=20=20=20=20=20=20=20
                       XXXXX           XXXXX=20=20=20=20=20=20
                       XXXX             XXXX=20=20=20=20=20=20
                        XXX             XXX=20=20=20=20=20=20=20
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
 Execution terminated due to the detection of a fatal error.

                    ABNORMAL TERMINATION
                    MOST SEVERE WARNING WAS AT LEVEL  1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.11  SECONDS=20
                         CPU TIME:     2.11  SECONDS 


All the Best,
Zeynab
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boundary="000000000000e2c96205c8066e17" X-Proofpoint-ORIG-GUID: P3SzM_tCs5gT_DRc6r2-bXMCcka64bCH X-CLX-Shades: MLX X-Proofpoint-GUID: P3SzM_tCs5gT_DRc6r2-bXMCcka64bCH X-CLX-Response: 1TFkXGRgeEQpMehcZGhwRCllEF3piTn4BS0JQSGcfEQpYWBdgXGdaHWlhZHt eGREKeE4XY1Nja3sTWH4aX14RCnlMF21NYkNkQkYSWnxaEQpDSBcHGBkcEQpDWRcHHBIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwfcRsGGxkadwYSEwYbGhpCGxoGGgYbGhoGGRpxGxAadwYaBhoGG gYHHBoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04Xehl5UGd1XmlZH01+ dW54SRxYGAdIcmdpSUFLHB5IaWIRClhcFx8EGgQYGRkFGxoEGxoaBB4SBBgYEBseGh8aEQpeWRd zZGxNQREKTVwXHhMfEQpMWhd4aU1raxEKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2 sRCkJPF2t8WVBYGWleGGZaEQpDWhcYGhMEEh8EGBoSBBsdGxEKQl4XGxEKREkXGxEKQlwXGxEKX k4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdiGXNtGBNyZh5zYhEKQk4X Y1Nja3sTWH4aX14RCkJMF2BcZ1odaWFke14ZEQpCbBdvHkdeRx4YbhJgXxEKQkAXaHxhTV9oa2t mWE4RCkJYF2dzZXNAbmFhTF1iEQpaWBceEQp5QxdmaWdQW2tCYklMchEKWUsXEx4dExEKcGcXYx pjR0F/YUZ4GXwQHhIRCnBoF2xpYGlpG3hPTEdGEBkaEQpwaBdmTWQaTUJtWx9NZRAZGhEKcGgXZ B9PRhN6bxtibGQQHhIRCnBoF2JmWFJjGkZSQUh7EBkaEQpwaBduWwFScEx4GW9hQRAZGhEKcH0X Y3N7TQVdHQF4QXAQGRoRCnBnF2lDblABWXNHAR5TEB4SEQpwfRdpGmVOXEgTYEd5RhAZGhEKcH8 Xb0RhUBITfxscEn4QHRMRCnBfF2IYGhgfeEdMe3t7EBsbHhEKcGwXb1MYWRgSUnhAfxMQGRoRCm 1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 phishscore=0 lowpriorityscore=0 suspectscore=0 mlxscore=0 spamscore=0 adultscore=0 impostorscore=0 priorityscore=306 clxscore=324 mlxlogscore=846 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260073 domainage_hfrom=9479 X-Spam-Score: 0 X-Spam-OrigSender: anoopama.tiwari@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Anupama Tiwari" --000000000000e2c96205c8066e17 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Ashkan, I am still getting the same error. On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari wrote: > Dear friend, > Use the file "toppar_water_ions_namd.str". > > --- > ,Best > Ashkan Shekaari > PhD Candidate in Solid State Physics > Department of Physics > K. N. Toosi University of Technology, Tehran, 15875-4416, Iran > > > > ------------------------------ > *From: *"Dr. Anupama Tiwari" > *To: *"namd-l" > *Sent: *Sunday, July 25, 2021 6:37:10 PM > *Subject: *namd-l: namd-I: Request for help in error fixing > > Respected NAMD users, > I got this error after implementing the namd command in power shell for md > simulation: > > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE > ./toppar_water_ions.str > LINE=3D*set nat ?NATC* > FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE > ./toppar_water_ions.str > LINE=3D*set nat ?NATC* > > Kindly suggest a solution. > -- > > > *Regards,Dr.Anupama Tiwari* > > --=20 *Regards,Dr.Anupama TiwariAssociate Prof.Acropolis Institute Of Technology & Research, Indore* --000000000000e2c96205c8066e17 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Ashkan,

I am still getting the same = error.

On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari <shekaari@email.kntu.ac.ir> wrote:<= br>
Dear friend,
Use the file "toppar_water_ions_namd.str&= quot;.

<= div dir=3D"ltr">
---
,Best
<= /div>
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology,=C2=A0Tehran,=C2=A015875-4416,= Iran
<= /div>


From: <= /b>"Dr. Anupama Tiwari" <anoopama.tiwari@gmail.com>
To: &= quot;namd-l" <namd-l@ks.uiuc.edu>
Sent: Sunday, July 25, 2021 6:37:10= PM
Subject: namd-l: namd-I: Request for help in error fixing
=

Respected NAMD users,
I = got this error after implementing the namd command in power shell for md si= mulation:

Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARA= METERS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_= water_ions.str
LINE=3D*set nat ?NATC*
FATAL ERROR: UNKNOWN PARAMETER = IN CHARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*<= br>

Kindly suggest a solution.
--
Regards,
Dr.Anupama Tiwari



--
Regards,<= /span>
Dr= .Anupama Tiwari
Associate Prof.
Acropolis Institute Of Technology & Researc= h, Indore
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boundary="0000000000008352c505c806a70a" X-CLX-Shades: MLX X-Proofpoint-GUID: XJULlFJ5SNr4yaiz_BKIXmLFu77At1u1 X-Proofpoint-ORIG-GUID: XJULlFJ5SNr4yaiz_BKIXmLFu77At1u1 X-CLX-Response: 1TFkXGxsfEQpMehcZGx8RCllEF3poR1wfbxtYXF5jEQpYWBdoWXhyHl5raGE TehEKeE4XY1Nja3sTWH4aX14RCnlMF2lZAW1lHW1wSWxaEQpDSBcHGBocEQpDWRcHHBIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYTH3ESEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF3Jgf2ZGbGAfeWRYHlNLQ1B1aGFjckdmbF8dHWteG18bEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NkbFxwEQpNXBcZGxsRCkxaF3hpTWtrEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx 0ZEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF29PeEMdZl5NY0JOEQpCThdjU2NrexNYfhpfXhEKQkwXaFl4ch5ea2hhE3oRCkJsF2Ff QEZGf11LaGRGEQpCQBdofGFNX2hra2ZYThEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF2ZpZ1B ba0JiSUxyEQpZSxcTHh0TEQpwZxdjGmNHQX9hRngZfBAZGhEKcGgXa2JCbm9Ff30ZfloQGxIRCn BoF2QfT0YTem8bYmxkEBkaEQpwaBduaHtpaHBHSEheZxAZGhEKcGgXYRJfXB0ZfX5eX1AQGRoRC nBoF2BGXVlLaU8cWExdEBkaEQpwfRdkenBLUkxITnNaehAZGhEKcH0XaWFfZFlhHEtjUloQGxIR CnBnF2lDblABWXNHAR5TEBkaEQpwfRdgYBpCchJ4bxpfWxAbEhEKcH8XZRl5Zl5HaRtkT3MQHhI RCnBfF2keR2lsYEgBZnhMEBkaEQpwfxdhZm9bGmdkQkgdWxAbHhoRCnBfF2NiElBIY3gffEJ9EB sbGhEKcGwXZH9oaWFTYmhCG38QGRoRCm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 impostorscore=0 mlxscore=0 spamscore=0 adultscore=0 malwarescore=0 clxscore=115 mlxlogscore=873 bulkscore=0 suspectscore=0 priorityscore=315 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260075 domainage_hfrom=9479 X-Spam-Score: 0 X-Spam-OrigSender: kushalrajroyfc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kushal Raj Roy --0000000000008352c505c806a70a Content-Type: text/plain; charset="UTF-8" Hello Professor, Please follow the given link. This information might help you. https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0582.html On Mon, 26 Jul, 2021, 7:09 pm Dr. Anupama Tiwari, wrote: > Hi Ashkan, > > I am still getting the same error. > > On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari > wrote: > >> Dear friend, >> Use the file "toppar_water_ions_namd.str". >> >> --- >> ,Best >> Ashkan Shekaari >> PhD Candidate in Solid State Physics >> Department of Physics >> K. N. Toosi University of Technology, Tehran, 15875-4416, Iran >> >> >> >> ------------------------------ >> *From: *"Dr. Anupama Tiwari" >> *To: *"namd-l" >> *Sent: *Sunday, July 25, 2021 6:37:10 PM >> *Subject: *namd-l: namd-I: Request for help in error fixing >> >> Respected NAMD users, >> I got this error after implementing the namd command in power shell for >> md simulation: >> >> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS >> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE >> ./toppar_water_ions.str >> LINE=*set nat ?NATC* >> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE >> ./toppar_water_ions.str >> LINE=*set nat ?NATC* >> >> Kindly suggest a solution. >> -- >> >> >> *Regards,Dr.Anupama Tiwari* >> >> > > -- > > > > *Regards,Dr.Anupama TiwariAssociate Prof.Acropolis Institute Of Technology > & Research, Indore* > --0000000000008352c505c806a70a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Professor,=C2=A0=C2=A0
=C2=A0
Please follow the given link. This information might hel= p you.





On Mon, 26 Jul, 2021, 7:09 pm Dr. Anupama Tiwari, <<= a href=3D"mailto:anoopama.tiwari@gmail.com" rel=3D"noreferrer noreferrer" t= arget=3D"_blank">anoopama.tiwari@gmail.com> wrote:
Hi Ashkan,

I am = still getting the same error.

On Sun, Jul 25, 2021 at 8:36 PM Ashkan S= hekaari <shekaari@email.kntu.ac.ir> = wrote:
Dear friend,
Use the file "toppar_water_ions_nam= d.str".

---,Best
=
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology,=C2=A0Tehran,=C2=A015875-44= 16, Iran
<= /div>


From: "Dr. Anupam= a Tiwari" <anoopama.tiwari@gmail.com>
To: "namd-l" <
namd-l@ks= .uiuc.edu>
Sent: Sunday, July 25, 2021 6:37:10 PM
Su= bject: namd-l: namd-I: Request for help in error fixing
<= br>
Respected NAMD users,
I got this err= or after implementing the namd command in power shell for md simulation:
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FA= TAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.s= tr
LINE=3D*set nat ?NATC*
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PA= RAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*

Kindly suggest a solution.
--
Regards,
Dr.Anupama Tiwari



= --
Regards,
Dr.Anupama Tiwari
Associate Prof.Acropolis = Institute Of Technology & Research, Indore

--0000000000008352c505c806a70a-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jul 26 08:23:48 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDNmJp015043; Mon, 26 Jul 2021 08:23:48 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QDNmxx015042; Mon, 26 Jul 2021 08:23:48 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDNlVV015031; Mon, 26 Jul 2021 08:23:47 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QDNlxn015030; Mon, 26 Jul 2021 08:23:47 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDNcmN014932 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 26 Jul 2021 08:23:38 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16QDF7T2000472 for ; Mon, 26 Jul 2021 13:23:37 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0a-00007101.pphosted.com with ESMTP id 3a09c03525-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 26 Jul 2021 13:23:37 +0000 Received: from [IPv6:2a02:810c:300:6724:d00:ff07:a4e8:e5b2] ([IPv6:2a02:810c:300:6724:d00:ff07:a4e8:e5b2]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 16QDNSv4113506 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 26 Jul 2021 15:23:32 +0200 Subject: Re: namd-l: namd-I: Request for help in error fixing To: namd-l@ks.uiuc.edu, "Dr. Anupama Tiwari" References: <1925807622.5385710.1627225587869.JavaMail.zimbra@email.kntu.ac.ir> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <313f1668-f8b6-30a9-55e8-8d7696a33ed8@physik.uni-kl.de> Date: Mon, 26 Jul 2021 15:23:30 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------DBAB5A84271BB45405EA0953" Content-Language: de-DE X-Spam-Status: No, hits=2.806, tests=DEAR_FRIEND=2.604,HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-1.091,URI_DOTEDU=1.291 X-Spam-Score: ** (2.806) X-Spam-Flag: NO X-CLX-Response: 1TFkXGxIZEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxgSGxEKQ1kXBxwTEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwZcR4YEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF00HRXJDcGBdZ29dHW9PZUtEcEJmHWVmQ3pmHR5nYBlfEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXc2RsXBoRCk1cFxsSEhEKTFoXfGFNQWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdsX2xmX3BMSxxSSxEKQ1oXGxkbBBgeHAQbGBoEGBgaEQ pCXhcbEQpEXhcYEQpCRRdsHVhyRR8cR0kFbhEKQk4XZBpJbnp6eBpkfVwRCkJMF2BgG1IZHRgaU nIFEQpCbBdma2JkGFlibUh+bBEKQkAXaHxhTV9oa2tmWE4RCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBceEQp5QxdmaWdQW2tCYklMchEKcGcXYxpjR0F/YUZ4GXwQGRoRCnBoF2kfGWwBBXliYgE FEBkaEQpwaBdvXkNHE2VteRxYQxAZGhEKcGgXbFASa0B6RHlvHVoQGRoRCnBoF2JZeXgbb0Rsf0 9ZEBkaEQpwaBdhaGReGR4beXNARBAZGhEKcH0XYH5Db1NEG2tHTl4QGRoRCnB9F2NlaVgYQl9ZT R1IEBkaEQpwfRdpYV9kWWEcS2NSWhAbEhEKcGcXaUNuUAFZc0cBHlMQGRoRCnB9F2ZoUBMYT31p c3BPEBkaEQpwZxdnTFISb19QX2ZbaBAZGhEKcH0XYGAaQnISeG8aX1sQGxIRCnB/F2UZeWZeR2k bZE9zEBkaEQpwXxdpHkdpbGBIAWZ4TBAZGhEKcH8XZWZEAR5IRmR8WhsQGxgaEQpwXxdiGx9JcH llZGJjBRAZGhEKcH8XYWZvWxpnZEJIHVsQGx4bEQpwXxdjYhJQSGN4H3xCfRAbGhsRCnBsF3ofe HlveExDX3BEEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-ORIG-GUID: g-oXiZJwMEw7EeOanZhL7OLiPL74MJ3u X-Proofpoint-GUID: g-oXiZJwMEw7EeOanZhL7OLiPL74MJ3u X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 priorityscore=0 clxscore=183 impostorscore=0 phishscore=0 malwarescore=0 bulkscore=0 spamscore=0 mlxlogscore=998 lowpriorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260075 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------DBAB5A84271BB45405EA0953 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi, =C2=A0=C2=A0=C2=A0 this has been discussed before=20 https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/0236.ht= ml =C2=A0=C2=A0=C2=A0 But those lines should **NOT** appear in the "_namd.str= " file..=20 (Just checked again the file on=20 https://urldefense.com/v3/__http://mackerell.umaryland.edu/*kenno/cgenff/pr= ogram.php*namd__;fiM!!DZ3fjg!v4-bY5vVDQ9TcUDk0ICNsaCg_8V-JD_Vm5QTFEDqlSpu70= ItWxO1Zqub5ZQXWa7RIA$ ) Be sure to use the correct file (and remove the other one!) Cheers Ren=C3=A9 On 7/26/2021 3:07 PM, Dr. Anupama Tiwari wrote: > Hi Ashkan, > > I am still getting the same error. > > On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari=20 > > wrote: > > Dear friend, > Use the file "toppar_water_ions_namd.str". > > --- > ,Best > Ashkan Shekaari > PhD Candidate in Solid State Physics > Department of Physics > K. N. Toosi University of Technology,=C2=A0Tehran,=C2=A015875-4416, > Iran > > ---------------------------------------------------------------------= --- > *From: *"Dr. Anupama Tiwari" > > *To: *"namd-l" > > *Sent: *Sunday, July 25, 2021 6:37:10 PM > *Subject: *namd-l: namd-I: Request for help in error fixing > > Respected NAMD users, > I got this error after implementing the namd command in power > shell for md simulation: > > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE > ./toppar_water_ions.str > LINE=3D*set nat ?NATC* > FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE > ./toppar_water_ions.str > LINE=3D*set nat ?NATC* > > Kindly suggest a solution. > --=20 > *Regards, > Dr.Anupama Tiwari > * > > > > --=20 > *Regards, > Dr.Anupama Tiwari > Associate Prof. > Acropolis Institute Of Technology & Research, Indore* --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------DBAB5A84271BB45405EA0953 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable

Hi,

=C2=A0=C2=A0=C2=A0 this has been discussed before https://www.ks.uiuc.edu/Rese= arch/namd/mailing_list/namd-l.2014-2015/0236.html

=C2=A0=C2=A0=C2=A0 But those lines should **NOT** appear in the "_na= md.str" file.. (Just checked again the file on htt= p://mackerell.umaryland.edu/~kenno/cgenff/program.php#namd)

Be sure to use the correct file (and remove the other one!)

Cheers

Ren=C3=A9

On 7/26/2021 3:07 PM, Dr. Anupama Tiwari wrote:
Hi Ashkan,

I am still getting the same error.

On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari <shekaari@email.kntu.ac.ir> wrote:
Dear friend,
Use the file "toppar_water_ions_namd.str".

---
,Best
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology,=C2=A0Tehran,=C2=A015875-4416, Iran


From: "Dr. Anupama Tiwari" <anoopama.tiwar= i@gmail.com>
To: "namd-l" <namd-l@ks.uiuc.edu>
Sent: Sunday, July 25, 2021 6:37:10 PM
Subject: namd-l: namd-I: Request for help in error fixing

Respected NAMD users,
I got this error after implementing the namd command in power shell for md simulation:

Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*

Kindly suggest a solution.
--
Regards,
Dr.Anupama Tiwari



--
Regards,
Dr.Anupama Tiwari
Associate Prof.
Acropolis Institute Of Technology & Research, Indore

--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--------------DBAB5A84271BB45405EA0953-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jul 26 08:29:54 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDTsIv018376; Mon, 26 Jul 2021 08:29:54 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QDTs2d018375; Mon, 26 Jul 2021 08:29:54 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDTrJZ018370; Mon, 26 Jul 2021 08:29:53 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QDTr9L018369; Mon, 26 Jul 2021 08:29:53 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDTiNA018361 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Dear users, I am running simulation on my laptop. I have activated all 8 cores of processor but when I run the simulation it shows 1 core processor is in use. How to bring all 8 processors in use ? Please help for the same. Kindly reply to this mail. Regards, Mr. Ruturaj Warake --000000000000f5073f05c806be00 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear users,
I am running simulation on m= y laptop.=C2=A0
I have activated all 8 cores of proc= essor but when I run the simulation it shows 1 core processor is in use. Ho= w to bring all 8 processors in use ?
Please help for= the same.

Kindly reply = to this mail.

Regards,
Mr. Ruturaj Warake
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charset="UTF-8" Use +p8 while running namd namd2 +p8 input.conf On Mon, 26 Jul 2021, 19:00 Ruturaj warake, wrote: > Dear users, > I am running simulation on my laptop. > I have activated all 8 cores of processor but when I run the simulation it > shows 1 core processor is in use. How to bring all 8 processors in use ? > Please help for the same. > > Kindly reply to this mail. > > Regards, > Mr. Ruturaj Warake > --000000000000d9dcea05c806cdd3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Use +p8 while running namd

namd2 +p8 input.conf

On Mon, 26 Jul 2021, 19:00 Ruturaj= warake, <ruturajwarake47@g= mail.com> wrote:
Dear users,
I am running simulation on my laptop.= =C2=A0
I have activated all 8 cores of processor but= when I run the simulation it shows 1 core processor is in use. How to brin= g all 8 processors in use ?
Please help for the same= .

Kindly reply to this m= ail.

Regards,
Mr. Ruturaj Warake
--000000000000d9dcea05c806cdd3-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jul 26 08:34:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDYq70020631; Mon, 26 Jul 2021 08:34:52 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QDYqm3020629; Mon, 26 Jul 2021 08:34:52 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDYpb3020616; Mon, 26 Jul 2021 08:34:51 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QDYppF020615; Mon, 26 Jul 2021 08:34:51 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QDYiBG020530 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 26 Jul 2021 08:34:45 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16QDXK7O003746 for ; Mon, 26 Jul 2021 13:34:44 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3a097s3e4m-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 26 Jul 2021 13:34:44 +0000 Received: from [IPv6:2a02:810c:300:6724:d00:ff07:a4e8:e5b2] ([IPv6:2a02:810c:300:6724:d00:ff07:a4e8:e5b2]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 16QDYe8W120038 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 26 Jul 2021 15:34:40 +0200 Subject: Re: namd-l: Error in running simulation To: namd-l@ks.uiuc.edu, Ruturaj warake References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <43f73245-09de-56b1-01c5-d5e6b1ea26e4@physik.uni-kl.de> Date: Mon, 26 Jul 2021 15:34:43 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------A47D51F59678706B96249E0D" Content-Language: de-DE X-Spam-Status: No, hits=0.202, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-1.091,URI_DOTEDU=1.291 X-Spam-Score: (0.202) X-Spam-Flag: NO X-CLX-Shades: MLX X-Proofpoint-GUID: zyvOox0996UByycLVfYfrLpPDANdrQYf X-Proofpoint-ORIG-GUID: zyvOox0996UByycLVfYfrLpPDANdrQYf X-CLX-Response: 1TFkXGxMZEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBx0SEQpDWRcHGx8SEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0ZcR8ZEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF1BTXGVFUhoTExx/aFNTSWZ8THNMWGZaem5rZE5Ye3NMEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NkbBx6EQpNXBcbHxgRCkxaF2l4YU1BTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2xfbGZfcExLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGB oRCkJeFxsRCkReFxgRCkJFF2wdWHJFHxxHSQVuEQpCThdkGkluenp4GmR9XBEKQkwXYGAbUhkdG BpScgURCkJsF2ZrYmQYWWJtSH5sEQpCQBdlTEJkYWxgG29yYREKQlgXZ3Nlc0BuYWFMXWIRCk1e FxsRClpYFxgRCnlDF20fZ15wWWddG017EQpwZxdmZgFfZ05MQXtsfBAaEQpwaBdnf08SAVtHcAF jQhAZGhEKcGgXZV5QeX4bb3BvTB8QGhEKcGgXYkxtYk9IW29QThMQHB8RCnBoF2VCYWlFaGJ6QU tbEAcZGhEKcGgXZFB4YG9pekRIfhoQGhEKcH0XZGNHWkFwE3J4eU8QGhEKcH8XZRl5Zl5HaRtkT 3MQHBoRCnBfF2taWHJYYmNCaUVCEBoRCnBsF3ofeHlveExDX3BEEB4SEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 impostorscore=0 mlxscore=0 spamscore=0 adultscore=0 malwarescore=0 clxscore=193 mlxlogscore=999 bulkscore=0 suspectscore=0 priorityscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260076 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------A47D51F59678706B96249E0D Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi, pathtonamd/namd2 +p     with X number of Cores should work. Always take a look into the manual and READMEs provided before using a software! https://www.ks.uiuc.edu/Research/namd/2.14/ug/node100.html Regards René On 7/26/2021 3:29 PM, Ruturaj warake wrote: > Dear users, > I am running simulation on my laptop. > I have activated all 8 cores of processor but when I run the > simulation it shows 1 core processor is in use. How to bring all 8 > processors in use ? > Please help for the same. > > Kindly reply to this mail. > > Regards, > Mr. Ruturaj Warake -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------A47D51F59678706B96249E0D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi,

  pathtonamd/namd2 +p<procs> <configfile>

    with X number of Cores

should work.

Always take a look into the manual and READMEs provided before using a software!

https://www.ks.uiuc.edu/Research/namd/2.14/ug/node100.html

Regards

René

On 7/26/2021 3:29 PM, Ruturaj warake wrote:
Dear users,
I am running simulation on my laptop. 
I have activated all 8 cores of processor but when I run the simulation it shows 1 core processor is in use. How to bring all 8 processors in use ?
Please help for the same.

Kindly reply to this mail.

Regards,
Mr. Ruturaj Warake
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="000000000000e3185905c808293e" X-Proofpoint-ORIG-GUID: I9vqHFavLsCSggqqvNz5vcXwdmVmUixP X-Proofpoint-GUID: I9vqHFavLsCSggqqvNz5vcXwdmVmUixP X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRwRCkx6FxkaHBEKWUQXbWxhG0ZrHn9nAVwRClhYF2RlYksYXG0BHX8 SEQp4ThdjU2NrexNYfhpfXhEKeUwXbRJpYnJvSHJMHFgRCkNIFwcYEh0RCkNZFwcbHxIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxgdcRsGHx53BhsbEwYaBhoGHRoGGRpxGxAadwYaBgcbHxoGGgYHH BoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XYxNcW2JsS1xmWWl5TU1b W1xkUB9cSXJdTkd8R39DUnoRClhcFx8EGgQYGRkFGxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc2R if1gRCk1cFxseGhEKTFoXfGlNa2sRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQ pCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGAQbHRoRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF 2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZXBiGm9/GmQaH2cRCkJOF2NTY2t7E1h+ Gl9eEQpCTBdkZWJLGFxtAR1/EhEKQmwXYlBje2Zvf1gaGWMRCkJAF2VMQmRhbGAbb3JhEQpCWBd nc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXbR9nXnBZZ10bTXsRCllLFxMeHRMRCnBoF21+GU 9/XkYBaWBrEBkaEQpwaBdiehNSTwFBE3BJWRAZGhEKcGgXZk18SG0dW1lCQEIQGhEKcGgXZUJha UVoYnpBS1sQGhEKcGgXZmlCHEQeQFxSehkQGRoRCnBsF2JFUhhkUB1GYENOEAcbEhEKbX4XGxEK WE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 suspectscore=0 priorityscore=306 adultscore=0 mlxscore=0 spamscore=0 lowpriorityscore=0 clxscore=36 mlxlogscore=479 malwarescore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260087 domainage_hfrom=9479 X-Spam-Score: 0 X-Spam-OrigSender: ruturajwarake47@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ruturaj warake --000000000000e3185905c808293e Content-Type: text/plain; charset="UTF-8" Dear Users, Thanks for replying. One more thing, I used the command +p8. Still it's taking 180 seconds for equilibration and 195 seconds for production to run 5000 numsteps with 2 fs time step. While running NAMD, We need to run equilibration step and then production. Suppose if I want to run simulation for 100 ns then do I need to run equilibration for 5,00,00,000 steps and then again production for same steps ? What if I reduce the equilibration steps ? Please do help me out. Thanks and Regards Ruturaj Warake, Niper, Hyderabad, India On Mon, 26 Jul 2021, 19:00 Ruturaj warake, wrote: > Dear users, > I am running simulation on my laptop. > I have activated all 8 cores of processor but when I run the simulation it > shows 1 core processor is in use. How to bring all 8 processors in use ? > Please help for the same. > > Kindly reply to this mail. > > Regards, > Mr. Ruturaj Warake > --000000000000e3185905c808293e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Users,
Thanks for replying.

One more thing,
I used the command +p8. Still it's taking 180 seconds for equ= ilibration and 195 seconds for production to run 5000 numsteps with 2 fs ti= me step.

While running N= AMD,
We need to run equilibration step and then prod= uction.
Suppose if I want to run simulation for 100 = ns then do I need to run equilibration for 5,00,00,000 steps and then again= production for same steps ?

What if I reduce the equilibration steps ?
Plea= se do help me out.

Thank= s and=C2=A0Regards

Rutur= aj Warake,
Niper, Hyderabad,
= India=C2=A0


On Mon, 26 Jul 2021, 19:00 Rut= uraj warake, <ruturajwarake= 47@gmail.com> wrote:
Dear users,
I am running simulation on my lapto= p.=C2=A0
I have activated all 8 cores of processor b= ut when I run the simulation it shows 1 core processor is in use. How to br= ing all 8 processors in use ?
Please help for the sa= me.

Kindly reply to this= mail.

Regards,
Mr. Ruturaj Warake
--000000000000e3185905c808293e-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jul 26 10:31:46 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QFVkCb027350; Mon, 26 Jul 2021 10:31:46 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QFVknY027349; Mon, 26 Jul 2021 10:31:46 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QFVjx2027345; Mon, 26 Jul 2021 10:31:45 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QFVjAt027344; Mon, 26 Jul 2021 10:31:45 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QFVXSE027334 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 26 Jul 2021 10:31:34 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16QFJbRF032508 for ; Mon, 26 Jul 2021 15:31:33 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3a0t5hrp90-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 26 Jul 2021 15:31:32 +0000 Received: from [IPv6:2a02:810c:300:6724:d00:ff07:a4e8:e5b2] ([IPv6:2a02:810c:300:6724:d00:ff07:a4e8:e5b2]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 16QFVSrJ009584 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 26 Jul 2021 17:31:28 +0200 Subject: Re: namd-l: Error in running simulation To: namd-l@ks.uiuc.edu, Ruturaj warake References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <5f0df1fd-5229-eac5-d841-cc1dba08c138@physik.uni-kl.de> Date: Mon, 26 Jul 2021 17:31:31 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------4C069A0F34077926FA2E437D" Content-Language: de-DE X-Spam-Status: No, hits=-1.089, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-1.091 X-Spam-Score: (-1.089) X-Spam-Flag: NO X-CLX-Response: 1TFkXGBofEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxgTHREKQ1kXBxsfEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsSH3EdGhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdkXFxFem1Pc2RCYnBHSXVgbHVfWklmYEdSX2tOUAdJGBEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzZGJEXREKTVwXGRoYEQpMWhd8YU1BTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2xfbGZfcExLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGB oRCkJeFxsRCkReFxgRCkJFF2wdWHJFHxxHSQVuEQpCThdkGkluenp4GmR9XBEKQkwXYGAbUhkdG BpScgURCkJsF2ZrYmQYWWJtSH5sEQpCQBdlTEJkYWxgG29yYREKQlgXZ3Nlc0BuYWFMXWIRClpY FxgRCnlDF20fZ15wWWddG017EQpwZxdlU31rH05vf3gabhAZGhEKcGgXbX4ZT39eRgFpYGsQGhE KcGgXYnoTUk8BQRNwSVkQGhEKcGgXZUJhaUVoYnpBS1sQBx4SEQpwaBdmaUIcRB5AXFJ6GRAaEQ pwaBdvEkZrWXNaWllbcBAaEQpwZxdpb2hccmBaSXwcSBAaEQpwbBd6H3h5b3hMQ19wRBAZGhEKb X4XGhEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-GUID: NvvoPGeYNhHZmc_JF_upcLJmxuAdz-c2 X-Proofpoint-ORIG-GUID: NvvoPGeYNhHZmc_JF_upcLJmxuAdz-c2 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 adultscore=0 priorityscore=0 lowpriorityscore=0 phishscore=0 clxscore=205 malwarescore=0 bulkscore=0 mlxlogscore=999 impostorscore=0 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260088 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------4C069A0F34077926FA2E437D Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi your runtime heavily depends on the number of atoms in your system. What I strongly recommend is reducing your system size as much as possible (might require testing of different system but it depends if its worth the time) usage of a GPU if available or at least a cluster node with more than 8 cores (if available), Equilibration time does not depend on production runtime. Equilibration means you run such that the temperature/volume/pressure/energy/density have settled down and e.g. no major structural changes occur in your protein  (RMSD) and other quantities. All depending on the ensemble and your quantities of interest. Though depending on your system maybe 10-100ps are enough of equilibration, but maybe you even need a few ns. Kind regards René On 7/26/2021 5:10 PM, Ruturaj warake wrote: > Dear Users, > Thanks for replying. > > One more thing, > I used the command +p8. Still it's taking 180 seconds for > equilibration and 195 seconds for production to run 5000 numsteps with > 2 fs time step. > > While running NAMD, > We need to run equilibration step and then production. > Suppose if I want to run simulation for 100 ns then do I need to run > equilibration for 5,00,00,000 steps and then again production for same > steps ? > > What if I reduce the equilibration steps ? > Please do help me out. > > Thanks and Regards > > Ruturaj Warake, > Niper, Hyderabad, > India > > > On Mon, 26 Jul 2021, 19:00 Ruturaj warake, > wrote: > > Dear users, > I am running simulation on my laptop. > I have activated all 8 cores of processor but when I run the > simulation it shows 1 core processor is in use. How to bring all 8 > processors in use ? > Please help for the same. > > Kindly reply to this mail. > > Regards, > Mr. Ruturaj Warake > -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------4C069A0F34077926FA2E437D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi

your runtime heavily depends on the number of atoms in your system.

What I strongly recommend is reducing your system size as much as possible (might require testing of different system but it depends if its worth the time) usage of a GPU if available or at least a cluster node with more than 8 cores (if available),

Equilibration time does not depend on production runtime.

Equilibration means you run such that the temperature/volume/pressure/energy/density have settled down and e.g. no major structural changes occur in your protein  (RMSD) and other quantities. All depending on the ensemble and your quantities of interest.

Though depending on your system maybe 10-100ps are enough of equilibration, but maybe you even need a few ns.

Kind regards

René

On 7/26/2021 5:10 PM, Ruturaj warake wrote:
Dear Users,
Thanks for replying.

One more thing,
I used the command +p8. Still it's taking 180 seconds for equilibration and 195 seconds for production to run 5000 numsteps with 2 fs time step.

While running NAMD,
We need to run equilibration step and then production.
Suppose if I want to run simulation for 100 ns then do I need to run equilibration for 5,00,00,000 steps and then again production for same steps ?

What if I reduce the equilibration steps ?
Please do help me out.

Thanks and Regards

Ruturaj Warake,
Niper, Hyderabad,
India 


On Mon, 26 Jul 2021, 19:00 Ruturaj warake, <ruturajwarake47@gmail.com> wrote:
Dear users,
I am running simulation on my laptop. 
I have activated all 8 cores of processor but when I run the simulation it shows 1 core processor is in use. How to bring all 8 processors in use ?
Please help for the same.

Kindly reply to this mail.

Regards,
Mr. Ruturaj Warake
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="000000000000d065a205c808e218" X-Proofpoint-GUID: znq80RqEEWugX8IvyiplaklXz13sHTmF X-Proofpoint-ORIG-GUID: znq80RqEEWugX8IvyiplaklXz13sHTmF X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBoSEQpMehcZHhIRCllEF21sYRtGax5/ZwFcEQpYWBdkZWJLGFxtAR1 /EhEKeE4XY1Nja3sTWH4aX14RCnlMF20SaWJyb0hyTBxYEQpDSBcHGRweEQpDWRcHGx8SEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcSHHEbEgYTdwYbGBkGGgYaBgcbHQYbGBxxGx0QGncGGgYHHxoGG gYHHBoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XUERbEhp4W29vfV9N chJjXFNDWkZLQUZyUBsZWWJ+R2wRClhcFx8EGgQYGRkFGxoEGxsaBB8aBBseGBAbHhofGhEKXlk Xc2RjbGERCk1cFwcZHhEKTFoXaXxpTWtNEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2 xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx0eEQpCXhcbEQpESRcbEQpCXBcbE QpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2VwYhpvfxpkGh9nEQpC ThdjU2NrexNYfhpfXhEKQkwXZGViSxhcbQEdfxIRCkJsF2JQY3tmb39YGhljEQpCQBdlTEJkYWx gG29yYREKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF20fZ15wWWddG017EQpZSxcTHh0TEQpwZx dgGUZFe05HGW1cRRAaEQpwaBdkTAVkWGNjT396eRAaEQpwaBdgGkhgXEVoGGB/RRAaEQpwaBdmT XxIbR1bWUJAQhAaEQpwaBdpHmAZSVBScHpwBRAaEQpwaBd6GkZPSXNzXmJ6SxAaEQpwbBdiRVIY ZFAdRmBDThAHGRoRCm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 suspectscore=0 spamscore=0 mlxscore=0 mlxlogscore=999 malwarescore=0 phishscore=0 priorityscore=348 impostorscore=0 adultscore=0 lowpriorityscore=0 clxscore=208 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260092 domainage_hfrom=9479 X-Spam-Score: 0 X-Spam-OrigSender: ruturajwarake47@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ruturaj warake --000000000000d065a205c808e218 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear users, Thank you for replying. Thanks to Mr. Diship & Mr. Rene hafner Mr. Ruturaj Warake NIPER, Hyderabad, India On Mon, 26 Jul 2021 at 21:01, Ren=C3=A9 Hafner TUK wrote: > Hi > > your runtime heavily depends on the number of atoms in your system. > > What I strongly recommend is reducing your system size as much as possibl= e > (might require testing of different system but it depends if its worth th= e > time) usage of a GPU if available or at least a cluster node with more th= an > 8 cores (if available), > > Equilibration time does not depend on production runtime. > > Equilibration means you run such that the > temperature/volume/pressure/energy/density have settled down and e.g. no > major structural changes occur in your protein (RMSD) and other > quantities. All depending on the ensemble and your quantities of interest= --000000000000d065a205c808e218-- From owner-namd-l@halifax.ks.uiuc.edu Mon Jul 26 11:28:23 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QGSNqX002113; Mon, 26 Jul 2021 11:28:23 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QGSNYS002112; Mon, 26 Jul 2021 11:28:23 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QGSM20002108; Mon, 26 Jul 2021 11:28:22 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16QGSMQD002107; Mon, 26 Jul 2021 11:28:22 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16QGSChT002098 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000003c76cb05c8093dad" X-Proofpoint-ORIG-GUID: a7rqAUfDCUTN7OR9yV_kwysGzCHFWz7u X-Proofpoint-GUID: a7rqAUfDCUTN7OR9yV_kwysGzCHFWz7u X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRwZEQpMehcZGhwRCllEF21sYRtGax5/ZwFcEQpYWBdkZWJLGFxtAR1 /EhEKeE4XY1Nja3sTWH4aX14RCnlMF20SaWJyb0hyTBxYEQpDSBcHHRgRCkNZFwcYGxMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxgaGnEYHwYZGncGGxgYBhsSQhoGGgYHGxwGGx4acRgeEBp3BhoGB xsaGgYaBhoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XSx1YW2t/TG5p f35kHWV4E1N8dUFdU1ltUGlibH1QHV8RClhcFx8EGgQYGRkFGxoEGxsaBB8aBBseGxAbHhofGhE KXlkXc2RjSRkRCk1cFwcZGREKTFoXaWxpTU1NEQpMRhdva2tra2sRCkJPF2tBU0weElpvTxJsEQ pDWhcYGhMEEh8EGxwaBBsdHBEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF 2NTY2t7E1h+Gl9eEQpCRRdlcGIab38aZBofZxEKQk4XY1Nja3sTWH4aX14RCkJMF2RlYksYXG0B HX8SEQpCbBdiUGN7Zm9/WBoZYxEKQkAXZ2Z8fXAYX14SbHARCkJYF2dzZXNAbmFhTF1iEQpaWBc YEQp5QxdhQhtfHmIYcmN4eBEKWUsXEx4dExEKcGgXZn9/RR4bGR8BAUcQGxIRCnBoF2IFXlhCc3 BfbWN8EBoRCnBoF2xcHl9BYWlOE1x6EBoRCnBoF2F/X255ZlxpTRp6EBoRCnBoF2xpa3B9a05OZ VJcEBoRCnBsF2JFUhhkUB1GYENOEAceEhEKbX4XGhEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 suspectscore=0 priorityscore=306 adultscore=0 mlxscore=0 spamscore=0 lowpriorityscore=0 clxscore=363 mlxlogscore=355 malwarescore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2104190000 definitions=main-2107260094 domainage_hfrom=9479 X-Spam-Score: 0 X-Spam-OrigSender: ruturajwarake47@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ruturaj warake --0000000000003c76cb05c8093dad Content-Type: text/plain; charset="UTF-8" Dear users, How to set cnt for production step. What's procedure to set it ? I am getting difficulty to set. Please reply. --0000000000003c76cb05c8093dad Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear users,

= How to set cnt for production step.

What's procedure to set it ?
I am ge= tting difficulty to set.
Please reply.


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boundary="_000_YTBPR01MB318345527D7EF2F880E59C76E6E89YTBPR01MB3183CANP_" MIME-Version: 1.0 X-OriginatorOrg: uwo.ca X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: YTBPR01MB3183.CANPRD01.PROD.OUTLOOK.COM X-MS-Exchange-CrossTenant-Network-Message-Id: dc04a95b-87ed-48cd-5b4e-08d9508d6d56 X-MS-Exchange-CrossTenant-originalarrivaltime: 26 Jul 2021 23:31:00.3963 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: ad93a64d-ad0d-4ecd-b2fd-e53ce15965be X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: +Liok4XstjRLd9YaJpXYucarzXvWaXWhZLsMvLrc+uaYsbFIkYW5rw3wRN06/RWB X-MS-Exchange-Transport-CrossTenantHeadersStamped: YT3PR01MB5272 X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: Gygyi7WfamuZPMHoGw4SXL4ypVU4EnWI X-CLX-Response: 1TFkXGxIaEQpMehcaEQpZRBdpHkBTbx1mWGEeQREKWFgXZ09DXntGXx9ATks RCnhOF20dQ0EFE2J5e3IeEQp5TBdoTEAYekYSXHlebxEKQ0gXBxkbGREKQ1kXBxsYHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGnEZExAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdtU01TQx19TEtHX3B6Z2JFbV0eeXJmHlNafH8eb0R9YxEKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3NkZVp4EQpNXBcbHhkRCkxaF3hhTUFrEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF2hEZBhAGURJTkRzEQpDWhceGgQbGh0EHBwEGx seEQpCXhcbEQpEXhcZEQpCRRdtZVpJTWB6fWVkbhEKQk4XbR1DQQUTYnl7ch4RCkJMF2dPQ157R l8fQE5LEQpCbBdnXHwdYnMccmV/QREKQkAXZUJOHkdAchlgRnsRCkJYF2dzZXNAbmFhTF1iEQpN XhcbEQpaWBceEQp5QxdmGV5aGxlkfHxocBEKcGcXbUdha01jGUxTaW4QGRoRCnBoF2N9QkZCWn1 bZlBEEBkaEQpwaBdsR39CUGhpRHN5chAZGhEKcGgXa0tsYGZNBU5/HmIQGRoRCnBoF2J6aH5eH3 AFTGxiEBkaEQpwaBdkTxMTYX9QeUZEWxAZGhEKcGcXbFJkYHABWhpiRXgQGRoRCnBnF2lDblABW XNHAR5TEB8eEQpwfRdjQQVnXUIaW1tbUhAeEhEKcH0XZ3JQWBJSflplS2wQHhIRCnB/F2Fmb1sa Z2RCSB1bEBsaHxEKcF8XY2ISUEhjeB98Qn0QHR0RCnBsF2l6WhtGGBtpS2laEB4SEQptfhcbEQp YTRdLESA= X-Proofpoint-GUID: Gygyi7WfamuZPMHoGw4SXL4ypVU4EnWI X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 impostorscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 clxscore=180 mlxlogscore=999 adultscore=0 mlxscore=0 bulkscore=0 phishscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107260136 X-Spam-Score: 0 X-Spam-OrigSender: vkwan8@uwo.ca X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Victor Kwan --_000_YTBPR01MB318345527D7EF2F880E59C76E6E89YTBPR01MB3183CANP_ Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: quoted-printable This is a CHARMM problem, isn't it? ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of zeyn= ab hosseini Sent: Sunday, July 25, 2021 3:07 PM To: NAMD list Subject: namd-l: Does CHARMM-GUI Drude-Prepper input generator work for MD = simulation of carbon nanotubes? Dear all, I have the intention to perform molecular dynamics (MD) simulation of carbo= n nanotubes (CNT) using the Drude polarizable force field implemented in NA= MD. I=9Dnitially, I used CHARMM-GUI to produce a solvated CNT inputs for NA= MD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation (u= sing non-polarizable FF) for this system. But as soon as I=9D use these inp= uts (.pdb & .psf files) to produce Drude-Prepper inputs for MD simulation o= f polarizable force field, I=9D receive a message mentioning CHARMM was ter= minated abnormally with the following error. It seems that the residue TUBE= is not recognized. My question is how it is recognized before (when perfor= ming MD with non-polarizable force field), but when it comes to polarizable= FF the TUBE residue is not recognized? CHARMM was terminated abnormally. Please check the output or report this failure to the CHARMM= -GUI developers. Output Excerpt from step2_drude.out: Comparing "NONE" and "CNEU". IF test evaluated as false. Skipping command CHARMM> if @cterpatch .eq. CT1 if @cname .eq. GLY set cterpatch CT1= G Parameter: CTERPATCH -> "NONE" Parameter: CNAME -> "TUBE" Comparing "NONE" and "CT1". IF test evaluated as false. Skipping command CHARMM> if @cterpatch .eq. CT2 if @cname .eq. GLY set cterpatch CT2= G Parameter: CTERPATCH -> "NONE" Parameter: CNAME -> "TUBE" Comparing "NONE" and "CT2". IF test evaluated as false. Skipping command CHARMM> CHARMM> set gene =3D 0 Parameter: GENE <- "0" CHARMM> if @type eq protein then Parameter: TYPE -> "ELSE" Comparing "ELSE" and "PROTEIN". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if @type eq rna then !UMB: explicitly for rna Parameter: TYPE -> "ELSE" Comparing "ELSE" and "RNA". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if @type eq dna then !UMB: explicitly for dna Parameter: TYPE -> "ELSE" Comparing "ELSE" and "DNA". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if @type eq carb then Parameter: TYPE -> "ELSE" Comparing "ELSE" and "CARB". IF test evaluated as false. Skip to ELSE or ENDIF CHARMM> CHARMM> if gene .eq. 0 then Comparing "0" and "0". IF test evaluated as true. Performing command CHARMM> ! default generate if not protein or water CHARMM> generate @segname first none last none setup warn drude d= mass 0.4 ! show Parameter: SEGNAME -> "NM" Drude polarizability will be setup for SEGID: NM mass of Drudes parti= cles =3D 0.4000 ***** ERROR in GENIC ***** Residue 'TUBE ' was not found. /---------\ / \ / \ / \ ! XXXX XXXX ! ! XXXX XXXX ! ! XXX XXX ! ! X ! --\ XXX /-- ! ! XXX ! ! ! ! ! ! ! I I I I I ! ! I I I I ! \ / -- -- \---/ XXX XXX XXXX XXXX XXXXX XXXXX XXX XXX XXX XXX XXXXX XXX XXX XXX XXX XXX XXX XXXXX XXXXX XXXX XXXX XXX XXX Execution terminated due to the detection of a fatal error. ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL 1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 2.11 SECONDS CPU TIME: 2.11 SECONDS All the Best, Zeynab --_000_YTBPR01MB318345527D7EF2F880E59C76E6E89YTBPR01MB3183CANP_ Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: quoted-printable
This is a CHARMM problem, isn't it?

From: owner-namd-l@ks.uiuc.= edu <owner-namd-l@ks.uiuc.edu> on behalf of zeynab hosseini <hosse= inizeynab93@gmail.com>
Sent: Sunday, July 25, 2021 3:07 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: namd-l: Does CHARMM-GUI Drude-Prepper input generator work = for MD simulation of carbon nanotubes?
 
Dear all,

I have the intention to perform molecular dynamics (MD) simulation of carbo= n nanotubes (CNT) using the Drude polarizable force field implemented in NA= MD. I=9Dnitially, I used CHARMM-GUI to produce a solvated CNT inputs for NA= MD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation (using non-polarizable FF) for this system. Bu= t as soon as I=9D use these inputs (.pdb & .psf files) to produce Drude= -Prepper inputs for MD simulation of polarizable force field, I=9D receive = a message mentioning CHARMM was terminated abnormally with the following error. It seems that the residue TUBE is not= recognized. My question is how it is recognized before (when performing MD= with non-polarizable force field), but when it comes to polarizable FF the= TUBE residue is not recognized?

CHARMM was terminated abnormally. 
Please check the output or report&nb= sp;this failure to the CHARMM-GUI developers.
Output Excerpt from step2_drude.out:
 Comparing "NONE" =
and "CNEU".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>       if @cterpatch .eq. CT1  if @cname .eq. GLY set cterpatch =
CT1G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT1".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>       if @cterpatch .eq. CT2  if @cname .eq. GLY set cterpatch =
CT2G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT2".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>    =20
 =20
 CHARMM>       set gene =3D 0
 Parameter: GENE <- "0"
 =20
 CHARMM>       if @type eq protein then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "PROTEIN".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq rna then  !UMB: explicitly for rna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "RNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq dna then     !UMB: explicitly for dna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "DNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq carb then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "CARB".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if gene .eq. 0 then
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 =20
 CHARMM>          ! default generate if not protein or water
 =20
 CHARMM>          generate @segname first none last none setup warn drud=
e dmass 0.4 ! show
 Parameter: SEGNAME -> "NM"
 Drude polarizability will be setup for SEGID: NM      mass of Drudes parti=
cles =3D    0.4000

 ***** ERROR in GENIC ***** Residue 'TUBE  ' was not found.


                                                 =20
                            /---------\          =20
                           /           \         =20
                          /             \        =20
                         /               \       =20
                         !  XXXX   XXXX  !       =20
                         !  XXXX   XXXX  !       =20
                         !  XXX     XXX  !       =20
                         !       X       !       =20
                          --\   XXX   /--        =20
                           ! !  XXX  ! !         =20
                           ! !       ! !         =20
                           ! I I I I I !         =20
                           !  I I I I  !         =20
                            \         /          =20
                             --     --           =20
                               \---/             =20
                        XXX             XXX      =20
                       XXXX             XXXX     =20
                       XXXXX           XXXXX     =20
                          XXX         XXX        =20
                            XXX     XXX          =20
                               XXXXX             =20
                              XXX XXX            =20
                            XXX     XXX          =20
                          XXX         XXX        =20
                       XXXXX           XXXXX     =20
                       XXXX             XXXX     =20
                        XXX             XXX      =20
                                                 =20
                                                 =20
 Execution terminated due to the detection of a fatal error.

                    ABNORMAL TERMINATION
                    MOST SEVERE WARNING WAS AT LEVEL  1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.11  SECONDS=20
                         CPU TIME:     2.11  SECONDS 


All the Best,
Zeynab
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boundary="000000000000ff8b1405c815b092" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 7DkA3I5J4HIru-kt_nrfYXDRW1kJe6gj X-CLX-Response: 1TFkXGxgZEQpMehcZHBsRCllEF3piTn4BS0JQSGcfEQpYWBdgXGdaHWlhZHt eGREKeE4XY1Nja3sTWH4aX14RCnlMF21NYkNkQkYSWnxaEQpDSBcHGBMbEQpDWRcHGR0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxwYcRsGGxgedwYSGQYbGhpCGx8GGgYSBhkacRsQGncGGgYHGxoaB hoGBxwaBhoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOFx1uQWsZYx9gHmJj WF8HQV51RFhMc3JueH0bQWBPHE1AEQpYXBcfBBoEGBkZBRsaBBsaGgQeEgQYGRAbHhofGhEKXlk Xc2R8TUMRCk1cFxsdEQpMWhd/aU1raxEKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2 sRCkJPF2t8WVBYGWleGGZaEQpDWhcYGhMEEh8EGBoSBBsdGhEKQl4XGxEKREkXGxEKQlwXGxEKX k4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdiGXNtGBNyZh5zYhEKQk4X Y1Nja3sTWH4aX14RCkJMF2BcZ1odaWFke14ZEQpCbBdvHkdeRx4YbhJgXxEKQkAXaHxhTV9oa2t mWE4RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcfEQp5QxdmaWdQW2tCYklMchEKWUsXEx4SGh EKcGcXYBlGRXtORxltXEUQGRoRCnBoF20cBRphUhkTcm1bEBkaEQpwaBdmTWQaTUJtWx9NZRAZG hEKcGgXZB9PRhN6bxtibGQQGRoRCnBoF2BDQllhW2kYX1JwEBkaEQpwaBdtRG1/Z0h+YBNaXhAZ GhEKcH0XYH5Db1NEG2tHTl4QGRoRCnB9F2NlaVgYQl9ZTR1IEBkaEQpwZxdjGmNHQX9hRngZfBA ZGhEKcH0XaWFfZFlhHEtjUloQGRoRCnBnF2lDblABWXNHAR5TEB0SEQpwfRdmaFATGE99aXNwTx AZGhEKcH0XYGAaQnISeG8aX1sQGRoRCnB/F2UZeWZeR2kbZE9zEBMaEQpwXxdpHkdpbGBIAWZ4T BAZGhEKcH8XZWZEAR5IRmR8WhsQGxkeEQpwXxdiGx9JcHllZGJjBRAZGhEKcH8XYWZvWxpnZEJI HVsQGxsdEQpwXxdjYhJQSGN4H3xCfRAdHREKcGwXb1MYWRgSUnhAfxMQGRoRCm1+FxsRClhNF0s RIA== X-Proofpoint-GUID: 7DkA3I5J4HIru-kt_nrfYXDRW1kJe6gj MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=361 impostorscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 clxscore=123 mlxlogscore=999 adultscore=0 mlxscore=0 bulkscore=0 phishscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107270041 domainage_hfrom=9480 X-Spam-Score: 0 X-Spam-OrigSender: anoopama.tiwari@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Anupama Tiwari" --000000000000ff8b1405c815b092 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks On Mon, 26 Jul 2021, 18:53 Ren=C3=A9 Hafner TUK, wrote: > Hi, > > this has been discussed before > https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/0236.= html > > But those lines should **NOT** appear in the "_namd.str" file.. (Just > checked again the file on > https://urldefense.com/v3/__http://mackerell.umaryland.edu/*kenno/cgenff/= program.php*namd__;fiM!!DZ3fjg!snX5iThSNwiRZAGyPPzfIMsKXxBjpA-cro18hET8RtW3= tZCbpH-FE77-hkhgFBlQFw$ ) > > Be sure to use the correct file (and remove the other one!) > > Cheers > > Ren=C3=A9 > On 7/26/2021 3:07 PM, Dr. Anupama Tiwari wrote: > > Hi Ashkan, > > I am still getting the same error. > > On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari > wrote: > >> Dear friend, >> Use the file "toppar_water_ions_namd.str". >> >> --- >> ,Best >> Ashkan Shekaari >> PhD Candidate in Solid State Physics >> Department of Physics >> K. N. Toosi University of Technology, Tehran, 15875-4416, Iran >> >> >> ------------------------------ >> *From: *"Dr. Anupama Tiwari" >> *To: *"namd-l" >> *Sent: *Sunday, July 25, 2021 6:37:10 PM >> *Subject: *namd-l: namd-I: Request for help in error fixing >> >> Respected NAMD users, >> I got this error after implementing the namd command in power shell for >> md simulation: >> >> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS >> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE >> ./toppar_water_ions.str >> LINE=3D*set nat ?NATC* >> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE >> ./toppar_water_ions.str >> LINE=3D*set nat ?NATC* >> >> Kindly suggest a solution. >> -- >> >> >> *Regards, Dr.Anupama Tiwari * >> >> > > -- > > > > *Regards, Dr.Anupama Tiwari Associate Prof. Acropolis Institute Of > Technology & Research, Indore* > > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --000000000000ff8b1405c815b092 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thanks

On Mon, 26 Jul 2021, 18:53 Ren=C3=A9 Hafner TUK, &l= t;hamburge@physik.uni-kl.de> wrote:
=20=20 =20=20=20=20 =20=20

Hi,

=C2=A0=C2=A0=C2=A0 this has been discussed before https://www.ks.uiuc.edu= /Research/namd/mailing_list/namd-l.2014-2015/0236.html

=C2=A0=C2=A0=C2=A0 But those lines should **NOT** appear in the &quo= t;_namd.str" file.. (Just checked again the file on http://mackerell.umaryland.edu/~kenno/cgenff/program.php#namd)

Be sure to use the correct file (and remove the other one!)

Cheers

Ren=C3=A9

On 7/26/2021 3:07 PM, Dr. Anupama Tiwari wrote:
=20=20=20=20=20=20
Hi Ashkan,

I am still getting the same error.

On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari <shekaari@email.kntu.ac.ir> wrote:
Dear friend,
Use the file "toppar_water_ions_namd.str".

---
,Best
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology,=C2=A0Tehran,=C2=A015875-4416, Iran


From: "Dr. Anupama Tiwari" <= anoopama.tiwari@gmail.com>
To: "namd-l" <namd-l@ks.uiuc.edu>= ;
Sent: Sunday, July 25, 2021 6:37:10 PM
Subject: namd-l: namd-I: Request for help in error fixing

Respected NAMD users,
I got this error after implementing the namd command in power shell for md simulation:

Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str
LINE=3D*set nat ?NATC*

Kindly suggest a solution.
--
Regards,
Dr.Anupama Tiwari



--
Regards,
Dr.Anupama Tiwari
Associate Prof.
Acropolis Institute Of Technology & Research, Indore

--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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During the diffusio= n > process (where I want to observe the input of an ion to a channel), I hav= e been > using the wrapAll and wrapWater on options in the config file, at the end= of > the simulation I have been able to see that there is really the input of = ions, > but Many authors say that you have to "unwrap" the trajectory, when doing > diffusion analysis, You need to unwrap if you are interested in the diffusive dynamics of the i= on, because you don't want big artificial jumps.=20 > then, I have done it, using pbc both only for the ions and for the whole = system > and in both cases it is not seen that the ion penetrates, The ion is still inside the channel even it is far away. You can imagine th= at it is inside a periodic image of the channel (you can display them in VM= D). Here it is simpler to look at wrapped coordinates, with the channel cen= tered.=20 > so I thought about extending the dynamics, but what happens is that when = I > extend the dynamics, the structure with which I start is the one that is = inside > the channel, so all this causes me enormous confusion. > Please, could you tell me in which cases wrapAll or wrapWater can be used= in a > dynamic. For the simulation it does not matter. To analyze binding, look at wrapped = coordinates. For diffusion, look at unwrapped coordinates.=20 Jerome=20 --=_eb623d32-3ea5-48a0-8270-685093ecaab5 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Geo,

----- On 16 Jui= l 21, at 0:45, Rop=C3=B3n-Palacios <biodano.geo@gmail.com> wrote:
=

Dear NAMD Users,

I really have a prob= lem, which does not let me sleep. During the diffusion process (where I wan= t to observe the input of an ion to a channel), I have been using the wrapA= ll and wrapWater on options in the config file, at the end of the simulatio= n I have been able to see that there is really the input of ions, but Many = authors say that you have to "unwrap" the trajectory, when doing diffusion = analysis,

You need to unwrap if you are = interested in the diffusive dynamics of the ion, because you don't want big= artificial jumps.

then, I have done it, us= ing pbc both only for the ions and for the whole system and in both cases i= t is not seen that the ion penetrates,

Th= e ion is still inside the channel even it is far away. You can imagine that= it is inside a periodic image of the channel (you can display them in VMD)= . Here it is simpler to look at wrapped coordinates, with the channel cente= red.

so I thought about extending the dyna= mics, but what happens is that when I extend the dynamics, the structure wi= th which I start is the one that is inside the channel, so all this causes = me enormous confusion.

Please, could you tell me in whi= ch cases wrapAll or wrapWater can be used in a dynamic.

For the simulation it does not matter. To analyze binding, l= ook at wrapped coordinates. For diffusion, look at unwrapped coordinates.

Jerome

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Thread-Topic: namd-l: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. 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charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable You absolutely can continue a NAMD2 run with NAMD3 and the CUDA integrator.= I've done it with membrane systems without issue. Your first error looks u= nusual to me. Are the configuration files identical except for turning on t= he CUDA integrator (and removing margin and stepspercycle)? You could also try switching from NAMD2 to 3 at a different time, just in c= ase you had something pathological about your system. Best, JC ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of Ryan= Woltz Sent: Tuesday, July 20, 2021 7:06 PM To: namd-l@ks.uiuc.edu Subject: namd-l: difficulty converting namd2 channel system to namd3 Atom v= elocity too fast, box too small errors. Dear community, I have a 300k atom membrane embedded channel system that is stable on= NAMD2.14 but wanted to upgrade to take advantage of the increased speed. = I downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on EXPANSE if tha= t matters. I've had several errors which I fixed a few but not sure how it = affects my system, I don't expect they did but I'll state them as I go alon= g just in case. Almost all errors relate to cudasoaintegrate. My system is set up as follows. Minimize, equilibrate system (step6= .1-6.6), slowly release restraints on protein to prevent large RMSD jumps (= Step7.1-7.13), production (step7.14). 1. My first attempt was to use NAMD3 to continue a NAMD2.14 run that was= in production for 30ns. This failed immediately with error: OPENING EXTENDED SYSTEM TRAJECTORY FILE FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, 0,= 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, li= ne 4263 on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202 >From what I gathered from posts you cannot continue a NAMD2 simulation with= NAMD3. Or more specifically the post said I cannot continue a simulation t= hat did not previously include cudasoaintegrate turned on.B.I then tried st= arting it from scratch by separating the minimize step and the equilibratio= n steps (6.1-6.6) but the cudasoaintegrate turned on is not compatible with= reassigntemp or reassignfreq. 1. I then turned off cudasoaintegrate for steps 6.1-6.6 and then turned = it on for steps 7.1 and beyond as the steps with protein restraints on the = CA atoms which are slowly released in steps 7.1-7.13 do not require reassig= nment. I used suggested options such as 1) margin 8 2) outputEnergies/outpu= tTiming=3D 400 3) pairlistpercycle =3D 4 4) stepspercycle =3D 40. Simulatio= n fails quickly with atoms moving too fast. 2. I then readjusted outputEnergies/outputTiming to 5000 (charmm-gui def= ault). However, step7.1 fails after 105000 steps due to fatal error Periodi= c cell has become too small for original patch grid! Possible solutions are= to restart from a recent checkpoint, increase margin, or disable useFlexib= leCell for liquid simulation.. 3. I played with the margins 0-20 and once I no longer got the atoms esc= aping error I then got the allocated memory exceeded, too many atoms in a p= atch error. 4. Finally I also took out pairlistpercycle and stepspercycle as noted o= n NAMD3 website that these are obsolete. Now the error of ERROR: Atoms movi= ng too fast at timestep 135902; simulation has become unstable (0 atoms on = pe 0). FATAL ERROR: SequencerCUDA: Atoms moving too fast I was able to collect bits and pieces from the forums but mostly it is on N= AMD2 or on NAMD3 but the errors were similar but not the same. From error E= ) I don=92t think I=92m running out of RAM since I have 93GB allocated and = it runs fine on NAMD2. I=92ve gotten most of my information from Nvidia=92s website and NAMD3 webs= ite and adjusted .inp files based on these sites. https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up= -to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!t-8Svjahoy1Ml50wu7S= ldEpeWnNxGXDPzIxoKtC9JTt6nuYUdYhrDfRIm7SV_Z3z5g$ I have a suspicion that the reason things are failing after equilibration i= s because I=92m turning on cudasoaintegrate after dynamics has started. How= ever, I don=92t know how to equilibrate with cudasoaintegrate on and reassi= gnTemp/reassingFreq. I=92ve worked a year to get this system stable so don= =92t want to play around too much with options I=92m unfamiliar with. Again= system is stable with NAMD2 and most of the errors I get is failure due to= the cudasoaintegrate option on. If any of these steps or errors could be f= ixed even if there was an option to do steps6.1-7.13 without cudasoaintegra= te on and turn it on for the production I=92d be happy. I=92m also wonderin= g if cudasoaintegrate doesn=92t like restraints on the protein as I=92ve be= en told by others that use very early versions. Any suggestions on how to fix any of these errors? Do I just need to keep p= laying with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ stepsper= cycle parameters until it works? Thank you, Ryan --_000_BN7PR07MB4481BAFE73FB34CDE2F8A21383E99BN7PR07MB4481namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
You absolutely can continue a NAMD2 run with NAMD3 and the CUDA integrator.= I've done it with membrane systems without issue. Your first error looks u= nusual to me. Are the configuration files identical except for turning on t= he CUDA integrator (and removing margin and stepspercycle)?

You could also try switching from NAMD2 to 3 at a different time, just in c= ase you had something pathological about your system.

Best,
JC

From: owner-namd-l@ks.uiuc.= edu <owner-namd-l@ks.uiuc.edu> on behalf of Ryan Woltz <rlwoltz@uc= davis.edu>
Sent: Tuesday, July 20, 2021 7:06 PM
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>
Subject: namd-l: difficulty converting namd2 channel system to namd3= Atom velocity too fast, box too small errors.
 

Dear community,


   = ;   I have a 300k atom membrane embedded channel system that is stable on NAMD2.= 14 but wanted to upgrade to take advantage of the increased speed.  I = downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on EXPANSE if that = matters. I've had several errors which I fixed a few but not sure how it affects my system, I don't expect they d= id but I'll state them as I go along just in case. Almost all errors relate= to cudasoaintegrate.


   = ;     My system is set up as follows. Minimize, equilibrate system (step6.1-6.6), s= lowly release restraints on protein to prevent large RMSD jumps (Step7.1-7.= 13), production (step7.14). 


  1. My = first attempt was to use NAMD3 to continue a NAMD2.14 run that was in produ= ction for 30ns. This failed immediately with error:

OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, 0,= 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, li= ne 4263
 on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202
From what I gathered from= posts you cannot continue a NAMD2 simulation with NAMD3. Or more specifica= lly the post said I cannot continue a simulation that did not previously include cudasoaintegrate turned on.B.= I then tried starting i= t from scratch by separating the minimize step and the equilibration steps (6.1-6.6) but the cudasoaintegrate turned= on is not compatible with reassigntemp or reassignfreq. 
  1. I t= hen turned off cudasoaintegrate for steps 6.1-6.6 and then turned it on for= steps 7.1 and beyond as the steps with protein restraints on the CA atoms which are slowly released in steps= 7.1-7.13 do not require reassignment. I used suggested options such as 1) = margin 8 2) outputEnergies/outputTiming=3D 400 3) pairlistpercycle =3D 4 4)= stepspercycle =3D 40. Simulation fails quickly with atoms moving too fast.

  2. I t= hen readjusted outputEnergies/outputTiming to 5000 (charmm-gui default). Ho= wever, step7.1 fails after 105000 steps due to fatal error Periodic cell has become too small for original p= atch grid! Possible solutions are to restart from a recent checkpoint, incr= ease margin, or disable useFlexibleCell for liquid simulation.. 

  3. I p= layed with the margins 0-20 and once I no longer got the atoms escaping err= or I then got the allocated memory exceeded, too many atoms in a patch error.

  4. Fin= ally I also took out pairlistpercycle and stepspercycle as noted on NAMD3 w= ebsite that these are obsolete. Now the error of ERROR: Atoms moving too fast at timestep 135902; simulation has beco= me unstable (0 atoms on pe 0).

    FATAL ERROR: SequencerCUDA: Atoms moving too fast

I was able to collect bits and pieces from the forums but mostly it is on NA= MD2 or on NAMD3 but the errors were similar but not the same. From error E)= I don=92t think I=92m running out of RAM since I have 93GB allocated and i= t runs fine on NAMD2.


I=92ve gotten most of my information from Nvidia=92s website and NAMD3 website an= d adjusted .inp files based on these sites.


https://www.ks.uiuc.edu/Research= /namd/alpha/3.0alpha/

https://developer.nvidia.com/blog/deli= vering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/


I have a suspicion that the reason things are failing after equilibration is= because I=92m turning on cudasoaintegrate after dynamics has started. Howe= ver, I don=92t know how to equilibrate with cudasoaintegrate on and reassig= nTemp/reassingFreq. I=92ve worked a year to get this system stable so don=92t want to play around too much with opt= ions I=92m unfamiliar with. Again system is stable with NAMD2 and most of t= he errors I get is failure due to the cudasoaintegrate option on. If any of= these steps or errors could be fixed even if there was an option to do steps6.1-7.13 without cudasoaintegrate o= n and turn it on for the production I=92d be happy. I=92m also wondering if= cudasoaintegrate doesn=92t like restraints on the protein as I=92ve been t= old by others that use very early versions.


Any suggestions on how to fix any of these errors? Do I just need to keep play= ing with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ stepspercyc= le parameters until it works?


Thank you,


Ryan

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To: Victor Kwan Cc: "namd-l@ks.uiuc.edu" Content-Type: multipart/alternative; boundary="000000000000b4ab8305c81d6ef9" X-Proofpoint-ORIG-GUID: n8_TUYVEsXaWiiWGbTYtXkIS7vacPjbX X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0TEQpMehcZHh4RCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHGR0YEQpDWRcHGxgYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8TcRkSEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0QSdX5/c3xvWXJLfUNDfW1IfnNeckFjeR1cS0l6QEhyEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NkTkVsEQpNXBceEhMRCkxaF3tpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHB wEGx0fEQpCXhcbEQpESRcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF298TxtvXkVfchgYEQpCThdjU2NrexNYfhpfXhEKQkwXaHp7YG5wUnNwWl8RCkJs F29QBX9PYWYZT0VyEQpCQBdlQk4eR0ByGWBGexEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF2Y ZXlobGWR8fGhwEQpZSxcTHhIaEQpwZxdvaxtjHRhaUnh6ZxAeEhEKcGgXZUZtHnBsbU9NEhsQGR oRCnBoF2sYfB0fXRp6cAVSEB4SEQpwaBdjbHkcX3oFWXBneRAZGhEKcGgXYHxrHVxhTBNvbnkQG RoRCnBoF2cbYEVdf0x+Zm56EBkaEQpwfRdoTGRnRRNSYxJDTxAZGhEKcGcXbUdha01jGUxTaW4Q HhIRCnBnF2lDblABWXNHAR5TEB0aEQpwfRdjQQVnXUIaW1tbUhAdEhEKcH0XZBN8G1tnX3J4Y2I QGRoRCnB9F2dyUFgSUn5aZUtsEB0aEQpwfxdpHx0SX2BhbhNkYxAeEhEKcF8XZGUZZWFlf1hcWX 0QHhIRCnB/F2Fmb1saZ2RCSB1bEBsZGBEKcF8XY2ISUEhjeB98Qn0QGxobEQpwbBdsUh1baWZsX nJIYRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: n8_TUYVEsXaWiiWGbTYtXkIS7vacPjbX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 priorityscore=344 clxscore=179 bulkscore=0 impostorscore=0 suspectscore=0 phishscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 mlxlogscore=999 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107270099 domainage_hfrom=9480 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --000000000000b4ab8305c81d6ef9 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Victor Well, I know that to use NAMD in order to implement MD simulation with Drude polarizable FF, CHARMM is needed to generate a CHARMM-compatible .psf file. I don't have access to the CHARMM program and I decided to use CHARMM-GUI. I posted the question in both the NAMD and CHARMM forum (link ) but nobody answered. It seems the CHARMM forum is not as active as the NAMD one. I also posted the question in the VMD mailing list. Would be so thankful if anybody could give me a hint.. All the best, Zeynab On Mon, Jul 26, 2021 at 7:31 PM Victor Kwan wrote: > This is a CHARMM problem, isn't it? > ------------------------------ > *From:* owner-namd-l@ks.uiuc.edu on behalf of > zeynab hosseini > *Sent:* Sunday, July 25, 2021 3:07 PM > *To:* NAMD list > *Subject:* namd-l: Does CHARMM-GUI Drude-Prepper input generator work for > MD simulation of carbon nanotubes? > > Dear all, > > I have the intention to perform molecular dynamics (MD) simulation of > carbon nanotubes (CNT) using the Drude polarizable force field implemented > in NAMD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CNT = inputs for > NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation > (using non-polarizable FF) for this system. But as soon as I=E2=80=8C use= these > inputs (.pdb & .psf files) to produce Drude-Prepper inputs for MD > simulation of polarizable force field, I=E2=80=8C receive a message menti= oning > CHARMM was terminated abnormally with the following error. It seems that > the residue TUBE is not recognized. My question is how it is recognized > before (when performing MD with non-polarizable force field), but when it > comes to polarizable FF the TUBE residue is not recognized? > > CHARMM was terminated abnormally. > Please check the output or report > this > failure to the CHARMM-GUI developers. > Output Excerpt from step2_drude.out: > > Comparing "NONE" and "CNEU". > IF test evaluated as false. Skipping command > > CHARMM> if @cterpatch .eq. CT1 if @cname .eq. GLY set cterpatch C= T1G > Parameter: CTERPATCH -> "NONE" > Parameter: CNAME -> "TUBE" > Comparing "NONE" and "CT1". > IF test evaluated as false. Skipping command > > CHARMM> if @cterpatch .eq. CT2 if @cname .eq. GLY set cterpatch C= T2G > Parameter: CTERPATCH -> "NONE" > Parameter: CNAME -> "TUBE" > Comparing "NONE" and "CT2". > IF test evaluated as false. Skipping command > > CHARMM> > > CHARMM> set gene =3D 0 > Parameter: GENE <- "0" > > CHARMM> if @type eq protein then > Parameter: TYPE -> "ELSE" > Comparing "ELSE" and "PROTEIN". > IF test evaluated as false. Skip to ELSE or ENDIF > > CHARMM> > > CHARMM> if @type eq rna then !UMB: explicitly for rna > Parameter: TYPE -> "ELSE" > Comparing "ELSE" and "RNA". > IF test evaluated as false. Skip to ELSE or ENDIF > > CHARMM> > > CHARMM> if @type eq dna then !UMB: explicitly for dna > Parameter: TYPE -> "ELSE" > Comparing "ELSE" and "DNA". > IF test evaluated as false. Skip to ELSE or ENDIF > > CHARMM> > > CHARMM> if @type eq carb then > Parameter: TYPE -> "ELSE" > Comparing "ELSE" and "CARB". > IF test evaluated as false. Skip to ELSE or ENDIF > > CHARMM> > > CHARMM> if gene .eq. 0 then > Comparing "0" and "0". > IF test evaluated as true. Performing command > > CHARMM> ! default generate if not protein or water > > CHARMM> generate @segname first none last none setup warn drude= dmass 0.4 ! show > Parameter: SEGNAME -> "NM" > Drude polarizability will be setup for SEGID: NM mass of Drudes par= ticles =3D 0.4000 > > ***** ERROR in GENIC ***** Residue 'TUBE ' was not found. > > > > /---------\ > / \ > / \ > / \ > ! XXXX XXXX ! > ! XXXX XXXX ! > ! XXX XXX ! > ! X ! > --\ XXX /-- > ! ! XXX ! ! > ! ! ! ! > ! I I I I I ! > ! I I I I ! > \ / > -- -- > \---/ > XXX XXX > XXXX XXXX > XXXXX XXXXX > XXX XXX > XXX XXX > XXXXX > XXX XXX > XXX XXX > XXX XXX > XXXXX XXXXX > XXXX XXXX > XXX XXX > > > Execution terminated due to the detection of a fatal error. > > ABNORMAL TERMINATION > MOST SEVERE WARNING WAS AT LEVEL 1 > > $$$$$ JOB ACCOUNTING INFORMATION $$$$$ > ELAPSED TIME: 2.11 SECONDS > CPU TIME: 2.11 SECONDS > > > > All the Best, > Zeynab > --000000000000b4ab8305c81d6ef9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Victor

Well, I know that to use NAMD= in order to implement MD simulation with Drude polarizable FF, CHARMM is n= eeded to generate a CHARMM-compatible .psf file. I don't have access to= the CHARMM program and I decided to use CHARMM-GUI. I posted the question = in both the NAMD and CHARMM forum (link) but nobody answered. It seems the CHARM= M forum is not as active as the NAMD one. I also posted the question in the= VMD mailing list. Would be so thankful if anybody could give me a hint..

All the best,
Zeynab

On Mon, Jul 26,= 2021 at 7:31 PM Victor Kwan <vkwan8@uw= o.ca> wrote:
This is a CHARMM problem, isn't it?

From= : owner-n= amd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.edu> on behalf of zeynab hosseini = <hossein= izeynab93@gmail.com>
Sent: Sunday, July 25, 2021 3:07 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: namd-l: Does CHARMM-GUI Drude-Prepper input generator work = for MD simulation of carbon nanotubes?
=C2=A0
Dear all,

I have the intention to perform molecular dynamics (MD) simulation of carbo= n nanotubes (CNT) using the Drude polarizable force field implemented in NA= MD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CNT inputs = for NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation (using non-polarizable FF) for this system. Bu= t as soon as I=E2=80=8C use these inputs (.pdb & .psf files) to produce= Drude-Prepper inputs for MD simulation of polarizable force field, I=E2=80= =8C receive a message mentioning CHARMM was terminated abnormally with the following error. It seems that the residue TUBE is not= recognized. My question is how it is recognized before (when performing MD= with non-polarizable force field), but when it comes to polarizable FF the= TUBE residue is not recognized?

CHARMM was terminated abnormally.=C2=A0
Please check the output or=C2=A0report=C2=A0this failure to the CHARMM-GUI developers.
Output Excerpt from=C2=A0step2_drude.out
 Comparing "NONE" a=
nd "CNEU".
 IF test evaluated as false.  Skipping command
=20=20
 CHARMM>       if @cterpatch .eq. CT1  if @cname .eq. GLY set cterpatch =
CT1G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT1".
 IF test evaluated as false.  Skipping command
=20=20
 CHARMM>       if @cterpatch .eq. CT2  if @cname .eq. GLY set cterpatch =
CT2G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT2".
 IF test evaluated as false.  Skipping command
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       set gene =3D 0
 Parameter: GENE <- "0"
=20=20
 CHARMM>       if @type eq protein then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "PROTEIN".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if @type eq rna then  !UMB: explicitly for rna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "RNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if @type eq dna then     !UMB: explicitly for dna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "DNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if @type eq carb then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "CARB".
 IF test evaluated as false.  Skip to ELSE or ENDIF
=20=20
 CHARMM>=20=20=20=20=20
=20=20
 CHARMM>       if gene .eq. 0 then
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
=20=20
 CHARMM>          ! default generate if not protein or water
=20=20
 CHARMM>          generate @segname first none last none setup warn drud=
e dmass 0.4 ! show
 Parameter: SEGNAME -> "NM"
 Drude polarizability will be setup for SEGID: NM      mass of Drudes parti=
cles =3D    0.4000

 ***** ERROR in GENIC ***** Residue 'TUBE  ' was not found.


=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
                            /---------\=20=20=20=20=20=20=20=20=20=20=20
                           /           \=20=20=20=20=20=20=20=20=20=20
                          /             \=20=20=20=20=20=20=20=20=20
                         /               \=20=20=20=20=20=20=20=20
                         !  XXXX   XXXX  !=20=20=20=20=20=20=20=20
                         !  XXXX   XXXX  !=20=20=20=20=20=20=20=20
                         !  XXX     XXX  !=20=20=20=20=20=20=20=20
                         !       X       !=20=20=20=20=20=20=20=20
                          --\   XXX   /--=20=20=20=20=20=20=20=20=20
                           ! !  XXX  ! !=20=20=20=20=20=20=20=20=20=20
                           ! !       ! !=20=20=20=20=20=20=20=20=20=20
                           ! I I I I I !=20=20=20=20=20=20=20=20=20=20
                           !  I I I I  !=20=20=20=20=20=20=20=20=20=20
                            \         /=20=20=20=20=20=20=20=20=20=20=20
                             --     --=20=20=20=20=20=20=20=20=20=20=20=20
                               \---/=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20
                        XXX             XXX=20=20=20=20=20=20=20
                       XXXX             XXXX=20=20=20=20=20=20
                       XXXXX           XXXXX=20=20=20=20=20=20
                          XXX         XXX=20=20=20=20=20=20=20=20=20
                            XXX     XXX=20=20=20=20=20=20=20=20=20=20=20
                               XXXXX=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20
                              XXX XXX=20=20=20=20=20=20=20=20=20=20=20=20=20
                            XXX     XXX=20=20=20=20=20=20=20=20=20=20=20
                          XXX         XXX=20=20=20=20=20=20=20=20=20
                       XXXXX           XXXXX=20=20=20=20=20=20
                       XXXX             XXXX=20=20=20=20=20=20
                        XXX             XXX=20=20=20=20=20=20=20
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
 Execution terminated due to the detection of a fatal error.

                    ABNORMAL TERMINATION
                    MOST SEVERE WARNING WAS AT LEVEL  1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.11  SECONDS=20
                         CPU TIME:     2.11  SECONDS 


All the Best,
Zeynab
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ABdhPJwlW1AsX+tKZmj+PsvJcPFBSST14jEZFUUB/jdGdkbsD/gOoHi6RIcHe6seFkWqDbExsUzwawsce1oy0VhjFig= X-Received: by 2002:a17:907:1b11:: with SMTP id mp17mr25331566ejc.1.1627445028442; Tue, 27 Jul 2021 21:03:48 -0700 (PDT) MIME-Version: 1.0 From: samaneh ghanbari Date: Wed, 28 Jul 2021 08:33:37 +0430 Message-ID: Subject: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000cfd60c05c8271281" X-CLX-Response: 1TFkXGxwTEQpMehcYHRkRCllEF3oFfAUfQnxjUntwEQpYWBdgUGMFHgVde0Z ARBEKeE4XY1Nja3sTWH4aX14RCnlMF259bV95eBpTeFxcEQpDSBcHGRwRCkNZFwcfHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGBpxGwYZE3cGEhsGGgYaBhwTBhpxGhAadwYaBhoGGgYaBhoGGnEaE Bp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF19aRWZAUFt+E25Cfn5CZUt/QmdHBx9O Wx1HWlsafHtEEQpYXBcfBBoEGBkZBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NkRFxoEQpNXBc bGRMRCkxaF2hpTWtrEQpMRhdva2tra2sRCkJPF2V+XFlbW0djU2FsEQpDWhcYGhMEEh8EGBsSBB 8YEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF 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namd-l@ks.uiuc.edu, samaneh ghanbari --000000000000cfd60c05c8271281 Content-Type: text/plain; charset="UTF-8" Dear all I have the following error to run namd2: "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NHL". I use parameter files: par_all36_lipid.prm par_all36_prot.prm par_all36_carb.prm par_all36_na.prm toppar_water_ions_namd.str par_all36_cgenff.prm par_all27_prot_lipid_na.inp par_interface.prm but I unable to understand the reason it. Could you help me, please? -- Sincerly Yours Miss.Ghanbari --000000000000cfd60c05c8271281 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear all

I have the following error to run namd2: "FATAL ERROR: DIDN'T FIND vdW PARAME= TER FOR ATOM TYPE NHL". I use parameter files:

=C2=A0

par_all36_lipid.prm
par_all36_prot.prm
par_all36_carb.prm
par_all36_na.prm
toppar_water_ions_namd.str
par_all36_cgenff.prm
par_all27_prot_lipid_na.inp
par_interface.prm

=C2=A0

but I unable to understand the reason it. Could you help me, please?





--
Sincerly Yours Miss.Ghanbari
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boundary="=_0a7da2b5-f5a0-465a-8f70-659a7c942572" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC73 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER Thread-Index: U6LCaqkiI6Oa9L9D4cW2NcYm8XaV9w== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 9wpbxRJhf8qMqnwff9Zho_b2IpQZc28h X-Proofpoint-GUID: 9wpbxRJhf8qMqnwff9Zho_b2IpQZc28h X-CLX-Response: 1TFkXGx0dEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxgdGREKQ1kXBx8ZEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8dcRkcEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOFxNdWkhSeGBCTBJbZ1tEXUxME3BCRXVIGGNae3BJGBJCEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NkWUZsEQpNXBcYHxoRCkxaF3xpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYgVoQ0BMWkBFck4RCkNaFxMeBBsSHgQbHRwEGx sbEQpCXhcbEQpEXhcYEQpCXBcbEQpCSxd6Hm1bS3xHX2IFehEKQkkXaF96YUYBYkBBT3kRCkJFF 2EdHmZrckFSGRl4EQpCThdoX3phRgFiQEFPeREKQkwXbRNBQVpBREMTfXgRCkJsF2FkGWddQhlF fGt4EQpCQBdoBRsbSVpvREN5eREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2xdSHh mGk4aYGQaEQpZSxcHGREKcGcXYxpjR0F/YUZ4GXwQGRoRCnBoF2R4Y30bfExvXGt6EBkaEQpwaB dmYFB5UAVdWgEeSRAZGhEKcGgXZ20YYx8eEn5hTmIQGRoRCnBoF2FPcmZNAUYfRW1AEBkaEQpwa BdoWUFCW21/bGxvZBAZGhEKcH0XY3N7TQVdHQF4QXAQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpw fRdpGmVOXEgTYEd5RhAZGhEKcH8Xb0RhUBITfxscEn4QHhsRCnBfF2IYGhgfeEdMe3t7EBsbGRE KcGwXb2B/bXlMQURrTk4QGRoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 spamscore=0 bulkscore=0 mlxlogscore=864 mlxscore=0 clxscore=177 suspectscore=0 phishscore=0 priorityscore=0 lowpriorityscore=0 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107280054 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_0a7da2b5-f5a0-465a-8f70-659a7c942572 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable First, remove " par_all27_prot_lipid_na.inp ";=20 Second, you probably are not using the proper force field containing NHL pa= rameters. So=20 1- include all charmm 36 parameter files within your namd input file;=20 2- or alternatively, open any of the parameter files and write in "NHL 0 0 = 0",=20 then save the changes and run. That might be helpful.=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!sROS6gvXJP-FhjMUbMlI-G8roLrf8BorYDq9Xrnxy5UQdB42wBNXElGt= YgOIUQW4fQ$ ]=20 From: "samaneh ghanbari" =20 To: "namd-l" =20 Sent: Wednesday, July 28, 2021 8:33:37 AM=20 Subject: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER=20 Dear all=20 I have the following error to run namd2: "FATAL ERROR: DIDN'T FIND vdW PARA= METER FOR ATOM TYPE NHL". I use parameter files:=20 par_all36_lipid.prm=20 par_all36_prot.prm=20 par_all36_carb.prm=20 par_all36_na.prm=20 toppar_water_ions_namd.str=20 par_all36_cgenff.prm=20 par_all27_prot_lipid_na.inp=20 par_interface.prm=20 but I unable to understand the reason it. Could you help me, please ?=20 --=20 Sincerly Yours Miss.Ghanbari=20 --=_0a7da2b5-f5a0-465a-8f70-659a7c942572 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
First, remove "par_all27_prot_lipid_na.in= p";
Second, you pr= obably are not using the proper force field containing NHL parameters. So
1- include all charmm 36 p= arameter files within your namd input file;
2- or alternatively, open any of the parameter files and= write in "NHL      0       0  &nbs= p;    0",
then = save the changes and run. That might be helpful.

---
,Best
<= /div>
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology= , Tehran, 15875-4416, Iran<= /font>


From: "samaneh ghanbari" <ghanbari.samaneh@gmail.com>
To: "namd= -l" <namd-l@ks.uiuc.edu>
Sent: Wednesday, July 28, 2021 8:3= 3:37 AM
Subject: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER

Dear a= ll

I have the following error to run namd2: "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NHL". I use parameter files:

 

par_all36_lipid.prm
par_all36_prot.prm
par_all36_carb.prm
par_all36_na.prm
toppar_water_ions_namd.str
par_all36_cgenff.prm
par_all27_prot_lipid_na.inp
par_interface.prm

 

but I unable to understand the reason it. Could you help me, please?





--
Sin= cerly Yours Miss.Ghanbari

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Wed, 28 Jul 2021 10:09:21 +0000 Date: Wed, 28 Jul 2021 10:09:19 +0000 (UTC) From: Vidhya Sankar To: NAMD List Message-ID: <1853243581.524208.1627466959957@mail.yahoo.com> Subject: namd-l: Mail about path CV MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_524207_1931023972.1627466959956" References: <1853243581.524208.1627466959957.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18749 YMailNorrin X-CLX-Response: 1TFkXGxkfEQpMehcZGxIRCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHGBgYEQpDWRcHGxkbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxsfcRsZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0MaTh9JGW1oa2sTYVsbGn1MGWh5ZHxcX39mGWFbcB5EEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NkXmxdEQpNXBceGRgRCkxaF2xpa2trEQpMRhdva2t va2sRCkJPF2JJH3pcWB9beRseEQpDWhcbGhwEGxoEGB4eBBgaExEKQl4XGxEKQlwXGxEKXk4XGx EKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmEQpCRRd6GW1DW0VfaGl9ZREKQk4XekQcH W9FbG1EQ2YRCkJMF2ZhYhNhbWJrSVxCEQpCbBdrHR9wGWxpRW94XBEKQkAXem97ZWFhbnJATl8R CkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdmEntZeBtPSWJTeBEKWUsXExwSEhEKcGgXbX1lWHp tWx5cW0AQGRoRCnBoF2IdaHpFX3NiZBIFEBkaEQpwaBdmG119G2VPcmVLbBAZGhEKcGgXY2MTSx lZTFprRBIQGRoRCnBoF25lT0BvE3p/Z3p8EBkaEQpwbBdkb05cRn5TaHxZWhAZGhEKcEwXZgVhH EcdRmF5Q38QGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: i0d5c3GBAA9Kq10Wf3BSNVvuUL3KqZ4n X-Proofpoint-GUID: i0d5c3GBAA9Kq10Wf3BSNVvuUL3KqZ4n X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 malwarescore=0 spamscore=0 clxscore=135 priorityscore=318 suspectscore=0 mlxscore=0 adultscore=0 mlxlogscore=708 phishscore=0 lowpriorityscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107280056 domainage_hfrom=9688 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_524207_1931023972.1627466959956 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd users =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I= =C2=A0 am using=C2=A0 pdb file at specific interval as path CV=C2=A0 but th= en i=C2=A0 run the calculation i got error as follows colvars:=C2=A0=C2=A0 Initializing a new collective variable.=20 colvars:=C2=A0=C2=A0 # name =3D "colvar2" [default]=20 colvars: Error: no valid components were provided for this collective varia= ble.=20 FATAL ERROR: Error in the collective variables module: exiting. It would be highly appreciable=C2=A0if someone help me to rectify error = =C2=A0 my CVinput file as follows colvar {=20 name=C2=A0=C2=A0=C2=A0 gs=20 =C2=A0lowerBoundary 70=20 =C2=A0upperBoundary 145=20 =C2=A0 width 1=20 # The path is defined by 5 reference frames (from string-00.pdb to string-0= 4.pdb)=20 # Use atomic coordinate from atoms 1, 2 and 3 to compute the path=20 gspath {=20 atoms { atomNumbersRange { 1-1589 } }=20 refPositionsFile1 0.pdb=20 refPositionsFile2 100.pdb=20 refPositionsFile3 200.pdb=20 refPositionsFile4 300.pdb=20 refPositionsFile5 400.pdb=20 refPositionsFile6 500.pdb=20 refPositionsFile7 600.pdb=20 refPositionsFile8 700.pdb=20 refPositionsFile9 800.pdb=20 refPositionsFile10 900.pdb=20 refPositionsFile11 1000.pdb=20 }=20 } With High Regards S.VIDHYA SANKAR ------=_Part_524207_1931023972.1627466959956 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Namd users
           &n= bsp; I  am using  pdb file at specific interval as path CV  = but then i  run the calculation i got error as follows
colvars= :   Initializing a new collective variable.
colvars: &nb= sp; # name =3D "colvar2" [default]
colvars: Error: no valid components = were provided for this collective variable.
FATAL ERROR: Error in = the collective variables module: exiting.
It wo= uld be highly appreciable if someone help me to rectify error &= nbsp; my CVinput file as follows

colvar {
name&n= bsp;   gs
 lowerBoundary 70
 upperBoundary 145 =
  width 1
# The path is defined by 5 reference frames (from st= ring-00.pdb to string-04.pdb)
# Use atomic coordinate from atoms 1, 2 a= nd 3 to compute the path
gspath {
atoms { atomNumbersRange { 1-1589= } }
refPositionsFile1 0.pdb
refPositionsFile2 100.pdb
refPosit= ionsFile3 200.pdb
refPositionsFile4 300.pdb
refPositionsFile5 400.p= db
refPositionsFile6 500.pdb
refPositionsFile7 600.pdb
refPosit= ionsFile8 700.pdb
refPositionsFile9 800.pdb
refPositionsFile10 900.= pdb
refPositionsFile11 1000.pdb
}
}

With High Regards
S.VIDHYA = SANKAR



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boundary="000000000000dd374a05c82ee3a6" X-CLX-Shades: MLX X-Proofpoint-GUID: GqGiH9PdMcY8tyBIwnPpiOj8RYAfKqQ2 X-CLX-Response: 1TFkXGxIbEQpMehcZGR4RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGRsZEQpDWRcHGxkaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwbcR4aEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF21bbUNiE3pOZ0lzEl5TaGNdRHpaQ2VAEnhza0xhW3sYEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NkXB1BEQpNXBcYHR8RCkxaF3hpa01rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGxIaEQpCXhcbEQpEXhcaEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY 1Nja3sTWH4aX14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9Y eGARCkJsF2FfelMZQ0Qaeht+EQpCQBdnaH99YGJCehlSQhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxs RClpYFxkRCnlDF24YBWN4fX5Le38YEQpZSxcTHhIbEQpwaBduYVscQ1pBbENNUBAZGhEKcGgXYx 5De3pvUxhhX1sQGRoRCnBoF3pMe299W0JLWVhkEB4SEQpwaBdma0Nme2BicEZ6GRAZGhEKcGgXa VlSTgVebGVrXHMQGRoRCnB9F2xHGRpaa3pGQxNaEBkaEQpwfxdiTgUBcEReaUR7ZRAbGxIRCnBf F25ZZWdsGWZZGEhZEBkaEQpwbBdmH3tYXGIFS1hkHxAZGhEKcEwXZgVhHEcdRmF5Q38QHhIRCm1 +FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: GqGiH9PdMcY8tyBIwnPpiOj8RYAfKqQ2 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=334 impostorscore=0 mlxscore=0 bulkscore=5 malwarescore=0 lowpriorityscore=5 clxscore=181 phishscore=0 suspectscore=0 spamscore=0 mlxlogscore=974 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107280076 domainage_hfrom=9481 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000dd374a05c82ee3a6 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi, can you make sure that your NAMD build supports gspath? This means not only *version 2.14 or higher*, but also an executable built with C++11 features enabled (not the default in older systems, which are still nonetheless operational): https://urldefense.com/v3/__https://colvars.github.io/README-c**A11.html__;= Kys!!DZ3fjg!rKbt0VPgrT4ThZiem335_Se87rKEZNjd-tVRQrlAPU508Lxbn9q-LWy6GSn1aKl= JxQ$=20 Giacomo On Wed, Jul 28, 2021 at 6:12 AM Vidhya Sankar < vidhyasankar7928@remove_yahoo.com> wrote: > Dear Namd users > I am using pdb file at specific interval as path CV but > then i run the calculation i got error as follows > colvars: Initializing a new collective variable. > colvars: # name =3D "colvar2" [default] > colvars: Error: no valid components were provided for this collective > variable. > FATAL ERROR: Error in the collective variables module: exiting. > It would be highly appreciable if someone help me to rectify error my > CVinput file as follows > > > > > > > > > > > > > > > > > > > > > > > *colvar { name gs lowerBoundary 70 upperBoundary 145 width 1 # The > path is defined by 5 reference frames (from string-00.pdb to string-04.pd= b) > # Use atomic coordinate from atoms 1, 2 and 3 to compute the path gspath { > atoms { atomNumbersRange { 1-1589 } } refPositionsFile1 0.pdb > refPositionsFile2 100.pdb refPositionsFile3 200.pdb refPositionsFile4 > 300.pdb refPositionsFile5 400.pdb refPositionsFile6 500.pdb > refPositionsFile7 600.pdb refPositionsFile8 700.pdb refPositionsFile9 > 800.pdb refPositionsFile10 900.pdb refPositionsFile11 1000.pdb } * > > *}* > > With High Regards > S.VIDHYA SANKAR > > > > --000000000000dd374a05c82ee3a6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi, can you make sure th= at your NAMD build supports gspath?=C2=A0 This means not only version 2.= 14 or higher, but also an executable built with C++11 features enabled= =C2=A0(not the default in older systems, which are still nonetheless operat= ional):


Dear Namd users
=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I=C2= =A0 am using=C2=A0 pdb file at specific interval as path CV=C2=A0 but then = i=C2=A0 run the calculation i got error as follows
colvars:=C2=A0= =C2=A0 Initializing a new collective variable.
colvars:=C2=A0=C2=A0 # n= ame =3D "colvar2" [default]
colvars: Error: no valid componen= ts were provided for this collective variable.
FATAL ERROR: Error = in the collective variables module: exiting.
=
It would be highly appreciable=C2=A0if someone= help me to rectify error =C2=A0 my CVinput file as follows
colvar {
name=C2=A0=C2=A0=C2=A0 gs
=C2=A0lowerBounda= ry 70
=C2=A0upperBoundary 145
=C2=A0 width 1
# The path is defi= ned by 5 reference frames (from string-00.pdb to string-04.pdb)
# Use a= tomic coordinate from atoms 1, 2 and 3 to compute the path
gspath { atoms { atomNumbersRange { 1-1589 } }
refPositionsFile1 0.pdb
refP= ositionsFile2 100.pdb
refPositionsFile3 200.pdb
refPositionsFile4 3= 00.pdb
refPositionsFile5 400.pdb
refPositionsFile6 500.pdb
refP= ositionsFile7 600.pdb
refPositionsFile8 700.pdb
refPositionsFile9 8= 00.pdb
refPositionsFile10 900.pdb
refPositionsFile11 1000.pdb
}=
}

With High Regards<= br>S.VIDHYA SANKAR

<= /div>

--000000000000dd374a05c82ee3a6-- From owner-namd-l@halifax.ks.uiuc.edu Wed Jul 28 20:57:59 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16T1vxM9029106; Wed, 28 Jul 2021 20:57:59 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16T1vxOj029105; Wed, 28 Jul 2021 20:57:59 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16T1vwjo029101; Wed, 28 Jul 2021 20:57:58 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16T1vwC8029100; Wed, 28 Jul 2021 20:57:58 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16T1vlAL029090 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 28 Jul 2021 20:57:48 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16T1s7DO005507 for ; Thu, 29 Jul 2021 01:57:47 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=michael.robinson1@monash.edu; dkim=pass header.s=google header.d=monash.edu Received: from mail-ot1-f46.google.com (mail-ot1-f46.google.com [209.85.210.46]) by mx0a-00007101.pphosted.com with ESMTP id 3a3fsd0x56-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 29 Jul 2021 01:57:46 +0000 Received: by mail-ot1-f46.google.com with SMTP id x15-20020a05683000cfb02904d1f8b9db81so4172947oto.12 for ; Wed, 28 Jul 2021 18:57:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=monash.edu; s=google; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=CkYpF7suDqUUlj1bRKq6k4MUNMfLFB7W8z3lECiQR38=; b=fm6r4nH+r+FTVJ8VqiIfbMRPg58UA94lOvHibdFO1BMhl2gjgS3GFMnVEWq78CSVsa bYHmsLUUIO+cUKrTP4vOojAUfDODZBbF8g7Z6WD7Ea+UlmBI7eRXmFzhyaPfPwCTGeLA IFQhzkATQSEzgcBcXA9UwydySl/rumy8jFsM5dgJIBik4EzL01jJdCnOSvPxq6dlKlC9 j7fuYXhJAIfRswNhdp3z/t4GfMxCwiSVjDOLjFHh2JRdVYdJ7SJP/yPwQF+2MNms6O6c KcdRbg6Ciso/WgED75rnxCvKIvnCJhc8WvA2FcIGbdFNPhhvczy3EzVbsNUbVn2bDz1Q 05EQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=CkYpF7suDqUUlj1bRKq6k4MUNMfLFB7W8z3lECiQR38=; b=kV5k6PS/F+lQR1Q7nt/ayGoWYm+glOrIrya4Mj1jn9Q5Jgn2biL2FSTQmH4IoLD3Cz c8VbrTsxOpwpBHmjXXMJgBqSWKhD07PLFQz2Ev4JKXTBCp7hiXdC9iri6EKYo5HumNhV ISCjEEkTfNHS5J7ZOI8tdRzvfCuRR80HC7RoJYyp5tUjIcJFAUTCkQbf+RzZezYGTFT7 bZFR7fSYtzkR0TePw5/h5dmuN9PstDNWSHjYIY4Im74fn/AWK4j2d87em9XJJH7iNFtp JHjI1A5J6C6AD3Rr75lyVeegr3rK67aT1JwNTOvgmzPMHK9w1BlSE06JYub2UZN3jWy9 JUaQ== X-Gm-Message-State: AOAM532idyv8aBYhN37VDrAonyM0bf1KFZ6BL8h2SdFe0dlFa9977uPW 82UYeavjNkE/hBjT/u5r/e2JTgYzcKN6kkejxFcTwCZCKd0Tsw== X-Google-Smtp-Source: ABdhPJzasxKONdTQI7rBvL1wt19+xIkzeVOZ2J92ifHuPS4IiqxDsNRwEAercmliK6CWxiqQATAWToZEP1l/6AJ/JZo= X-Received: by 2002:a05:6830:1184:: with SMTP id u4mr1827122otq.29.1627523860796; Wed, 28 Jul 2021 18:57:40 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Michael Robinson Date: Thu, 29 Jul 2021 11:57:29 +1000 Message-ID: Subject: Re: namd-l: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? To: namd-l@ks.uiuc.edu, zeynab hosseini Content-Type: multipart/alternative; boundary="000000000000967eb805c8396d2f" X-Proofpoint-ORIG-GUID: QQDzEOg0NKICo-dHmR_z2ADbrGb_lWZU X-Proofpoint-GUID: QQDzEOg0NKICo-dHmR_z2ADbrGb_lWZU X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehceEhEKWUQXZGZbXRoBQkMbfV8RClhYF2ZFS3xkTVsecFh vEQp4ThdvGBIbTAVFQWdoehEKeUwXbx9uTEZHRB9wbxIRCkNIFwceExkRCkNZFwcbHhkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBNxHhIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xe3tuUG9lTRpkYWNpRQdOYkd4dVAYa25IWG1IdUZ9cH8RClhcFx8EGgQYGRkF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdzZBwBGBEKTVwXGBsdEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pMQ0lzaXkBW0B7EQpDWhcYGhMEEh8EGBsaBB 4cEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdvGBIbTAVFQWdoehEKQkkXbxgSG0wFRUFna HoRCkJFF2Z/AUFAf2NZYVJaEQpCThdvGBIbTAVFQWdoehEKQkwXZkVLfGRNWx5wWG8RCkJsF3oa ZgFpblt6EklwEQpCQBdlQk4eR0ByGWBGexEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnl DF2YZXlobGWR8fGhwEQpZSxcdEh4fEQpwZxdsUmRgcAFaGmJFeBAeEhEKcGgXZm1rWl5vS2xLTH sQGRoRCnBoF2sYfB0fXRp6cAVSEBkaEQpwaBdjbHkcX3oFWXBneRAZGhEKcGgXeh4YZ31Ca2FfS EsQGRoRCnBoF2huQkkcb1lsYnpaEBkaEQpwfRdlYVIeTGtIH29lcxAZGhEKcH0XZ0BBb0hab2F7 cl0QGRoRCnBnF29rG2MdGFpSeHpnEBkaEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGcXaUNuUAFZc0c BHlMQGRoRCnB9F2NBBWddQhpbW1tSEBkaEQpwfRdpcmtLSFkeXQVaXxAZGhEKcH0XZ2dMYWgbQ1 ppQEcQGRoRCnB9F2dyUFgSUn5aZUtsEBkaEQpwfxdlGXlmXkdpG2RPcxAeEhEKcF8XY0dnT2Z6Y HJtE1oQGRoRCnB/F2Fmb1saZ2RCSB1bEBsaGREKcF8XY2ISUEhjeB98Qn0QHB0RCnBsF2VdZ0Rl WHlQS0BEEBIaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 impostorscore=0 priorityscore=48 phishscore=0 spamscore=0 suspectscore=0 lowpriorityscore=0 mlxscore=0 bulkscore=0 clxscore=189 malwarescore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107290008 domainage_hfrom=7845 X-Spam-Score: 0 X-Spam-OrigSender: michael.robinson1@monash.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Robinson --000000000000967eb805c8396d2f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Zeynab, I'm unfamiliar with the application of MD to carbon nanotubes, but I just want to add that you no longer need to use CHARMM or CHARMM-GUI to generate a Drude FF .psf file. Psfgen 2.0 was released last year, and can handle structure preparation for the Drude force field in basically the same way as a classical force field - see the latest user's guide: https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf. Psfgen 2.0 comes bundled with the latest alphas of VMD, and my local installation of NAMD 2.14 is also reporting the use of psfgen 2.0. Hopefully that's helpful! Regards, Michael Robinson On Wed, 28 Jul 2021 at 02:37, zeynab hosseini wrote: > Hi Victor > > Well, I know that to use NAMD in order to implement MD simulation with > Drude polarizable FF, CHARMM is needed to generate a CHARMM-compatible .p= sf > file. I don't have access to the CHARMM program and I decided to use > CHARMM-GUI. I posted the question in both the NAMD and CHARMM forum (link > ) > but nobody answered. It seems the CHARMM forum is not as active as the NA= MD > one. I also posted the question in the VMD mailing list. Would be so > thankful if anybody could give me a hint.. > > All the best, > Zeynab > > On Mon, Jul 26, 2021 at 7:31 PM Victor Kwan wrote: > >> This is a CHARMM problem, isn't it? >> ------------------------------ >> *From:* owner-namd-l@ks.uiuc.edu on behalf of >> zeynab hosseini >> *Sent:* Sunday, July 25, 2021 3:07 PM >> *To:* NAMD list >> *Subject:* namd-l: Does CHARMM-GUI Drude-Prepper input generator work >> for MD simulation of carbon nanotubes? >> >> Dear all, >> >> I have the intention to perform molecular dynamics (MD) simulation of >> carbon nanotubes (CNT) using the Drude polarizable force field implement= ed >> in NAMD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CNT= inputs for >> NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulati= on >> (using non-polarizable FF) for this system. But as soon as I=E2=80=8C us= e these >> inputs (.pdb & .psf files) to produce Drude-Prepper inputs for MD >> simulation of polarizable force field, I=E2=80=8C receive a message ment= ioning >> CHARMM was terminated abnormally with the following error. It seems that >> the residue TUBE is not recognized. My question is how it is recognized >> before (when performing MD with non-polarizable force field), but when i= t >> comes to polarizable FF the TUBE residue is not recognized? >> >> CHARMM was terminated abnormally. >> Please check the output or report >> this >> failure to the CHARMM-GUI developers. >> Output Excerpt from step2_drude.out: >> >> Comparing "NONE" and "CNEU". >> IF test evaluated as false. Skipping command >> >> CHARMM> if @cterpatch .eq. CT1 if @cname .eq. GLY set cterpatch = CT1G >> Parameter: CTERPATCH -> "NONE" >> Parameter: CNAME -> "TUBE" >> Comparing "NONE" and "CT1". >> IF test evaluated as false. Skipping command >> >> CHARMM> if @cterpatch .eq. CT2 if @cname .eq. GLY set cterpatch = CT2G >> Parameter: CTERPATCH -> "NONE" >> Parameter: CNAME -> "TUBE" >> Comparing "NONE" and "CT2". >> IF test evaluated as false. Skipping command >> >> CHARMM> >> >> CHARMM> set gene =3D 0 >> Parameter: GENE <- "0" >> >> CHARMM> if @type eq protein then >> Parameter: TYPE -> "ELSE" >> Comparing "ELSE" and "PROTEIN". >> IF test evaluated as false. Skip to ELSE or ENDIF >> >> CHARMM> >> >> CHARMM> if @type eq rna then !UMB: explicitly for rna >> Parameter: TYPE -> "ELSE" >> Comparing "ELSE" and "RNA". >> IF test evaluated as false. Skip to ELSE or ENDIF >> >> CHARMM> >> >> CHARMM> if @type eq dna then !UMB: explicitly for dna >> Parameter: TYPE -> "ELSE" >> Comparing "ELSE" and "DNA". >> IF test evaluated as false. Skip to ELSE or ENDIF >> >> CHARMM> >> >> CHARMM> if @type eq carb then >> Parameter: TYPE -> "ELSE" >> Comparing "ELSE" and "CARB". >> IF test evaluated as false. Skip to ELSE or ENDIF >> >> CHARMM> >> >> CHARMM> if gene .eq. 0 then >> Comparing "0" and "0". >> IF test evaluated as true. Performing command >> >> CHARMM> ! default generate if not protein or water >> >> CHARMM> generate @segname first none last none setup warn drud= e dmass 0.4 ! show >> Parameter: SEGNAME -> "NM" >> Drude polarizability will be setup for SEGID: NM mass of Drudes pa= rticles =3D 0.4000 >> >> ***** ERROR in GENIC ***** Residue 'TUBE ' was not found. >> >> >> >> /---------\ >> / \ >> / \ >> / \ >> ! XXXX XXXX ! >> ! XXXX XXXX ! >> ! XXX XXX ! >> ! X ! >> --\ XXX /-- >> ! ! XXX ! ! >> ! ! ! ! >> ! I I I I I ! >> ! I I I I ! >> \ / >> -- -- >> \---/ >> XXX XXX >> XXXX XXXX >> XXXXX XXXXX >> XXX XXX >> XXX XXX >> XXXXX >> XXX XXX >> XXX XXX >> XXX XXX >> XXXXX XXXXX >> XXXX XXXX >> XXX XXX >> >> >> Execution terminated due to the detection of a fatal error. >> >> ABNORMAL TERMINATION >> MOST SEVERE WARNING WAS AT LEVEL 1 >> >> $$$$$ JOB ACCOUNTING INFORMATION $$$$$ >> ELAPSED TIME: 2.11 SECONDS >> CPU TIME: 2.11 SECONDS >> >> >> >> All the Best, >> Zeynab >> > --000000000000967eb805c8396d2f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Zeynab,

I'm unfamilia= r with the application of MD to carbon nanotubes, but I just want to add th= at you no longer need to use CHARMM or CHARMM-GUI to generate a Drude FF .p= sf file. Psfgen 2.0 was released last year, and can handle structure prepar= ation for the Drude force field in basically the same way as a classical fo= rce field - see the latest user's guide: https://www.ks.uiuc.edu/Research/v= md/plugins/psfgen/ug.pdf.

Psfgen 2.0 comes bun= dled with the latest alphas of VMD, and my local installation of NAMD 2.14 = is also reporting the use of psfgen 2.0. Hopefully that's helpful!
Regards,
Michael Robinson

On Wed, 28 Jul 2021 at 0= 2:37, zeynab hosseini <hos= seinizeynab93@gmail.com> wrote:
Hi Victor

Well, = I know that to use NAMD in order to implement MD simulation with Drude pola= rizable FF, CHARMM is needed to generate a CHARMM-compatible .psf file. I d= on't have access to the CHARMM program and I decided to use CHARMM-GUI.= I posted the question in both the NAMD and CHARMM forum (link)= but nobody answered. It seems the CHARMM forum is not as active as the NAM= D one. I also posted the question in the VMD mailing list. Would be so than= kful if anybody could give me a hint..

All the bes= t,
Zeynab

On Mon, Jul 26, 2021 at 7:31 PM Victor Kwan <vkwan8@uwo.ca> wrot= e:
This is a CHARMM problem, isn't it?

From: owner-namd-l@ks.uiuc.edu <owner-namd-l@ks.uiuc.edu> o= n behalf of zeynab hosseini <hosseinizeynab93@gmail.com>
Sent: Sunday, July 25, 2021 3:07 PM
To: NAMD list <namd-l@ks.uiuc.edu>
Subject: namd-l: Does CHARMM-GUI Drude-Prepper input generator work = for MD simulation of carbon nanotubes?
=C2=A0
Dear all,

I have the intention to perform molecular dynamics (MD) simulation of carbo= n nanotubes (CNT) using the Drude polarizable force field implemented in NA= MD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CNT inputs = for NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation (using non-polarizable FF) for this system. Bu= t as soon as I=E2=80=8C use these inputs (.pdb & .psf files) to produce= Drude-Prepper inputs for MD simulation of polarizable force field, I=E2=80= =8C receive a message mentioning CHARMM was terminated abnormally with the following error. It seems that the residue TUBE is not= recognized. My question is how it is recognized before (when performing MD= with non-polarizable force field), but when it comes to polarizable FF the= TUBE residue is not recognized?

CHARMM was terminated abnormally.=C2=A0
Please check the output or=C2=A0report=C2=A0this failure to the CHARMM-GUI developers.
Output Excerpt from=C2=A0step2_drude.out
 Comparing "NONE" a=
nd "CNEU".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>       if @cterpatch .eq. CT1  if @cname .eq. GLY set cterpatch =
CT1G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT1".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>       if @cterpatch .eq. CT2  if @cname .eq. GLY set cterpatch =
CT2G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT2".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>    =20
 =20
 CHARMM>       set gene =3D 0
 Parameter: GENE <- "0"
 =20
 CHARMM>       if @type eq protein then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "PROTEIN".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq rna then  !UMB: explicitly for rna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "RNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq dna then     !UMB: explicitly for dna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "DNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq carb then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "CARB".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if gene .eq. 0 then
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 =20
 CHARMM>          ! default generate if not protein or water
 =20
 CHARMM>          generate @segname first none last none setup warn drud=
e dmass 0.4 ! show
 Parameter: SEGNAME -> "NM"
 Drude polarizability will be setup for SEGID: NM      mass of Drudes parti=
cles =3D    0.4000

 ***** ERROR in GENIC ***** Residue 'TUBE  ' was not found.


                                                 =20
                            /---------\          =20
                           /           \         =20
                          /             \        =20
                         /               \       =20
                         !  XXXX   XXXX  !       =20
                         !  XXXX   XXXX  !       =20
                         !  XXX     XXX  !       =20
                         !       X       !       =20
                          --\   XXX   /--        =20
                           ! !  XXX  ! !         =20
                           ! !       ! !         =20
                           ! I I I I I !         =20
                           !  I I I I  !         =20
                            \         /          =20
                             --     --           =20
                               \---/             =20
                        XXX             XXX      =20
                       XXXX             XXXX     =20
                       XXXXX           XXXXX     =20
                          XXX         XXX        =20
                            XXX     XXX          =20
                               XXXXX             =20
                              XXX XXX            =20
                            XXX     XXX          =20
                          XXX         XXX        =20
                       XXXXX           XXXXX     =20
                       XXXX             XXXX     =20
                        XXX             XXX      =20
                                                 =20
                                                 =20
 Execution terminated due to the detection of a fatal error.

                    ABNORMAL TERMINATION
                    MOST SEVERE WARNING WAS AT LEVEL  1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.11  SECONDS=20
                         CPU TIME:     2.11  SECONDS 


All the Best,
Zeynab
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charset="UTF-8" X-Proofpoint-ORIG-GUID: ymiHyA8-SF0cLpBfan5wsCiNgV8FhAiq X-Proofpoint-GUID: ymiHyA8-SF0cLpBfan5wsCiNgV8FhAiq X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx4ZEQpMehcZHxkRCllEF2NtGF5wU1prbE9PEQpYWBdpeh99RRhlfwV BQREKeE4XY1Nja3sTWH4aX14RCnlMF25GemVDaFtbAX4aEQpDSBcHGB4eEQpDWRcHGxkTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxgZcRscEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1NHQ2JTaxIHeWwaSWZaaExLRB9dWWlDZE18EmxCa0NbEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc2QFXW8RCk1cFxgeHhEKTFoXaGFNb2sRCkxGF29ra2t raxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx0YEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2McXltoe196ZHxoEQpCThdjU2Nre xNYfhpfXhEKQkwXaXoffUUYZX8FQUERCkJsF21GYXBiH2VwWF1zEQpCQBdjUnxERnpSGFNgGxEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2EYXWNhHWtrY3sZEQpZSxcTHhIYEQpwaBd oGFxlYWNdE0F/WBAZGhEKcGgXbWETclAZbUsaE3wQGRoRCnBoF2JBb0ZobR5cZHpwEBkaEQpwaB dgHnJDeUNkWHkfeBAZGhEKcGgXaXx5YEdrfUF5aFMQGRoRCnBsF3p7fxxmUB1QWGdkEBkaEQptf hcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=714 impostorscore=0 priorityscore=353 phishscore=0 spamscore=0 suspectscore=0 lowpriorityscore=0 mlxscore=0 bulkscore=0 clxscore=143 malwarescore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107290049 domainage_hfrom=9482 X-Spam-Score: 0 X-Spam-OrigSender: shootgoaltag@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 16T7NNlC003641 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Gawtak Kim Hi, I have experience running molecular dynamics simulations using “NAMD_2.14_Win64-multicoreâ€. At that time, I ran NAMD by typing "namd2 +auto-provision" into the Command Prompt, and as a result, CPU 0~39 (40 logical processors) of NUMA Node 0 were used for computation, while CPU 0~39 (40 logical processors) of NUMA Node 1 were not used for computation. For your information, the specifications of the workstation I used at that time are as follows. OS: Windows 10 Pro CPU: Intel Xeon Gold 6242R 3.10 GHz (2 CPUs) 20 physical cores per CPU 2 logical processors per physical core 2 CPUs * 20 cores * 2 logical processors = 80 logical processors GPU: NVIDIA Quadro P2200 (1 GPU) RAM: 512GB However, I want to use both CPU 0~39 (40 logical processors) of NUMA Node 0 and CPU 0~39 (40 logical processors) of NUMA Node 1 at the same time to use the total of 80 logical processors simultaneously. What should I enter in Command Prompt to make this possible? If this is possible, will the simulation speed be twice as fast as the simulation speed at that time? Also, as far as I know, the NVIDIA Quadro P2200 GPU supports CUDA GPU Acceleration. If I use “NAMD_2.14_Win64-multicore-CUDAâ€, can I expect an increase in simulation speed due to CUDA GPU Acceleration? What should I enter in Command Prompt to make this possible? If I should use both 80 logical processors and CUDA GPU Acceleration to maximize simulation speed, what should I enter in Command Prompt to make this possible? Do I need to install one more identical GPU on the workstation to maximize simulation speed? In other words, should the number of CPUs and GPUs be the same? I'd appreciate it if you could answer my question. Thank you. Best regards, Gawtak Kim From owner-namd-l@halifax.ks.uiuc.edu Thu Jul 29 04:11:08 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16T9B8Lg006773; Thu, 29 Jul 2021 04:11:08 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16T9B8Fs006772; Thu, 29 Jul 2021 04:11:08 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16T9B7vX006768; Thu, 29 Jul 2021 04:11:07 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16T9B7Xg006767; Thu, 29 Jul 2021 04:11:07 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16T9B0js006752 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Thu, 29 Jul 2021 09:10:55 +0000 Date: Thu, 29 Jul 2021 09:10:52 +0000 (UTC) From: Vidhya Sankar To: NAMD List Message-ID: <1781506330.509072.1627549852953@mail.yahoo.com> Subject: namd-l: about usage of eABF method MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_509071_1982093072.1627549852952" References: <1781506330.509072.1627549852953.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18762 YMailNorrin X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 3HA06MHIeGDN8K3wMyCIJ98kRjMpjDRm X-CLX-Response: 1TFkXGx0dEQpMehcZGRIRCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHGxIZEQpDWRcHGx8ZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcTcRsGGx13BhscEwYaBhoGHxoGGnEaEBp3BhoGBx8aBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThcZYmsaHGdiY09tbmQSYRldZ1Np Y2ATEkF4QGdaQG54RxEKWFwXHwQaBBgZGQUbGgQbGxoEHxoEGx4YEBseGh8aEQpeWRdzZWh/BRE KTVwXGxobEQpMWhdsaWtraxEKTEYXb2trb2trEQpCTxdiSR96XFgfW3kbHhEKQ1oXGxocBBsaBB geHgQYGhMRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0VsbURDZ hEKQkUXehltQ1tFX2hpfWURCkJOF3pEHB1vRWxtRENmEQpCTBdmYWITYW1ia0lcQhEKQmwXax0f cBlsaUVveFwRCkJAF2hsR2FETnlgH0loEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxgRCnl DF2ViSXhZfFxCQRxMEQpZSxcTHBITEQpwaBdsT0V7UF1yT0RcYRAHGRoRCnBoF2AdGWtFEm5gHE gfEAcZGhEKcGgXa0BSeEcbb2VkT38QBxkaEQpwaBdhYXoFGF1kaBt/eBAHGRoRCnBoF2V4TVgFT WBkeVNHEAcZGhEKcGwXZG9OXEZ+U2h8WVoQBxkaEQpwTBdmBWEcRx1GYXlDfxAHGRoRCm1+Fwcb EQpYTRdLESA= X-Proofpoint-GUID: 3HA06MHIeGDN8K3wMyCIJ98kRjMpjDRm X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=177 adultscore=0 impostorscore=0 suspectscore=0 phishscore=0 mlxlogscore=643 bulkscore=0 spamscore=0 malwarescore=0 priorityscore=338 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107290060 domainage_hfrom=9689 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_509071_1982093072.1627549852952 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd users =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 I ma applying Elecric field=C2=A0during My simulation=C2=A0 for t= ranlocation of molecule through nano pore=C2=A0 =C2=A0So it becomes Non Equ= librium MD . So can i apply eABF method to calculate free energy also it it= suitable to apply eABF method Kindly=C2=A0=C2=A0 give me clarification With High Regards S . Vidhya sankar =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=20 ------=_Part_509071_1982093072.1627549852952 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Dear Namd users
               I ma applying Elecric field during My simulation  for tranlocation of molecule through nano pore 
 So it becomes Non Equlibrium MD . So can i apply eABF method to calculate free energy also it it suitable to apply eABF method
Kindly   give me clarification

With High Regards
S . Vidhya sankar

                          
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X-Proofpoint-ORIG-GUID: sTE-JtzK1Kqcexp4K6fP1eWv6gz666fR X-Proofpoint-GUID: sTE-JtzK1Kqcexp4K6fP1eWv6gz666fR X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxkSEQpMehcZHhkRCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHGxkTEQpDWRcHGBsfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxsScRseEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1l+bwdgXlBhG2FbSU9SWh5hHEx6G099XBxNUBwcHEx4EQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3Nlb0NaEQpNXBcYHh4RCkxaF2hpa2trEQpMRhdva2t va2sRCkJPF2JJH3pcWB9beRseEQpDWhcbGhwEGxoEGB4aBB0SEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRCkJFF3oZbUNbRV9oaX1lEQpCThd6RBwdb 0VsbURDZhEKQkwXZmFiE2FtYmtJXEIRCkJsF2sdH3AZbGlFb3hcEQpCQBdoUkBbclJaeElnYBEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF21hb0xpcBhjWkRvEQpZSxcTHBITEQpwaBd lWGcTZn5JG2JlSxAZGhEKcGgXbRNBHkhNXGVoZmMQGRoRCnBoF3pecF9ZbB5aXmxyEBkaEQpwaB dkYkUfX3pHEk5MZRAZGhEKcGgXekFaZ2V6bGRtfGsQGRoRCnBsF2RvTlxGflNofFlaEBwaEQpwT BdmBWEcRx1GYXlDfxAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 phishscore=0 suspectscore=0 bulkscore=0 spamscore=0 malwarescore=0 mlxlogscore=917 priorityscore=343 impostorscore=0 clxscore=138 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107290082 domainage_hfrom=9689 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_886747_440196778.1627563015804 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd users i tried form metadybamics us RMSD as CV i have following in= put files =C2=A0 colvar {=20 =C2=A0=C2=A0 name=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s=20 =C2=A0 =C2=A0=C2=A0 width=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1=20 =C2=A0 =C2=A0=C2=A0 lowerboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 70=20 =C2=A0=C2=A0 upperboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 145=20 =C2=A0 =C2=A0=C2=A0 lowerwallconstant=C2=A0=C2=A0=C2=A0=C2=A0 10.0=20 =C2=A0=C2=A0 upperwallconstant=C2=A0=C2=A0=C2=A0=C2=A0 10.0=20 =C2=A0 =C2=A0=C2=A0 scriptedFunction=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 source.tcl=20 =C2=A0 =C2=A0=C2=A0 # extendedLagrangian=C2=A0=C2=A0=C2=A0 on=20 =C2=A0 # extendedFluctuation=C2=A0=C2=A0 0.01=20 =C2=A0 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group1=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 0.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 1 }=20 =C2=A0=C2=A0 rmmsd {=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group2=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589=20 =C2=A0refpositionsfile=C2=A0=C2=A0=C2=A0 1000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 2 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0=C2=A0 group3=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 2000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 3 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0=C2=A0 group4=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 3000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 4 }=20 =C2=A0=C2=A0 group5=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 4000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 5 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0 group6=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 5000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 6 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0=C2=A0 group7=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 6000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 7 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0 group8=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 7000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 8 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0 group9=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 8000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 9 }=20 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0 group10=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589=20 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 9000.pdb =C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 10 }=20 =C2=A0 }=20 =C2=A0 #############################################################=20 # ABF section=20 #############################################################=20 =C2=A0 abf {=20 =C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s=20 =C2=A0=C2=A0 fullSamples=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 500=20 }=20 =C2=A0 But when i run the meta dynamics i gt the following error colvars: ------------------------------------------------------------------= ----=20 colvars: Reading new configuration:=20 colvars: # smp =3D on [default]=20 colvars: # analysis =3D off [default]=20 colvars: # colvarsTrajFrequency =3D 1000=20 colvars: # colvarsRestartFrequency =3D 10000 [default]=20 colvars: # scriptedColvarForces =3D off [default]=20 colvars: # scriptingAfterBiases =3D off [default]=20 colvars: Warning: no collective variables defined.=20 colvars: Collective variables initialized, 0 in total.=20 colvars: No collective variables biases were defined.=20 colvars: ------------------------------------------------------------------= ----=20 colvars: Collective variables module (re)initialized.=20 colvars: ------------------------------------------------------------------= ----=20 colvars: ------------------------------------------------------------------= ----=20 colvars: Reading new configuration from file "pathCV1.in":=20 colvars: Error: unmatched curly braces in configuration.=20 FATAL ERROR: Error in the collective variables module: exiting.=20 =C2=A0 ------------- Processor 0 Exiting: Called CmiAbort ------------=20 Reason: FATAL ERROR: Error in the collective variables module: exiting.=20 What are the mistake i did=C2=A0 it would be useful if any one of you point= ed out Even=C2=A0 i tried lot i could not trace out error With regards S.VIDHYASNKAR ------=_Part_886747_440196778.1627563015804 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Namd users i tried form metadybamics us RMSD a= s CV i have following input files

 
colvar {
   name     =              s =
 
   width       &= nbsp;         1
 
 = ;  lowerboundary         70    upperboundary        = ; 145
 
   lowerwallconstant     = 10.0
   upperwallconstant     10.0
&n= bsp;
   scriptedFunction      source.= tcl
 
   # extendedLagrangian    on   # extendedFluctuation   0.01
 
   = rmsd {
      group1
   &nbs= p;  atomNumbersRange  1-1589
 
   &nbs= p; refpositionsfile    0.pdb
     co= mponentExp        1 }
   r= mmsd {
      group2
   &nbs= p;   atomNumbersRange  1-1589
 refpositionsfile&nbs= p;   1000.pdb
     componentExp &nbs= p;      2 }
   rmsd {
 &nbs= p;   group3
       atomNumbersR= ange   1-1589
 
     refpositions= file    2000.pdb
     componentExp&n= bsp;       3 }
   rmsd {
&n= bsp;    group4
       atom= NumbersRange  1-1589
 
     refpositio= nsfile    3000.pdb
     componentExp=         4 }
   group5
=        atomNumbersRange  1-1589
&nbs= p;
     refpositionsfile    4000.pdb =
     componentExp     &nbs= p;  5 }
   rmsd {
    group6
&nbs= p;      atomNumbersRange   1-1589
&n= bsp;
     refpositionsfile    5000.pd= b
     componentExp     &n= bsp;  6 }
   rmsd {
     group7 =
       atomNumbersRange   1-158= 9
 
     refpositionsfile   = 6000.pdb
     componentExp    =     7 }
   rmsd {
    group= 8
       atomNumbersRange   1-1= 589
 
     refpositionsfile  &nbs= p; 7000.pdb
     componentExp   &nbs= p;    8 }
   rmsd {
    gro= up9
       atomNumbersRange   1= -1589
 
     refpositionsfile  &n= bsp; 8000.pdb
     componentExp   &n= bsp;    9 }
   rmsd {
   group10=
      atomNumbersRange  1-1589
 = ;
     refpositionsfile    9000.pdb  componentExp      10 }
 
}  
############################################################# <= br># ABF section
######################################################= #######
 
abf {
   colvars    = ;            s
&= nbsp;  fullSamples        &nbs= p;  500
}
 
But when i run the meta dynamics i= gt the following error
colvars: ----------------------------------------------------= ------------------
colvars: Reading new configuration:
colvars: # s= mp =3D on [default]
colvars: # analysis =3D off [default]
colvars: = # colvarsTrajFrequency =3D 1000
colvars: # colvarsRestartFrequency =3D = 10000 [default]
colvars: # scriptedColvarForces =3D off [default]
c= olvars: # scriptingAfterBiases =3D off [default]
colvars: Warning: no c= ollective variables defined.
colvars: Collective variables initialized,= 0 in total.
colvars: No collective variables biases were defined.
= colvars: ------------------------------------------------------------------= ----
colvars: Collective variables module (re)initialized.
colvars:= ---------------------------------------------------------------------- colvars: -----------------------------------------------------------------= -----
colvars: Reading new configuration from file "pathCV1.in":
co= lvars: Error: unmatched curly braces in configuration.
FATAL ERROR: Err= or in the collective variables module: exiting.
 
-------------= Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR:= Error in the collective variables module: exiting.


What are the mistake i did  = it would be useful if any one of you pointed out Even  i tried lot i c= ould not trace out error

With regards
S.VIDHYASNKAR
=

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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello Vidhya, the presence of an electric field, which I assume to be constant over time (it may or may not change across the simulation cell), means an additional force for each atom. This force *will* be counted in the PMF via different mechanisms, depending on what you use. - Traditional ABF measures the total atomic forces as part of the time integration scheme, and applies the thermodynamic integration (TI) method to these forces to compute a PMF. The external electric potential is th= us included in the PMF in an exact manner. https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-nam= d/colvars-refman-namd.html*sec:colvarbias_abf__;Iw!!DZ3fjg!qd5FTn7rSngKVUB0= 5RcAwMkhlk8dTRj7LtesQia5X80XYJGoeQ_Tj5F0JIJjIfdJUw$=20 - eABF, as well as nearly all other methods (metadynamics, umbrella sampling, SMD, ...) use the resulting trajectory of the variable to estimate the PMF. The external electric potential is thus *sampled* like all other terms of the PMF (both enthalpic and entropic). https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-nam= d/colvars-refman-namd.html*sec:colvarbias_ti_ext_czar__;Iw!!DZ3fjg!qd5FTn7r= SngKVUB05RcAwMkhlk8dTRj7LtesQia5X80XYJGoeQ_Tj5F0JIJWGlPkGw$=20 In either case, the external electric potential becomes part of the PMF, and whether this is representative of a system where there is no such potential, it is up to you. Only in the special case where you're computing a PMF for a single atom using as CV its absolute position (i.e. distance from a dummy atom or from a very large group that effectively doesn't move) you may subtract the electric potential to have an *approximate* idea of how the PMF would be without it. Giacomo On Thu, Jul 29, 2021 at 5:13 AM Vidhya Sankar < vidhyasankar7928@remove_yahoo.com> wrote: > Dear Namd users > I ma applying Elecric field during My simulation for > tranlocation of molecule through nano pore > So it becomes Non Equlibrium MD . So can i apply eABF method to calculate > free energy also it it suitable to apply eABF method > Kindly give me clarification > > With High Regards > S . Vidhya sankar > > > --000000000000f73c3005c842d62b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello Vidhya, the presence of an electric field, which I a= ssume to be constant over time (it may or may not change across the simulat= ion cell), means an additional force for each atom.=C2=A0 This force wil= l be counted in the PMF via different mechanisms, depending on what you= use.
In either case, the external electric potential becomes = part of the PMF, and whether this is representative of a system where there= is no such potential, it is up to you.=C2=A0 Only in the special case wher= e you're computing a PMF for a single atom using as CV its absolute pos= ition (i.e. distance from a dummy atom or from a very large group that effe= ctively doesn't move) you may subtract the electric potential to have a= n approximate idea of how the PMF would be without it.

Giacomo

On Thu, Jul 29, 2021 at 5:13 AM Vidhya Sankar <= vidh= yasankar7928@remove_yahoo.com> wrote:
Dear Namd users
=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I = ma applying Elecric field=C2=A0during My simulation=C2=A0 for = tranlocation of molecule through nano pore=C2=A0
=C2=A0So it bec= omes Non Equlibrium MD . So can i apply eABF method to calculate free energ= y also it it suitable to apply eABF method
Kindly=C2=A0=C2=A0 = give me clarification

With High Regards
S .= Vidhya sankar

=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0
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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello Vidhya, I'm not sure where you have line break characters (which may have changed when you pasted into the email), but their position will matter. I would begin by checking the documentation for what you're using here, which is the Colvars module. Because Colvars is distributed with NAMD for your own convenience, you may also check the embedded chapter in the NAMD user's guide, but I would argue that the one on the Colvars webpage is easier to navigate: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvars_config_syntax__;Iw!!DZ3fjg!riXNzsraGMI_= H1QpHtDzXVDWCPWPvP4b-V_0iXhlAAKAJG__IJQzNgJvVWt5mvyGLA$=20 If you appreciate this distinction, it would make it easier for you to find the correct information. I can't say for sure what is the problem there (there are a few issues that may play into the Colvar parser's weaknesses). Try writing down a simple CV with just one RMSD function: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:cvc_rmsd__;Iw!!DZ3fjg!riXNzsraGMI_H1QpHtDzXVDWC= PWPvP4b-V_0iXhlAAKAJG__IJQzNgJvVWsB-1W1tQ$=20 without scriptedFunction for now. I'm all in favor of using someone else's input as a starting template, but if you don't check yourself what the keywords mean in the doc, you won't get very far with advanced methodology such as enhanced sampling. When you can make it work for one RMSD by fixing all the typos, it's straightforward to add the other RMSD terms. It is also tedious to try and start a new NAMD simulation each time, so why not download the latest VMD alpha build and try the Dashboard GUI? https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-vmd/co= lvars-refman-vmd.html*sec:dashboard__;Iw!!DZ3fjg!riXNzsraGMI_H1QpHtDzXVDWCP= WPvP4b-V_0iXhlAAKAJG__IJQzNgJvVWuOT71IAA$=20 On Thu, Jul 29, 2021 at 8:52 AM Vidhya Sankar < vidhyasankar7928@remove_yahoo.com> wrote: > Dear Namd users i tried form metadybamics us RMSD as CV i have following > input files > > > colvar { > name s > > width 1 > > lowerboundary 70 > upperboundary 145 > > lowerwallconstant 10.0 > upperwallconstant 10.0 > > scriptedFunction source.tcl > > # extendedLagrangian on > # extendedFluctuation 0.01 > > rmsd { > group1 > atomNumbersRange 1-1589 > > refpositionsfile 0.pdb > componentExp 1 } > rmmsd { > group2 > atomNumbersRange 1-1589 > refpositionsfile 1000.pdb > componentExp 2 } > rmsd { > group3 > atomNumbersRange 1-1589 > > refpositionsfile 2000.pdb > componentExp 3 } > rmsd { > group4 > atomNumbersRange 1-1589 > > refpositionsfile 3000.pdb > componentExp 4 } > group5 > atomNumbersRange 1-1589 > > refpositionsfile 4000.pdb > componentExp 5 } > rmsd { > group6 > atomNumbersRange 1-1589 > > refpositionsfile 5000.pdb > componentExp 6 } > rmsd { > group7 > atomNumbersRange 1-1589 > > refpositionsfile 6000.pdb > componentExp 7 } > rmsd { > group8 > atomNumbersRange 1-1589 > > refpositionsfile 7000.pdb > componentExp 8 } > rmsd { > group9 > atomNumbersRange 1-1589 > > refpositionsfile 8000.pdb > componentExp 9 } > rmsd { > group10 > atomNumbersRange 1-1589 > > refpositionsfile 9000.pdb > componentExp 10 } > > } > > ############################################################# > # ABF section > ############################################################# > > abf { > colvars s > fullSamples 500 > } > > > *But when i run the meta dynamics i gt the following error* > > > > > > > > > > > > > > > > > > > > > > > *colvars: > ---------------------------------------------------------------------- > colvars: Reading new configuration: colvars: # smp =3D on [default] colva= rs: > # analysis =3D off [default] colvars: # colvarsTrajFrequency =3D 1000 col= vars: > # colvarsRestartFrequency =3D 10000 [default] colvars: # scriptedColvarFo= rces > =3D off [default] colvars: # scriptingAfterBiases =3D off [default] colva= rs: > Warning: no collective variables defined. colvars: Collective variables > initialized, 0 in total. colvars: No collective variables biases were > defined. colvars: > ---------------------------------------------------------------------- > colvars: Collective variables module (re)initialized. colvars: > ---------------------------------------------------------------------- > colvars: > ---------------------------------------------------------------------- > colvars: Reading new configuration from file "pathCV1.in": colvars: Error: > unmatched curly braces in configuration. FATAL ERROR: Error in the > collective variables module: exiting. ------------- Processor 0 Exiting: > Called CmiAbort ------------ Reason: FATAL ERROR: Error in the collective > variables module: exiting. * > > > What are the mistake i did it would be useful if any one of you pointed > out Even i tried lot i could not trace out error > > With regards > S.VIDHYASNKAR > > > --000000000000dc684505c843210e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello Vidhya, I'm not sure where you have line break c= haracters (which may have changed when you pasted into the email), but thei= r position will matter.

I would begin by checking the do= cumentation for what you're using here, which is the Colvars module.=C2= =A0 Because Colvars is distributed with NAMD for your own convenience, you = may also check the embedded chapter in the NAMD user's guide, but I wou= ld argue that the one on the Colvars webpage is easier to navigate:
http= s://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colv= ars_config_syntax
If you appreciate this distinction, it woul= d make it easier for you to find the correct information.

I can't say for sure what is the problem there (there are a few= issues that may play=C2=A0into the Colvar parser's weaknesses).=C2=A0 = Try writing down a simple CV with just one RMSD function:
= without scriptedFunction for now.=C2=A0 I'm all in favor of using someo= ne else's input as a starting template, but if you don't check your= self what the keywords mean in the doc, you won't get very far with adv= anced methodology such as enhanced sampling.=C2=A0 When you can make it wor= k for one RMSD by fixing all the typos, it's straightforward to add the= other RMSD terms.

It is also tedious to try and s= tart a new NAMD simulation each time, so why not download the latest VMD al= pha build and try the Dashboard GUI?

On Thu, Jul 29, 2021 at 8:52= AM Vidhya Sankar <vidhyasankar7928@remove_yahoo.com> wrote:
Dear Namd users i tried form metadybamics us RMSD= as CV i have following input files

=C2=A0
colvar {
=C2=A0=C2=A0 name=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 s
=C2=A0
=C2=A0=C2=A0 width=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
= =C2=A0
=C2=A0=C2=A0 lowerboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 70
=C2=A0=C2=A0 upperboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 145
=C2=A0
=C2=A0=C2=A0 lowerwallconstant=C2=A0= =C2=A0=C2=A0=C2=A0 10.0
=C2=A0=C2=A0 upperwallconstant=C2=A0=C2=A0=C2= =A0=C2=A0 10.0
=C2=A0
=C2=A0=C2=A0 scriptedFunction=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 source.tcl
=C2=A0
=C2=A0=C2=A0 # extendedLagrangian= =C2=A0=C2=A0=C2=A0 on
=C2=A0 # extendedFluctuation=C2=A0=C2=A0 0.01 =C2=A0
=C2=A0=C2=A0 rmsd {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group1 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 0.pdb
=C2= =A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 1 }
=C2=A0=C2=A0 rmmsd {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group2 =
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589
= =C2=A0refpositionsfile=C2=A0=C2=A0=C2=A0 1000.pdb
=C2=A0=C2=A0=C2=A0=C2= =A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 2 }
=C2=A0= =C2=A0 rmsd {
=C2=A0=C2=A0=C2=A0=C2=A0 group3
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589
=C2=A0
=C2=A0=C2= =A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 2000.pdb
=C2=A0=C2= =A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 3 } =
=C2=A0=C2=A0 rmsd {
=C2=A0=C2=A0=C2=A0=C2=A0 group4
=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNumbersRange=C2=A0 1-1589
=C2=A0
=C2= =A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 3000.pdb
=C2= =A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 4 }
=C2=A0=C2=A0 group5
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 at= omNumbersRange=C2=A0 1-1589
=C2=A0
=C2=A0=C2=A0=C2=A0=C2=A0 refposit= ionsfile=C2=A0=C2=A0=C2=A0 4000.pdb
=C2=A0=C2=A0=C2=A0=C2=A0 componentE= xp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 5 }
=C2=A0=C2=A0 rmsd { =C2=A0=C2=A0=C2=A0 group6
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomNu= mbersRange=C2=A0=C2=A0 1-1589
=C2=A0
=C2=A0=C2=A0=C2=A0=C2=A0 refpos= itionsfile=C2=A0=C2=A0=C2=A0 5000.pdb
=C2=A0=C2=A0=C2=A0=C2=A0 componen= tExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 6 }
=C2=A0=C2=A0 rmsd { =
=C2=A0=C2=A0=C2=A0=C2=A0 group7
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 atomNumbersRange=C2=A0=C2=A0 1-1589
=C2=A0
=C2=A0=C2=A0=C2=A0=C2= =A0 refpositionsfile=C2=A0=C2=A0=C2=A0 6000.pdb
=C2=A0=C2=A0=C2=A0=C2= =A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 7 }
=C2=A0= =C2=A0 rmsd {
=C2=A0=C2=A0=C2=A0 group8
=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589
=C2=A0
=C2=A0=C2=A0=C2= =A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 7000.pdb
=C2=A0=C2=A0=C2= =A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 8 }
= =C2=A0=C2=A0 rmsd {
=C2=A0=C2=A0=C2=A0 group9
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNumbersRange=C2=A0=C2=A0 1-1589
=C2=A0
=C2=A0=C2= =A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 8000.pdb
=C2=A0=C2= =A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 9 } =
=C2=A0=C2=A0 rmsd {
=C2=A0=C2=A0 group10
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 atomNumbersRange=C2=A0 1-1589
=C2=A0
=C2=A0=C2=A0=C2=A0=C2= =A0 refpositionsfile=C2=A0=C2=A0=C2=A0 9000.pdb
=C2=A0 componentExp=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 10 }
=C2=A0
}
=C2=A0
############= #################################################
# ABF section
###= ##########################################################
=C2=A0
ab= f {
=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s
=C2=A0=C2=A0 fullSample= s=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 500
} =C2=A0
But when i run the meta dynamics i gt the following erro= r

colvars: ---------------------= -------------------------------------------------
colvars: Reading new = configuration:
colvars: # smp =3D on [default]
colvars: # analysis = =3D off [default]
colvars: # colvarsTrajFrequency =3D 1000
colvars:= # colvarsRestartFrequency =3D 10000 [default]
colvars: # scriptedColva= rForces =3D off [default]
colvars: # scriptingAfterBiases =3D off [defa= ult]
colvars: Warning: no collective variables defined.
colvars: Co= llective variables initialized, 0 in total.
colvars: No collective vari= ables biases were defined.
colvars: -----------------------------------= -----------------------------------
colvars: Collective variables modul= e (re)initialized.
colvars: -------------------------------------------= ---------------------------
colvars: ----------------------------------= ------------------------------------
colvars: Reading new configuration= from file "pathCV1.in":
colvars: Error: unmatched curly brac= es in configuration.
FATAL ERROR: Error in the collective variables mod= ule: exiting.
=C2=A0
------------- Processor 0 Exiting: Called CmiAb= ort ------------
Reason: FATAL ERROR: Error in the collective variables= module: exiting.


What are the m= istake i did=C2=A0 it would be useful if any one of you pointed out Even=C2= =A0 i tried lot i could not trace out error

Wi= th regards
S.VIDHYASNKAR

--000000000000dc684505c843210e-- From owner-namd-l@halifax.ks.uiuc.edu Thu Jul 29 10:42:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16TFgJai017603; Thu, 29 Jul 2021 10:42:19 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16TFgJbJ017602; Thu, 29 Jul 2021 10:42:19 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16TFgIkv017598; Thu, 29 Jul 2021 10:42:18 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16TFgIOT017597; Thu, 29 Jul 2021 10:42:18 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16TFg6Ub017589 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 29 Jul 2021 10:42:06 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16TFXbme007832 for ; Thu, 29 Jul 2021 15:42:06 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=hosseinizeynab93@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-il1-f173.google.com (mail-il1-f173.google.com [209.85.166.173]) by mx0b-00007101.pphosted.com with ESMTP id 3a3kwpufpp-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 29 Jul 2021 15:42:05 +0000 Received: by mail-il1-f173.google.com with SMTP id r5so6324615ilc.13 for ; Thu, 29 Jul 2021 08:42:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=CikjG28LxMcLtLMX7ne802siIXAm8Z8+FfGSKfN2twc=; b=dJ4Apn9aPUVADk3InIrODrUYh0gN4yNYqNPOnTapEzyF2M3qrw+cFlZBRtLeA5Y4Id rG0sWWPnv/D5g1uTbWx0VV2H4iGNYdSxSnAW/7zcQqzXYlnZaSRLehgk8Jg15Ctg1rLV LUZsGgbq++XglDDK1U0r+unIkp0zfcpEwCyWGwcrMsFlnLbrFlyh/9ylAA874xy/0PpX rUtYzfIJ5bF2QLXt+0scwlQqq6w6PSqqcTiZ10DlFZGZlTt6ARajQsSHZLBHd00P3coT Z9QA5UoT2cAeiQzk2tpP493gj6ns0s4E7qU8CvuccEzDbgykfP8BA2krMECrDInWTmKQ n7Aw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=CikjG28LxMcLtLMX7ne802siIXAm8Z8+FfGSKfN2twc=; b=rRMXUldvbpDOesIwAzOwO/NCYjSsIK1DOLiMAHJEuLmuzAiwRjVsHZRkG7ig+ql+Ef 2GbTyjMcjzLsZyhLjk0xaLAgjJUsQuJ4UWKUZu25KmAw0mSOzkQb25mkHtHIAA2PFllZ AzetsJbhztVKI06S+zHiS5YxNG4Oee97KweQLCeKuCdhzgw1EygJuZptFOUPjHDl+mdA g6vMvnipeb1LbdRxPEPopJjJtRdbsEsdVjneFBRgxPkgdi6pRnZcNZZt+9WrNXM1dmR/ 36k0JRbOo3Nqm8DXuGRrcClzaKu2JE7vw+eVBTGmImpi/GyhMo3lyqvrUbw5fVx2JSRt qTgw== X-Gm-Message-State: AOAM530pzH0MIjDqCAGrjoJB9j7vze6lNZUXqi08tsBkIRIAorBNRNy0 MbiPUWKN5TWawmhqzwxw1wsSNk6XCKPx0gwbyiU= X-Google-Smtp-Source: ABdhPJyfuLtSSMF4VSE+GRuh7/CHRMbcceefJjfMojMITf1gHgEBixtHn0kbQr2f1zlRNEpzu9v0DLk1g/nUmUjtifA= X-Received: by 2002:a92:1805:: with SMTP id 5mr4100860ily.138.1627573325075; Thu, 29 Jul 2021 08:42:05 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: zeynab hosseini Date: Thu, 29 Jul 2021 11:36:23 -0400 Message-ID: Subject: Re: namd-l: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? To: Michael Robinson Cc: NAMD list Content-Type: multipart/alternative; boundary="000000000000e3178905c844f186" X-Proofpoint-GUID: h0uN6B_BmEoprZGQh57isw-IGzckifzx X-CLX-Response: 1TFkXGxIZEQpMehcZGhkRCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHHhscEQpDWRcHGxkbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwZcR4YEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0IaX2QcaHVoR29FWlhwbXtCHx1DWV0HY21QSUFDTFBSEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NlYm5aEQpNXBcZHB4RCkxaF3hpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHB wEGx0ZEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF298TxtvXkVfchgYEQpCThdjU2NrexNYfhpfXhEKQkwXaHp7YG5wUnNwWl8RCkJs F29QBX9PYWYZT0VyEQpCQBdlQk4eR0ByGWBGexEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF2Y ZXlobGWR8fGhwEQpZSxcTHhIYEQpwZxdtXXJjeGNDE3AeXBAZGhEKcGgXbV9pW2UTSR1kZ3oQGR oRCnBoF2Zta1peb0tsS0x7EB4SEQpwaBdrGHwdH10aenAFUhAZGhEKcGgXY2x5HF96BVlwZ3kQH hIRCnBoF2huQkkcb1lsYnpaEB4SEQpwfRdlYVIeTGtIH29lcxAZGhEKcH0XZ0BBb0hab2F7cl0Q GRoRCnBnF29rG2MdGFpSeHpnEB4SEQpwZxdtR2FrTWMZTFNpbhAeEhEKcGcXaUNuUAFZc0cBHlM QGRoRCnB9F2NBBWddQhpbW1tSEBkaEQpwfRdpcmtLSFkeXQVaXxAZGhEKcH0XZ2dMYWgbQ1ppQE cQHhIRCnB9F2dyUFgSUn5aZUtsEBkaEQpwfxdlGXlmXkdpG2RPcxAcGhEKcF8XY0dnT2Z6YHJtE 1oQHhIRCnB/F2Fmb1saZ2RCSB1bEBsZGREKcF8XY2ISUEhjeB98Qn0QGxobEQpwbBdsUh1baWZs XnJIYRAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: h0uN6B_BmEoprZGQh57isw-IGzckifzx X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 suspectscore=0 phishscore=0 mlxlogscore=999 adultscore=0 priorityscore=303 mlxscore=0 clxscore=183 impostorscore=0 lowpriorityscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107290097 domainage_hfrom=9482 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --000000000000e3178905c844f186 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Michael, I really appreciate your help. I'll try it.. All the best, Zeynab On Wed, Jul 28, 2021 at 9:57 PM Michael Robinson < michael.robinson1@monash.edu> wrote: > Hi Zeynab, > > I'm unfamiliar with the application of MD to carbon nanotubes, but I just > want to add that you no longer need to use CHARMM or CHARMM-GUI to genera= te > a Drude FF .psf file. Psfgen 2.0 was released last year, and can handle > structure preparation for the Drude force field in basically the same way > as a classical force field - see the latest user's guide: > https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf. > > Psfgen 2.0 comes bundled with the latest alphas of VMD, and my local > installation of NAMD 2.14 is also reporting the use of psfgen 2.0. > Hopefully that's helpful! > Regards, > Michael Robinson > > On Wed, 28 Jul 2021 at 02:37, zeynab hosseini > wrote: > >> Hi Victor >> >> Well, I know that to use NAMD in order to implement MD simulation with >> Drude polarizable FF, CHARMM is needed to generate a CHARMM-compatible .= psf >> file. I don't have access to the CHARMM program and I decided to use >> CHARMM-GUI. I posted the question in both the NAMD and CHARMM forum (lin= k >> ) >> but nobody answered. It seems the CHARMM forum is not as active as the N= AMD >> one. I also posted the question in the VMD mailing list. Would be so >> thankful if anybody could give me a hint.. >> >> All the best, >> Zeynab >> >> On Mon, Jul 26, 2021 at 7:31 PM Victor Kwan wrote: >> >>> This is a CHARMM problem, isn't it? >>> ------------------------------ >>> *From:* owner-namd-l@ks.uiuc.edu on behalf >>> of zeynab hosseini >>> *Sent:* Sunday, July 25, 2021 3:07 PM >>> *To:* NAMD list >>> *Subject:* namd-l: Does CHARMM-GUI Drude-Prepper input generator work >>> for MD simulation of carbon nanotubes? >>> >>> Dear all, >>> >>> I have the intention to perform molecular dynamics (MD) simulation of >>> carbon nanotubes (CNT) using the Drude polarizable force field implemen= ted >>> in NAMD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CN= T inputs for >>> NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulat= ion >>> (using non-polarizable FF) for this system. But as soon as I=E2=80=8C u= se these >>> inputs (.pdb & .psf files) to produce Drude-Prepper inputs for MD >>> simulation of polarizable force field, I=E2=80=8C receive a message men= tioning >>> CHARMM was terminated abnormally with the following error. It seems tha= t >>> the residue TUBE is not recognized. My question is how it is recognized >>> before (when performing MD with non-polarizable force field), but when = it >>> comes to polarizable FF the TUBE residue is not recognized? >>> >>> CHARMM was terminated abnormally. >>> Please check the output or report >>> this >>> failure to the CHARMM-GUI developers. >>> Output Excerpt from step2_drude.out: >>> >>> Comparing "NONE" and "CNEU". >>> IF test evaluated as false. Skipping command >>> >>> CHARMM> if @cterpatch .eq. CT1 if @cname .eq. GLY set cterpatch= CT1G >>> Parameter: CTERPATCH -> "NONE" >>> Parameter: CNAME -> "TUBE" >>> Comparing "NONE" and "CT1". >>> IF test evaluated as false. Skipping command >>> >>> CHARMM> if @cterpatch .eq. CT2 if @cname .eq. GLY set cterpatch= CT2G >>> Parameter: CTERPATCH -> "NONE" >>> Parameter: CNAME -> "TUBE" >>> Comparing "NONE" and "CT2". >>> IF test evaluated as false. Skipping command >>> >>> CHARMM> >>> >>> CHARMM> set gene =3D 0 >>> Parameter: GENE <- "0" >>> >>> CHARMM> if @type eq protein then >>> Parameter: TYPE -> "ELSE" >>> Comparing "ELSE" and "PROTEIN". >>> IF test evaluated as false. Skip to ELSE or ENDIF >>> >>> CHARMM> >>> >>> CHARMM> if @type eq rna then !UMB: explicitly for rna >>> Parameter: TYPE -> "ELSE" >>> Comparing "ELSE" and "RNA". >>> IF test evaluated as false. Skip to ELSE or ENDIF >>> >>> CHARMM> >>> >>> CHARMM> if @type eq dna then !UMB: explicitly for dna >>> Parameter: TYPE -> "ELSE" >>> Comparing "ELSE" and "DNA". >>> IF test evaluated as false. Skip to ELSE or ENDIF >>> >>> CHARMM> >>> >>> CHARMM> if @type eq carb then >>> Parameter: TYPE -> "ELSE" >>> Comparing "ELSE" and "CARB". >>> IF test evaluated as false. Skip to ELSE or ENDIF >>> >>> CHARMM> >>> >>> CHARMM> if gene .eq. 0 then >>> Comparing "0" and "0". >>> IF test evaluated as true. Performing command >>> >>> CHARMM> ! default generate if not protein or water >>> >>> CHARMM> generate @segname first none last none setup warn dru= de dmass 0.4 ! show >>> Parameter: SEGNAME -> "NM" >>> Drude polarizability will be setup for SEGID: NM mass of Drudes p= articles =3D 0.4000 >>> >>> ***** ERROR in GENIC ***** Residue 'TUBE ' was not found. >>> >>> >>> >>> /---------\ >>> / \ >>> / \ >>> / \ >>> ! XXXX XXXX ! >>> ! XXXX XXXX ! >>> ! XXX XXX ! >>> ! X ! >>> --\ XXX /-- >>> ! ! XXX ! ! >>> ! ! ! ! >>> ! I I I I I ! >>> ! I I I I ! >>> \ / >>> -- -- >>> \---/ >>> XXX XXX >>> XXXX XXXX >>> XXXXX XXXXX >>> XXX XXX >>> XXX XXX >>> XXXXX >>> XXX XXX >>> XXX XXX >>> XXX XXX >>> XXXXX XXXXX >>> XXXX XXXX >>> XXX XXX >>> >>> >>> Execution terminated due to the detection of a fatal error. >>> >>> ABNORMAL TERMINATION >>> MOST SEVERE WARNING WAS AT LEVEL 1 >>> >>> $$$$$ JOB ACCOUNTING INFORMATION $$$$$ >>> ELAPSED TIME: 2.11 SECONDS >>> CPU TIME: 2.11 SECONDS >>> >>> >>> >>> All the Best, >>> Zeynab >>> >> --000000000000e3178905c844f186 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Michael,

I really appreciate=C2=A0yo= ur help. I'll try it..

All the best,
Zeynab

On Wed, Jul 28, 2021 at 9:57 PM Michael Robinson <michael.robinson1@monash.edu&g= t; wrote:
Hi Zeynab,

I'm unfamiliar with= the application of MD to carbon nanotubes, but I just want to add that you= no longer need to use CHARMM or CHARMM-GUI to generate a Drude FF .psf fil= e. Psfgen 2.0 was released last year, and can handle structure preparation = for the Drude force field in basically the same way as a classical force fi= eld - see the latest user's guide: https://www.ks.uiuc.ed= u/Research/vmd/plugins/psfgen/ug.pdf.

Psfgen 2= .0 comes bundled with the latest alphas of VMD, and my local installation o= f NAMD 2.14 is also reporting the use of psfgen 2.0. Hopefully that's h= elpful!
Regards,
Michael Robinson

On Wed, 28 J= ul 2021 at 02:37, zeynab hosseini <hosseinizeynab93@gmail.com> wrote:
Hi Vi= ctor

Well, I know that to use NAMD in order to implement= MD simulation with Drude polarizable FF, CHARMM is needed to generate a CH= ARMM-compatible .psf file. I don't have access to the CHARMM program an= d I decided to use CHARMM-GUI. I posted the question in both the NAMD and C= HARMM forum (link) but nobody answered. It seems the CHARMM foru= m is not as active as the NAMD one. I also posted the question in the VMD m= ailing list. Would be so thankful if anybody could give me a hint..

All the best,
Zeynab

On Mon, Jul 26, 2021= at 7:31 PM Victor Kwan <vkwan8@uwo.ca> wrote:
This is a CHARMM problem, isn't it?

From: owner-namd-l@ks.uiuc.edu <owner-n= amd-l@ks.uiuc.edu> on behalf of zeynab hosseini <hosseinizeynab93@gmail.com<= /a>>
Sent: Sunday, July 25, 2021 3:07 PM
To: NAMD list <
namd-l@ks.uiuc.edu>
Subject: namd-l: Does CHARMM-GUI Drude-Prepper input generator work = for MD simulation of carbon nanotubes?
=C2=A0
Dear all,

I have the intention to perform molecular dynamics (MD) simulation of carbo= n nanotubes (CNT) using the Drude polarizable force field implemented in NA= MD. I=E2=80=8Cnitially, I used CHARMM-GUI to produce a solvated CNT inputs = for NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation (using non-polarizable FF) for this system. Bu= t as soon as I=E2=80=8C use these inputs (.pdb & .psf files) to produce= Drude-Prepper inputs for MD simulation of polarizable force field, I=E2=80= =8C receive a message mentioning CHARMM was terminated abnormally with the following error. It seems that the residue TUBE is not= recognized. My question is how it is recognized before (when performing MD= with non-polarizable force field), but when it comes to polarizable FF the= TUBE residue is not recognized?

CHARMM was terminated abnormally.=C2=A0
Please check the output or=C2=A0report=C2=A0this failure to the CHARMM-GUI developers.
Output Excerpt from=C2=A0step2_drude.out
 Comparing "NONE" a=
nd "CNEU".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>       if @cterpatch .eq. CT1  if @cname .eq. GLY set cterpatch =
CT1G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT1".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>       if @cterpatch .eq. CT2  if @cname .eq. GLY set cterpatch =
CT2G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT2".
 IF test evaluated as false.  Skipping command
 =20
 CHARMM>    =20
 =20
 CHARMM>       set gene =3D 0
 Parameter: GENE <- "0"
 =20
 CHARMM>       if @type eq protein then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "PROTEIN".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq rna then  !UMB: explicitly for rna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "RNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq dna then     !UMB: explicitly for dna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "DNA".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if @type eq carb then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "CARB".
 IF test evaluated as false.  Skip to ELSE or ENDIF
 =20
 CHARMM>    =20
 =20
 CHARMM>       if gene .eq. 0 then
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 =20
 CHARMM>          ! default generate if not protein or water
 =20
 CHARMM>          generate @segname first none last none setup warn drud=
e dmass 0.4 ! show
 Parameter: SEGNAME -> "NM"
 Drude polarizability will be setup for SEGID: NM      mass of Drudes parti=
cles =3D    0.4000

 ***** ERROR in GENIC ***** Residue 'TUBE  ' was not found.


                                                 =20
                            /---------\          =20
                           /           \         =20
                          /             \        =20
                         /               \       =20
                         !  XXXX   XXXX  !       =20
                         !  XXXX   XXXX  !       =20
                         !  XXX     XXX  !       =20
                         !       X       !       =20
                          --\   XXX   /--        =20
                           ! !  XXX  ! !         =20
                           ! !       ! !         =20
                           ! I I I I I !         =20
                           !  I I I I  !         =20
                            \         /          =20
                             --     --           =20
                               \---/             =20
                        XXX             XXX      =20
                       XXXX             XXXX     =20
                       XXXXX           XXXXX     =20
                          XXX         XXX        =20
                            XXX     XXX          =20
                               XXXXX             =20
                              XXX XXX            =20
                            XXX     XXX          =20
                          XXX         XXX        =20
                       XXXXX           XXXXX     =20
                       XXXX             XXXX     =20
                        XXX             XXX      =20
                                                 =20
                                                 =20
 Execution terminated due to the detection of a fatal error.

                    ABNORMAL TERMINATION
                    MOST SEVERE WARNING WAS AT LEVEL  1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.11  SECONDS=20
                         CPU TIME:     2.11  SECONDS 


All the Best,
Zeynab
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boundary="00000000000023e7c705c8510594" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: xcGgR2jxCwZJfcc2bo_LC2RWvLaWHHYH X-CLX-Response: 1TFkXGxMaEQpMehcZHhIRCllEF3prYB9EQ0wbfEtPEQpYWBdoWUcSGQF8ZXJ HQREKeE4XY1Nja3sTWH4aX14RCnlMF2FLBR17fENHZGdHEQpDSBcHGxgYEQpDWRcHGB8aEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1JJbU14GEBSaV1wYExJSRhIRXVmaRh4fVxmS31iYnNiEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3Nlfl4FEQpNXBcbEhoRCkxaF2hpTU1NEQpMRhdva2t ra2sRCkJPF21tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBBsSGxEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdrRHNuGxgZZERfaBEKQk4XY1Nja 3sTWH4aX14RCkJMF2hZRxIZAXxlckdBEQpCbBduehhwfEV8Yn8baREKQkAXZGhwTW9uY35zZ0gR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxduQB5fclMSHWVwfREKWUsXEx4SGREKcGg XaHkTcG0YQ2h8XRkQGRoRCnBoF2AYTElPEm1kRk9pEBkaEQpwaBdiUGNnf3hAH05IeBAZGhEKcG gXZXtgYRtlGnlfWBgQGRoRCnBoF2NSX3JnWR5gZVxdEBkaEQpwbBdmRVhoGm5dTnBtRBAZGhEKb X4XGxEKWE0XSxEg X-Proofpoint-GUID: xcGgR2jxCwZJfcc2bo_LC2RWvLaWHHYH X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=190 adultscore=0 impostorscore=0 suspectscore=0 phishscore=0 mlxlogscore=473 bulkscore=0 spamscore=0 malwarescore=0 priorityscore=348 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107300036 domainage_hfrom=9483 X-Spam-Score: 0 X-Spam-OrigSender: zebamir85@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Amir Zeb --00000000000023e7c705c8510594 Content-Type: text/plain; charset="UTF-8" Hello NAMD users! I want to restart a simulation in NAMD, which was previously stopped/crashed. I'm getting an error "Fatal error: Errors in the configuration file" when I restart my simulation and I uncomment: firsttimestep 952000 ;# last step from previous simulation numteps 150000 ;# total number of steps but when I comment these steps as: #firsttimestep #numsteps The simulation restarts smoothly, but the dcd file will print the trajectory from the beginning. Could anyone please help me to solve this problem? I shall be thankful for the cooperation. Amir --00000000000023e7c705c8510594 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello NAMD users!

I wa= nt to restart a simulation in NAMD, which was previously stopped/crashed.
I'm getting an error "Fatal error: Errors in the con= figuration file" when I restart my simulation and I uncomment:
firsttimestep 952000=C2=A0 =C2=A0 =C2=A0 =C2=A0;# last step from previou= s=C2=A0simulation
numteps=C2=A0 =C2=A0 =C2=A0 =C2=A0150000=C2=A0 = =C2=A0 =C2=A0 =C2=A0;# total number of steps=C2=A0
but when I com= ment these steps as:
#firsttimestep=C2=A0=C2=A0
#numste= ps=C2=A0
The simulation restarts smoothly,=C2=A0but the=C2=A0dcd = file will print the trajectory from the beginning.
Could anyone p= lease help me to solve this problem?

I shall be th= ankful for the=C2=A0cooperation.

Amir
<= /div>
--00000000000023e7c705c8510594-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jul 30 01:18:34 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16U6IYom017101; Fri, 30 Jul 2021 01:18:34 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16U6IXQp017100; Fri, 30 Jul 2021 01:18:33 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16U6IXaw017096; Fri, 30 Jul 2021 01:18:33 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16U6IXCf017095; Fri, 30 Jul 2021 01:18:33 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16U6IJ7W017087 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 30 Jul 2021 01:18:20 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16U6DplH000493 for ; Fri, 30 Jul 2021 06:18:19 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3a3nxwf9ut-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 30 Jul 2021 06:18:19 +0000 Received: from [IPv6:2a02:810c:300:6724:65d6:eba6:aed8:b327] ([IPv6:2a02:810c:300:6724:65d6:eba6:aed8:b327]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 16U6I9Xo011983 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Fri, 30 Jul 2021 08:18:16 +0200 Subject: Re: namd-l: Fatal Error: Error in the configuration file To: namd-l@ks.uiuc.edu, Amir Zeb References: From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <4e6de6e3-0cc7-08de-b749-d249bd262f64@physik.uni-kl.de> Date: Fri, 30 Jul 2021 08:18:07 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: de-DE X-Spam-Status: No, hits=-0.124, tests=HELO_NO_DOMAIN=0.001,NICE_REPLY_A=-0.125 X-Spam-Score: (-0.124) X-Spam-Flag: NO X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: AzJ7_p9EwVMhqXz3kfizzviZ1g42qYoP X-CLX-Response: 1TFkXGx0TEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsZHREKQ1kXBxwZEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8TcRkSEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF2tQYB11WhNvXXxnQltyUBlBTENQUFxDcBtNHhhbc0V6EQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3Nlfh9tEQpNXBcZGxwRCkxaF3hhTUFNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF21Oc1hwWmVofQVbEQpCWBdnc2VzQG5hYUxdYhEKWlgX GBEKeUMXbF1IeGYaThpgZBoRCnBoF2MYWGtzWVgTQHp6EBkaEQpwaBdgGExJTxJtZEZPaRAcGhE KcGgXZlpQYF1QHFpbcGcQGRoRCnBoF2AeYkVQSXgFX19hEBkaEQpwaBdgZ0tpcGVTWQVMfBAZGh EKcGwXeh94eW94TENfcEQQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: AzJ7_p9EwVMhqXz3kfizzviZ1g42qYoP X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=179 adultscore=0 impostorscore=0 suspectscore=0 phishscore=0 mlxlogscore=999 bulkscore=0 spamscore=0 malwarescore=0 priorityscore=0 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107300037 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Hi Amir,     numsteps must be larger than firsttimestep in order for any step will be done. numsteps can be used to complete a certain number missing number of steps: i.e. setting it to 1.000.000 in your case makes namd run for the missing 48.000 timesteps.     And "run XXX" muste be removed when using numsteps. For any other guidance you need to give the specific error line. Cheers René On 7/30/2021 8:06 AM, Amir Zeb wrote: > Hello NAMD users! > > I want to restart a simulation in NAMD, which was previously > stopped/crashed. > I'm getting an error "Fatal error: Errors in the configuration file" > when I restart my simulation and I uncomment: > firsttimestep 952000       ;# last step from previous simulation > numteps       150000       ;# total number of steps > but when I comment these steps as: > #firsttimestep > #numsteps > The simulation restarts smoothly, but the dcd file will print the > trajectory from the beginning. > Could anyone please help me to solve this problem? > > I shall be thankful for the cooperation. > > Amir -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany From owner-namd-l@halifax.ks.uiuc.edu Fri Jul 30 04:43:51 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16U9hpSu022039; Fri, 30 Jul 2021 04:43:51 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16U9hp80022038; Fri, 30 Jul 2021 04:43:51 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16U9horT022034; Fri, 30 Jul 2021 04:43:50 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16U9hoqa022033; Fri, 30 Jul 2021 04:43:50 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 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7mr1763791ilx.269.1627647055584; Fri, 30 Jul 2021 05:10:55 -0700 (PDT) MIME-Version: 1.0 From: zeynab hosseini Date: Fri, 30 Jul 2021 08:05:13 -0400 Message-ID: Subject: namd-l: Problem with creating Drude-compatible .psf file for amino acid To: NAMD list Content-Type: multipart/alternative; boundary="0000000000009165b605c8561ca0" X-Proofpoint-ORIG-GUID: cwiB7ntPQAJtX7qHb9GS96waaJ3CFfzP X-Proofpoint-GUID: cwiB7ntPQAJtX7qHb9GS96waaJ3CFfzP X-CLX-Response: 1TFkXGxIfEQpMehcZGR0RCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHGRobEQpDWRcHGBoZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0ldQ2gdRF56e2tgXnIdW2JIE215ExxdS0tgGWlsTFB6EQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc2VwblgRCk1cFxgTHhEKTFoXaWhpa01NEQpMRhdva2t ra2sRCkJPF21tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBBsSGhEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdvfE8bb15FX3IYGBEKQk4XY1Nja 3sTWH4aX14RCkJMF2h6e2BucFJzcFpfEQpCbBdvUAV/T2FmGU9FchEKQkAXYhxGfxMfXEZDRHgR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcfEQp5QxdlGEQfaRh+bEYZWBEKWUsXEx4SGREKcGc XbXxLXmZFR01LSR0QGRoRCnBoF2cYWWFaG3NGRR0TEBoRCnBoF2VMelB7eEZkaVxZEBoRCnBoF2 dSE3gSWHkcRR94EBoRCnBoF2NJH24bUEx5UnkFEBkaEQpwaBdkQn5gWUEFTFhHEhAaEQpwfRdtH R0BWnx6YnhAHRAZGhEKcH0XbB0Telp/W05eGVoQGRoRCnB9F25vYRtJQxxuemQfEBkaEQpwfRdg XVluW2FzGkJgfxAZGhEKcH8XYWZvWxpnZEJIHVsQGxgbEQpwXxdjYhJQSGN4H3xCfRAdEhEKcH8 XZVhyGB1JGF5GaXwQGxkaEQpwXxdiUAFJGWV7f0caaBAZGhEKcGwXbFIdW2lmbF5ySGEQHhIRCn BMF21oZRlBUn17GEVSEBoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=337 impostorscore=0 bulkscore=0 mlxscore=0 mlxlogscore=999 lowpriorityscore=0 spamscore=0 adultscore=0 suspectscore=0 clxscore=185 phishscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107300078 domainage_hfrom=9483 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --0000000000009165b605c8561ca0 Content-Type: text/plain; charset="UTF-8" Dear all, I wanted to do a test run for the molecular dynamics simulation of an amino acid (AA) using Drude polarizable force field (FF). I picked ASP AA ( ASP_autopsf.pdb ) and used psfgen (vmd-1.9.4a51) to create ASP .psf and .pdb files compatible with Drude FF. Initially, I performed the following script without the terminal patches (first NTER; last CTER) and I noticed that some atoms from the ASP terminals are missing. Then, I added the terminal patches as follows, but the produced .pdb file ( ASP-p.pdb & ASP-p.psf ) contains an extra Oxygen atom (and related lone-pair) located at the origin which is far from the ASP itself. ############ package require psfgen topology drude_toppar_2019/toppar_drude_master_protein_2019g.str segment AP1 { pdb ASP_autopsf.pdb first NTER last CTER auto angles dihedrals } coordpdb ASP_autopsf.pdb AP1 guesscoord writepdb ASP-p.pdb writepsf ASP-p.psf ###################### Here is the output for the script including the terminal patches: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64) Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to vmd@ks.uiuc.edu Info) Please include this reference in published work using VMD: Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Info) ------------------------------------------------------------- Info) Multithreading available, 8 CPUs detected. Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT Info) Free system memory: 4988MB (63%) Info) No CUDA accelerator devices available. Info) Dynamically loaded 3 plugins in directory: Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile 2.0 psfgen) reading topology file drude_toppar_2019/toppar_drude_master_protein_2019g.str psfgen) DRUDE master topology and parameter stream file psfgen) Includes water, 2013 psfgen) Ions updated, June 2018 psfgen) Nucleic acid/carbohydrate/lipid update January 2017 psfgen) Opt molecular ions, fylin 2018 psfgen) Halogen and NBFIX terms, fylin 2018 psfgen) Updated protein FF with opt alpha/Thole, fylin 2018 psfgen) psfgen) reading topology from stream file psfgen) Topology for drude water, ions and proteins psfgen) psfgen) Created by CHARMM version 41 psfgen) cross-term entries present in topology definitions psfgen) skipping parameters in stream file psfgen) Drude polarizable FF parameters psfgen) psfgen) building segment AP1 psfgen) reading residues from pdb file ASP_autopsf.pdb psfgen) extracted 1 residues from pdb file psfgen) setting patch for first residue to NTER psfgen) setting patch for last residue to CTER psfgen) enabling angle autogeneration psfgen) enabling dihedral autogeneration Info: generating structure... psfgen) Info: skipping bond C-N at beginning of segment. psfgen) Info: skipping improper N-C-CA-HN at beginning of segment. psfgen) Info: skipping improper C-CA-N-O at beginning of segment. psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment. psfgen) Info: skipping conformation CA-C-N-CA at beginning of segment. psfgen) Info: skipping conformation N-CA-C-O at beginning of segment. psfgen) Info: skipping conformation N-CA-C-N at beginning of segment. psfgen) Info: skipping conformation C-N-CA-C at beginning of segment. psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment. segment complete. psfgen) reading coordinates from pdb file ASP_autopsf.pdb for segment AP1 psfgen) Info: guessing coordinates for 3 atoms (1 non-hydrogen) psfgen) Info: guessing coordinates for 8 lonepairs psfgen) Warning: failed to guess coordinates for 3 atoms psfgen) Info: writing pdb file ASP-p.pdb psfgen) Info: pdb file complete. psfgen) Info: writing psf file ASP-p.psf psfgen) total of 36 atoms psfgen) total of 10 drude particles psfgen) total of 4 anisotropy entries psfgen) total of 8 lone pairs psfgen) total of 32 bonds psfgen) total of 24 angles psfgen) total of 30 dihedrals psfgen) total of 2 impropers psfgen) total of 0 explicit exclusions psfgen) Structure requires EXTended PSF format psfgen) total of 0 cross-terms psfgen) Info: psf file complete. vmd > ######################## The relate lines of .pdb are as following: ################### REMARK original generated coordinate pdb file ATOM 1 N ASP A 201 54.031 29.991 188.076 1.00 0.00 AP1 N ATOM 2 DN ASP A 201 54.031 29.991 188.076 1.00 0.00 AP1 N ATOM 3 HT1 ASP A 201 54.797 30.563 188.371 1.00 0.00 AP1 H ATOM 4 HT2 ASP A 201 53.531 29.653 188.874 1.00 0.00 AP1 H ATOM 5 HT3 ASP A 201 53.418 30.519 187.488 1.00 0.00 AP1 H ATOM 6 CA ASP A 201 54.552 28.848 187.319 1.00 0.00 AP1 C ATOM 7 DCA ASP A 201 54.552 28.848 187.319 1.00 0.00 AP1 C ATOM 8 HA ASP A 201 55.030 29.254 186.434 1.00 0.00 AP1 H ATOM 9 C ASP A 201 53.431 27.920 186.831 1.00 0.00 AP1 C ATOM 10 DC ASP A 201 53.431 27.920 186.831 1.00 0.00 AP1 C *ATOM 11 O ASP A 201 0.000 0.000 0.000 -1.00 0.00 AP1 OATOM 12 DO ASP A 201 0.000 0.000 0.000 -1.00 0.00 AP1 OATOM 13 LPOA ASP A 201 0.000 0.000 0.000 -1.00 0.00 AP1 HATOM 14 LPOB ASP A 201 0.000 0.000 0.000 -1.00 0.00 AP1 H* ATOM 15 OT1 ASP A 201 52.551 28.286 187.132 1.00 0.00 AP1 O ATOM 16 DOT1 ASP A 201 52.551 28.286 187.132 1.00 0.00 AP1 O ATOM 17 OT2 ASP A 201 53.836 27.160 186.323 1.00 0.00 AP1 O ATOM 18 DOT2 ASP A 201 53.836 27.160 186.323 1.00 0.00 AP1 O ################## Would you kindly guide me on what is wrong? All the best, Zeynab --0000000000009165b605c8561ca0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear all,

I wanted to do a test run for= the molecular dynamics simulation of an amino acid (AA) using Drude polari= zable force field (FF). I picked=C2=A0ASP AA (ASP_autopsf.pdb) and used ps= fgen (vmd-1.9.4a51) to create ASP .psf and .pdb files compatible with Drude= FF. Initially, I performed the following script without the terminal patch= es (first NTER; last CTER) and I noticed=C2=A0 that some atoms from the ASP= terminals are missing. Then, I added the terminal patches as follows, but = the produced .pdb file (=C2=A0ASP-p.pdb=C2=A0&=C2=A0ASP-p.psf) contai= ns an extra Oxygen atom (and related lone-pair) located at the origin which= is far from the ASP itself.=C2=A0
############
package= require psfgen
topology drude_toppar_2019/toppar_drude_master_protein_2= 019g.str
segment AP1 {
pdb ASP_autopsf.pdb
first NTER
last CTER=
auto angles dihedrals
}
coordpdb ASP_autopsf.pdb AP1
guesscoor= d
writepdb=C2=A0ASP-p.pdb
writepsf=C2=A0ASP-p.psf
###= ###################

Here is the output for the scr= ipt including the terminal=C2=A0patches:
rlwrap: Command not found.=
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1= : no version information available (required by /usr/local/lib/vmd/vmd_LINU= XAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)Info)=C2=A0http://www.ks.uiuc.edu/Research/vmd/=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0
Info) = Email questions and bug reports to=C2=A0vmd@ks.uiuc.edu=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0=C2=A0
Info) Please include this reference in published work using VM= D: =C2=A0=C2=A0
Info) =C2=A0 =C2=A0Humphrey, W., Dalke, A. and Schulten,= K., `VMD - Visual =C2=A0=C2=A0
Info) =C2=A0 =C2=A0Molecular Dynamics= 9;, J. Molec. Graphics 1996, 14.1, 33-38.
Info) ------------------------= -------------------------------------
Info) Multithreading available, 8 = CPUs detected.
Info) =C2=A0 CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 H= T=C2=A0
Info) Free system memory: 4988MB (63%)
Info) No CUDA accelera= tor devices available.
Info) Dynamically loaded 3 plugins in directory:<= br>Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
2.0
psfgen) re= ading topology file drude_toppar_2019/toppar_drude_master_protein_2019g.str=

psfgen) =C2=A0DRUDE master topology and parameter stream file=C2=A0=
psfgen) =C2=A0Includes water, 2013
psfgen) =C2=A0Ions updated, June = 2018
psfgen) =C2=A0Nucleic acid/carbohydrate/lipid update January 2017psfgen) =C2=A0Opt molecular ions, fylin 2018
psfgen) =C2=A0Halogen and= NBFIX terms, fylin 2018
psfgen) =C2=A0Updated protein FF with opt alpha= /Thole, fylin 2018
psfgen) =C2=A0
psfgen) reading topology from strea= m file
psfgen) =C2=A0Topology for drude water, ions and proteins
psfg= en) =C2=A0
psfgen) Created by CHARMM version 41
psfgen) cross-term en= tries present in topology definitions
psfgen) skipping parameters in str= eam file
psfgen) =C2=A0Drude polarizable FF parameters=C2=A0
psfgen) = =C2=A0
psfgen) building segment AP1
psfgen) reading residues from pdb= file ASP_autopsf.pdb
psfgen) extracted 1 residues from pdb file
psfg= en) setting patch for first residue to NTER
psfgen) setting patch for la= st residue to CTER
psfgen) enabling angle autogeneration
psfgen) enab= ling dihedral autogeneration
Info: generating structure...
psfgen) In= fo: skipping bond C-N at beginning of segment.
psfgen) Info: skipping im= proper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping imprope= r C-CA-N-O at beginning of segment.
psfgen) Info: skipping cross-term C-= N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conforma= tion CA-C-N-CA at beginning of segment.
psfgen) Info: skipping conformat= ion N-CA-C-O at beginning of segment.
psfgen) Info: skipping conformatio= n N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation = C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-= CA-N-HN at beginning of segment.


segment complete.
psfgen) re= ading coordinates from pdb file ASP_autopsf.pdb for segment AP1
psfgen) = Info: guessing coordinates for 3 atoms (1 non-hydrogen)
psfgen) Info: gu= essing coordinates for 8 lonepairs
psfgen) Warning: failed to guess coor= dinates for 3 atoms
psfgen) Info: writing pdb file ASP-p.pdb
psfgen) = Info: pdb file complete.
psfgen) Info: writing psf file ASP-p.psf
psf= gen) total of 36 atoms
psfgen) total of 10 drude particles
psfgen) to= tal of 4 anisotropy entries
psfgen) total of 8 lone pairs
psfgen) tot= al of 32 bonds
psfgen) total of 24 angles
psfgen) total of 30 dihedra= ls
psfgen) total of 2 impropers
psfgen) total of 0 explicit exclusion= s
psfgen) Structure requires EXTended PSF format
psfgen) total of 0 c= ross-terms
psfgen) Info: psf file complete.
vmd >=C2=A0

########################

The = relate lines of .pdb are as following:

###########= ########
REMARK original generated coordinate pdb file
ATO= M =C2=A0 =C2=A0 =C2=A01 =C2=A0N =C2=A0 ASP A 201 =C2=A0 =C2=A0 =C2=A054.031= =C2=A029.991 188.076 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0N=
ATOM =C2=A0 =C2=A0 =C2=A02 =C2=A0DN =C2=A0ASP A 201 =C2=A0 =C2=A0 =C2= =A054.031 =C2=A029.991 188.076 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP= 1 =C2=A0N
ATOM =C2=A0 =C2=A0 =C2=A03 =C2=A0HT1 ASP A 201 =C2=A0 =C2=A0 = =C2=A054.797 =C2=A030.563 188.371 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2= =A0AP1 =C2=A0H
ATOM =C2=A0 =C2=A0 =C2=A04 =C2=A0HT2 ASP A 201 =C2=A0 =C2= =A0 =C2=A053.531 =C2=A029.653 188.874 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 = =C2=A0AP1 =C2=A0H
ATOM =C2=A0 =C2=A0 =C2=A05 =C2=A0HT3 ASP A 201 =C2=A0 = =C2=A0 =C2=A053.418 =C2=A030.519 187.488 =C2=A01.00 =C2=A00.00 =C2=A0 =C2= =A0 =C2=A0AP1 =C2=A0H
ATOM =C2=A0 =C2=A0 =C2=A06 =C2=A0CA =C2=A0ASP A 20= 1 =C2=A0 =C2=A0 =C2=A054.552 =C2=A028.848 187.319 =C2=A01.00 =C2=A00.00 =C2= =A0 =C2=A0 =C2=A0AP1 =C2=A0C
ATOM =C2=A0 =C2=A0 =C2=A07 =C2=A0DCA ASP A = 201 =C2=A0 =C2=A0 =C2=A054.552 =C2=A028.848 187.319 =C2=A01.00 =C2=A00.00 = =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0C
ATOM =C2=A0 =C2=A0 =C2=A08 =C2=A0HA =C2= =A0ASP A 201 =C2=A0 =C2=A0 =C2=A055.030 =C2=A029.254 186.434 =C2=A01.00 =C2= =A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0H
ATOM =C2=A0 =C2=A0 =C2=A09 =C2= =A0C =C2=A0 ASP A 201 =C2=A0 =C2=A0 =C2=A053.431 =C2=A027.920 186.831 =C2= =A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0C
ATOM =C2=A0 =C2=A0 10= =C2=A0DC =C2=A0ASP A 201 =C2=A0 =C2=A0 =C2=A053.431 =C2=A027.920 186.831 = =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0C
ATOM =C2=A0 =C2= =A0 11 =C2=A0O =C2=A0 ASP A 201 =C2=A0 =C2=A0 =C2=A0 0.000 =C2=A0 0.000 =C2= =A0 0.000 -1.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0O
ATOM =C2=A0 = =C2=A0 12 =C2=A0DO =C2=A0ASP A 201 =C2=A0 =C2=A0 =C2=A0 0.000 =C2=A0 0.000 = =C2=A0 0.000 -1.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0O
ATOM =C2= =A0 =C2=A0 13 LPOA ASP A 201 =C2=A0 =C2=A0 =C2=A0 0.000 =C2=A0 0.000 =C2=A0= 0.000 -1.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0H
ATOM =C2=A0 =C2= =A0 14 LPOB ASP A 201 =C2=A0 =C2=A0 =C2=A0 0.000 =C2=A0 0.000 =C2=A0 0.000 = -1.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0H

ATOM =C2=A0 =C2=A0 = 15 =C2=A0OT1 ASP A 201 =C2=A0 =C2=A0 =C2=A052.551 =C2=A028.286 187.132 =C2= =A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0O
ATOM =C2=A0 =C2=A0 16= DOT1 ASP A 201 =C2=A0 =C2=A0 =C2=A052.551 =C2=A028.286 187.132 =C2=A01.00 = =C2=A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0O
ATOM =C2=A0 =C2=A0 17 =C2=A0O= T2 ASP A 201 =C2=A0 =C2=A0 =C2=A053.836 =C2=A027.160 186.323 =C2=A01.00 =C2= =A00.00 =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0O
ATOM =C2=A0 =C2=A0 18 DOT2 ASP A= 201 =C2=A0 =C2=A0 =C2=A053.836 =C2=A027.160 186.323 =C2=A01.00 =C2=A00.00 = =C2=A0 =C2=A0 =C2=A0AP1 =C2=A0O
##################
=
Would you kindly guide me on what is wrong?

All the best,
Zeynab
--0000000000009165b605c8561ca0-- From owner-namd-l@halifax.ks.uiuc.edu Fri Jul 30 16:57:51 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16ULvp1T004748; Fri, 30 Jul 2021 16:57:51 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16ULvpVe004747; Fri, 30 Jul 2021 16:57:51 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16ULvokV004743; Fri, 30 Jul 2021 16:57:50 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 16ULvoje004742; Fri, 30 Jul 2021 16:57:50 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 16ULvfuX004735 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 30 Jul 2021 16:57:41 -0500 (CDT) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 16ULrF4d009076 for ; Fri, 30 Jul 2021 21:57:40 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=rlwoltz@ucdavis.edu; dkim=pass header.d=ucdavis.edu header.s=google Received: from mail-lj1-f181.google.com (mail-lj1-f181.google.com [209.85.208.181]) by mx0b-00007101.pphosted.com with ESMTP id 3a3ju8df3j-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 30 Jul 2021 21:57:40 +0000 Received: by mail-lj1-f181.google.com with SMTP id a7so14338743ljq.11 for ; Fri, 30 Jul 2021 14:57:39 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=ucdavis.edu; s=google; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=h8LOXVHUV6AIK2/47Je3qUn2XyEk9ZPvrKgsvU4k9Sw=; b=AItGcqXH2zo2mzeppYNmRSXWP7ursrDYc6CghWZLvPAUu8u+r45NjTxf/90elfSGVJ DCXVWx9jMgiastLb038X02TH/AuuJYAXGF6sjyCTSv9iZEDOelIj5u289Vgz/9+dCv2l dO97c2bYYvESvH5i7IXrlmrDTZBL0bmx7amBM= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=h8LOXVHUV6AIK2/47Je3qUn2XyEk9ZPvrKgsvU4k9Sw=; b=W6HUNe6yao3xn3Fs556mjVq4AL4JdTKdZHzi/mmZtJRVV4L4rHbceuMmdblD32iBN7 I3QX99Ye3LgbHMhHR22OAbE5k55B+ik52rIkCqkSmYmgqV9NqKdTCt+DCP/nbtEH7ge8 B6D3sYyk/nEP44RWtVg54tWzpeKxW73AsbVk6376THlBniwcmub4whhtL4EETqGRMhsI P9RKRALgjSgfQGdEamJESP9IZSKkLOvhwc5O+7DPKCH0tyWTPG/Oy02lfDBRpl7iqk4+ j9RBn6nId3KlXIpiBqh5AFjfdW74Djy5Ng2Pq02rB27vmFDkx9aKTVWh8l/Bm/MiFi94 4EHw== X-Gm-Message-State: AOAM530ZxjXJXIEQ0ML4rgDFsOaTmFy7oCxIgEfgZ5W2kGxOQuoivw5+ HOWXms6ufsdZ/wTh37KvQuyw2IjqMZ6jUzimyBpc X-Google-Smtp-Source: ABdhPJxHqhS6a9XpEjvJe2if1jm/wM0obR7/RZls9DxXkmvEyg6c1xto5mx4ew96SNLFGakUFJ4FrDU1SzeQxA2LJcs= X-Received: by 2002:a2e:a78c:: with SMTP id c12mr3089849ljf.319.1627682258007; Fri, 30 Jul 2021 14:57:38 -0700 (PDT) References: <21F183D7-03E4-42ED-BA48-659C976C3953@msu.edu> In-Reply-To: <21F183D7-03E4-42ED-BA48-659C976C3953@msu.edu> From: Ryan Woltz Date: Fri, 30 Jul 2021 14:57:27 -0700 Message-ID: Subject: Re: namd-l: Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. To: "Vermaas, Josh" Cc: "namd-l@ks.uiuc.edu" Content-Type: multipart/alternative; boundary="000000000000cc14d005c85e4e8f" X-Proofpoint-ORIG-GUID: GMFmqZlRzN9Hdyf6EC49xpKGx4IT-IbV X-Proofpoint-GUID: GMFmqZlRzN9Hdyf6EC49xpKGx4IT-IbV X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIZEQpMehcbHBwRCllEF25BW1sfQnx4RWYFEQpYWBdnaUQcbhpbYHt uYREKeE4XYm5hExJ7aW17SHwRCnlMF2hcXn9LZn8dc15oEQpDSBcHHxoTEQpDWRcHEx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBlxHhgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XbWdsR1twRnhQZBNiTlNMHG9pHhNSWmFtUh5jfgdjSHwRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc2VCWlwRCk1cFxgfGxEKTFoXfGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrfFlQWBlpXhhmWhEKQ1oXGBoTBBIfBBgaEg QbEhsRCkJeFxsRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2JuYRMSe2lte0h8EQpCSRdibmETEntpb XtIfBEKQkUXY1p6QmUdcnljUAURCkJOF2JuYRMSe2lte0h8EQpCTBdnaUQcbhpbYHtuYREKQmwX bEZBehlyWF8cb2URCkJAF2lfGGAaS3NyZxsfEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXEhE KeUMXb3B4ZGEYbmYdE18RCnBnF21HYWtNYxlMU2luEBkaEQpwaBdtYWMfX0wFeh9pBRAZGhEKcG gXZF1NTH9JAQFhRX4QGRoRCnBoF2cfbkhsTHxhUBlFEBkaEQpwaBdvek5wTGRlW0RzehAZGhEKc GgXYmkBcGViSENnb3gQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwfRdgQVpwUhsceWJvZxAZGhEK cH0XehlFXkBNQkNgRmEQGRoRCnB9F2ZQexkcE2ZiTUxSEBkaEQpwfRduHBhDRBkcWXJDexAZGhE KcH0Xa1x7T0tGHFhTc0cQGRoRCnB9F2NbGlsYbhpwZmhMEBkaEQpwfxdlGXlmXkdpG2RPcxASHx EKcF8XZlBAYGUTWGJtYngQGRoRCnB/F2Fmb1saZ2RCSB1bEBsYGxEKcF8XY1AcemlSHV0YZ0IQG x4ZEQpwfxdsBXpDGkBHWxMYYxAdHxEKcF8Xb15NHGwFT0BQW10QGRoRCnBfF2deZHlOSWhDZ39k EBsZExEKcH8Xb0RhUBITfxscEn4QGBwRCnBfF25uR2dAEmF7X3wBEBkaEQpwXxdtfG5EchpAZl4 bRBAbHhoRCnBsF2hZfHxEfkFlU19vEBkaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 phishscore=0 suspectscore=0 bulkscore=0 spamscore=0 malwarescore=0 mlxlogscore=999 priorityscore=166 impostorscore=0 clxscore=183 mlxscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2107300149 X-Spam-Score: 0 X-Spam-OrigSender: rlwoltz@ucdavis.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ryan Woltz --000000000000cc14d005c85e4e8f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Josh, Thank you for your advice and apologies for such a delay. I wanted to make sure things were working correctly and with your help I think I found the solution. While on the NAMD3 website it says it can handle constraints. Here are my constraints I use for namd2.14: constraints on #delete for namd3 consref restraints/ca_prot_step7_13.ref #delete for namd3 conskfile restraints/ca_prot_step7_13.ref #delete for namd3 conskcol B #delete for namd3 constraintScaling 1.0 #delete for namd3 The "delete for namd3" I add in as a way for my .inp creation script to know which lines to remove when converting to namd3. Again I have 2 wquilibration steps the standard charmm-gui step6.1-6.6 and a 13 step process that slowly releases constraints from the CA atom of the protein (step7.1-7.13). This is from step7.13 and at step7.14 which is the production step I run for the system. I normally had the above options for step7.14 where the beta value in the constraints files were 0.00 but even having these options cause the cuRAND error which seems to be a CUDA failure based on the websites I pasted. Removing these options fixed the CUDA incompatibility. But you are right that I'm getting instability with namd3. The biggest issue is I have a Selectivity filter of an ion channel that starts with potassium in the filter. However, some of the outer most potassiums leave and are replaced by smaller waters and cause the selectivity filter to collapse region by region. This is just going to be testing out parameters to fix it or go back to NAMD2.14 but thought I'd put that in for developers. I hope this helps people in the future that got the CUDA incompatibility errors I did. I also noticed that if I ran with cudasoaintegrate off I didn't get the any errors in NAMD3 with the constraint options presented above. Thanks for some good direction in solving this Josh, have a good day. Cheers, Ryan On Wed, Jul 21, 2021 at 7:56 AM Vermaas, Josh wrote: > Hi Ryan, > > > > In my experience, NAMD3.0a9 can restart from 2.14 inputs, and I=E2=80=99v= e done it > for membrane systems. However, I=E2=80=99ll admit that I don=E2=80=99t us= e CHARMM-GUI=E2=80=99s > recommended scheme for equilibrating the membrane, which I think is too > conservative. There isn=E2=80=99t anything obviously wrong with your inpu= t deck. > One thing I=E2=80=99d check is the intermediate structures, particularly = near the > indices that NAMD is barfing on. One thing I **have** noticed is that > minimization with 3.0a9 is broken, with or without CUDASOAIntegrate. In > some cases, it is possible to end up with very unphysical structures, and > the structures rattle themselves apart once dynamics starts. Otherwise, y= ou > may have an inadvertent ring piercing, which will also cause dynamics to > blow up. > > > > -Josh > > > > *From: * on behalf of Ryan Woltz < > rlwoltz@ucdavis.edu> > *Reply-To: *"namd-l@ks.uiuc.edu" , Ryan Woltz < > rlwoltz@ucdavis.edu> > *Date: *Tuesday, July 20, 2021 at 7:18 PM > *To: *"namd-l@ks.uiuc.edu" > *Subject: *namd-l: Please ignore previous poor formatted: difficulty > converting namd2 channel system to namd3 Atom velocity too fast, box too > small errors. > > > > Dear community, > > > > I have a 300k atom membrane embedded channel system that is stable > on NAMD2.14 but wanted to upgrade to take advantage of the increased > speed. I downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on > EXPANSE if that matters. I've had several errors which I fixed a few but > not sure how it affects my system, I don't expect they did but I'll state > them as I go along just in case. Almost all errors relate to > cudasoaintegrate. > > > > My system is set up as follows. Minimize, equilibrate system > (step6.1-6.6), slowly release restraints on protein to prevent large RMSD > jumps (Step7.1-7.13), production (step7.14). > > > > A. My first attempt was to use NAMD3 to continue a NAMD2.14 run that > was in production for 30ns. This failed immediately with error: > > OPENING EXTENDED SYSTEM TRAJECTORY FILE > FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, > 0, 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, > line 4263 > on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202 > > From what I gathered from posts you cannot continue a NAMD2 simulation > with NAMD3. Or more specifically the post said I cannot continue a > simulation that did not previously include cudasoaintegrate turned on. > > > > Working with NAMD3 from beginning: > > 1. I then tried starting it from scratch by separating the minimize > step and the equilibration steps (6.1-6.6) but the cudasoaintegrate > turned on is not compatible with reassigntemp or reassignfreq. > 2. I then turned off cudasoaintegrate for steps 6.1-6.6 and then > turned it on for steps 7.1 and beyond as the steps with protein restra= ints > on the CA atoms which are slowly released in steps 7.1-7.13 do not req= uire > reassignment. I used suggested options such as 1) margin 8 2) > outputEnergies/outputTiming=3D 400 3) pairlistpercycle =3D 4 4) stepsp= ercycle =3D > 40. Simulation fails quickly with atoms moving too fast. > > C. I then readjusted outputEnergies/outputTiming to 5000 (charmm-gui > default). However, step7.1 fails after 105000 steps due to fatal error > Periodic cell has become too small for original patch grid! Possible > solutions are to restart from a recent checkpoint, increase margin, or > disable useFlexibleCell for liquid simulation.. > > D. I played with the margins 0-20 and once I no longer got the atoms > escaping error I then got the allocated memory exceeded, too many atoms in > a patch error. > > E. Finally I also took out pairlistpercycle and stepspercycle as noted > on NAMD3 website that these are obsolete. Now the error of ERROR: Atoms > moving too fast at timestep 135902; simulation has become unstable (0 ato= ms > on pe 0). > > FATAL ERROR: SequencerCUDA: Atoms moving too fast > > > > I was able to collect bits and pieces from the forums but mostly it is on > NAMD2 or on NAMD3 but the errors were similar but not the same. From error > E) I don=E2=80=99t think I=E2=80=99m running out of RAM since I have 93GB= allocated and it > runs fine on NAMD2. > > > > I=E2=80=99ve gotten most of my information from Nvidia=E2=80=99s website = and NAMD3 website > and adjusted .inp files based on these sites. > > > > https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ > > > > https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-= up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!rOr1R5qxMp08_Zhow= TZDdM9_tNyocI-3NJ1sUj2B8O5tBuS_wnEuK2eN_a-3cKjLFQ$=20 > > > > > I have a suspicion that the reason things are failing after equilibration > is because I=E2=80=99m turning on cudasoaintegrate after dynamics has sta= rted. > However, I don=E2=80=99t know how to equilibrate with cudasoaintegrate on= and > reassignTemp/reassingFreq. I=E2=80=99ve worked a year to get this system = stable so > don=E2=80=99t want to play around too much with options I=E2=80=99m unfam= iliar with. Again > system is stable with NAMD2 and most of the errors I get is failure due to > the cudasoaintegrate option on. If any of these steps or errors could be > fixed even if there was an option to do steps6.1-7.13 without > cudasoaintegrate on and turn it on for the production I=E2=80=99d be happ= y. I=E2=80=99m > also wondering if cudasoaintegrate doesn=E2=80=99t like restraints on the= protein > as I=E2=80=99ve been told by others that use very early versions. > > > > Any suggestions on how to fix any of these errors? Do I just need to keep > playing with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ > stepspercycle parameters until it works? > > > > Attachments > > > > > https://urldefense.com/v3/__https://drive.google.com/drive/folders/1NgNWL= rDFQLdcB77I0U9U_sGD2KVEoJ_X?usp=3Dsharing__;!!DZ3fjg!rOr1R5qxMp08_ZhowTZDdM= 9_tNyocI-3NJ1sUj2B8O5tBuS_wnEuK2eN_a_6FCk_Ng$=20 > > > > > Thank you, > > > > Ryan > --000000000000cc14d005c85e4e8f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Josh,

=C2=A0 =C2=A0 =C2=A0 Thank you= for your advice and apologies for such a delay. I wanted to make sure thin= gs were working correctly and with your help I think I found the solution. = While on the NAMD3 website it says it can handle constraints. Here are my c= onstraints I use for namd2.14:

constraints =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0#delete for namd3consref =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 restraints= /ca_prot_step7_13.ref=C2=A0 =C2=A0 #delete for namd3
conskfile =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 restraints/ca_prot_step7_13.ref= =C2=A0 =C2=A0 #delete for namd3
conskcol =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0B=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 #delete for namd3
c= onstraintScaling =C2=A0 =C2=A0 =C2=A0 1.0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 #delete for namd3

= The "delete for namd3" I add in as a way for my .inp creation scr= ipt to know which lines to remove when converting=C2=A0to namd3. Again I ha= ve 2 wquilibration steps the standard charmm-gui step6.1-6.6 and a 13 step = process that slowly=C2=A0releases constraints from the CA atom of the prote= in (step7.1-7.13). This is from step7.13 and at step7.14 which is the produ= ction step I run for the system. I normally had the above options for step7= .14 where the beta value in the constraints files were 0.00 but even having= these options cause the cuRAND error which seems to be a CUDA failure base= d on the websites I pasted. Removing these options fixed the CUDA incompati= bility. But you are right that I'm getting instability with namd3. The = biggest issue is I have a Selectivity filter of an ion channel that starts = with potassium in the filter. However, some of the outer most=C2=A0potassiu= ms leave and are replaced by smaller waters and cause the selectivity filte= r to collapse region by region. This is just going to be testing out parame= ters to fix it or go back to NAMD2.14 but thought I'd put that in for d= evelopers.=C2=A0

I hope this helps people in the f= uture that got the CUDA incompatibility errors I did. I also noticed that i= f I ran with cudasoaintegrate=C2=A0 =C2=A0 off I didn't get the any err= ors in NAMD3 with the constraint options presented above. Thanks for some g= ood direction in solving this Josh, have a good day.

Cheers,

Ryan

On Wed, Jul 21, 2021 at 7:56 = AM Vermaas, Josh <vermaasj@msu.edu> wrote:

Hi Ryan,

=C2=A0

In my experience, NAMD3.0a9 can restart from 2.14 in= puts, and I=E2=80=99ve done it for membrane systems. However, I=E2=80=99ll = admit that I don=E2=80=99t use CHARMM-GUI=E2=80=99s recommended scheme for = equilibrating the membrane, which I think is too conservative. There isn=E2=80=99t anything obviously wrong with your input deck. One thing I= =E2=80=99d check is the intermediate structures, particularly near the indi= ces that NAMD is barfing on. One thing I *have* noticed is that mini= mization with 3.0a9 is broken, with or without CUDASOAIntegrate. In some cases, it is possible to end up with very unphysical structures, a= nd the structures rattle themselves apart once dynamics starts. Otherwise, = you may have an inadvertent ring piercing, which will also cause dynamics t= o blow up.

=C2=A0

-Josh

=C2=A0

From: = <owner-namd-l@ks.uiuc.edu&g= t; on behalf of Ryan Woltz <rlwoltz@ucdavis.edu>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, Ryan Woltz <rlwoltz@ucdavis.edu>
Date: Tuesday, July 20, 2021 at 7:18 PM
To: "na= md-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>
Subject: namd-l: Please ignore previous poor formatted: difficulty c= onverting namd2 channel system to namd3 Atom velocity too fast, box too sma= ll errors.

=C2=A0

Dear community,

=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0I have a 300k atom membrane embed= ded channel system that is stable on NAMD2.14 but wanted to upgrade to take= advantage of the increased speed.=C2=A0 I downloaded NAMD3.0 alpha9. I'm also using the V100 GPUs on EXPANSE if that matters. I've had = several errors which I fixed a few but not sure how it affects my system, I= don't expect they did but I'll state them as I go along just in ca= se. Almost all errors relate to cudasoaintegrate.

=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0My system is set up a= s follows. Minimize, equilibrate system (step6.1-6.6), slowly release restr= aints on protein to prevent large RMSD jumps (Step7.1-7.13), production (st= ep7.14).=C2=A0

=C2=A0

A.=C2=A0=C2=A0=C2=A0 My first attempt was to use NAMD3 to continue a NAMD2.14 run that= was in production for 30ns. This failed immediately with error:<= /u>

OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: CUDA cuRAND error curandGenerateNormal(gen, gaussrand_x, n, 0,= 1) in file src/SequencerCUDAKernel.cu, function langevinVelocitiesBBK2, li= ne 4263
=C2=A0on Pe 0 (exp-12-57 device 0 pci 0:af:0): status value 202

From what I gathered from posts you cannot continue a NAMD2 simulation= with NAMD3. Or more specifically the post said I cannot continue a simulat= ion that did not previously include cudasoaintegrate turned on.



Working with NAMD3 from beginning:

  1. I then tried start= ing it from scratch by separating the minimize step and the equilibration s= teps (6.1-6.6) but the cudasoaintegrate turned on is not compatible with reassigntemp or reassignfreq.=C2= =A0
  2. I then turned off = cudasoaintegrate for steps 6.1-6.6 and then turned it on for steps 7.1 and = beyond as the steps with protein restraints on the CA atoms which are slowl= y released in steps 7.1-7.13 do not require reassignment. I used suggested options such as 1) margin 8 2) = outputEnergies/outputTiming=3D 400 3) pairlistpercycle =3D 4 4) stepspercyc= le =3D 40. Simulation fails quickly with atoms moving too fast.

C.=C2=A0=C2=A0 I then readjusted outputEnergies/outputTiming to 5000 (charmm-gui= default). However, step7.1 fails after 105000 steps due to fatal error Per= iodic cell has become too small for original patch grid! Possible solutions are to restart from a recent c= heckpoint, increase margin, or disable useFlexibleCell for liquid simulatio= n..=C2=A0

D.=C2=A0=C2=A0 I played with the margins 0-20 and once I no longer got the atoms= escaping error I then got the allocated memory exceeded, too many atoms in= a patch error.

E.=C2=A0=C2=A0=C2=A0 Finally I also took out pairlistpercycle and stepspercycle as not= ed on NAMD3 website that these are obsolete. Now the error of ERROR: Atoms = moving too fast at timestep 135902; simulation has become unstable (0 atoms on pe 0).

FATAL ERROR: Seque= ncerCUDA: Atoms moving too fast

=C2=A0

I was able to collect bits and pieces from the forums but mostly it i= s on NAMD2 or on NAMD3 but the errors were similar but not the same. From e= rror E) I don=E2=80=99t think I=E2=80=99m running out of RAM since I have 93GB allocated and it runs fine on NAMD2.

=C2=A0

I=E2=80=99ve gotten most of my information from Nvidia=E2=80=99s webs= ite and NAMD3 website and adjusted .inp files based on these sites.<= u>

=C2=A0

https://www.ks.uiuc.edu/Research/namd/alp= ha/3.0alpha/

htt= ps://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-= and-a100-gpu/

=C2=A0

I have a suspicion that the reason things are failing after equilibra= tion is because I=E2=80=99m turning on cudasoaintegrate after dynamics has = started. However, I don=E2=80=99t know how to equilibrate with cudasoaintegrate on and reassignTemp/reassingFreq. I=E2=80=99ve worke= d a year to get this system stable so don=E2=80=99t want to play around too= much with options I=E2=80=99m unfamiliar with. Again system is stable with= NAMD2 and most of the errors I get is failure due to the cudasoaintegrate option on. If any of these steps or errors could be fixed= even if there was an option to do steps6.1-7.13 without cudasoaintegrate o= n and turn it on for the production I=E2=80=99d be happy. I=E2=80=99m also = wondering if cudasoaintegrate doesn=E2=80=99t like restraints on the protein as I=E2=80=99ve been told by others that use very early ver= sions.

=C2=A0

Any suggestions on how to fix any of these errors? Do I just need to = keep playing with margin/ outputenergy/ outputtimeing/ pairlistpercycle/ st= epspercycle parameters until it works?

=C2=A0

Attachments

=C2=A0

=C2=A0

Thank you,

=C2=A0

Ryan

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Mon, 2 Aug 2021 08:33:17 +0000 Date: Mon, 2 Aug 2021 08:31:16 +0000 (UTC) From: Vidhya Sankar To: NAMD List Message-ID: <626732336.1731946.1627893076516@mail.yahoo.com> Subject: namd-l: Mail About error in CV MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1731945_1451386583.1627893076514" References: <626732336.1731946.1627893076516.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18749 YMailNorrin X-Proofpoint-ORIG-GUID: ENk5jSvL3S2ebPY4p9BMzYeWaSuBNCFX X-CLX-Shades: MLX X-CLX-Response: 1TFkXHBIRCkx6FxkbHBEKWUQXYERTRBhzZ0BbX20RClhYF2ZhYhNhbWJrSVx CEQp4Thd6RBwdb0VsbURDZhEKeUwXaUMeT29hQkMFRB0RCkNIFwcbExkRCkNZFwcYGx8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYeEnEYEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF29kQR9AeVxmGXkYT0h6cx5aE2hnUHNPfUt5X2hkaWxyEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXc3p8YFgRCk1cFxgSExEKTFoXaGlra2sRCkxGF29ra29raxE KQk8XYkkfelxYH1t5Gx4RCkNaFxsaHAQbGgQYHhoEGxodEQpCXhcbEQpCXBcbEQpeThcbEQpCSx d6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRCkJFF3oZbUNbRV9oaX1lEQpCThd6RBwdb0Vsb URDZhEKQkwXZmFiE2FtYmtJXEIRCkJsF2sdH3AZbGlFb3hcEQpCQBdhXXxjRhxtRERIcBEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxsRCnlDF25HTFJBGBJDEhp+EQpZSxcTHBMZEQpwaBdvRAE bQFlrb3ASRRAZGhEKcGgXekt/e2JMTHxMTxkQGRoRCnBoF29/U35vfFBPGmhYEBkaEQpwaBdhRx tOEntuTR99XBAZGhEKcGgXZ2QYXm9aBUloQ2MQGRoRCnBsF2RvTlxGflNofFlaEBkaEQpwTBdmB WEcRx1GYXlDfxAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: ENk5jSvL3S2ebPY4p9BMzYeWaSuBNCFX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=630 suspectscore=0 adultscore=0 bulkscore=0 priorityscore=316 spamscore=0 phishscore=0 clxscore=68 lowpriorityscore=0 impostorscore=0 mlxscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108020059 domainage_hfrom=9693 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_1731945_1451386583.1627893076514 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd users =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I am using rmsd as CV in namd for that i have input fie=C2=A0 as follows colvar {=20 =C2=A0=C2=A0 name=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 r1= =20 =C2=A0 =C2=A0=C2=A0 width=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1=20 =C2=A0 =C2=A0=C2=A0 lowerboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 70=20 =C2=A0=C2=A0 upperboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 145=20 =C2=A0 =C2=A0=C2=A0 lowerwallconstant=C2=A0=C2=A0=C2=A0=C2=A0 10.0=20 =C2=A0=C2=A0 upperwallconstant=C2=A0=C2=A0=C2=A0=C2=A0 10.0=20 =C2=A0 #=C2=A0=C2=A0 scriptedFunction=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 source.tcl=20 =C2=A0 =C2=A0=C2=A0 # extendedLagrangian=C2=A0=C2=A0=C2=A0 on=20 =C2=A0 # extendedFluctuation=C2=A0=C2=A0 0.01=20 =C2=A0 =C2=A0=C2=A0 rmsd {=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms=C2=A0 { 1 2 3 4 5 }= =20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomsFile=C2=A0 0.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomsCol B=20 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomsColValue 1.0=20 =C2=A0#=C2=A0=C2=A0=C2=A0=C2=A0 }=20 =C2=A0=C2=A0=C2=A0=C2=A0 refpositionsfile=C2=A0=C2=A0=C2=A0 1000.pdb=20 =C2=A0=C2=A0=C2=A0=C2=A0 refpositiosCol B =C2=A0=C2=A0=C2=A0=C2=A0 refPositionsColvValue=C2=A0 1.0=20 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 1=20 }=20 }=20 But When i run the simulation=C2=A0 I got error as follows colvars: # scriptingAfterBiases =3D off [default]=20 colvars: ------------------------------------------------------------------= ----=20 colvars:=C2=A0=C2=A0 Initializing a new collective variable.=20 colvars:=C2=A0=C2=A0 # name =3D "r1"=20 colvars:=C2=A0=C2=A0 Initializing a new "rmsd" component.=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # name =3D "" [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # componentCoeff =3D 1 [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # componentExp =3D 1=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # period =3D 0 [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # wrapAround =3D 0 [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # forceNoPBC =3D off [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # scalable =3D on [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Initializing atom group "atoms= ".=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # name =3D "" [default]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # centerReference =3D off [def= ault]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # rotateReference =3D off [def= ault]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # atomsOfGroup =3D "" [default= ]=20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # indexGroup =3D "" [default]= =20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # psfSegID =3D=C2=A0 [default]= =20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # atomsFile =3D "" [default]= =20 colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # dummyAtom =3D ( 0 , 0 , 0 ) = [default]=20 colvars: Error: no atoms defined for atom group "atoms".=20 FATAL ERROR: Error in the collective variables module: exiting.=20 =C2=A0 ------------- Processor 0 Exiting: Called CmiAbort ------------=20 Reason: FATAL ERROR: Error in the collective variables module: exiting. It would be highly appreciable if any one point out and rectify the error f= or the past 10 days=C2=A0 to me it was tedious to solve the error=C2=A0=C2= =A0=20 With High regards S.VIDHYA sankar ------=_Part_1731945_1451386583.1627893076514 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Namd users
    &nb= sp;            =     I am using rmsd as CV in namd
for that i ha= ve input fie  as follows
colvar {
   name      &nb= sp;   r1
 
   width    =              1 =
 
   lowerboundary      = ;   70
   upperboundary    &nbs= p;    145
 
   lowerwallconstant =     10.0
   upperwallconstant   = ;  10.0
 
#   scriptedFunction   =    source.tcl
 
   # extendedLagrangian&nbs= p;   on
  # extendedFluctuation   0.01
&nb= sp;
   rmsd {
       &n= bsp; atoms  { 1 2 3 4 5 }
      &nbs= p; atomsFile  0.pdb
        ato= msCol B
        atomsColValue 1.0  #     }
     refpositio= nsfile    1000.pdb
     refpositiosC= ol B
     refPositionsColvValue  1.0
 =     componentExp        1=
}
}

But = When i run the simulation  I got error as follows


colvars: # scriptingAft= erBiases =3D off [default]
colvars: -----------------------------------= -----------------------------------
colvars:   Initializing a= new collective variable.
colvars:   # name =3D "r1"
colv= ars:   Initializing a new "rmsd" component.
colvars: &nb= sp;   # name =3D "" [default]
colvars:    = ; # componentCoeff =3D 1 [default]
colvars:     # c= omponentExp =3D 1
colvars:     # period =3D 0 [defa= ult]
colvars:     # wrapAround =3D 0 [default]
= colvars:     # forceNoPBC =3D off [default]
colvars= :     # scalable =3D on [default]
colvars: &nb= sp;     Initializing atom group "atoms".
colvars:&n= bsp;      # name =3D "" [default]
colvars:&nbs= p;      # centerReference =3D off [default]
co= lvars:       # rotateReference =3D off [defau= lt]
colvars:       # atomsOfGroup =3D "" = [default]
colvars:       # indexGroup =3D= "" [default]
colvars:       # psfSegID = =3D  [default]
colvars:       # atom= sFile =3D "" [default]
colvars:       # d= ummyAtom =3D ( 0 , 0 , 0 ) [default]
colvars: Error: no atoms defined f= or atom group "atoms".
FATAL ERROR: Error in the collective variables m= odule: exiting.
 
------------- Processor 0 Exiting: Called Cmi= Abort ------------
Reason: FATAL ERROR: Error in the collec= tive variables module: exiting.

It would be highly appreciable if any one point out and rect= ify the error for the past 10 days  to me it was tedious to solve the = error  

<= b>With High regards
S.VIDHYA sankar




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boundary="000000000000fc1e9605c894b656" X-Proofpoint-ORIG-GUID: 4Leo2TzsZ4SPH9DPmjFIRBwJNW7QG7Fs X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0cEQpMehcZHBoRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGRIdEQpDWRcHGx8fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx5mT0UYflBZcB55emITbnpHQGxjeGhdYGR9HXttHWxZEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc3pLWRwRCk1cFxkdGREKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbEhoRCkJeFxsRCkReFxoRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4 YBEKQmwXYV96UxlDRBp6G34RCkJAF2VHSEReTBpJaHh7EQpCWBdnc2VzQG5hYUxdYhEKWlgXGRE KeUMXZmZFHWJdQExmHVARCllLFxMeEhwRCnBoF2xSWkhwTF4TGEVmEBkaEQpwaBduW2RzQklrZx 5fTxAZGhEKcGgXZnlvWhpnaFtjYBsQGRoRCnBoF25ATkNBb1t5XlBfEBkaEQpwaBdseR9HRAUdc xN7fBAZGhEKcH0XekMBQ2FebXNFU3gQGRoRCnB/F2JOBQFwRF5pRHtlEBsaGREKcF8XYhpfUExG AUYcGlIQGRoRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdmBWEcRx1GYXlDfxAZGhEKbX4XGhEKWE0 XSxEg X-Proofpoint-GUID: 4Leo2TzsZ4SPH9DPmjFIRBwJNW7QG7Fs MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 suspectscore=0 adultscore=0 bulkscore=0 priorityscore=360 spamscore=0 phishscore=0 clxscore=176 lowpriorityscore=0 impostorscore=0 mlxscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108020095 domainage_hfrom=9486 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000fc1e9605c894b656 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable There are multiple keywords to select atoms, one is atomNumbers followed by numeric indices, or atomsFile as you have used. These two and other ones live inside a block that is named like the group that is used by a variable (e.g. for RMSD that group is called "atoms"). There are not a ton of examples in the Colvars doc. But selecting atoms is a central topic and *there is actually one*: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvar_atom_groups_sel__;Iw!!DZ3fjg!s-QsiY4Gh_Z= F8IaOcHWtxNM347secG374HFzVgavlTK0ETF7Sn4QbqMvy4A5dg-2TA$=20 There are also a couple more typos, which would give you additional errors once you fix the syntax of the atom selection. You can easily fix them yourself by giving a second read to what you put in. Giacomo On Mon, Aug 2, 2021 at 4:36 AM Vidhya Sankar < vidhyasankar7928@remove_yahoo.com> wrote: > Dear Namd users > I am using rmsd as CV in namd > for that i have input fie as follows > > colvar { > name r1 > > width 1 > > lowerboundary 70 > upperboundary 145 > > lowerwallconstant 10.0 > upperwallconstant 10.0 > > # scriptedFunction source.tcl > > # extendedLagrangian on > # extendedFluctuation 0.01 > > rmsd { > atoms { 1 2 3 4 5 } > atomsFile 0.pdb > atomsCol B > atomsColValue 1.0 > # } > refpositionsfile 1000.pdb > refpositiosCol B > refPositionsColvValue 1.0 > componentExp 1 > } > } > > But When i run the simulation I got error as follows > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *colvars: # scriptingAfterBiases =3D off [default] colvars: > ---------------------------------------------------------------------- > colvars: Initializing a new collective variable. colvars: # name =3D = "r1" > colvars: Initializing a new "rmsd" component. colvars: # name =3D "" > [default] colvars: # componentCoeff =3D 1 [default] colvars: # > componentExp =3D 1 colvars: # period =3D 0 [default] colvars: # > wrapAround =3D 0 [default] colvars: # forceNoPBC =3D off [default] > colvars: # scalable =3D on [default] colvars: Initializing atom > group "atoms". colvars: # name =3D "" [default] colvars: # > centerReference =3D off [default] colvars: # rotateReference =3D off > [default] colvars: # atomsOfGroup =3D "" [default] colvars: # > indexGroup =3D "" [default] colvars: # psfSegID =3D [default] > colvars: # atomsFile =3D "" [default] colvars: # dummyAtom = =3D ( 0 > , 0 , 0 ) [default] colvars: Error: no atoms defined for atom group > "atoms". FATAL ERROR: Error in the collective variables module: exiting. > ------------- Processor 0 Exiting: Called CmiAbort ------------ * > > *Reason: FATAL ERROR: Error in the collective variables module: exiting.* > > > *It would be highly appreciable if any one point out and rectify the error > for the past 10 days to me it was tedious to solve the error * > > > > *With High regardsS.VIDHYA sankar* > > > > > --000000000000fc1e9605c894b656 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
There are multiple keywords to select atoms, one is atomNu= mbers followed by numeric indices, or atomsFile as you have used.=C2=A0 The= se two and other ones live inside a block that is named like the group that= is used by a variable (e.g. for RMSD that group is called "atoms"= ;).

There are not a ton of examples in the Colvars doc.= =C2=A0 But selecting atoms is a central topic and there is actually one<= /i>:

Th= ere are also a couple more typos, which would give you additional errors on= ce you fix the=C2=A0syntax of the atom selection.=C2=A0 You can easily fix = them yourself by giving a second read to what you put in.

Giacomo



On Mon, Aug 2, 202= 1 at 4:36 AM Vidhya Sankar <vidhyasankar7928@remove_yahoo.com> wrote:=
Dear Namd users
=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I am using rmsd as CV in namd
f= or that i have input fie=C2=A0 as follows

colv= ar {
=C2=A0=C2=A0 name=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 r1
=C2=A0
=C2=A0=C2=A0 width=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
=C2= =A0
=C2=A0=C2=A0 lowerboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 70
=C2=A0=C2=A0 upperboundary=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 145
=C2=A0
=C2=A0=C2=A0 lowerwallconstant=C2=A0=C2= =A0=C2=A0=C2=A0 10.0
=C2=A0=C2=A0 upperwallconstant=C2=A0=C2=A0=C2=A0= =C2=A0 10.0
=C2=A0
#=C2=A0=C2=A0 scriptedFunction=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 source.tcl
=C2=A0
=C2=A0=C2=A0 # extendedLagrangian=C2= =A0=C2=A0=C2=A0 on
=C2=A0 # extendedFluctuation=C2=A0=C2=A0 0.01
= =C2=A0
=C2=A0=C2=A0 rmsd {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 atoms=C2=A0 { 1 2 3 4 5 }
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 atomsFile=C2=A0 0.pdb
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 atomsCol B
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atomsColValue= 1.0
=C2=A0#=C2=A0=C2=A0=C2=A0=C2=A0 }
=C2=A0=C2=A0=C2=A0=C2=A0 ref= positionsfile=C2=A0=C2=A0=C2=A0 1000.pdb
=C2=A0=C2=A0=C2=A0=C2=A0 refpo= sitiosCol B
=C2=A0=C2=A0=C2=A0=C2=A0 refPositionsColvValue=C2=A0 1.0 =C2=A0=C2=A0=C2=A0=C2=A0 componentExp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 1
}
}

But When i run the= simulation=C2=A0 I got error as follows



colvars: # scriptingAfterBiases =3D off [default]
colva= rs: ---------------------------------------------------------------------- =
colvars:=C2=A0=C2=A0 Initializing a new collective variable.
colvar= s:=C2=A0=C2=A0 # name =3D "r1"
colvars:=C2=A0=C2=A0 Initializ= ing a new "rmsd" component.
colvars:=C2=A0=C2=A0=C2=A0=C2=A0 = # name =3D "" [default]
colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # co= mponentCoeff =3D 1 [default]
colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # compone= ntExp =3D 1
colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # period =3D 0 [default] <= br>colvars:=C2=A0=C2=A0=C2=A0=C2=A0 # wrapAround =3D 0 [default]
colvar= s:=C2=A0=C2=A0=C2=A0=C2=A0 # forceNoPBC =3D off [default]
colvars:=C2= =A0=C2=A0=C2=A0=C2=A0 # scalable =3D on [default]
colvars:=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 Initializing atom group "atoms".
col= vars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # name =3D "" [default]=
colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # centerReference =3D off= [default]
colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # rotateReferen= ce =3D off [default]
colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # ato= msOfGroup =3D "" [default]
colvars:=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 # indexGroup =3D "" [default]
colvars:=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 # psfSegID =3D=C2=A0 [default]
colvars:=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # atomsFile =3D "" [default] colvars:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 # dummyAtom =3D ( 0 , 0 , 0 = ) [default]
colvars: Error: no atoms defined for atom group "atoms= ".
FATAL ERROR: Error in the collective variables module: exiting.=
=C2=A0
------------- Processor 0 Exiting: Called CmiAbort ---------= ---
Reason: FATAL ERROR: Error in the collective variables = module: exiting.

It would be highly app= reciable if any one point out and rectify the error for the past 10 days=C2= =A0 to me it was tedious to solve the error=C2=A0=C2=A0

With High regards
S.VIDHYA sankar
<= /div>



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charset="UTF-8" Dear Users, I am running simulation for 100ns. But due to large system size, it's taking lot of time to run the simulation. So I need to reduce the system size. How can I reduce it ? Please help me out. Mr. Ruturaj Warake Niper, Hyderabad India --000000000000c4809e05c894d168 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Users,
I am running simulation for = 100ns. But due to large system size, it's taking lot of time to run the= simulation. So I need to reduce the system size.=C2=A0
How can I reduce it ? Please help me out.=C2=A0
=
Mr. Ruturaj Warake
Niper= , Hyderabad
India=C2=A0

<= /div>
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Mon, 2 Aug 2021 21:37:24 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3a6qus8dgu-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Mon, 02 Aug 2021 21:37:24 +0000 Received: from [IPv6:2a02:810c:300:6724:35c2:4972:a0a5:bcb1] ([IPv6:2a02:810c:300:6724:35c2:4972:a0a5:bcb1]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 172LbCNa110604 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 2 Aug 2021 23:37:19 +0200 Subject: Re: namd-l: Reducing the system size To: namd-l@ks.uiuc.edu, Ruturaj warake References: <1f108eda-0e48-4485-adf3-801196cf9906@email.android.com> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: Date: Mon, 2 Aug 2021 23:37:12 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 In-Reply-To: <1f108eda-0e48-4485-adf3-801196cf9906@email.android.com> Content-Type: multipart/alternative; boundary="------------181CB20AF3C7990A62C27167" Content-Language: de-DE X-Spam-Status: No, hits=1.919, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.08,URI_DOTEDU=1.997 X-Spam-Score: * (1.919) X-Spam-Flag: NO X-CLX-Shades: MLX X-Proofpoint-GUID: UFnP0ZeXmG11tt-lDMvIzVqBndf12EeI X-Proofpoint-ORIG-GUID: UFnP0ZeXmG11tt-lDMvIzVqBndf12EeI X-CLX-Response: 1TFkXGxISEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxgbGREKQ1kXBxgeGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscEnEeHRAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThd/bER6GnBPckdtGxteXgdGbmdcY1B8W2hETkwbGG9PYxEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdzek1FXBEKTVwXHBwRCkxaF3thTUFNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF29Mfx1OYk1sQVlhEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXHxEKeUMXZ0RjAXJCfRt9E10RCnBnF2VTfWsfTm9/eBpuEB4SEQpwaBdpAWVpHxNQZHp SehAZGhEKcGgXbkBjY3NsZUl4QFAQGRoRCnBoF2JZRmR8WmBAWx5sEBwaEQpwaBdsfkFlWwFJTG scSRAZGhEKcGgXa216Z3NOEk5uU3IQGRoRCnB9F2YaZhMZW08dUm9+EBkaEQpwfRdiaHlZAXwcA RNsbBAZGhEKcH0XYlB5UkhpaBhjaHoQGRoRCnB9F2xtGQVpcn0aaG1jEBkaEQpwfRdlX0l7bUQf cHAFcBAZGhEKcH0XYVgBTAEFQm9mElsQGRoRCnBnF2ZFYkFNSENYU1xAEBkaEQpwfxdiHE1Fa2x CYHBoYBAbGBkRCnBfF2JNXkgFHl9LRXtnEBseHBEKcH8XZRl5Zl5HaRtkT3MQEh8RCnBfF2keR2 lsYEgBZnhMEBkaEQpwfxdlWHIYHUkYXkZpfBAbHh8RCnBfF2hPeWVORFtcQ2FzEBkaEQpwbBd6H 3h5b3hMQ19wRBAZGhEKbX4XGxEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 clxscore=188 lowpriorityscore=0 priorityscore=0 bulkscore=0 mlxlogscore=968 mlxscore=0 spamscore=0 phishscore=0 malwarescore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108020137 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------181CB20AF3C7990A62C27167 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi it mainly depends on what you simulate. One things the (water) solvation layers you add to your system in z and xy directions respectively. In case of membranes you might just build a smaller one (at least in XY plane of membrane bc this can also drastically reduce the solvation layer volume size). One further option is you might check out if HMR (https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/acs.j= ctc.9b00160__;!!DZ3fjg!pfngaJtp-At6padjIqr91VOvRvs4s5hQDu-QATgK7h16ugElye7i= cdVP_-QNdX78bA$ ) & (e.g. checkout previous post for hints, https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/155= 5.html) =C2=A0This basically makes all non-solvent hydrogens heavier (and connected heavy atoms lighter) and one can increase timestep to 4fs (with nbbonded and fullelect set to one 2). =C2=A0=C2=A0=C2=A0 For standard mass and case I use the timestepping s= cheme of 2-1-2. And last but not least if you do not need any special things but have a somewhat recent GPU at hand you may wanna try out NAMD3.0alpha (http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/) =C2=A0=C2=A0=C2=A0 This helped me a lot too in a rather simple equilibration/stability check for longer simulations. For any further guidance, as always, one needs to provide more information. Regards Ren=C3=A9 On 8/2/2021 11:15 PM, ashkan shekaari wrote: > No way. > > On Aug 2, 2021 7:29 PM, Ruturaj warake wrote: > > Dear Users, > I am running simulation for 100ns. But due to large system size, > it's taking lot of time to run the simulation. So I need to reduce > the system size. > How can I reduce it ? Please help me out. > > Mr. Ruturaj Warake > Niper, Hyderabad > India > > --=20 -- Dipl.-Phys. Ren=C3=A9 Hafner TU Kaiserslautern Germany --------------181CB20AF3C7990A62C27167 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable

Hi

it mainly depends on what you simulate.

One things the (water) solvation layers you add to your system in z and xy directions respectively.

In case of membranes you might just build a smaller one (at least in XY plane of membrane bc this can also drastically reduce the solvation layer volume size).


One further option is you might check out if HMR (https://pub= s.acs.org/doi/abs/10.1021/acs.jctc.9b00160) & (e.g. checkout previous post for hints, https://www.ks.uiuc.edu/Rese= arch/namd/mailing_list/namd-l.2017-2018/1555.html)

=C2=A0This basically makes all non-solvent hydrogens heavier (and connected heavy atoms lighter) and one can increase timestep to 4fs (with nbbonded and fullelect set to one 2).

=C2=A0=C2=A0=C2=A0 For standard mass and case I use the timesteppi= ng scheme of 2-1-2.


And last but not least if you do not need any special things but have a somewhat recent GPU at hand you may wanna try out NAMD3.0alpha (http://www.ks.uiuc.edu/Research/namd/alpha/3= .0alpha/)

=C2=A0=C2=A0=C2=A0 This helped me a lot too in a rather simple equilibration/stability check for longer simulations.


For any further guidance, as always, one needs to provide more information.

Regards

Ren=C3=A9


On 8/2/2021 11:15 PM, ashkan shekaari wrote:
No way.

On Aug 2, 2021 7:29 PM, Ruturaj warake <ruturajwarake47@gmail.com> wrote:
Dear Users,
I am running simulation for 100ns. But due to large system size, it's taking lot of time to run the simulation. So I need to reduce the system size.=C2=A0
How can I reduce it ? Please help me out.= =C2=A0

Mr. Ruturaj Warake
Niper, Hyderabad
India=C2=A0


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
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charset="UTF-8" X-CLX-Shades: MLX X-Proofpoint-GUID: U4Nq9gdwSaDzLHAJMCbyjl93r5ym8QM4 X-Proofpoint-ORIG-GUID: U4Nq9gdwSaDzLHAJMCbyjl93r5ym8QM4 X-CLX-Response: 1TFkXGxwTEQpMehcZGBIRCllEF2BkGmkeckh4Xx5gEQpYWBdhW3Noc28ZSWF yXBEKeE4XY1Nja3sTWH4aX14RCnlMF2YSfXlJX2BjQWNFEQpDSBcHGxgcEQpDWRcHExoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhNxGRoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xfx5kWxNNTl15S25QZmJrYGdpSFNARhMZWB9TRxJ7Zx4RClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc3pGH04RCk1cFxsfGhEKTFoXaGlrTU0RCkxGF29ra2t raxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx0SEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2R+c3x5cx1rS0xAEQpCThdjU2Nre xNYfhpfXhEKQkwXYVtzaHNvGUlhclwRCkJsF3p7Yh9QekVnBUdoEQpCQBdrXl17GVwdUH4SfBEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2RTGlBFZ1l5f24ZEQpZSxcTHhIdEQpwaBd ifVxJYHpvQFMFHBAZGhEKcGgXb2ZMW0JfeEdyHH8QGRoRCnBoF2tTfWRGWRhsW3lvEBkaEQpwaB dlflMfW0VlGUhzHhAZGhEKcGgXbkZIY1gaGm9vHX8QGRoRCnB9F2NBY3praQUeYhpZEBkaEQpwf xdjQWN6a2kFHmIaWRAZGhEKcGwXaEkbbx8TU0VOQlsQGRoRCnBMF21oZRlBUn17GEVSEBkaEQpt fhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 clxscore=169 lowpriorityscore=0 priorityscore=328 bulkscore=0 mlxlogscore=554 mlxscore=0 spamscore=0 phishscore=0 malwarescore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108030019 domainage_hfrom=9487 X-Spam-Score: 0 X-Spam-OrigSender: jeffcomer@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 1733aZeg029460 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeff Comer It appears that constant pH simulations should be possible with NAMD3alpha9 since thermodynamic integration is included. Has anyone tried this? I have constant pH simulations that run with NAMD 2.14 (no CUDA). These crash with the error "Floating point exception(core dumped)" after the first constant pH switching iteration in NAMD3alpha9. Has anyone encountered this? Thanks, Jeff –––––––––––––––––––––––––––––––––––——————— Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!pYK0zGl1AjLKdvKWpTdanUC4C7cHJGWSr_Hw2Y-ctuSxE0XO477rJFtF6lxL9HkDbw$ From owner-namd-l@halifax.ks.uiuc.edu Mon Aug 2 22:48:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1733mG9E001314; Mon, 2 Aug 2021 22:48:16 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1733mGDK001313; Mon, 2 Aug 2021 22:48:16 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1733mGud001309; Mon, 2 Aug 2021 22:48:16 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1733mGos001308; 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Mon, 02 Aug 2021 20:48:04 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Jeff Comer Date: Mon, 2 Aug 2021 22:47:53 -0500 Message-ID: Subject: Re: namd-l: constant pH with NAMD3 To: NAMD list Content-Type: text/plain; charset="UTF-8" X-CLX-Response: 1TFkXGxwTEQpMehcZHhMRCllEF2BkGmkeckh4Xx5gEQpYWBdhW3Noc28ZSWF yXBEKeE4XY1Nja3sTWH4aX14RCnlMF2YSfXlJX2BjQWNFEQpDSBcHGxMbEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4TcRwaEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1xibVBaHGJDY0wfW31SU3pMdR9rcGBzYxJ8QhtZSEdnEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc3pHb3sRCk1cFxscEQpMWhd4aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2FZHHkYSAUSG0J4EQpDWhcYGhMEEh8EGBsTBB sdHBEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCR RdkfnN8eXMda0tMQBEKQk4XY1Nja3sTWH4aX14RCkJMF2Fbc2hzbxlJYXJcEQpCbBd6e2IfUHpF ZwVHaBEKQkAXaBN6W1pGRntrfGkRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcfEQp5QxdsTUh aTGN8WUNGHhEKWUsXEx4SHREKcGgXZXhobn1aZnhIThkQGRoRCnBoF28TUlhgQHkeHF5GEB4SEQ pwaBdlaUFoQ3kFGEh+ZxAeEhEKcGgXZVB9G1x7Gl94E14QGRoRCnBoF2xQHU8BUlhQSX5nEBkaE QpwfRduT2VuQ10FG2NGSBAeEhEKcH8XbURfRkVtfUh5GW4QGxoSEQpwXxdrRksTeWhpbnwTeBAc EhEKcGwXaEkbbx8TU0VOQlsQHhIRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: vHGzp6HiIf5qWxyPf_5AZJYI8Vh1sbmM X-Proofpoint-ORIG-GUID: vHGzp6HiIf5qWxyPf_5AZJYI8Vh1sbmM X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=349 mlxscore=0 phishscore=0 adultscore=0 bulkscore=0 mlxlogscore=832 malwarescore=0 spamscore=0 impostorscore=0 clxscore=169 lowpriorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108030020 domainage_hfrom=9487 X-Spam-Score: 0 X-Spam-OrigSender: jeffcomer@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 1733m73x001301 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeff Comer PS: I tried to run the acetate constant pH example that ships with NAMD, lib/namdcph/examples/ace. For NAMD 3alpha8, I got a segmentation fault. On Mon, Aug 2, 2021 at 10:38 PM Jeff Comer wrote: > > It appears that constant pH simulations should be possible with > NAMD3alpha9 since thermodynamic integration is included. Has anyone > tried this? I have constant pH simulations that run with NAMD 2.14 (no > CUDA). These crash with the error "Floating point exception(core > dumped)" after the first constant pH switching iteration in > NAMD3alpha9. Has anyone encountered this? > > Thanks, > Jeff > > –––––––––––––––––––––––––––––––––––——————— > Jeffrey Comer, PhD > Associate Professor > Department of Anatomy and Physiology > Kansas State University > Office: P-213 Mosier Hall > Phone: 785-532-6311 > Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!pYK0zGl1AjLKdvKWpTdanUC4C7cHJGWSr_Hw2Y-ctuSxE0XO477rJFtF6lxL9HkDbw$ > From owner-namd-l@halifax.ks.uiuc.edu Tue Aug 3 04:46:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1739kerS006132; Tue, 3 Aug 2021 04:46:40 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1739kdwp006131; Tue, 3 Aug 2021 04:46:39 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1739kdMr006127; 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Tue, 03 Aug 2021 02:46:24 -0700 (PDT) MIME-Version: 1.0 From: Ruturaj warake Date: Tue, 3 Aug 2021 15:16:14 +0530 Message-ID: Subject: namd-l: Running NAMD 3.0 To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000001b4bd905c8a48f0c" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxsaEQpMehcZHxMRCllEF21sYRtGax5/ZwFcEQpYWBdkZWJLGFxtAR1 /EhEKeE4XY1Nja3sTWH4aX14RCnlMF20SaWJyb0hyTBxYEQpDSBcHHRgRCkNZFwcbHRgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYTGnEdEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF0JraUBvS2BebnJmGh57XElAR0lhdV4fdWcdbH5eXkBwEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXc3pYf2QRCk1cFwcZHxEKTFoXaGFNb2sRCkxGF29ra2traxE KQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGBgEGx0bEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2VwYhpvfxpkGh9nEQpCThdjU2NrexNYf hpfXhEKQkwXZGViSxhcbQEdfxIRCkJsF2JQY3tmb39YGhljEQpCQBdpEk5kEn9hRF4eYhEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2JaRGxHfmJfaV1AEQpZSxcTHhIdEQpwaBdpQG9 AHXBrRVNcHxAZGhEKcGgXZX1Dcl4eZBJGRXoQGRoRCnBoF2sTSXlPaFMFWHtOEBkaEQpwbBdiRV IYZFAdRmBDThAeEhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: hACjEaJtDXL04QvcjmcK_t5_M7FTttjZ X-Proofpoint-GUID: hACjEaJtDXL04QvcjmcK_t5_M7FTttjZ X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=359 suspectscore=0 mlxscore=0 clxscore=110 spamscore=0 phishscore=0 malwarescore=0 adultscore=0 impostorscore=0 mlxlogscore=356 lowpriorityscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108030066 domainage_hfrom=9487 X-Spam-Score: 0 X-Spam-OrigSender: ruturajwarake47@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ruturaj warake --0000000000001b4bd905c8a48f0c Content-Type: text/plain; charset="UTF-8" Dear users, Could anyone please guide me how to run NAMD 3.0 on linux OS ? I downloaded it from the website. What to do further ? --0000000000001b4bd905c8a48f0c Content-Type: text/html; charset="UTF-8"
Dear users,
Could anyone please guide me how to run NAMD 3.0 on linux OS ?
I downloaded it from the website.
What to do further ?
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Tue, 03 Aug 2021 02:57:15 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Oscar Bastidas Date: Tue, 3 Aug 2021 04:57:01 -0500 Message-ID: Subject: Re: namd-l: Running NAMD 3.0 To: NAMD list , Ruturaj warake Content-Type: multipart/alternative; boundary="000000000000e17beb05c8a4b520" X-CLX-Response: 1TFkXGxwbEQpMehcbEhsRCllEF21hZERJWx1LYAUYEQpYWBdoZENLcmVoAUF QYREKeE4XY0N5REZeUmVrUG8RCnlMF2J8fn5lRk1jeVh4EQpDSBcHGxodEQpDWRcHGxoSEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4bcR8aEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF08fSBxGfX96TW5MXX1zZ0RMHkVhG0JnUHN9eV14aXNMEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc3pYT3MRCk1cFx0bEQpMWhd4aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2BPXWJ5WGNvRxJaEQpDWhcbGR4EEh4EGxMcBB gaHBEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY0N5REZeUmVrUG8RCkJJF2NDeURGXlJla 1BvEQpCRRdic2lAaEhzWhtuGBEKQk4XY0N5REZeUmVrUG8RCkJMF2hkQ0tyZWgBQVBhEQpCbBd6 RmJYUk1MBXhbThEKQkAXZHJOfk1+WEFmZW4RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp 5QxdmBW1tUwF+SGBTWREKWUsXGxgcGxkRCnBnF2VTfWsfTm9/eBpuEB4SEQpwaBdoTkJ9GE0fWF 97SRAZGhEKcGgXZX1Dcl4eZBJGRXoQGRoRCnBoF2NObxhCS35IGVBFEBkaEQpwaBdoW39CYFIeY 2hhUBAZGhEKcGgXaEJpYx5vZmR+WmEQGRoRCnBsF29tHWhhUENCYB9IEBkaEQpwTBdtaGUZQVJ9 exhFUhAeEhEKcEMXb0tHfE5iExhoUGIQGxsYEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: e5b6lWUPgDfwWYMnf4oK1hMzYWSwRCYf X-Proofpoint-ORIG-GUID: e5b6lWUPgDfwWYMnf4oK1hMzYWSwRCYf X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=181 mlxscore=0 phishscore=0 adultscore=0 bulkscore=0 mlxlogscore=780 malwarescore=0 spamscore=0 impostorscore=0 clxscore=161 lowpriorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108030067 domainage_hfrom=12613 X-Spam-Score: 0 X-Spam-OrigSender: obastida@umn.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Oscar Bastidas --000000000000e17beb05c8a4b520 Content-Type: text/plain; charset="UTF-8" It's run exclusively on the commandline. If you're working on a Linux cluster, include the command to run namd in a batch script file of some sort that you submit to the job scheduler. This assumes you've prepped your protein structure already using CHARMM-GUI or a downloaded version of CHARMM. On Tue, Aug 3, 2021, 4:52 AM Ruturaj warake wrote: > Dear users, > Could anyone please guide me how to run NAMD 3.0 on linux OS ? > I downloaded it from the website. > What to do further ? > --000000000000e17beb05c8a4b520 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
It's run exclusively on the commandline.=C2=A0 If you= 're working on a Linux cluster, include the command to run namd in a ba= tch script file of some sort that you submit to the job scheduler.=C2=A0 Th= is assumes you've prepped your protein structure already using CHARMM-G= UI or a downloaded version of CHARMM.

<= div dir=3D"ltr" class=3D"gmail_attr">On Tue, Aug 3, 2021, 4:52 AM Ruturaj w= arake <ruturajwarake47@gmai= l.com> wrote:
Dear users,
Could anyone please guide me how to run NA= MD 3.0 on linux OS ?
I downloaded it from the websit= e.
What to do further ?
--000000000000e17beb05c8a4b520-- From owner-namd-l@halifax.ks.uiuc.edu Tue Aug 3 07:25:31 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 173CPVT6010650; Tue, 3 Aug 2021 07:25:31 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 173CPVxO010649; Tue, 3 Aug 2021 07:25:31 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 173CPU42010645; Tue, 3 Aug 2021 07:25:30 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 173CPU9h010644; Tue, 3 Aug 2021 07:25:30 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 173CPIPm010635 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000004e65f205c8a6c755" X-CLX-Shades: MLX X-Proofpoint-GUID: 8A2PBDbAp6G4_ULEWbWhff9ajYfA8wwf X-Proofpoint-ORIG-GUID: 8A2PBDbAp6G4_ULEWbWhff9ajYfA8wwf X-CLX-Response: 1TFkXGx0eEQpMehcZGhoRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGxwfEQpDWRcHGxsYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ecRkeEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxJrGHpobkhrWhxtHnV/Zm99SH1CTEwTS0BzTGsSXV1MEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3N6XlpgEQpNXBcYEh4RCkxaF3xpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHwQbHB wEHhwRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaxMaYU5fXlgYHWURCkJOF2NTY2t7E1h+Gl9eEQpCTBdpSUgaS35pRht4cxEKQmwX YR4ZeFpubGdjX2IRCkJAF2gTeltaRkZ7a3xpEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHBE KeUMXbE1IWkxjfFlDRh4RCllLFxMeEh0RCnBoF21GUmZNellTaEh+EBkaEQpwaBdtGWBIb1BOT2 ZsbRAZGhEKcGgXekxsU09yaVxtXUYQGRoRCnBoF2wbZGNOXVpYHENkEBkaEQpwaBdgX1N5cnhoH 31sZBAZGhEKcH0Xbk9lbkNdBRtjRkgQGxIRCnB9F2RHTUtaSHocTE5SEBkaEQpwfxdtRF9GRW19 SHkZbhAbHhgRCnBfF2tGSxN5aGlufBN4EBsaEhEKcH8XYWZvWxpnZEJIHVsQGxkZEQpwXxdjYhJ QSGN4H3xCfRAbGhsRCnBsF24dZnsSSxp4ElxtEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 clxscore=174 lowpriorityscore=0 priorityscore=300 bulkscore=0 mlxlogscore=939 mlxscore=0 spamscore=0 phishscore=0 malwarescore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108030083 domainage_hfrom=9487 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --0000000000004e65f205c8a6c755 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Jeff, I actually never had time to try this myself. There could be a lot of small issues with unusual features like dynamic lambda and topology reloading (my top guess). I'll see if I can get access to namd3 binary and give it a go. Cheers, Brian On Mon, Aug 2, 2021, 11:49 PM Jeff Comer wrote: > PS: I tried to run the acetate constant pH example that ships with > NAMD, lib/namdcph/examples/ace. For NAMD 3alpha8, I got a segmentation > fault. > > On Mon, Aug 2, 2021 at 10:38 PM Jeff Comer wrote: > > > > It appears that constant pH simulations should be possible with > > NAMD3alpha9 since thermodynamic integration is included. Has anyone > > tried this? I have constant pH simulations that run with NAMD 2.14 (no > > CUDA). These crash with the error "Floating point exception(core > > dumped)" after the first constant pH switching iteration in > > NAMD3alpha9. Has anyone encountered this? > > > > Thanks, > > Jeff > > > > =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94= =E2=80=94 > > Jeffrey Comer, PhD > > Associate Professor > > Department of Anatomy and Physiology > > Kansas State University > > Office: P-213 Mosier Hall > > Phone: 785-532-6311 > > Website: > https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!pYK0zGl1AjLKdv= KWpTdanUC4C7cHJGWSr_Hw2Y-ctuSxE0XO477rJFtF6lxL9HkDbw$ > > > > --0000000000004e65f205c8a6c755 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Jeff,=C2=A0

I actually never had time to try this myself. There could be = a lot of small issues with unusual features like dynamic lambda and topolog= y reloading (my top guess). I'll see if I can get access to namd3 binar= y and give it a go.=C2=A0

Cheers,
Brian=C2=A0

On Mon, Aug 2, 2021,= 11:49 PM Jeff Comer <jeffcomer@g= mail.com> wrote:
PS: I tried= to run the acetate constant pH example that ships with
NAMD, lib/namdcph/examples/ace. For NAMD 3alpha8, I got a segmentation
fault.

On Mon, Aug 2, 2021 at 10:38 PM Jeff Comer <jeffcomer@gmail.com>= wrote:
>
> It appears that constant pH simulations should be possible with
> NAMD3alpha9 since thermodynamic integration is included. Has anyone > tried this? I have constant pH simulations that run with NAMD 2.14 (no=
> CUDA). These crash with the error "Floating point exception(core<= br> > dumped)" after the first constant pH switching iteration in
> NAMD3alpha9. Has anyone encountered this?
>
> Thanks,
> Jeff
>
> =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94= =E2=80=94
> Jeffrey Comer, PhD
> Associate Professor
> Department of Anatomy and Physiology
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: https://urldefense.com/v= 3/__http://jeffcomer.us__;!!DZ3fjg!pYK0zGl1AjLKdvKWpTdanUC4C7cHJGWSr_Hw2Y-c= tuSxE0XO477rJFtF6lxL9HkDbw$
>

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charset="UTF-8" Dear all Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alternatively I had this problem for other atom types that I wrote like ATOM TYPE NHL in the parameter file. However, now I am getting a new error stating, " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)" I am unable to understand the reason behind it. Could you help me, please? -- Sincerly Yours Miss.Ghanbari --000000000000ca637605c8a82ea5 Content-Type: text/html; charset="UTF-8"

Dear all
Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alternatively I had this problem for other atom types that I wrote like ATOM TYPE NHL in the parameter file. However, now I am getting a new error stating, " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)"
I am unable to understand the reason behind it. Could you help me, please?
--
Sincerly Yours Miss.Ghanbari
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Tue, 03 Aug 2021 07:15:56 -0700 (PDT) Content-Type: multipart/alternative; boundary=Apple-Mail-2B5FA78E-F30C-4F6E-974E-0C0CA150FF38 Content-Transfer-Encoding: 7bit From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Date: Tue, 3 Aug 2021 09:15:53 -0500 Message-Id: <6A8A4B64-E9C6-4E54-87D1-CA9C7737CCF2@gmail.com> References: In-Reply-To: To: namd-l@ks.uiuc.edu, samaneh ghanbari X-Mailer: iPhone Mail (18B92) X-CLX-Shades: MLX X-Proofpoint-GUID: AD5KWovQ5HJpX0cUnFmieGJ_Fzr-bUZQ X-Proofpoint-ORIG-GUID: AD5KWovQ5HJpX0cUnFmieGJ_Fzr-bUZQ X-CLX-Response: 1TFkXGxIeEQpMehcZHhwRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGRsfEQpDWRcHGRMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB5xHhkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04Xa24fYX1FXHsfYmBachpJf0RsR0NPbWB1bFBYB0h/cHsRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXc3pcexwRCk1cFxsdGREKTFoXfGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdkflhPZm5zSXBbTxEKQ1oXGBoTBBIfBBgbHA QeGREKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmS21YRhhPY0VDQBEKQk4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdv T2RBWkJQbWZrWREKQkAXaExpZRluXGxwfhsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdsXUh4ZhpOGmBkGhEKWUsXEx4SHREKcGgXYn5FX0FGe3N6ElAQHhIRCnBoF2ddQFkcTVpAaV lmEB4SEQpwaBdrWB5/QGkdGlByaBAZGhEKcGgXYHtceHAebHsZZ0QQGRoRCnBoF3oZXFluTEhMG WASEBkaEQpwbBdnaENrcxJ5GE1iXBAZGhEKcEMXYnBvWWZ/U11QQkIQGRoRCm1+FxsRClhNF0sR IA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 suspectscore=0 clxscore=184 lowpriorityscore=0 priorityscore=346 bulkscore=0 mlxlogscore=999 mlxscore=0 spamscore=0 phishscore=0 malwarescore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108030095 domainage_hfrom=9487 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= --Apple-Mail-2B5FA78E-F30C-4F6E-974E-0C0CA150FF38 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable You have missing parameters for it bonds, check where it atoms are and them a= dd appropriate parameters.=20 Not sure , but it is atoms are from sphingomielyn.=20 Best,=20 Geo.=20 Enviado desde mi iPhone > El 3 ago. 2021, a la(s) 9:07 a. m., samaneh ghanbari escribi=C3=B3: >=20 > =EF=BB=BF >=20 > Dear all > Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alt= ernatively I had this problem for other atom types that I wrote like ATOM TY= PE NHL in the parameter file. However, now I am getting a new error stating,= " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)= " > I am unable to understand the reason behind it. Could you help me, please?= =20 > --=20 > Sincerly Yours Miss.Ghanbari --Apple-Mail-2B5FA78E-F30C-4F6E-974E-0C0CA150FF38 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable You have missing parameters for it bonds, c= heck where it atoms are and them add appropriate parameters. 

<= /div>
Not sure , but it is atoms are from sphingomielyn. 

Best, 

Geo. 

Enviado desde mi iPhone

El 3 ago. 2021, a la(s) 9:07 a. m., samaneh ghanbari <gha= nbari.samaneh@gmail.com> escribi=C3=B3:

=EF=BB=BF

Dear all
Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alternativel= y I had this problem for other atom types that I wrote like ATOM TYPE NHL in t= he parameter file. However, now I am getting a new error stating, " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)" =
I am unable to understand the reason behind it. Could you help me, please?
--
Sincerly Yours Miss.Ghanbari
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charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable In your system, there is a bond between atom types CEL3 and CTL2. In the=20 force field parameter files you provided in the input script for NAMD,=20 no parameters are defined for that combination of atom types. NAMD thus=20 doesn't know how to compute forces for that pair of atoms, and bails. A=20 quick grep through CHARMM parameter files suggests that you are missing=20 toppar_all36_lipid_sphingo.str, which is where the parameters for=20 sphingolipids are defined. -Josh On 8/3/21 10:05 AM, samaneh ghanbari wrote: > > Dear all > Thanks for the help Mr Shekaari. Your suggestion solved the issue. But=20 > alternatively I had this problem for other atom types that I wrote=20 > like ATOM TYPE NHL in the parameter file. However, now I am getting a=20 > new error stating, " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR=20 > CEL3 CTL2 (ATOMS 490 488)" > I am unable to understand the reason behind it. Could you help me,=20 > please? > --=20 > Sincerly Yours Miss.Ghanbari --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!omJmNVPlO-Fx3T-honMdksP_g2XcIvMtGye1XVrcwyg402hiWuDIRY4= bRWiY3_dxmg$=20 --------------870020E9FA019BC490632F3A Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable In your system, there is a bond between atom types CEL3 and CTL2. In the force field parameter files you provided in the input script for NAMD, no parameters are defined for that combination of atom types. NAMD thus doesn't know how to compute forces for that pair of atoms, and bails. A quick grep through CHARMM parameter files suggests that you are missing toppar_all36_lipid_sphingo.str, which is where the parameters for sphingolipids are defined.

-Josh

On 8/3/21 10:05 AM, samaneh ghanbari wrote:
=20=20=20=20=20=20

Dear all
Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alternatively I had this problem for other atom types that I wrote like ATOM TYPE NHL in the parameter file. However, now I am getting a new error stating, " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)"
I am unable to understand the reason behind it. Could you help me, please?
--
Sincerly Yours Miss.Ghanbari

--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
--------------870020E9FA019BC490632F3A-- From owner-namd-l@halifax.ks.uiuc.edu Wed Aug 4 10:52:11 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 174FqBWm029487; Wed, 4 Aug 2021 10:52:11 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 174FqBL5029486; Wed, 4 Aug 2021 10:52:11 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 174FqAKX029482; Wed, 4 Aug 2021 10:52:10 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 174FqAab029481; Wed, 4 Aug 2021 10:52:10 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 174Fq1D1029472 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 4 Aug 2021 10:52:01 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 174FYHKl031778 for ; Wed, 4 Aug 2021 15:52:00 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=ruturajwarake47@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-qv1-f53.google.com (mail-qv1-f53.google.com [209.85.219.53]) by mx0b-00007101.pphosted.com with ESMTP id 3a7wke86jg-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 04 Aug 2021 15:52:00 +0000 Received: by mail-qv1-f53.google.com with SMTP id f91so1291406qva.9 for ; Wed, 04 Aug 2021 08:52:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=3dGdfsf88R/hlwLy1+/16sAc8msJABgEGHltvmIeRZw=; b=A3Zi5isS9BCoeZZUAEbt7pGvano4dMPZv0QFOsey1SY6MqbsC3o/L74Nj4VGkVZD5D ETM9LUZfmWtfIAJ3oKKp/mfV+jqgJNRQKPyvUDsGw+L1i2Nj5EjAHBEQyejRPRAV35SF oAareJEQm8EcuVipga7/qpBKYSxg1WVv1SzSEAYB7ImMU8k4M3ayZcUDw65/2xuni+28 LGDAzcypbEXvuXtkAtpque6bk/T4q/187UPd428DizOhK+BOrHsmZa2TqqWlUelWMPjy Y5ENtil3kovf8+8StG2DJLmjurIjVdgcUdMiox0BSqqjSX1jDUtfy85ymYwc0e0Z3qVm ysFg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=3dGdfsf88R/hlwLy1+/16sAc8msJABgEGHltvmIeRZw=; b=qWyGpNFrQWUPpyb+kRrWHnDVXEV1qX0VD6qGg4tLwQnd6gyw5/ebCNnSYTGVhgb2y8 VheO9fH4L9eUdiBqFdU8QRXXAYqmjHGn0uhKArayAsFU9kT4aihZQXHJ8XMTqO9xyqIZ skInbNEBVHlR5txWdUT9QS2ofDtwKb6S+6siNFg4l9pgPkgOt9/7b7/X+5ourCTHdtgE WQw7ioobfYDXQzEL1/ORP5e8p6phAQz7zjQ9+ovXIoDw1CS0Bcx5nl7jBQi/sK84otmm Ypt21QC1u/kt6B1LkvyIe3/OWpPWlW6TZSlkoojoCJcSFrzdUWFG9kGY9llTl9t5myMa 1xvg== X-Gm-Message-State: AOAM532ENr9omXuDiBFdUMdR1ElwaFAYwOnQn5TFf1+0rhMwj6/TRi64 7+BVL94Q5F9QqGvSQTYOeJ+9BkRZLeXe6nqlJfML3af2TvQ= X-Google-Smtp-Source: ABdhPJyd9EnAgL2IUe+PQIX//U/ZwlVfrbJbm5uN635nBeOHd+c9sq3uFT9lwCWfetaIvlKQqpJAhsFBolqNZzOAxqo= X-Received: by 2002:a05:6214:b33:: with SMTP id w19mr77624qvj.50.1628092319841; Wed, 04 Aug 2021 08:51:59 -0700 (PDT) MIME-Version: 1.0 From: Ruturaj warake Date: Wed, 4 Aug 2021 21:21:48 +0530 Message-ID: Subject: namd-l: Numsteps or Runs? To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="00000000000062c28205c8bdc831" X-Proofpoint-GUID: raJD6Oth7PlZ2amwQxURYeqo6cUrVus- X-Proofpoint-ORIG-GUID: raJD6Oth7PlZ2amwQxURYeqo6cUrVus- X-CLX-Response: 1TFkXGxwZEQpMehcZHh4RCllEF21sYRtGax5/ZwFcEQpYWBdkZWJLGFxtAR1 /EhEKeE4XY1Nja3sTWH4aX14RCnlMF20SaWJyb0hyTBxYEQpDSBcHGxsfEQpDWRcHHxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhlxGBwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWEtgbhxlXkIdekZwGEtHXXtSf3hzT1tFHEl/WHxfWQcRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc3tsXR0RCk1cFxwaEQpMWhdoaU1NTREKTEYXb2tra2t rEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEwQfGREKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdlcGIab38aZBofZxEKQk4XY1Nja3sTW H4aX14RCkJMF2RlYksYXG0BHX8SEQpCbBdiUGN7Zm9/WBoZYxEKQkAXZ0xIY05cBQVlHEARCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdpExNmZ3gaUnASZhEKWUsXEx4SEhEKcGgXbUM eU1lLU1tgQh4QGRoRCnBsF2JFUhhkUB1GYENOEBkaEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=1 malwarescore=0 mlxlogscore=192 mlxscore=1 bulkscore=0 impostorscore=0 spamscore=1 lowpriorityscore=0 priorityscore=344 adultscore=0 suspectscore=0 clxscore=163 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108040089 domainage_hfrom=9488 X-Spam-Score: 1 X-Spam-OrigSender: ruturajwarake47@gmail.com X-Spam-Bar: * Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ruturaj warake --00000000000062c28205c8bdc831 Content-Type: text/plain; charset="UTF-8" Dear users, Running simulation, the system need to be equilibrated. For that equilibration step is run. Suppose, I wish to equilibrate the system for 100 ps. Then where should I put this number? in front of numsteps ? Or Runs ? --00000000000062c28205c8bdc831 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear users,
Running simulation, the syst= em need to be equilibrated. For that equilibration step is run. Suppose, I = wish to equilibrate the system for 100 ps. Then where should I put this num= ber? in front of numsteps ? Or Runs ?
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Thread-Index: qQ6vrhqJQl/WALGgg19slErATqYGyA== X-Proofpoint-GUID: IENM4uCxLNrhqo82nuQSd6fEO-njyzkI X-Proofpoint-ORIG-GUID: IENM4uCxLNrhqo82nuQSd6fEO-njyzkI X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0eEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxgaHBEKQ1kXBx8fEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ecRwSEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF2NvZGceX2lSZmRYQltFEhhEX3t5ThxMb2UHREBTUEFjEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXc3tiWlIRCk1cFxseHhEKTFoXfGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGx sRCkJeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXY R0eZmtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8 a3gRCkJAF20Yb0VkAXJaE1lPEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXaUVLUx4 aeF56TVkRCllLFwcZEQpwZxdjGmNHQX9hRngZfBAZGhEKcGgXZH5PSEhgEx9sGnsQGRoRCnBoF2 liGRgcRWxhGx4fEBkaEQpwaBdoWUFCW21/bGxvZBAZGhEKcGgXYmdIZ0tub0wdWlAQGRoRCnBoF 2VBSFppclN5bHlCEBkaEQpwfRdjc3tNBV0dAXhBcBAZGhEKcGcXZVN9ax9Ob394Gm4QGRoRCnBn F2lDblABWXNHAR5TEBkaEQpwfRdpGmVOXEgTYEd5RhAZGhEKcH8Xb0RhUBITfxscEn4QHxgRCnB fF2IYGhgfeEdMe3t7EBsbHxEKcGwXb2B/bXlMQURrTk4QGRoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 mlxscore=0 phishscore=0 spamscore=0 priorityscore=0 malwarescore=0 impostorscore=0 suspectscore=0 adultscore=0 clxscore=174 bulkscore=0 mlxlogscore=574 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108040105 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_4e95dfb1-8d33-4304-a69e-51303d7abb43 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable run 100000000=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!q_qwDvWNLp2IJi1xUO8Ggj5n23euWXdOhC0PDgpdHmGTQ3CKLiSDPVOn= CdeKUFyqng$ ]=20 From: "Ruturaj warake" =20 To: "namd-l" =20 Sent: Wednesday, August 4, 2021 8:21:48 PM=20 Subject: namd-l: Numsteps or Runs?=20 Dear users,=20 Running simulation, the system need to be equilibrated. For that equilibrat= ion step is run. Suppose, I wish to equilibrate the system for 100 ps. Then= where should I put this number? in front of numsteps ? Or Runs ?=20 --=_4e95dfb1-8d33-4304-a69e-51303d7abb43 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
run       100000000

---
,Best
<= /div>
<= div dir=3D"ltr">
Ashkan Shekaari=
PhD Candidate in Solid State Physics
Department= of Physics
K. N. Toosi University= of Technology, Tehran, 15875-4416, Iran<= /font>
=

=
From: "Ruturaj warake" <ruturajwarake47@gmail.com>
To= : "namd-l" <namd-l@ks.uiuc.edu>
Sent: Wednesday, August= 4, 2021 8:21:48 PM
Subject: namd-l: Numsteps or Runs?
<= div>
Dear u= sers,
Running simulation, the system need to be equilibrat= ed. For that equilibration step is run. Suppose, I wish to equilibrate the = system for 100 ps. Then where should I put this number? in front of numstep= s ? Or Runs ?

= --=_4e95dfb1-8d33-4304-a69e-51303d7abb43-- From owner-namd-l@halifax.ks.uiuc.edu Wed Aug 4 14:27:48 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 174JRlu4004976; Wed, 4 Aug 2021 14:27:48 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 174JRlCR004975; Wed, 4 Aug 2021 14:27:47 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 174JRlMn004971; Wed, 4 Aug 2021 14:27:47 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 174JRlWv004970; Wed, 4 Aug 2021 14:27:47 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 174JReLG004963 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 4 Aug 2021 14:27:41 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 174JODYM019180 for ; Wed, 4 Aug 2021 19:27:40 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3a7wkh9tww-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 04 Aug 2021 19:27:39 +0000 Received: from [192.168.0.7] (ip2505f671.dynamic.kabel-deutschland.de [37.5.246.113]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 174JRamr020964 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 4 Aug 2021 21:27:37 +0200 To: "namd-l@ks.uiuc.edu" From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Subject: namd-l: Lowe-Andersen Thermostat default damping value Message-ID: <4963b79a-d72f-114e-2117-d62284d828e7@physik.uni-kl.de> Date: Wed, 4 Aug 2021 21:27:36 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: de-DE X-Spam-Status: No, hits=0.398, tests=KHOP_HELO_FCRDNS=0.398 X-Spam-Score: (0.398) X-Spam-Flag: NO X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxsdGhEKQ1kXBxsbExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseGXEfGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdhY3loXEVeExxBfkxIYWBlfk1eQUNacnBbGUNhHx5zTBEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdze2MdYhEKTVwXHBwRCkxaF2hhTUFNEQpCTxdsX2xmX3B MSxxSSxEKQ1oXGxkbBBgeHAQbGBoEGBgaEQpCXhcbEQpEXhcYEQpCRRdsHVhyRR8cR0kFbhEKQk 4XZBpJbnp6eBpkfVwRCkJMF2BgG1IZHRgaUnIFEQpCbBdma2JkGFlibUh+bBEKQkAXaFtOHXN9a GJ4aVwRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdiQEhFcBl5fkIbTBEKcGgXZBh4 RUNeY1tDZFIQGRoRCnBoF2kFU0FoQhpZc3NhEBkaEQpwaBdnGEdNHE9mU3lHYRAZGhEKcGgXZB5 NZh5wbmx8clwQGRoRCnBoF2N8eRIacFNgcgV+EBkaEQpwbBd6H3h5b3hMQ19wRBAZGhEKcEMXYm IYaHl8Z3pzUHgQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: KISBvot96kTfbKJOTgtkipXZq3iK54Yf X-Proofpoint-ORIG-GUID: KISBvot96kTfbKJOTgtkipXZq3iK54Yf X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 mlxlogscore=643 spamscore=0 priorityscore=0 impostorscore=0 lowpriorityscore=0 suspectscore=0 malwarescore=0 mlxscore=0 adultscore=0 clxscore=163 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108040116 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Dear NAMD maintainers,     I just want to want to reassure that for the Lowe-Andersen Thermostat     the default value for damping 50 ps^-1 given, is really the recommended one.     I am doing an investigation of viscosity and see somewhat strange behaviour for values around 50ps-^1         but that might just arise from the nature of this thermostat. Kind regards René -- -- Dipl.-Phys. 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boundary="_000_TYCP286MB12847329C9A91A3ECD69634EF6F29TYCP286MB1284JPNP_" MIME-Version: 1.0 X-OriginatorOrg: connect.ust.hk X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: TYCP286MB1284.JPNP286.PROD.OUTLOOK.COM X-MS-Exchange-CrossTenant-Network-Message-Id: 96f62e4d-9ec4-46a9-52bc-08d957c19c5c X-MS-Exchange-CrossTenant-originalarrivaltime: 05 Aug 2021 03:32:11.2400 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 6c1d4152-39d0-44ca-88d9-b8d6ddca0708 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: VpTzO/Xb6Lys7TjdyCxVhJkPN8QW/zpNJEADALKo/rHzltYK117gTKJ57ZvTqH+BJsLfk16gNtida4BjPOTZsg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: TYYP286MB1212 X-CLX-Shades: MLX X-Proofpoint-GUID: BMoorXZ9qLb-eWfqf3ywye5n9iuXH8gi X-Proofpoint-ORIG-GUID: BMoorXZ9qLb-eWfqf3ywye5n9iuXH8gi X-CLX-Response: 1TFkXGBsYEQpMehcaEQpZRBdka2lpZRkTWEJcQBEKWFgXZ2RlbX1Lbh8YQhI RCnhOF2EaEk5vYhpdcHMaEQp5TBdoGWcFbXl4HWtGfBEKQ0gXBxgdGxEKQ1kXBxgdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxMYcRscHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdoZ0VFWHJwE1tmSAdPfUxbTBlTXVNPH0QTQ19yYhJNQxEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdze3toSBEKTVwXGxwZEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdvb2trbGtrEQpCTxdtZ2JHckZlX09+ThEKQ1oXHhoEGxodBBseGw QbGB0RCkJeFxsRCkReFxkRCkJcFxsRCl5OFxsRCkJLF2EaEk5vYhpdcHMaEQpCSRdhGhJOb2IaX XBzGhEKQkUXbn9uTkRse1JAelIRCkJOF2EaEk5vYhpdcHMaEQpCTBdnZGVtfUtuHxhCEhEKQmwX aV19bH5BHHBoS1sRCkJAF2hMaWUZblxscH4bEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGxE KeUMXbF1IeGYaThpgZBoRCnBnF21HYWtNYxlMU2luEBkaEQpwaBdoRH0bGRISQF5nTxAZGhEKcG gXa2xHeml7ZHhzRHMQGRoRCnBoF25DYRIceBtSWxxGEBkaEQpwaBdiQR4TY31CZn1GfxAZGhEKc GgXaHpybU5LQlBMGWEQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwbBdpXXIbThNzRX9PUhAZGhEK bX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 lowpriorityscore=0 adultscore=0 clxscore=212 spamscore=0 suspectscore=0 mlxscore=0 mlxlogscore=999 priorityscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108050018 X-Spam-Score: 0 X-Spam-OrigSender: atyagiaa@connect.ust.hk X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Abhishek TYAGI --_000_TYCP286MB12847329C9A91A3ECD69634EF6F29TYCP286MB1284JPNP_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable hi, it is simple as stated that the information for the bond between the two at= oms is missing in your parameter file. Please check this in your parameter = file, and to solve this or to get the bond length you may check search the = CHARMM repository or look for literature. If you still can't find this information, then you have to go to the CHARMM= -GUI and upload the molecule to get the parameters. You may also try to che= ck with CGENFF server, by uploading mol2 format of your molecules. If none = of this work, then you need to procced for the structure optimization using= FFTK toolkit available in VMD. Good luck Abhi ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of sama= neh ghanbari Sent: Tuesday, August 3, 2021 22:05 To: namd-l@ks.uiuc.edu Subject: namd-l: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Dear all Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alte= rnatively I had this problem for other atom types that I wrote like ATOM TY= PE NHL in the parameter file. However, now I am getting a new error stating= , " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 48= 8)" I am unable to understand the reason behind it. Could you help me, please? -- Sincerly Yours Miss.Ghanbari --_000_TYCP286MB12847329C9A91A3ECD69634EF6F29TYCP286MB1284JPNP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
hi,

it is simple as stated that the information for the bond between the two at= oms is missing in your parameter file. Please check this in your parameter = file, and to solve this or to get the bond length you may check search the = CHARMM repository or look for literature. 
If you still can't find this information, then you have to go to the CHARMM= -GUI and upload the molecule to get the parameters. You may also try to check with CGENFF server, by uploading mol2 format of your molecules. If none of this work, = then you need to procced for the structure optimization using FFTK toolkit = available in VMD.

Good luck
Abhi

<= /span>



From: owner-namd-l@ks.uiuc.= edu <owner-namd-l@ks.uiuc.edu> on behalf of samaneh ghanbari <ghan= bari.samaneh@gmail.com>
Sent: Tuesday, August 3, 2021 22:05
To: namd-l@ks.uiuc.edu <namd-l@ks.uiuc.edu>
Subject: namd-l: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS
 

Dear all
Thanks for the help Mr Shekaari. Your suggestion solved the issue. = But alternatively I had this problem for other atom types that I wrote like= ATOM TYPE NHL in the parameter file. However, now I am getting a new error stating, " FATAL ERROR: UNABLE TO FIND B= OND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)"
I am unable to understand the reason behind it. Could you help me, pleas= e?
--
Sincerly Yours Miss.Ghanbari
--_000_TYCP286MB12847329C9A91A3ECD69634EF6F29TYCP286MB1284JPNP_-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 7 14:16:55 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177JGt7Y022053; Sat, 7 Aug 2021 14:16:55 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 177JGt87022052; Sat, 7 Aug 2021 14:16:55 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177JGtHq022048; Sat, 7 Aug 2021 14:16:55 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 177JGs9b022047; Sat, 7 Aug 2021 14:16:54 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177JGlCV022040 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 7 Aug 2021 14:16:48 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 177JD8qO017666 for ; Sat, 7 Aug 2021 19:16:47 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0a-00007101.pphosted.com with ESMTP id 3a9gnxkrwa-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 07 Aug 2021 19:16:47 +0000 Received: from [IPv6:2a02:810c:300:6724:adc4:8909:aa62:54c4] ([IPv6:2a02:810c:300:6724:adc4:8909:aa62:54c4]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 177JGiZt007313 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 7 Aug 2021 21:16:44 +0200 To: "namd-l@ks.uiuc.edu" From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Subject: namd-l: Compiling issue: selfcompiled NAMD2.14 multicore version factor ~2x slower Message-ID: <389d8cf4-2cf5-69b0-cc2b-e852b2ee021d@physik.uni-kl.de> Date: Sat, 7 Aug 2021 21:16:44 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="------------5F3EA0322D6B1CBA2B943D39" Content-Language: de-DE X-Spam-Status: No, hits=0.002, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001 X-Spam-Score: (0.002) X-Spam-Flag: NO X-Proofpoint-GUID: 4kmce1flo_y3tDIem3CuQJsu00724jNp X-Proofpoint-ORIG-GUID: 4kmce1flo_y3tDIem3CuQJsu00724jNp X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMeEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxgcGBEKQ1kXBxsTGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsdHnEfHhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThceQUdJTxtMRkV1UxlebmNPRxlpX3tgWV8aGh0YHkBkWhEKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3N4Y2kcEQpNXBceHxsRCkxaF2loYU1BTREKQk8XbF9sZl9 wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGhEKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCk JOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YGlJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF2ZPSXtIS 25ZSHxjEQpCWBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXaEhzWnx6U2J7E28RCnBoF2QdfV4bQl5L E08cEBoRCnBoF3pwbmRwQBNNel5oEBoRCnBoF2QFU0JkbB5nR3lCEBoRCnBoF3pnU0IYHXkBQBh 7EBoRCnBoF2IeQk5nTFN9fV5oEBoRCnBsF3ofeHlveExDX3BEEBkaEQptfhcaEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=194 bulkscore=0 suspectscore=0 malwarescore=0 priorityscore=0 mlxscore=0 adultscore=0 impostorscore=0 spamscore=0 mlxlogscore=778 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108070140 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------5F3EA0322D6B1CBA2B943D39 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit    Dear NAMD maintainers,     I tried implementing a new colvar (which was successful) but wondered about speed reduction by it.     Though I compared my self compiled version plain MD simulations (finally without colvars) with the precompiled binary from the website.     The only thing changed in the code is in colvars module files that is not active for the following comparism.     I obtain the following speed of simulations for a single standard cutoff etc. simulation (membrane + water, 7k atoms)         Precompiled: 300 ns/day (4fs ,HMR)         Selfcompiled: 162 ns/day (4fs timestep, HMR) This is not CUDA Version dependent as this results is stable with both CUDA 11.3 as well as with CUDA 10.1 (this latter version was used in the precompiled binary). Any help is appreciated. Kind regards René I compiled it with the following settings: """ # building charmm module purge module load gcc/8.4 ./build charm++ multicore-linux-x86_64 gcc  -j16 --with-production ### module purge module load gcc/8.4 module load nvidia/10.1 ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64-gcc --with-tcl --with-python --with-fftw --with-cuda --arch-suffix SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def cd Linux-x86_64-g++ # append the line CXXOPTS=-lstdc++ -std=c++11 to the Make.config ## if no CXXOPTS like --with-debug are defined then it will not work echo "CXXOPTS=-lstdc++ -std=c++11" >> Make.config echo "showin Make.config" cat Make.config # then run it make -j 12 | tee make_log_SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def.txt """ -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------5F3EA0322D6B1CBA2B943D39 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

   Dear NAMD maintainers,


    I tried implementing a new colvar (which was successful) but wondered about speed reduction by it.

    Though I compared my self compiled version plain MD simulations (finally without colvars) with the precompiled binary from the website.

    The only thing changed in the code is in colvars module files that is not active for the following comparism.


    I obtain the following speed of simulations for a single standard cutoff etc. simulation (membrane + water, 7k atoms)

        Precompiled: 300 ns/day (4fs ,HMR)

        Selfcompiled: 162 ns/day (4fs timestep, HMR)


This is not CUDA Version dependent as this results is stable with both CUDA 11.3 as well as with CUDA 10.1 (this latter version was used in the precompiled binary).


Any help is appreciated.

Kind regards

René

I compiled it with the following settings:

"""

# building charmm
module purge
module load gcc/8.4
./build charm++ multicore-linux-x86_64 gcc  -j16  --with-production

###
module purge
module load gcc/8.4
module load nvidia/10.1
./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64-gcc --with-tcl --with-python --with-fftw --with-cuda --arch-suffix SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def
cd Linux-x86_64-g++
# append the line CXXOPTS=-lstdc++ -std=c++11 to the Make.config
## if no CXXOPTS like --with-debug are defined then it will not work
echo "CXXOPTS=-lstdc++ -std=c++11" >> Make.config

echo "showin Make.config"
cat Make.config
# then run it
make -j 12 | tee make_log_SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def.txt

"""


--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
--------------5F3EA0322D6B1CBA2B943D39-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 7 15:41:34 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177KfYvX024440; Sat, 7 Aug 2021 15:41:34 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 177KfXb8024439; Sat, 7 Aug 2021 15:41:33 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177KfXls024435; Sat, 7 Aug 2021 15:41:33 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 177KfXKe024434; Sat, 7 Aug 2021 15:41:33 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177KfKCY024426 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="00000000000091e3a705c8fe2c5d" X-Proofpoint-ORIG-GUID: 6vnO4Dqhn5llexsIb80IuJjQkNPdLsD1 X-Proofpoint-GUID: 6vnO4Dqhn5llexsIb80IuJjQkNPdLsD1 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0dEQpMehcZHxsRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHhsfEQpDWRcHGxIZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8dcRkcEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxxcRGUebltCRB9GRk9SWWNIEhpjX2BAe0Fkek5mWW4bEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc3hgeWYRCk1cFx4cGhEKTFoXfGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbEhgRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2tDHm5ZQmlAARpIEQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXYWV EeVpDGH98RhwRCllLFxMeExsRCnBnF2AZRkV7TkcZbVxFEBIfEQpwaBdrEnhOS1liGXN5WxAZGh EKcGgXYXtDRk0fYB1CclIQGRoRCnBoF2dDQGkeGxweUF4ZEBkaEQpwaBdhWR1ZQV8BeERcWhAZG hEKcGgXYkkdE2VvZVxcTl0QGRoRCnB9F2gcc0hAW39QXGhuEBkaEQpwfxdlWHIYHUkYXkZpfBAb Hh8RCnBfF2gcc0hAW39QXGhuEBkaEQpwbBdmH3tYXGIFS1hkHxAZGhEKcEwXbWhlGUFSfXsYRVI QGRoRCm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=351 suspectscore=0 adultscore=0 mlxscore=0 malwarescore=0 phishscore=0 mlxlogscore=999 clxscore=177 lowpriorityscore=0 bulkscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108070147 domainage_hfrom=9491 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000091e3a705c8fe2c5d Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Ren=C3=A9, if Colvars is not active in both runs (with pre-compiled a= nd self-compiled) it is very unlikely that changes in its source files can impact performance. You could probably confirm this by using your own build of an *unmodified* 2.14 source tree, which I would expect to behave the same way. One thing to note is that most pre-compiled builds of NAMD are built with the Intel compiler, see e.g. the following when you launch the "Linux-x86_64-multicore-CUDA" build: Info: Based on Charm++/Converse 61002 for *multicore-linux-x86_64-iccstatic= * Info: Built Mon Aug 24 10:10:58 CDT 2020 by jim on belfast.ks.uiuc.edu Jim Phillips, or one of the other core maintainers at UIUC may be able to comment further about what you could do on your end to reproduce the optimizations of the pre-compiled build on your own build. In general, I would also look into changing the number of CPU threads associated in 2.x NAMD. You have a fairly good performance to begin with, consistent with such a small system. The CPU-GPU communication step is one of the main factors limiting simulation speed, and this is definitely affected by how many CPU threads communicate with the GPU. For such a small system, fewer CPU threads per GPU would be more appropriate. (Note that this is valid for 2.x, NAMD 3.0 is entirely different). Giacomo On Sat, Aug 7, 2021 at 3:18 PM Ren=C3=A9 Hafner TUK wrote: > Dear NAMD maintainers, > > > I tried implementing a new colvar (which was successful) but wondered > about speed reduction by it. > > Though I compared my self compiled version plain MD simulations > (finally without colvars) with the precompiled binary from the website. > > The only thing changed in the code is in colvars module files that is > not active for the following comparism. > > > I obtain the following speed of simulations for a single standard > cutoff etc. simulation (membrane + water, 7k atoms) > > Precompiled: 300 ns/day (4fs ,HMR) > > Selfcompiled: 162 ns/day (4fs timestep, HMR) > > > This is not CUDA Version dependent as this results is stable with both > CUDA 11.3 as well as with CUDA 10.1 (this latter version was used in the > precompiled binary). > > > Any help is appreciated. > > Kind regards > > Ren=C3=A9 > > I compiled it with the following settings: > > """ > > # building charmm > module purge > module load gcc/8.4 > ./build charm++ multicore-linux-x86_64 gcc -j16 --with-production > > ### > module purge > module load gcc/8.4 > module load nvidia/10.1 > ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64-gcc > --with-tcl --with-python --with-fftw --with-cuda --arch-suffix > SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def > cd Linux-x86_64-g++ > # append the line CXXOPTS=3D-lstdc++ -std=3Dc++11 to the Make.config > ## if no CXXOPTS like --with-debug are defined then it will not work > echo "CXXOPTS=3D-lstdc++ -std=3Dc++11" >> Make.config > > echo "showin Make.config" > cat Make.config > # then run it > make -j 12 | tee > make_log_SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def.= txt > > """ > > > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --00000000000091e3a705c8fe2c5d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Ren=C3=A9, if Colvars is not active in both runs (wi= th pre-compiled and self-compiled) it is very unlikely that changes in its = source files can impact=C2=A0performance.=C2=A0 You could probably confirm = this by using your own build of an unmodified 2.14 source tree, whic= h I would expect to behave the same=C2=A0way.

One thing = to note is that most pre-compiled builds of NAMD are built with the Intel c= ompiler, see e.g. the following when you launch the "Linux-x86_64-mult= icore-CUDA" build:

Info: Based on Charm++/Con= verse 61002 for multicore-linux-x86_64-iccstatic
Info: Built Mon = Aug 24 10:10:58 CDT 2020 by jim on b= elfast.ks.uiuc.edu

Jim Phillips, or one of= the other core maintainers at UIUC may be able to comment further about wh= at you could do on your=C2=A0end to reproduce the optimizations of the pre-= compiled build on your own build.

In general, I wo= uld also look into changing the number of CPU threads associated in 2.x NAM= D.=C2=A0 You have a fairly good performance to begin with, consistent with = such a small system.=C2=A0 The CPU-GPU communication step is one of the mai= n factors limiting simulation speed, and this is definitely affected by how= many CPU threads communicate with the GPU.

For su= ch a small system, fewer CPU threads per GPU would be more appropriate.=C2= =A0 (Note that this is valid for 2.x, NAMD 3.0 is entirely different).
<= /div>

Giacomo

=
On Sat, Aug 7, 2021 at 3:18 PM Ren=C3= =A9 Hafner TUK <hamburge@ph= ysik.uni-kl.de> wrote:
=20 =20 =20

=C2=A0=C2=A0 Dear NAMD maintainers,


=C2=A0=C2=A0=C2=A0 I tried implementing a new colvar (which was succ= essful) but wondered about speed reduction by it.

=C2=A0=C2=A0=C2=A0 Though I compared my self compiled version plain = MD simulations (finally without colvars) with the precompiled binary from the website.

=C2=A0=C2=A0=C2=A0 The only thing changed in the code is in colvars = module files that is not active for the following comparism.


=C2=A0=C2=A0=C2=A0 I obtain the following speed of simulations for a= single standard cutoff etc. simulation (membrane + water, 7k atoms)

=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 Precompiled: 300 ns/day (4fs ,= HMR)

=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 Selfcompiled: 162 ns/day (4fs = timestep, HMR)


This is not CUDA Version dependent as this results is stable with both CUDA 11.3 as well as with CUDA 10.1 (this latter version was used in the precompiled binary).


Any help is appreciated.

Kind regards

Ren=C3=A9

I compiled it with the following settings:

"""

# building charmm
module purge
module load gcc/8.4
./build charm++ multicore-linux-x86_64 gcc=C2=A0 -j16=C2=A0 --with-production

###
module purge
module load gcc/8.4
module load nvidia/10.1
./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64-gcc --with-tcl --with-python --with-fftw --with-cuda --arch-suffix SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def
cd Linux-x86_64-g++
# append the line CXXOPTS=3D-lstdc++ -std=3Dc++11 to the Make.confi= g
## if no CXXOPTS like --with-debug are defined then it will not work
echo "CXXOPTS=3D-lstdc++ -std=3Dc++11" >> Make.conf= ig

echo "showin Make.config"
cat Make.config
# then run it
make -j 12 | tee make_log_SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def.tx= t

"""


--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--00000000000091e3a705c8fe2c5d-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 7 17:44:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177MiKQh026869; Sat, 7 Aug 2021 17:44:20 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 177MiKpb026868; Sat, 7 Aug 2021 17:44:20 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177MiJpd026864; Sat, 7 Aug 2021 17:44:20 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 177MiJdk026863; Sat, 7 Aug 2021 17:44:19 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 177Mi5x7026855 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 7 Aug 2021 17:44:06 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 177Mhw3d019065 for ; Sat, 7 Aug 2021 22:44:05 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3a9j5dv2rt-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 07 Aug 2021 22:44:05 +0000 Received: from [IPv6:2a02:810c:300:6724:adc4:8909:aa62:54c4] ([IPv6:2a02:810c:300:6724:adc4:8909:aa62:54c4]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 177Mi0fX105671 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Sun, 8 Aug 2021 00:44:00 +0200 Subject: Re: namd-l: Compiling issue: selfcompiled NAMD2.14 multicore version factor ~2x slower - SOLVED To: namd-l@ks.uiuc.edu, Giacomo Fiorin References: <389d8cf4-2cf5-69b0-cc2b-e852b2ee021d@physik.uni-kl.de> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <51f6f2b6-1360-88f3-c8ae-3c215b8c1aef@physik.uni-kl.de> Date: Sun, 8 Aug 2021 00:44:01 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.12.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------677FFD459034FB71FCEC2F18" Content-Language: de-DE X-Spam-Status: No, hits=-2.616, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-2.619,URIBL_BLOCKED=0.001 X-Spam-Score: (-2.616) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: GNBX6SHbdaKq92VdLqhCjCZHjFj1oEML X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBsdEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBx4aHREKQ1kXBxsSGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsTHXETGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdtZGhyHHliSE5LYVsTGHxOZltCaUBpcGJAbEAbRW9nZhEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdzeGZsexEKTVwXHh4ZEQpMWhd4YU1BTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2xfbGZfcExLHFJLEQpDWhcbGRsEGB4cBBsYGgQYGB oRCkJeFxsRCkReFxgRCkJFF2wdWHJFHxxHSQVuEQpCThdkGkluenp4GmR9XBEKQkwXYGAbUhkdG BpScgURCkJsF2ZrYmQYWWJtSH5sEQpCQBdrQx5uWUJpQAEaSBEKQlgXZ3Nlc0BuYWFMXWIRClpY FxkRCnlDF2FlRHlaQxh/fEYcEQpwZxdgGUZFe05HGW1cRRATHxEKcGgXb0FMS2tgcxgfZWIQGhE KcGgXYXpcZGBYHG1BQGEQGhEKcGgXaR0cQWB+e2FSZE4QGhEKcGgXegFFGE1yfEkdeW0QGhEKcG gXYW4cH0tcUn1nHk8QGhEKcH0XaBxzSEBbf1BcaG4QGRoRCnBnF2EaBVwfAQEeYWxEEBoRCnB/F 2VYchgdSRheRml8EBsfGREKcF8XaBxzSEBbf1BcaG4QGRoRCnBsF3ofeHlveExDX3BEEB4SEQpt fhcaEQpYTRdLESA= X-Proofpoint-GUID: GNBX6SHbdaKq92VdLqhCjCZHjFj1oEML X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 malwarescore=0 phishscore=0 spamscore=0 priorityscore=0 suspectscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 impostorscore=0 clxscore=217 mlxlogscore=945 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108070161 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------677FFD459034FB71FCEC2F18 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Giacomo,     yes I noticed that icc was used in the precompiled one but did not think it had such a big influence wether its gcc or icc.. But indeed it does very much! FYI: Using intel/2019 compiler and comparim performances on hardware like: * 12cores (of XEON SP 6126, best available at the cluster) +1xV100 gpu            Now I even get a slightly higher speed than the precompiled one (compared without colvars)! :) With colvars I now get: * on 12cores + V100: ~350ns/day. * 6cores +V100: ~ 250 ns/day. And intel + CUDA 11.3 or CUDA 10.1 still makes no differences. Best René On 8/7/2021 10:40 PM, Giacomo Fiorin wrote: > Hello René, if Colvars is not active in both runs (with pre-compiled > and self-compiled) it is very unlikely that changes in its source > files can impact performance.  You could probably confirm this by > using your own build of an /unmodified/ 2.14 source tree, which I > would expect to behave the same way. > > One thing to note is that most pre-compiled builds of NAMD are built > with the Intel compiler, see e.g. the following when you launch the > "Linux-x86_64-multicore-CUDA" build: > > Info: Based on Charm++/Converse 61002 for > *multicore-linux-x86_64-iccstatic* > Info: Built Mon Aug 24 10:10:58 CDT 2020 by jim on belfast.ks.uiuc.edu > > > Jim Phillips, or one of the other core maintainers at UIUC may be able > to comment further about what you could do on your end to reproduce > the optimizations of the pre-compiled build on your own build. > > In general, I would also look into changing the number of CPU threads > associated in 2.x NAMD.  You have a fairly good performance to begin > with, consistent with such a small system.  The CPU-GPU communication > step is one of the main factors limiting simulation speed, and this is > definitely affected by how many CPU threads communicate with the GPU. > > For such a small system, fewer CPU threads per GPU would be more > appropriate.  (Note that this is valid for 2.x, NAMD 3.0 is entirely > different). > > Giacomo > > On Sat, Aug 7, 2021 at 3:18 PM René Hafner TUK > > wrote: > >    Dear NAMD maintainers, > > >     I tried implementing a new colvar (which was successful) but > wondered about speed reduction by it. > >     Though I compared my self compiled version plain MD > simulations (finally without colvars) with the precompiled binary > from the website. > >     The only thing changed in the code is in colvars module files > that is not active for the following comparism. > > >     I obtain the following speed of simulations for a single > standard cutoff etc. simulation (membrane + water, 7k atoms) > >         Precompiled: 300 ns/day (4fs ,HMR) > >         Selfcompiled: 162 ns/day (4fs timestep, HMR) > > > This is not CUDA Version dependent as this results is stable with > both CUDA 11.3 as well as with CUDA 10.1 (this latter version was > used in the precompiled binary). > > > Any help is appreciated. > > Kind regards > > René > > I compiled it with the following settings: > > """ > > # building charmm > module purge > module load gcc/8.4 > ./build charm++ multicore-linux-x86_64 gcc  -j16 --with-production > > ### > module purge > module load gcc/8.4 > module load nvidia/10.1 > ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64-gcc > --with-tcl --with-python --with-fftw --with-cuda --arch-suffix > SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def > cd Linux-x86_64-g++ > # append the line CXXOPTS=-lstdc++ -std=c++11 to the Make.config > ## if no CXXOPTS like --with-debug are defined then it will not work > echo "CXXOPTS=-lstdc++ -std=c++11" >> Make.config > > echo "showin Make.config" > cat Make.config > # then run it > make -j 12 | tee > make_log_SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def.txt > > """ > > > -- > Dipl.-Phys. René Hafner > TU Kaiserslautern > Germany > -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------677FFD459034FB71FCEC2F18 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Giacomo,

    yes I noticed that icc was used in the precompiled one but did not think it had such a big influence wether its gcc or icc..

But indeed it does very much!

FYI:

Using intel/2019 compiler

and comparim performances on hardware like:

* 12cores (of XEON SP 6126, best available at the cluster) +1xV100 gpu

           Now I even get a slightly higher speed than the precompiled one (compared without colvars)! :)


With colvars I now get:

* on 12cores + V100: ~350ns/day.

* 6cores +V100: ~ 250 ns/day.


And intel + CUDA 11.3 or CUDA 10.1 still makes no differences.


Best

René

On 8/7/2021 10:40 PM, Giacomo Fiorin wrote:
Hello René, if Colvars is not active in both runs (with pre-compiled and self-compiled) it is very unlikely that changes in its source files can impact performance.  You could probably confirm this by using your own build of an unmodified 2.14 source tree, which I would expect to behave the same way.

One thing to note is that most pre-compiled builds of NAMD are built with the Intel compiler, see e.g. the following when you launch the "Linux-x86_64-multicore-CUDA" build:

Info: Based on Charm++/Converse 61002 for multicore-linux-x86_64-iccstatic
Info: Built Mon Aug 24 10:10:58 CDT 2020 by jim on belfast.ks.uiuc.edu

Jim Phillips, or one of the other core maintainers at UIUC may be able to comment further about what you could do on your end to reproduce the optimizations of the pre-compiled build on your own build.

In general, I would also look into changing the number of CPU threads associated in 2.x NAMD.  You have a fairly good performance to begin with, consistent with such a small system.  The CPU-GPU communication step is one of the main factors limiting simulation speed, and this is definitely affected by how many CPU threads communicate with the GPU.

For such a small system, fewer CPU threads per GPU would be more appropriate.  (Note that this is valid for 2.x, NAMD 3.0 is entirely different).

Giacomo

On Sat, Aug 7, 2021 at 3:18 PM René Hafner TUK <hamburge@physik.uni-kl.de> wrote:

   Dear NAMD maintainers,


    I tried implementing a new colvar (which was successful) but wondered about speed reduction by it.

    Though I compared my self compiled version plain MD simulations (finally without colvars) with the precompiled binary from the website.

    The only thing changed in the code is in colvars module files that is not active for the following comparism.


    I obtain the following speed of simulations for a single standard cutoff etc. simulation (membrane + water, 7k atoms)

        Precompiled: 300 ns/day (4fs ,HMR)

        Selfcompiled: 162 ns/day (4fs timestep, HMR)


This is not CUDA Version dependent as this results is stable with both CUDA 11.3 as well as with CUDA 10.1 (this latter version was used in the precompiled binary).


Any help is appreciated.

Kind regards

René

I compiled it with the following settings:

"""

# building charmm
module purge
module load gcc/8.4
./build charm++ multicore-linux-x86_64 gcc  -j16  --with-production

###
module purge
module load gcc/8.4
module load nvidia/10.1
./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64-gcc --with-tcl --with-python --with-fftw --with-cuda --arch-suffix SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def
cd Linux-x86_64-g++
# append the line CXXOPTS=-lstdc++ -std=c++11 to the Make.config
## if no CXXOPTS like --with-debug are defined then it will not work
echo "CXXOPTS=-lstdc++ -std=c++11" >> Make.config

echo "showin Make.config"
cat Make.config
# then run it
make -j 12 | tee make_log_SelfCompiledNAMD214MultiCoreCUDA_cuda101_gcc_with_newcolvar_def.txt

"""


--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="0000000000006ac9ae05c906fde5" X-Proofpoint-ORIG-GUID: iw8cy7nmld_Xch6E28lgp5jZ2NcW0xx_ X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwfEQpMehcZHh4RCllEF21sYRtGax5/ZwFcEQpYWBdkZWJLGFxtAR1 /EhEKeE4XY1Nja3sTWH4aX14RCnlMF20SaWJyb0hyTBxYEQpDSBcHGx0eEQpDWRcHGxgdEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4fcRgdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0NdEklTHURHRk51cklCHG8YEkZNWh9AcBhkSX0aUlJ1EQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3N4eUJTEQpNXBcZGhoRCkxaF2xpTU1rEQpMRhdva2t ra2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBBsdEhEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdlcGIab38aZBofZxEKQk4XY1Nja 3sTWH4aX14RCkJMF2RlYksYXG0BHX8SEQpCbBdiUGN7Zm9/WBoZYxEKQkAXbHNuGXpkHUddE0kR CkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxd6cHxJX2xORn8SchEKWUsXEx4TGBEKcGgXYUtjR30 FQF1SXBgQGRoRCnBoF2x+YG1rZmFMZFN+EBkaEQpwaBd6RwF/GE1gYlJBXRAZGhEKcGgXaEdrBU EFfhMYQmMQGRoRCnBoF2BbTWAZeRh5WnwcEBkaEQpwbBdiRVIYZFAdRmBDThAZGhEKbX4XGhEKW E0XSxEg X-Proofpoint-GUID: iw8cy7nmld_Xch6E28lgp5jZ2NcW0xx_ X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 malwarescore=0 phishscore=0 spamscore=0 priorityscore=344 suspectscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 impostorscore=0 clxscore=165 mlxlogscore=439 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108080044 domainage_hfrom=9492 X-Spam-Score: 0 X-Spam-OrigSender: ruturajwarake47@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ruturaj warake --0000000000006ac9ae05c906fde5 Content-Type: text/plain; charset="UTF-8" Dear users, I am running normal protein ligand docked complex simulation. I have less computer configuration so I did 10 ns run first. Then I again did 10 ns and so on till 30 ns by changing the inputname and outputname in production.inp file. But as I am seeing now, production.dcd file is being smaller in size (kB) after every run. So I am not sure whether it works or not. Whether I can achieve 30 ns or I am repeating same 10 ns again and again ? Please guide me for the same. Ruturaj Warake, Niper, Hyderabad --0000000000006ac9ae05c906fde5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear users,
I am running normal protein = ligand docked complex simulation.
I have less comput= er configuration so I did 10 ns run first. Then I again did 10 ns and so on= till 30 ns by changing the inputname and outputname in production.inp file= .=C2=A0
But as I am seeing now, production.dcd file = is being smaller in size (kB) after every run.=C2=A0
So I am not sure whether it works=C2=A0or not. Whether I can achieve 30 ns= or I am repeating same 10 ns again and again ? Please guide=C2=A0me for th= e same.=C2=A0

Ruturaj Wa= rake,
Niper, Hyderabad
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charset="UTF-8" Post your conf files for all 3 runs. You seem to have overwritten your files. On Sun, 8 Aug, 2021, 12:44 pm Ruturaj warake, wrote: > Dear users, > I am running normal protein ligand docked complex simulation. > I have less computer configuration so I did 10 ns run first. Then I again > did 10 ns and so on till 30 ns by changing the inputname and outputname in > production.inp file. > But as I am seeing now, production.dcd file is being smaller in size (kB) > after every run. > So I am not sure whether it works or not. Whether I can achieve 30 ns or I > am repeating same 10 ns again and again ? Please guide me for the same. > > Ruturaj Warake, > Niper, Hyderabad > --000000000000b8e5dd05c90709d9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Post your conf files for all 3 runs. You seem to have ove= rwritten your files.=C2=A0

On Sun, 8 Aug, 2021, 12:44 pm Ruturaj warake, <= ;ruturajwarake47@gmail.com= > wrote:
Dear = users,
I am running normal protein ligand docked complex s= imulation.
I have less computer configuration so I d= id 10 ns run first. Then I again did 10 ns and so on till 30 ns by changing= the inputname and outputname in production.inp file.=C2=A0
But as I am seeing now, production.dcd file is being smaller in s= ize (kB) after every run.=C2=A0
So I am not sure whe= ther it works=C2=A0or not. Whether I can achieve 30 ns or I am repeating sa= me 10 ns again and again ? Please guide=C2=A0me for the same.=C2=A0

Ruturaj Warake,
Niper, Hyderabad
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charset="UTF-8" Can anyone please respond to this ? On Sun, 8 Aug 2021, 12:55 Ruturaj warake, wrote: > attached 3 config files. > step5 for 10ns > step6 and step7 are for 5 ns respectively. > total 20ns > > please do guide. > > On Sun, 8 Aug 2021 at 12:45, Pratik Narain Srivastava < > pratik.narain@gmail.com> wrote: > >> Post your conf files for all 3 runs. You seem to have overwritten your >> files. >> >> On Sun, 8 Aug, 2021, 12:44 pm Ruturaj warake, >> wrote: >> >>> Dear users, >>> I am running normal protein ligand docked complex simulation. >>> I have less computer configuration so I did 10 ns run first. Then I >>> again did 10 ns and so on till 30 ns by changing the inputname and >>> outputname in production.inp file. >>> But as I am seeing now, production.dcd file is being smaller in size >>> (kB) after every run. >>> So I am not sure whether it works or not. Whether I can achieve 30 ns or >>> I am repeating same 10 ns again and again ? Please guide me for the same. >>> >>> Ruturaj Warake, >>> Niper, Hyderabad >>> >> --000000000000e57d4c05c90d4e64 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Can anyone please respond to this ?

On Sun, 8 Aug 2021, = 12:55 Ruturaj warake, <rutu= rajwarake47@gmail.com> wrote:
attached 3 config files.
step5 for 10ns
st= ep6 and step7 are for 5 ns respectively.
total 20ns
please do guide.

On Sun, 8 Aug 2021 at 12:45, Pratik Narai= n Srivastava <pratik.narain@gmail.com> wrote:
Post your co= nf files for all 3 runs. You seem to have overwritten your files.=C2=A0
On S= un, 8 Aug, 2021, 12:44 pm Ruturaj warake, <ruturajwarake47@gmail.= com> wrote:
Dear users,
I am running normal prote= in ligand docked complex simulation.
I have less com= puter configuration so I did 10 ns run first. Then I again did 10 ns and so= on till 30 ns by changing the inputname and outputname in production.inp f= ile.=C2=A0
But as I am seeing now, production.dcd fi= le is being smaller in size (kB) after every run.=C2=A0
So I am not sure whether it works=C2=A0or not. Whether I can achieve 30= ns or I am repeating same 10 ns again and again ? Please guide=C2=A0me for= the same.=C2=A0

Ruturaj= Warake,
Niper, Hyderabad
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Tue, 10 Aug 2021 21:33:58 -0700 (PDT) Content-Type: multipart/alternative; boundary=Apple-Mail-4CFA7588-58AB-4629-8326-2C5D7727E7FA Content-Transfer-Encoding: 7bit From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: MD simulation Date: Tue, 10 Aug 2021 23:33:54 -0500 Message-Id: <14F46D66-ED9C-4030-B87F-483629434219@gmail.com> References: Cc: Pratik Narain Srivastava In-Reply-To: To: namd-l@ks.uiuc.edu, Ruturaj warake X-Mailer: iPhone Mail (18B92) X-CLX-Shades: MLX X-Proofpoint-GUID: GgjHWu0BXOQ1BXrKNoFSo-LHZe8WHYL_ X-Proofpoint-ORIG-GUID: GgjHWu0BXOQ1BXrKNoFSo-LHZe8WHYL_ X-CLX-Response: 1TFkXGx0cEQpMehcZHhIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGRsdEQpDWRcHGxocEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF21NQGJ9XxpocmV7G2hyWGFkRWx5RQdmYnBPEn1ic2Z1EQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3N5ekx5EQpNXBcYGB8RCkxaF3tpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZH5YT2Zuc0lwW08RCkNaFxgaEwQSHwQYGx wEHh0RCkJeFxsRCkReFxgRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXZkttWEYYT2NFQ0ARCkJOF2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9y SxEKQmwXb09kQVpCUG1ma1kRCkJAF2cZAXhfbRJvExt+EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxE KWlgXGBEKeUMXYEFdaFBAGRhiTEgRCnBnF2VTfWsfTm9/eBpuEBkaEQpwaBdoU0N7HQFOfFtuQB AZGhEKcGgXbxtHRlBNSURmaWUQGRoRCnBoF2B7WHBaY20eX21kEBkaEQpwaBdrSH1ua0x9YFtkW hAZGhEKcGgXYn8aBUcfZlJkREIQGRoRCnBsF2doQ2tzEnkYTWJcEBkaEQpwQxdgRh5hWB4dSGRc cxAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 adultscore=0 spamscore=0 clxscore=176 mlxlogscore=913 priorityscore=348 mlxscore=0 suspectscore=0 phishscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108110027 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= --Apple-Mail-4CFA7588-58AB-4629-8326-2C5D7727E7FA Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Post your conf file=20 Enviado desde mi iPhone > El 8 ago. 2021, a la(s) 9:46 a. m., Ruturaj warake escribi=C3=B3: >=20 > =EF=BB=BF > Can anyone please respond to this ? >=20 >> On Sun, 8 Aug 2021, 12:55 Ruturaj warake, wro= te: >> attached 3 config files. >> step5 for 10ns >> step6 and step7 are for 5 ns respectively. >> total 20ns >>=20 >> please do guide. >>=20 >>> On Sun, 8 Aug 2021 at 12:45, Pratik Narain Srivastava wrote: >>> Post your conf files for all 3 runs. You seem to have overwritten your f= iles.=20 >>>=20 >>>> On Sun, 8 Aug, 2021, 12:44 pm Ruturaj warake, wrote: >>>> Dear users, >>>> I am running normal protein ligand docked complex simulation. >>>> I have less computer configuration so I did 10 ns run first. Then I aga= in did 10 ns and so on till 30 ns by changing the inputname and outputname i= n production.inp file.=20 >>>> But as I am seeing now, production.dcd file is being smaller in size (k= B) after every run.=20 >>>> So I am not sure whether it works or not. Whether I can achieve 30 ns o= r I am repeating same 10 ns again and again ? Please guide me for the same.=20= >>>>=20 >>>> Ruturaj Warake, >>>> Niper, Hyderabad --Apple-Mail-4CFA7588-58AB-4629-8326-2C5D7727E7FA Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Post your conf file 


Enviado desde mi iPhone

El 8 ago. 2021, a la(s) 9:46 a. m., Ruturaj wara= ke <ruturajwarake47@gmail.com> escribi=C3=B3:

=EF=BB=BF
Can a= nyone please respond to this ?

On Sun, 8 Aug 2021, 12:55 Ruturaj warake, <ruturajwarake47@gmail.com> w= rote:
attached 3 con= fig files.
step5 for 10ns
step6 and step7 are for 5 ns respect= ively.
total 20ns

please do guide.
<= /div>
On= Sun, 8 Aug 2021 at 12:45, Pratik Narain Srivastava <pratik.narain@gm= ail.com> wrote:
Post your conf files for all 3 runs. You seem to have= overwritten your files. 

On Sun, 8 Aug, 2021, 12:44 pm Ruturaj warake, <= ;ruturajwarake47@gmail.com> wrote:
Dear users,
= I am running normal protein ligand docked complex simulation.
I have less computer configuration so I did 10 ns run first. Then I a= gain did 10 ns and so on till 30 ns by changing the inputname and outputname= in production.inp file. 
But as I am seeing now= , production.dcd file is being smaller in size (kB) after every run. 
So I am not sure whether it works or not. Whether= I can achieve 30 ns or I am repeating same 10 ns again and again ? Please g= uide me for the same. 

Ruturaj Warake,
Niper, Hyderabad
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charset="UTF-8" Hi, I am trying to do a constant ph namd job on a small protein containing GLU and LYS residues using NAMD2.14. While running namd my job crashes with "FATAL ERROR: TCL: argument list must have multiple of 2 arguments! " just after reading the top_cph36_prot.rtf file. I am following the cph tutorial distributed along with namd2.14.I have completed normal equilibration of the same system using the same configuration file ( without consph specific keywords) and using its restart files as input files for position and velocity in current consph job. Any help in solving this problem will be most appreciated. A snippet of my configuration file is as follows : #-------------------------------------------------------------- ## constph specific keywords paraTypeCharmm on parameters par_all36_prot.prm parameters toppar_water_ions.str parameters par_cph36_prot.prm # Load constant-pH specific topology files cphConfigFile conf_cph36_prot.json topology top_cph36_prot.rtf set pH 5 pH $pH outputname $pH/c6pep_310 cphMDBasename $pH/namdcph.md cphSwitchBasename $pH/namdcph.sw # switch at 15ps cphNumstepsPerSwitch 7500 # Minimize after randomizing protonation states at start. cphNumMinSteps 100 # numsteps = 500 => number of steps of conventional MD to be run in between switches # numcycles = 5000 => number of MC/MD cycles cphRun 500 5000 #------------------------------------------------ My logfile is as follows: PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore psfgen) reading topology file top_cph36_prot.rtf psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable Proteins < psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> Jun 2017 <<<<<<<<<<<<<<<<<<<<<<<<<<< psfgen) Patches and residues for constant-pH MD in NAMD psfgen) psfgen) Created by CHARMM version 36 1 psfgen) cross-term entries present in topology definitions FATAL ERROR: TCL: argument list must have multiple of 2 arguments! ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: TCL: argument list must have multiple of 2 arguments! [0] Stack Traceback: [0:0] namd2 0x4f16c4 [0:1] namd2 0xdcf3d7 [0:2] namd2 0x1425658 TclInvokeStringCommand [0:3] namd2 0x1428170 [0:4] namd2 0x146af53 [0:5] namd2 0x14a5cc7 [0:6] namd2 0x1428170 [0:7] namd2 0x146af53 [0:8] namd2 0x14a5cc7 [0:9] namd2 0x1428170 [0:10] namd2 0x1429556 [0:11] namd2 0x1429d36 [0:12] namd2 0x148bb41 [0:13] namd2 0x148bcfe [0:14] namd2 0xdc2bd0 [0:15] namd2 0x50cb80 [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main [0:17] namd2 0x4118f5 CHARM++ FATAL ERROR: FATAL ERROR: TCL: argument list must have multiple of 2 arguments! Segmentation fault (core dumped) -- Diship Srivastava JRF Department of Chemistry IIT(ISM) - Dhanbad India --000000000000a07ccd05c94abf82 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
I am trying to do a constant ph namd job on a smal= l protein containing GLU and LYS residues using NAMD2.14.=C2=A0 While runni= ng namd=C2=A0 my job crashes with "FATAL ERROR: TCL: argument list mus= t have multiple of 2 arguments! " just after reading the=C2=A0top_cph3= 6_prot.rtf file. I am following the cph tutorial distributed along with nam= d2.14.I have completed=C2=A0 normal equilibration of the same system using = the same configuration file ( without consph specific keywords) and=C2=A0 u= sing its restart files as input files for position and velocity in current = consph job. Any help in solving this problem will be most appreciated.

=C2=A0A snippet of my configuration file is as follows= :=C2=A0
#-------------------------------------------------------= -------
## constph specific keywords
paraTypeCharmm =C2=A0 =C2= =A0 =C2=A0on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all36_prot= .prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_water_ions.str<= br>parameters par_cph36_prot.prm
# Load constant-pH specific topology fi= les
cphConfigFile conf_cph36_prot.json
topology =C2=A0 =C2=A0 =C2=A0= top_cph36_prot.rtf


set pH 5

pH $pH
outputname =C2=A0 = =C2=A0 =C2=A0 =C2=A0$pH/c6pep_310
cphMDBasename =C2=A0 =C2=A0 $pH/namdcp= h.md
cphSwitchBasename $pH/namdcph.sw

# switch at 15ps=
cphNumstepsPerSwitch 7500
# Minimize after randomizing protonation s= tates at start.
cphNumMinSteps 100
# numsteps =3D 500 =3D> number = of steps of conventional MD to be run in between switches
# numcycles = =3D 5000 =3D> number of MC/MD cycles
cphRun 500 5000
<= br>
#------------------------------------------------
<= br>
My logfile is as follows:=C2=A0

PSFG= EN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore
psfgen) rea= ding topology file top_cph36_prot.rtf

psfgen) > CHARMM36 All-Hydr= ogen Topology File for Titratable Proteins <
psfgen) >>>>= >>>>>>>>>>>>>>>>>>>= ;>>> Jun 2017 <<<<<<<<<<<<<= <<<<<<<<<<<<<<
psfgen) =C2=A0P= atches and residues for constant-pH MD in NAMD
psfgen)
psfgen) Creat= ed by CHARMM version 36 1
psfgen) cross-term entries present in topology= definitions
FATAL ERROR: TCL: argument list must have multiple of 2 arg= uments!
------------- Processor 0 Exiting: Called CmiAbort ------------<= br>Reason: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0TCL: argument list must have multiple of 2 arguments!

[0] = Stack Traceback:
=C2=A0 [0:0] namd2 0x4f16c4
=C2=A0 [0:1] namd2 0xdc= f3d7
=C2=A0 [0:2] namd2 0x1425658 TclInvokeStringCommand
=C2=A0 [0:3= ] namd2 0x1428170
=C2=A0 [0:4] namd2 0x146af53
=C2=A0 [0:5] namd2 0= x14a5cc7
=C2=A0 [0:6] namd2 0x1428170
=C2=A0 [0:7] namd2 0x146af53 =
=C2=A0 [0:8] namd2 0x14a5cc7
=C2=A0 [0:9] namd2 0x1428170
=C2= =A0 [0:10] namd2 0x1429556
=C2=A0 [0:11] namd2 0x1429d36
=C2=A0 [0:= 12] namd2 0x148bb41
=C2=A0 [0:13] namd2 0x148bcfe
=C2=A0 [0:14] nam= d2 0xdc2bd0
=C2=A0 [0:15] namd2 0x50cb80
=C2=A0 [0:16] libc.so.6 0x= 7fc6afc20bf7 __libc_start_main
=C2=A0 [0:17] namd2 0x4118f5
CHARM++ = FATAL ERROR: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0TCL: argument list must have multiple of 2 arguments!

Segm= entation fault (core dumped)


-- <= br>
Diship Srivastava=C2=A0
JRF=C2=A0
Depa= rtment of Chemistry
IIT(ISM) - Dhanbad
India
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boundary="00000000000037e86905c960144c" X-Proofpoint-ORIG-GUID: 5X2EyfSGEeLNHnxhGmNXmRb5OCZU_Jwr X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBoZEQpMehcZGR4RCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHHxobEQpDWRcHGxoZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIZcRsZHhAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThcfchhvU0x5bW9PZmRiRFJCbUdkckd4SB9laXB/dWBdWBEKWFwXHwQaBBgZ GQUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzeVwSSREKTVwXHhkZEQpMWhd8aU1NTREKRVkXb2s RCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh8EGx wcBB4eEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2sTGmFOX15YGB1lEQpCThdjU2NrexNYfhpfXhEKQkwXaUlIGkt+aUYbeHMRCkJs F2EeGXhabmxnY19iEQpCQBdhU1t4UB5eQHAfQhEKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF29 6WRsSQnhnZmMeEQpwaBdgYxtlbmdNExsBUhAZGhEKcGgXYgUYTX9OekkaGUYQGRoRCnBoF28cZ3 h6fkNYbBwFEBkaEQpwaBdpbmhIRBpib1hZQBAZGhEKcGgXaGhoGmkTfkdFWVsQGRoRCnBsF24dZ nsSSxp4ElxtEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 5X2EyfSGEeLNHnxhGmNXmRb5OCZU_Jwr X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 adultscore=0 malwarescore=0 suspectscore=0 impostorscore=0 clxscore=203 bulkscore=0 mlxlogscore=999 priorityscore=334 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108120113 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --00000000000037e86905c960144c Content-Type: text/plain; charset="UTF-8" I don't see anything wrong from the snippet you posted. Though based on the error message one of the commands expected an even number of arguments, presumably as a list of labeled values. Are there other relevant keywords to show? BKR On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava wrote: > Hi, > I am trying to do a constant ph namd job on a small protein containing GLU > and LYS residues using NAMD2.14. While running namd my job crashes with > "FATAL ERROR: TCL: argument list must have multiple of 2 arguments! " just > after reading the top_cph36_prot.rtf file. I am following the cph tutorial > distributed along with namd2.14.I have completed normal equilibration of > the same system using the same configuration file ( without consph specific > keywords) and using its restart files as input files for position and > velocity in current consph job. Any help in solving this problem will be > most appreciated. > > A snippet of my configuration file is as follows : > #-------------------------------------------------------------- > ## constph specific keywords > paraTypeCharmm on > parameters par_all36_prot.prm > parameters toppar_water_ions.str > parameters par_cph36_prot.prm > # Load constant-pH specific topology files > cphConfigFile conf_cph36_prot.json > topology top_cph36_prot.rtf > > > set pH 5 > > pH $pH > outputname $pH/c6pep_310 > cphMDBasename $pH/namdcph.md > cphSwitchBasename $pH/namdcph.sw > > # switch at 15ps > cphNumstepsPerSwitch 7500 > # Minimize after randomizing protonation states at start. > cphNumMinSteps 100 > # numsteps = 500 => number of steps of conventional MD to be run in > between switches > # numcycles = 5000 => number of MC/MD cycles > cphRun 500 5000 > > #------------------------------------------------ > > My logfile is as follows: > > PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore > psfgen) reading topology file top_cph36_prot.rtf > > psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable Proteins < > psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> Jun 2017 <<<<<<<<<<<<<<<<<<<<<<<<<<< > psfgen) Patches and residues for constant-pH MD in NAMD > psfgen) > psfgen) Created by CHARMM version 36 1 > psfgen) cross-term entries present in topology definitions > FATAL ERROR: TCL: argument list must have multiple of 2 arguments! > ------------- Processor 0 Exiting: Called CmiAbort ------------ > Reason: FATAL ERROR: > > TCL: argument list must have multiple of 2 > arguments! > > [0] Stack Traceback: > [0:0] namd2 0x4f16c4 > [0:1] namd2 0xdcf3d7 > [0:2] namd2 0x1425658 TclInvokeStringCommand > [0:3] namd2 0x1428170 > [0:4] namd2 0x146af53 > [0:5] namd2 0x14a5cc7 > [0:6] namd2 0x1428170 > [0:7] namd2 0x146af53 > [0:8] namd2 0x14a5cc7 > [0:9] namd2 0x1428170 > [0:10] namd2 0x1429556 > [0:11] namd2 0x1429d36 > [0:12] namd2 0x148bb41 > [0:13] namd2 0x148bcfe > [0:14] namd2 0xdc2bd0 > [0:15] namd2 0x50cb80 > [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main > [0:17] namd2 0x4118f5 > CHARM++ FATAL ERROR: FATAL ERROR: > > TCL: argument list must have > multiple of 2 arguments! > > Segmentation fault (core dumped) > > > -- > Diship Srivastava > JRF > Department of Chemistry > IIT(ISM) - Dhanbad > India > --00000000000037e86905c960144c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I don't see anything wrong from the snippet you poste= d. Though based on the error message one of the commands expected an even n= umber of arguments, presumably as a list of labeled values. Are there other= relevant keywords to show?

BK= R

On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava <dishipsrivastava@gmail.com> wrote:
Hi,
I am trying = to do a constant ph namd job on a small protein containing GLU and LYS resi= dues using NAMD2.14.=C2=A0 While running namd=C2=A0 my job crashes with &qu= ot;FATAL ERROR: TCL: argument list must have multiple of 2 arguments! "= ; just after reading the=C2=A0top_cph36_prot.rtf file. I am following the c= ph tutorial distributed along with namd2.14.I have completed=C2=A0 normal e= quilibration of the same system using the same configuration file ( without= consph specific keywords) and=C2=A0 using its restart files as input files= for position and velocity in current consph job. Any help in solving this = problem will be most appreciated.

=C2=A0A snippet = of my configuration file is as follows :=C2=A0
#-----------------= ---------------------------------------------
## constph specific= keywords
paraTypeCharmm =C2=A0 =C2=A0 =C2=A0on
parameters =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0par_all36_prot.prm
parameters =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0toppar_water_ions.str
parameters par_cph36_prot.prm
= # Load constant-pH specific topology files
cphConfigFile conf_cph36_pro= t.json
topology =C2=A0 =C2=A0 =C2=A0top_cph36_prot.rtf


set pH= 5

pH $pH
outputname =C2=A0 =C2=A0 =C2=A0 =C2=A0$pH/c6pep_310
= cphMDBasename =C2=A0 =C2=A0 $pH/namdcph.md
cphSwitchBasename $pH/namdcph= .sw

# switch at 15ps
cphNumstepsPerSwitch 7500
# Mi= nimize after randomizing protonation states at start.
cphNumMinSteps 100=
# numsteps =3D 500 =3D> number of steps of conventional MD to be run= in between switches
# numcycles =3D 5000 =3D> number of MC/MD cycles=
cphRun 500 5000

#------------------------= ------------------------

My logfile is as follows:= =C2=A0

PSFGEN 1.6.7 from NAMD Git-2019-12-01 for L= inux-x86_64-multicore
psfgen) reading topology file top_cph36_prot.rtf
psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable Prote= ins <
psfgen) >>>>>>>>>>>>>>= ;>>>>>>>>>>>> Jun 2017 <<<<= <<<<<<<<<<<<<<<<<<<= ;<<<<
psfgen) =C2=A0Patches and residues for constant-pH MD = in NAMD
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) cr= oss-term entries present in topology definitions
FATAL ERROR: TCL: argum= ent list must have multiple of 2 arguments!
------------- Processor 0 Ex= iting: Called CmiAbort ------------
Reason: FATAL ERROR: =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: argument list must have m= ultiple of 2 arguments!

[0] Stack Traceback:
=C2=A0 [0:0] namd2 0= x4f16c4
=C2=A0 [0:1] namd2 0xdcf3d7
=C2=A0 [0:2] namd2 0x1425658 Tc= lInvokeStringCommand
=C2=A0 [0:3] namd2 0x1428170
=C2=A0 [0:4] namd2= 0x146af53
=C2=A0 [0:5] namd2 0x14a5cc7
=C2=A0 [0:6] namd2 0x142817= 0
=C2=A0 [0:7] namd2 0x146af53
=C2=A0 [0:8] namd2 0x14a5cc7
=C2= =A0 [0:9] namd2 0x1428170
=C2=A0 [0:10] namd2 0x1429556
=C2=A0 [0:1= 1] namd2 0x1429d36
=C2=A0 [0:12] namd2 0x148bb41
=C2=A0 [0:13] namd= 2 0x148bcfe
=C2=A0 [0:14] namd2 0xdc2bd0
=C2=A0 [0:15] namd2 0x50cb= 80
=C2=A0 [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main
=C2=A0 [= 0:17] namd2 0x4118f5
CHARM++ FATAL ERROR: FATAL ERROR: =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: argument list must have m= ultiple of 2 arguments!

Segmentation fault (core dumped)

--
Diship Srivastava=C2=A0
JRF=C2=A0
=
Department of Chemistry
IIT(ISM) - Dhanbad
India
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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear all, I faced a problem with running MD simulation of phenylalanine (PHE) amino acid, which has an aromatic side chain, using a polarizable force field. I= =E2=80=8C used the following script (using psfgen 2.0) to create drude-compatible .psf and .pdb files: package require psfgen topology drude_toppar_2019/toppar_drude_master_protein_2019g.str segment AP1 { pdb PHE2.pdb first NTES last CTES auto angles dihedrals } coordpdb PHE2.pdb AP1 guesscoord writepdb phe.pdb writepsf phe.psf Uploading the phe.psf (file link ) and phe.pdb (file link ) files in vmd shows that there is a bond (a rendered image is available here ) between the lone pair located in the middle of aromatic ring (type LPA1) and CG atom of PHE (type CD2R6A ) which is the Carbon atom located on the ring and interfacing the ring and backbone. However when I run a short minimization simulation initially I receive the following error mentioning no bond parameter file is found. I looked into the topology file (file link ) and couldn't find such a bond. I have to say that I followed the same procedure with aspartic acid (ASP), which has no aromatic ring, and everything was OK. It seems this problem arises when using aromatic rings. I would really appreciate it if anyone could guide me. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 20 0 0 Info: PERIODIC CELL BASIS 2 0 20 0 Info: PERIODIC CELL BASIS 3 0 0 20 Info: PERIODIC CELL CENTER 62 36 101 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: MIN ATOMS PER PATCH 40 Info: INITIAL TEMPERATURE 310 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 ELECTROSTATICS SCALED BY 1 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: DCD FILENAME phe_min-heat.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 1000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME phe_min-heat Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME phe_min-heat Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 13.5 Info: PAIRLIST SHRINK RATE 0.01 Info: PAIRLIST GROW RATE 0.01 Info: PAIRLIST TRIGGER 0.3 Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16 Info: ENERGY OUTPUT STEPS 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 2 INVERSE PS Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.257952 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 20 20 20 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from FFTW_NAMD_2.13_Linux-x86_64-netlrts.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.13_Linux-x86_64-netlrts.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: RIGID BONDS TO HYDROGEN : ALL Info: ERROR TOLERANCE : 1e-08 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1628838807 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB phe.pdb Info: STRUCTURE FILE phe.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS drude_toppar_2019/toppar_drude_master_protein_2019g.str Info: PARAMETERS drude_toppar_2019/toppar_drude_d_aminoacids_2019g.str Info: PARAMETERS drude_toppar_2019/toppar_drude_carbohydrate_2019a.str Info: PARAMETERS drude_toppar_2019/toppar_drude_nucleic_acid_2017c.str Info: PARAMETERS drude_toppar_2019/toppar_drude_lipid_2017c.str Info: PARAMETERS drude_toppar_2019/toppar_drude_model_2019g.str Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SUMMARY OF PARAMETERS: Info: 453 BONDS Info: 1097 ANGLES Info: 3641 DIHEDRAL Info: 121 IMPROPER Info: 15 CROSSTERM Info: 173 VDW Info: 343 VDW_PAIRS Info: 38 NBTHOLE_PAIRS Warning: Reading PSF supporting DRUDE without enabling the Drude model in the simulation config file FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 (ATOMS 40 23) ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 (ATOMS 40 23) [0] Stack Traceback: [0:0] [0x4f9dfd] [0:1] [0xdb1481] Links: image: https://urldefense.com/v3/__https://drive.google.com/file/d/1Xlqzhq5JEiIRUa= 5YYoG9V-l5fBwG_-Eq/view?usp=3Dsharing__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILf= WkZo-v_L3rMHmwTe1-80_HSg2xAn23DHAKkL-4zA$=20 psf file: https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7= c7z0Xrvv83vGZv4Enl/view__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmw= Te1-80_HSg2xAn23DHBbtfmvhQ$=20 pdb file: https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcK= T8kYYux3aMd0PHDRL2/view__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmw= Te1-80_HSg2xAn23DHDZMuhApQ$=20 topology file: https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr= 8Lc2FQmO13wCmx65pp/view__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmw= Te1-80_HSg2xAn23DHBv4ZwJtg$=20 All the best, Zeynab --000000000000e9adf005c96cae10 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear all,

I faced a problem with running MD simulat= ion of phenylalanine (PHE) amino acid, which has an aromatic side chain, us= ing a polarizable force field. I=E2=80=8C used the following script (using = psfgen 2.0) to create drude-compatible .psf and .pdb files:
package requ= ire psfgen
topology drude_toppar_2019/toppar_drude_master_protein_2019g.= str
segment AP1 {
pdb PHE2.pdb
first NTES
last CTES
auto ang= les dihedrals
}
coordpdb PHE2.pdb AP1
guesscoord
writepdb phe.p= db
writepsf phe.psf

Uploading the phe.psf (file=C2=A0link)=C2=A0and phe.pdb (file= =C2=A0link) files= in vmd shows that there is a bond (a rendered image is available here) between the lone p= air located in the middle of aromatic ring (type LPA1) and CG atom of PHE (= type CD2R6A ) which is the Carbon atom located on the ring and interfacing = the ring and backbone. However when I run a short minimization simulation i= nitially I receive the following error mentioning no bond parameter file is= found. I looked into the topology file (file=C2=A0link) and couldn't find such a bond. = I have to say that I followed the same procedure with aspartic acid (ASP), = which has no aromatic=C2=A0ring, and everything was OK. It seems this=C2=A0= problem arises when using aromatic=C2=A0rings. I would really appreciate it= if anyone could guide me.

Info: SIMULATION PARAMETERS:
Info: TI= MESTEP =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1
Info: NUMBER O= F STEPS =C2=A0 =C2=A0 =C2=A0 =C2=A00
Info: STEPS PER CYCLE =C2=A0 =C2=A0= =C2=A0 =C2=A020
Info: PERIODIC CELL BASIS 1 =C2=A020 0 0
Info: PERIO= DIC CELL BASIS 2 =C2=A00 20 0
Info: PERIODIC CELL BASIS 3 =C2=A00 0 20Info: PERIODIC CELL CENTER =C2=A0 62 36 101
Info: WRAPPING WATERS AROU= ND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER =C2=A0Centralized<= br>Info: LOAD BALANCING STRATEGY =C2=A0New Load Balancers -- DEFAULT
Inf= o: LDB PERIOD =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4000 steps
Info:= FIRST LDB TIMESTEP =C2=A0 =C2=A0 100
Info: LAST LDB TIMESTEP =C2=A0 =C2= =A0 -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1<= br>Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH =C2=A0 =C2= =A040
Info: INITIAL TEMPERATURE =C2=A0 =C2=A0310
Info: CENTER OF MASS= MOVING INITIALLY? NO
Info: DIELECTRIC =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 1
Info: EXCLUDE =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: = MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 phe_min-heat.dcd
Info: DCD FREQUENCY =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A01000
Info: DCD FIRST STEP =C2=A0 =C2=A0 =C2=A0 = =C2=A0 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTEN= DED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FO= RCE DCD OUTPUT
Info: OUTPUT FILENAME =C2=A0 =C2=A0 =C2=A0 =C2=A0phe_min-= heat
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME = =C2=A0 =C2=A0 =C2=A0 phe_min-heat
Info: RESTART FREQUENCY =C2=A0 =C2=A0 = =C2=A01000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING AC= TIVE
Info: SWITCHING ON =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 10
Info: S= WITCHING OFF =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012
Info: PAIRLIST DISTANC= E =C2=A0 =C2=A0 =C2=A013.5
Info: PAIRLIST SHRINK RATE =C2=A0 0.01
Inf= o: PAIRLIST GROW RATE =C2=A0 =C2=A0 0.01
Info: PAIRLIST TRIGGER =C2=A0 = =C2=A0 =C2=A0 0.3
Info: PAIRLISTS PER CYCLE =C2=A0 =C2=A02
Info: PAIR= LISTS ENABLED
Info: MARGIN =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0
Info: HYDROGEN GROUP CUTOFF =C2=A02.5
Info: PATCH DIMENS= ION =C2=A0 =C2=A0 =C2=A0 =C2=A016
Info: ENERGY OUTPUT STEPS =C2=A0 =C2= =A01000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTP= UT STEPS =C2=A0 =C2=A01000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGE= VIN TEMPERATURE =C2=A0 310
Info: LANGEVIN USING BBK INTEGRATOR
Info: = LANGEVIN DAMPING COEFFICIENT IS 2 INVERSE PS
Info: LANGEVIN DYNAMICS APP= LIED TO HYDROGENS
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TO= LERANCE =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1e-06
Info: PME= EWALD COEFFICIENT =C2=A0 =C2=A0 =C2=A0 0.257952
Info: PME INTERPOLATION= ORDER =C2=A0 =C2=A0 4
Info: PME GRID DIMENSIONS =C2=A0 =C2=A0 =C2=A0 = =C2=A0 20 20 20
Info: PME MAXIMUM GRID SPACING =C2=A0 =C2=A01
Info: A= ttempting to read FFTW data from FFTW_NAMD_2.13_Linux-x86_64-netlrts.txtInfo: Optimizing 6 FFT steps. =C2=A01... 2... 3... 4... 5... 6... =C2=A0 D= one.
Info: Writing FFTW data to FFTW_NAMD_2.13_Linux-x86_64-netlrts.txt<= br>Info: FULL ELECTROSTATIC EVALUATION FREQUENCY =C2=A0 =C2=A0 =C2=A01
I= nfo: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RAN= GE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
I= nfo: RIGID BONDS TO HYDROGEN : ALL
Info: =C2=A0 =C2=A0 =C2=A0 =C2=A0 ERR= OR TOLERANCE : 1e-08
Info: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0MAX ITERATI= ONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBE= R SEED =C2=A0 =C2=A0 1628838807
Info: USE HYDROGEN BONDS? =C2=A0 =C2=A0N= O
Info: COORDINATE PDB =C2=A0 =C2=A0 =C2=A0 =C2=A0 phe.pdb
Info: STRU= CTURE FILE =C2=A0 =C2=A0 =C2=A0 =C2=A0 phe.psf
Info: PARAMETER file: CHA= RMM format!
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 d= rude_toppar_2019/toppar_drude_master_protein_2019g.str
Info: PARAMETERS = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 drude_toppar_2019/toppar_drude_d_= aminoacids_2019g.str
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 drude_toppar_2019/toppar_drude_carbohydrate_2019a.str
Info: PARA= METERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 drude_toppar_2019/toppar_d= rude_nucleic_acid_2017c.str
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 drude_toppar_2019/toppar_drude_lipid_2017c.str
Info: PARA= METERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 drude_toppar_2019/toppar_d= rude_model_2019g.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PA= RAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf= SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Inf= o: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STR= EAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF P= ARAMETERS:
Info: 453 BONDS
Info: 1097 ANGLES
Info: 3641 DIHEDRALInfo: 121 IMPROPER
Info: 15 CROSSTERM
Info: 173 VDW
Info: 343 VD= W_PAIRS
Info: 38 NBTHOLE_PAIRS
Warning: Reading PSF supporting DRUDE = without enabling the Drude model in the simulation config file
FATAL ERR= OR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 (ATOMS 40 23)
-------= ------ Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL E= RROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 (ATOMS 40 23)

[= 0] Stack Traceback:
=C2=A0 [0:0] =C2=A0 [0x4f9dfd]
=C2=A0 [0:1] =C2= =A0 [0xdb1481]


Links:
image: https://drive.google.co= m/file/d/1Xlqzhq5JEiIRUa5YYoG9V-l5fBwG_-Eq/view?usp=3Dsharing
=

All = the best,
Zeynab
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boundary="000000000000b5457505c985bb0e" X-Proofpoint-GUID: RJKacB9t2R5CmW1TUHjqxvL0nie1YqQO X-CLX-Response: 1TFkXExoRCkx6FxkcGxEKWUQXZlsBQkRuTxxbT2gRClhYF2YfE3sZXxtaRW9 YEQp4ThdjU2NrexNYfhpfXhEKeUwXaEZYSElwRktAAUERCkNIFwcfGxgRCkNZFwcbHhwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYdGnEeEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF3hgYUtJaBNeGHgfaUd9G35/YkBbUlxmGkRDTxtzW3tlEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXc35ySHARCk1cFx4bHhEKTFoXfGlNa2sRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxduHGcdWXJnZl5IchEKQ1oXGBoTBBIfBBgaEgQeHR EKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eE QpCRRdsf0FSQ25jE2RQHhEKQk4XY1Nja3sTWH4aX14RCkJMF2YfE3sZXxtaRW9YEQpCbBdjEk5a QV9MbFocGhEKQkAXYVNbeFAeXkBwH0IRCkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5QxdvelkbEkJ 4Z2ZjHhEKcGgXYgUYTX9OekkaGUYQGRoRCnBoF28cZ3h6fkNYbBwFEBkaEQpwaBdiHVptHhlCYG 54GRAZGhEKcGgXaW5oSEQaYm9YWUAQGRoRCnBoF2EcfBJuREFCWk5IEBkaEQpwfRdnG0l8QGRBX HtzYxAZGhEKcH8Xbmkfch9cXgVEQhMQGxgcEQpwXxdlTWlPaF1QHUVcHxAZGhEKcGwXbXoZe0Zs Um1NZGYQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: RJKacB9t2R5CmW1TUHjqxvL0nie1YqQO X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 phishscore=0 malwarescore=0 mlxlogscore=999 suspectscore=0 priorityscore=361 adultscore=0 bulkscore=0 impostorscore=0 clxscore=90 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108140088 X-Spam-Score: 0 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --000000000000b5457505c985bb0e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks for the reply. No I did not used any other keywords. I am attaching my psf and pdb file in attachment. You can check if I am making some mistake. https://urldefense.com/v3/__https://www.dropbox.com/sh/9mdtoabtgnmh0ca/AAA2= 9qDi_a2sj9LYUgdTeN_Va?dl=3D0__;!!DZ3fjg!p2CK3Kp2sCUcQFE96TyZlIIYMM-tL8XUyBT= y7qu6IRMtjtsgSda1oI07gLONUJGtBQ$=20 On Thu, 12 Aug 2021 at 22:59, Brian Radak wrote: > I don't see anything wrong from the snippet you posted. Though based on > the error message one of the commands expected an even number of argument= s, > presumably as a list of labeled values. Are there other relevant keywords > to show? > > BKR > > On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava < > dishipsrivastava@gmail.com> wrote: > >> Hi, >> I am trying to do a constant ph namd job on a small protein containing >> GLU and LYS residues using NAMD2.14. While running namd my job crashes >> with "FATAL ERROR: TCL: argument list must have multiple of 2 arguments!= " >> just after reading the top_cph36_prot.rtf file. I am following the cph >> tutorial distributed along with namd2.14.I have completed normal >> equilibration of the same system using the same configuration file ( >> without consph specific keywords) and using its restart files as input >> files for position and velocity in current consph job. Any help in solvi= ng >> this problem will be most appreciated. >> >> A snippet of my configuration file is as follows : >> #-------------------------------------------------------------- >> ## constph specific keywords >> paraTypeCharmm on >> parameters par_all36_prot.prm >> parameters toppar_water_ions.str >> parameters par_cph36_prot.prm >> # Load constant-pH specific topology files >> cphConfigFile conf_cph36_prot.json >> topology top_cph36_prot.rtf >> >> >> set pH 5 >> >> pH $pH >> outputname $pH/c6pep_310 >> cphMDBasename $pH/namdcph.md >> cphSwitchBasename $pH/namdcph.sw >> >> # switch at 15ps >> cphNumstepsPerSwitch 7500 >> # Minimize after randomizing protonation states at start. >> cphNumMinSteps 100 >> # numsteps =3D 500 =3D> number of steps of conventional MD to be run in >> between switches >> # numcycles =3D 5000 =3D> number of MC/MD cycles >> cphRun 500 5000 >> >> #------------------------------------------------ >> >> My logfile is as follows: >> >> PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore >> psfgen) reading topology file top_cph36_prot.rtf >> >> psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable Proteins < >> psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> Jun 2017 <<<<<<<<<<<<<<<<<<<<<<<<<<< >> psfgen) Patches and residues for constant-pH MD in NAMD >> psfgen) >> psfgen) Created by CHARMM version 36 1 >> psfgen) cross-term entries present in topology definitions >> FATAL ERROR: TCL: argument list must have multiple of 2 arguments! >> ------------- Processor 0 Exiting: Called CmiAbort ------------ >> Reason: FATAL ERROR: >> >> TCL: argument list must have multiple= of >> 2 arguments! >> >> [0] Stack Traceback: >> [0:0] namd2 0x4f16c4 >> [0:1] namd2 0xdcf3d7 >> [0:2] namd2 0x1425658 TclInvokeStringCommand >> [0:3] namd2 0x1428170 >> [0:4] namd2 0x146af53 >> [0:5] namd2 0x14a5cc7 >> [0:6] namd2 0x1428170 >> [0:7] namd2 0x146af53 >> [0:8] namd2 0x14a5cc7 >> [0:9] namd2 0x1428170 >> [0:10] namd2 0x1429556 >> [0:11] namd2 0x1429d36 >> [0:12] namd2 0x148bb41 >> [0:13] namd2 0x148bcfe >> [0:14] namd2 0xdc2bd0 >> [0:15] namd2 0x50cb80 >> [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main >> [0:17] namd2 0x4118f5 >> CHARM++ FATAL ERROR: FATAL ERROR: >> >> TCL: argument list must h= ave >> multiple of 2 arguments! >> >> Segmentation fault (core dumped) >> >> >> -- >> Diship Srivastava >> JRF >> Department of Chemistry >> IIT(ISM) - Dhanbad >> India >> > --000000000000b5457505c985bb0e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thanks for the reply.=C2=A0
No I did not used any othe= r keywords.=C2=A0 I am attaching my psf and pdb file in attachment.=C2=A0 Y= ou can check=C2=A0if=C2=A0 I am making some mistake.

https://www.dropbox.com/sh/= 9mdtoabtgnmh0ca/AAA29qDi_a2sj9LYUgdTeN_Va?dl=3D0

On Thu, 12 Aug 20= 21 at 22:59, Brian Radak <brian= .radak@gmail.com> wrote:
I don't see anything wrong from the s= nippet you posted. Though based on the error message one of the commands ex= pected an even number of arguments, presumably as a list of labeled values.= Are there other relevant keywords to show?

BKR

On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava <= ;dishipsriv= astava@gmail.com> wrote:
Hi,
I am trying to do a constant ph na= md job on a small protein containing GLU and LYS residues using NAMD2.14.= =C2=A0 While running namd=C2=A0 my job crashes with "FATAL ERROR: TCL:= argument list must have multiple of 2 arguments! " just after reading= the=C2=A0top_cph36_prot.rtf file. I am following the cph tutorial distribu= ted along with namd2.14.I have completed=C2=A0 normal equilibration of the = same system using the same configuration file ( without consph specific key= words) and=C2=A0 using its restart files as input files for position and ve= locity in current consph job. Any help in solving this problem will be most= appreciated.

=C2=A0A snippet of my configuration = file is as follows :=C2=A0
#-------------------------------------= -------------------------
## constph specific keywords
paraTyp= eCharmm =C2=A0 =C2=A0 =C2=A0on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0par_all36_prot.prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0to= ppar_water_ions.str
parameters par_cph36_prot.prm
# Load constant-pH = specific topology files
cphConfigFile conf_cph36_prot.json
topology = =C2=A0 =C2=A0 =C2=A0top_cph36_prot.rtf


set pH 5

pH $pHoutputname =C2=A0 =C2=A0 =C2=A0 =C2=A0$pH/c6pep_310
cphMDBasename =C2= =A0 =C2=A0 $pH/namdcph.md
cphSwitchBasename $pH/namdcph.sw

=
# switch at 15ps
cphNumstepsPerSwitch 7500
# Minimize after rand= omizing protonation states at start.
cphNumMinSteps 100
# numsteps = =3D 500 =3D> number of steps of conventional MD to be run in between swi= tches
# numcycles =3D 5000 =3D> number of MC/MD cycles
cphRun 500= 5000

#---------------------------------------= ---------

My logfile is as follows:=C2=A0

PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-mul= ticore
psfgen) reading topology file top_cph36_prot.rtf

psfgen) &= gt; CHARMM36 All-Hydrogen Topology File for Titratable Proteins <
psf= gen) >>>>>>>>>>>>>>>>>&g= t;>>>>>>>> Jun 2017 <<<<<<<<= ;<<<<<<<<<<<<<<<<<<&l= t;
psfgen) =C2=A0Patches and residues for constant-pH MD in NAMD
psfg= en)
psfgen) Created by CHARMM version 36 1
psfgen) cross-term entrie= s present in topology definitions
FATAL ERROR: TCL: argument list must h= ave multiple of 2 arguments!
------------- Processor 0 Exiting: Called C= miAbort ------------
Reason: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: argument list must have multiple of 2 a= rguments!

[0] Stack Traceback:
=C2=A0 [0:0] namd2 0x4f16c4
= =C2=A0 [0:1] namd2 0xdcf3d7
=C2=A0 [0:2] namd2 0x1425658 TclInvokeStrin= gCommand
=C2=A0 [0:3] namd2 0x1428170
=C2=A0 [0:4] namd2 0x146af53 <= br>=C2=A0 [0:5] namd2 0x14a5cc7
=C2=A0 [0:6] namd2 0x1428170
=C2=A0= [0:7] namd2 0x146af53
=C2=A0 [0:8] namd2 0x14a5cc7
=C2=A0 [0:9] na= md2 0x1428170
=C2=A0 [0:10] namd2 0x1429556
=C2=A0 [0:11] namd2 0x1= 429d36
=C2=A0 [0:12] namd2 0x148bb41
=C2=A0 [0:13] namd2 0x148bcfe =
=C2=A0 [0:14] namd2 0xdc2bd0
=C2=A0 [0:15] namd2 0x50cb80
=C2= =A0 [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main
=C2=A0 [0:17] namd= 2 0x4118f5
CHARM++ FATAL ERROR: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: argument list must have multiple of = 2 arguments!

Segmentation fault (core dumped)


--
Diship Srivast= ava=C2=A0
JRF=C2=A0
Department of Chemistry
IIT(ISM= ) - Dhanbad
India
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([2601:184:497f:b2a0:8cf9:b728:49f5:b024]) by smtp.gmail.com with ESMTPSA id j11sm2972536qkl.87.2021.08.14.08.22.16 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sat, 14 Aug 2021 08:22:16 -0700 (PDT) Subject: Re: namd-l: Problem in running constant pH NAMD job To: Diship Srivastava Cc: namd-l References: From: Brian Radak Message-ID: Date: Sat, 14 Aug 2021 11:22:16 -0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------4205B60A4345F061B8D97972" Content-Language: en-US X-Proofpoint-GUID: SZ0zWEstAneCzDIIJofEFSpPJHUlgaKL X-CLX-Response: 1TFkXGxMaEQpMehcZGRMRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHHhIcEQpDWRcHGx4cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3lwGlB9b1lea0RPaVBuY2NgRUxvbHlaemBif0ZNS2FmEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc35zeGwRCk1cFxkfGhEKTFoXe2lNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGB gEGx0SEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2sTGmFOX15YGB1lEQpCThdjU2NrexNYfhpfXhEKQkwXaUlIGkt+aUYbeHMRCkJs F2EeGXhabmxnY19iEQpCQBdhU1t4UB5eQHAfQhEKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF29 6WRsSQnhnZmMeEQpwZxdnXGRoSGkcX2N+YBAZGhEKcGgXZmNgYUFaQF9+HEsQGRoRCnBoF2JFfX MfW2Z9aWscEBkaEQpwaBdlZmV5Yx1GYWVCZRAZGhEKcGgXb1MBRl5TfFtPengQGRoRCnBoF29EQ m5sGX9PX3oSEBkaEQpwfRdnG0l8QGRBXHtzYxAeEhEKcH8Xbmkfch9cXgVEQhMQGxgdEQpwXxdl TWlPaF1QHUVcHxAeEhEKcGwXbh1mexJLGngSXG0QGRoRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: SZ0zWEstAneCzDIIJofEFSpPJHUlgaKL MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=190 bulkscore=0 priorityscore=339 mlxlogscore=999 impostorscore=0 lowpriorityscore=0 mlxscore=0 spamscore=0 suspectscore=0 malwarescore=0 adultscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108140095 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------4205B60A4345F061B8D97972 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable There's unlikely to be anything wrong with your psf. The flag indicates=20 that you are specifying too many/few arguments, likely to=20 cphNumstepsPerSwitch. I would double check that you don't have any stray=20 characters on that line -- for example, you /cannot/ put comments on the=20 same line as keywords. I'm not even sure this works with semicolons. On 8/14/21 10:24 AM, Diship Srivastava wrote: > Thanks for the reply. > No I did not used any other keywords.=C2=A0 I am attaching my psf and pdb= =20 > file in attachment.=C2=A0 You can check=C2=A0if=C2=A0 I am making some mi= stake. > > https://urldefense.com/v3/__https://www.dropbox.com/sh/9mdtoabtgnmh0ca/AA= A29qDi_a2sj9LYUgdTeN_Va?dl=3D0__;!!DZ3fjg!psF_-aD-q0gkSvrWh-N8Tp86FmHDHM_WO= RQgrHi0HDAs1gKAEM2Q4dUdAbfJ3GNmZg$=20=20 > > > On Thu, 12 Aug 2021 at 22:59, Brian Radak > wrote: > > I don't see anything wrong from the snippet you posted. Though > based on the error message one of the commands expected an even > number of arguments, presumably as a list of labeled values. Are > there other relevant keywords to show? > > BKR > > On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava > > > wrote: > > Hi, > I am trying to do a constant ph namd job on a small protein > containing GLU and LYS residues using NAMD2.14.=C2=A0 While runni= ng > namd=C2=A0 my job crashes with "FATAL ERROR: TCL: argument list > must have multiple of 2 arguments! " just after reading > the=C2=A0top_cph36_prot.rtf file. I am following the cph tutorial > distributed along with namd2.14.I have completed=C2=A0 normal > equilibration of the same system using the same configuration > file ( without consph specific keywords) and=C2=A0 using its > restart files as input files for position and velocity in > current consph job. Any help in solving this problem will be > most appreciated. > > =C2=A0A snippet of my configuration file is as follows : > #-------------------------------------------------------------- > ## constph specific keywords > paraTypeCharmm =C2=A0 =C2=A0 =C2=A0on > parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all36_prot.prm > parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_water_ions.str > parameters par_cph36_prot.prm > # Load constant-pH specific topology files > cphConfigFile conf_cph36_prot.json > topology =C2=A0 =C2=A0 =C2=A0top_cph36_prot.rtf > > > set pH 5 > > pH $pH > outputname =C2=A0 =C2=A0 =C2=A0 =C2=A0$pH/c6pep_310 > cphMDBasename =C2=A0 =C2=A0 $pH/namdcph.md > cphSwitchBasename $pH/namdcph.sw > > # switch at 15ps > cphNumstepsPerSwitch 7500 > # Minimize after randomizing protonation states at start. > cphNumMinSteps 100 > # numsteps =3D 500 =3D> number of steps of conventional MD to be > run in between switches > # numcycles =3D 5000 =3D> number of MC/MD cycles > cphRun 500 5000 > > #------------------------------------------------ > > My logfile is as follows: > > PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore > psfgen) reading topology file top_cph36_prot.rtf > > psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable > Proteins < > psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> Jun 2017 > <<<<<<<<<<<<<<<<<<<<<<<<<<< > psfgen) =C2=A0Patches and residues for constant-pH MD in NAMD > psfgen) > psfgen) Created by CHARMM version 36 1 > psfgen) cross-term entries present in topology definitions > FATAL ERROR: TCL: argument list must have multiple of 2 arguments! > ------------- Processor 0 Exiting: Called CmiAbort ------------ > Reason: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: argument list > must have multiple of 2 arguments! > > [0] Stack Traceback: > =C2=A0 [0:0] namd2 0x4f16c4 > =C2=A0 [0:1] namd2 0xdcf3d7 > =C2=A0 [0:2] namd2 0x1425658 TclInvokeStringCommand > =C2=A0 [0:3] namd2 0x1428170 > =C2=A0 [0:4] namd2 0x146af53 > =C2=A0 [0:5] namd2 0x14a5cc7 > =C2=A0 [0:6] namd2 0x1428170 > =C2=A0 [0:7] namd2 0x146af53 > =C2=A0 [0:8] namd2 0x14a5cc7 > =C2=A0 [0:9] namd2 0x1428170 > =C2=A0 [0:10] namd2 0x1429556 > =C2=A0 [0:11] namd2 0x1429d36 > =C2=A0 [0:12] namd2 0x148bb41 > =C2=A0 [0:13] namd2 0x148bcfe > =C2=A0 [0:14] namd2 0xdc2bd0 > =C2=A0 [0:15] namd2 0x50cb80 > =C2=A0 [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main > =C2=A0 [0:17] namd2 0x4118f5 > CHARM++ FATAL ERROR: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 > =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: argument list must have multiple = of 2 arguments! > > Segmentation fault (core dumped) > > > --=20 > Diship Srivastava > JRF > Department of Chemistry > IIT(ISM) - Dhanbad > India > --------------4205B60A4345F061B8D97972 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable

There's unlikely to be anything wrong with your psf. The flag indicates that you are specifying too many/few arguments, likely to cphNumstepsPerSwitch. I would double check that you don't have any stray characters on that line -- for example, you cannot put comments on the same line as keywords. I'm not even sure this works with semicolons.

On 8/14/21 10:24 AM, Diship Srivastava wrote:
Thanks for the reply.=C2=A0
No I did not used any other keywords.=C2=A0 I am attaching my psf and pdb file in attachment.=C2=A0 You can check=C2=A0if=C2=A0= I am making some mistake.


On Thu, 12 Aug 2021 at 22:59, Brian Radak <brian.radak@gmail.com> wrote:
I don't see anything wrong from the snippet you posted. Though based on the error message one of the commands expected an even number of arguments, presumably as a list of labeled values. Are there other relevant keywords to show?

BKR

On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava <dishipsrivastava@gmail.com> wrote:
Hi,
I am trying to do a constant ph namd job on a small protein containing GLU and LYS residues using NAMD2.14.=C2=A0 While running namd=C2=A0 my job crashes w= ith "FATAL ERROR: TCL: argument list must have multiple of 2 arguments! " just after reading the=C2=A0top_cph36_prot.rtf file. I am following the cph tutorial distributed along with namd2.14.I have completed=C2=A0 normal equilibration of the same system using the same configuration file ( without consph specific keywords) and=C2=A0 using its restart files as input files for position and velocity in current consph job. Any help in solving this problem will be most appreciated.

=C2=A0A snippet of my configuration file is as follows :=C2=A0
#-----------------------------------------------------= ---------
## constph specific keywords
paraTypeCharmm =C2=A0 =C2=A0 =C2=A0on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0par_all36_pr= ot.prm
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_water= _ions.str
parameters par_cph36_prot.prm
# Load constant-pH specific topology files
cphConfigFile conf_cph36_prot.json
topology =C2=A0 =C2=A0 =C2=A0top_cph36_prot.rtf


set pH 5

pH $pH
outputname =C2=A0 =C2=A0 =C2=A0 =C2=A0$pH/c6pep_310
cphMDBasename =C2=A0 =C2=A0 $pH/namdcph.md
cphSwitchBasename $pH/namdcph.sw

# switch at 15ps
cphNumstepsPerSwitch 7500
# Minimize after randomizing protonation states at start.
cphNumMinSteps 100
# numsteps =3D 500 =3D> number of steps of conventional MD to be run in between switches
# numcycles =3D 5000 =3D> number of MC/MD cycles
cphRun 500 5000

#------------------------------------------------

My logfile is as follows:=C2=A0

PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore
psfgen) reading topology file top_cph36_prot.rtf

psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable Proteins <
psfgen) >>>>>>>>>>>>>>>>>>>= ;>>>>>>> Jun 2017 <<<<<<<<<<<<<<<<<<<= ;<<<<<<<<
psfgen) =C2=A0Patches and residues for constant-pH MD in NAMD
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) cross-term entries present in topology definitions
FATAL ERROR: TCL: argument list must have multiple of 2 arguments!
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0TCL: argument list must have multiple of 2 arguments!

[0] Stack Traceback:
=C2=A0 [0:0] namd2 0x4f16c4
=C2=A0 [0:1] namd2 0xdcf3d7
=C2=A0 [0:2] namd2 0x1425658 TclInvokeStringCommand
=C2=A0 [0:3] namd2 0x1428170
=C2=A0 [0:4] namd2 0x146af53
=C2=A0 [0:5] namd2 0x14a5cc7
=C2=A0 [0:6] namd2 0x1428170
=C2=A0 [0:7] namd2 0x146af53
=C2=A0 [0:8] namd2 0x14a5cc7
=C2=A0 [0:9] namd2 0x1428170
=C2=A0 [0:10] namd2 0x1429556
=C2=A0 [0:11] namd2 0x1429d36
=C2=A0 [0:12] namd2 0x148bb41
=C2=A0 [0:13] namd2 0x148bcfe
=C2=A0 [0:14] namd2 0xdc2bd0
=C2=A0 [0:15] namd2 0x50cb80
=C2=A0 [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main<= br> =C2=A0 [0:17] namd2 0x4118f5
CHARM++ FATAL ERROR: FATAL ERROR: =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TCL: a= rgument list must have multiple of 2 arguments!

Segmentation fault (core dumped)


--
Diship Srivastava=C2=A0
JRF=C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
India
--------------4205B60A4345F061B8D97972-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 14 10:22:55 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EFMtxB024927; Sat, 14 Aug 2021 10:22:55 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17EFMtoQ024926; Sat, 14 Aug 2021 10:22:55 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EFMsOH024922; Sat, 14 Aug 2021 10:22:54 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17EFMsGs024921; Sat, 14 Aug 2021 10:22:54 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EFMllO024887 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 14 Aug 2021 10:22:47 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 17EFDG43012296 for ; Sat, 14 Aug 2021 15:22:46 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3ae46sjn13-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 14 Aug 2021 15:22:46 +0000 Received: from [IPv6:2a02:810c:300:6724:ade3:8eb6:93db:d706] ([IPv6:2a02:810c:300:6724:ade3:8eb6:93db:d706]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 17EFMbRa019388 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 14 Aug 2021 17:22:43 +0200 To: "namd-l@ks.uiuc.edu" From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Subject: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling Message-ID: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> Date: Sat, 14 Aug 2021 17:22:37 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.13.0 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="------------C4C6C21B27B6B12B99D898E7" Content-Language: en-US X-Spam-Status: No, hits=0.002, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001 X-Spam-Score: (0.002) X-Spam-Flag: NO X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: AK9hVOPb7enThHu3tY-UXyx9devXI-qR X-Proofpoint-GUID: AK9hVOPb7enThHu3tY-UXyx9devXI-qR X-CLX-Response: 1TFkXGxIfEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxkcHBEKQ1kXBxgfHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscH3EeHhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdrYRNCfGV6SB1PRH5CYl8ZXnMHf3JTUhNOT1xyYwdbeBEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzfnN4QhEKTVwXEhkRCkxaF2hhTUFNEQpCTxdsX2xmX3B MSxxSSxEKQ1oXGxkbBBgeHAQbGBoEGBgaEQpCXhcbEQpEXhcYEQpCRRdsHVhyRR8cR0kFbhEKQk 4XZBpJbnp6eBpkfVwRCkJMF2BgG1IZHRgaUnIFEQpCbBdma2JkGFlibUh+bBEKQkAXb2lzSHNIT EYBRU8RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdvXGBlcEBZR2d9YhEKcGgXaU9H YV1IX2FCbkwQGRoRCnBoF2ESZkIbSWheZU8SEBkaEQpwaBdmZlB6R3pGXXBNTxAZGhEKcGgXbBl aeB54b0tsWU4QGRoRCnBoF3pFYkBfZWsSY3pQEBkaEQpwbBd6H3h5b3hMQ19wRBAZGhEKbX4XGx EKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 lowpriorityscore=0 spamscore=0 mlxlogscore=351 priorityscore=0 clxscore=185 suspectscore=0 adultscore=0 phishscore=0 impostorscore=0 mlxscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108140095 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------C4C6C21B27B6B12B99D898E7 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi, I am trying to use a distance like colvar to sample a surface with a ligand using extended ABF. In order to speed up the surface sampling process I turned the abf line into a 3D one where I also sample the X and Y direction. My colvar file roughly looks like: colvar { name X; distanceZ ... } #  Ligand distance from Membrane Center in X direction colvar { name Y; distanceZ ... }  # Ligand distance from Membrane Center in Y direction colvar { name distanceFromMembrane}  # Ligand local distance from Membrane Surface (selfdefined) abf { colvars X Y distanceFromMembrane;  ... } This means the third variable is not independent from/orthogonal to X and Y but that shouldn't be and issue when using eABF. Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get PMF(distMembrane) ) * When I did 1D sampling ( only distanceFromMembrane) I obtained rougly 5.5kcal/mol as dG (difference from Minimum to a point far away from Membrane) * When I do *3D sampling* using "subtractAppliedForce *on*" *in all 3 colvars* I obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" because I initially used metadynamics +eABF) * When I do *3D sampling* using "subtractAppliedForce *off*" *in all 3 colvars* I obtained dG ~ 1-2kcal/mol. *What is the correct way to sample non-independent variables with proper guesses?* (I expect the 3D to reconstruct the 1D sampling case when done correctly and just help improving the sampling of the whole surface) Kind regards René -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------C4C6C21B27B6B12B99D898E7 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi,

I am trying to use a distance like colvar to sample a surface with a ligand using extended ABF.

In order to speed up the surface sampling process I turned the abf line into a 3D one where I also sample the X and Y direction.


My colvar file roughly looks like:

colvar { name X; distanceZ ... } #  Ligand distance from Membrane Center in X direction

colvar { name Y; distanceZ ... }  # Ligand distance from Membrane Center in Y direction

colvar { name distanceFromMembrane}  # Ligand local distance from Membrane Surface (selfdefined)

abf { colvars X Y distanceFromMembrane;  ... }


This means the third variable is not independent from/orthogonal to X and Y but that shouldn't be and issue when using eABF.


Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get PMF(distMembrane) )


* When I did 1D sampling ( only distanceFromMembrane) I obtained rougly 5.5kcal/mol as dG (difference from Minimum to a point far away from Membrane)

* When I do 3D sampling using "subtractAppliedForce on" in all 3 colvars I obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" because I initially used metadynamics +eABF)

* When I do 3D sampling using "subtractAppliedForce off" in all 3 colvars I obtained dG ~ 1-2kcal/mol.


What is the correct way to sample non-independent variables with proper guesses?

(I expect the 3D to reconstruct the 1D sampling case when done correctly and just help improving the sampling of the whole surface)


Kind regards

René


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
--------------C4C6C21B27B6B12B99D898E7-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 14 12:18:42 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EHIgXI029212; Sat, 14 Aug 2021 12:18:42 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17EHIg1d029211; Sat, 14 Aug 2021 12:18:42 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EHIfDB029207; Sat, 14 Aug 2021 12:18:41 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17EHIfJY029206; Sat, 14 Aug 2021 12:18:41 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EHIVNG029197 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 14 Aug 2021 12:18:31 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 17EHECkC032322 for ; Sat, 14 Aug 2021 17:18:31 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=giacomo.fiorin@gmail.com; dkim=pass header.d=gmail.com header.s=20161025 Received: from mail-yb1-f176.google.com (mail-yb1-f176.google.com [209.85.219.176]) by mx0a-00007101.pphosted.com with ESMTP id 3ae4ay34am-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Sat, 14 Aug 2021 17:18:30 +0000 Received: by mail-yb1-f176.google.com with SMTP id i8so2062438ybt.7 for ; Sat, 14 Aug 2021 10:18:30 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=UiasetidinQmlNjQK4cW3c1lt1UeO9cWTtvmawFQ6kg=; b=Cp+kqSfnhGHP/t2JbOjbTo5gfQ2rpQmEAEn++uT6ozE5nq+wLhSjVTW7pbnOmsUfb3 rwbN/+Sf0Juhnh2alNOEWQItRwpWPRitx8XqP5ckGXQZS+HZn2l9enzw/9Xt2zz+ZrhN RDShIsEoQGJ+iTW404/wce3yfG8W5WhnAc/0a3HjGS6ar8gVsjE1rJSMm++FJTFlM0X0 mnFhnZPN13wxWhf1vGn11gXgd3mCYtiltdFwZ3dsPn5de+WoJXpQD/Xq/hhlfSdDQIjH 7AKRHpikmVUS1QznyaRxORd7u6u4RwnI6DtBKmRMJBz75IoAslPHJTQL+N37Pdz22ysy 3+FQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=UiasetidinQmlNjQK4cW3c1lt1UeO9cWTtvmawFQ6kg=; b=oV6JJdbK/CD8dDWOkLBTXIVQavqVX1vHl8rkShjYCr+P0gFh/YIGrjGak1hVYeWEy4 5by8ubub1fhn/oTuMgX1CmOu0aOW9UIQ86PqYh4H7Kufrmqn1bb0Q1Vhl7vdQVgIwMMj iQrnu1YxyUPu8hIzpmgZghRN2KA9bY3GAp0lRMHUZBTMg5ZqrZVJ2KsYo+x8N8ed0c+5 myItKzWKca9stkxc8zomGmygYqdM8slTRenbxQAeZGYcF2aFvcsxoXuRY3b7xNHqyQF8 hwCNT4cb3wPy/PXFiamZbiQPlB/SZbvqYyej5B/kVKjLbf3dSbBJ4Mws0ewR8O0iWg0y 1s/A== X-Gm-Message-State: AOAM5307km+3kWmBesac0w+Wy/FDaF++kL5chNqylvBJPqtxw43M+xub W11JYBe4s1SuHmgoci+jiRCdiXEjtjF9GvbwN0DAmTCfatU= X-Google-Smtp-Source: ABdhPJwOLQNvhoTKRccpK8ALDyREFh1wjWnufMBaWC8Afu82LrOiu/vKkVgehU5zId8RvSwm67dDD5h40XBh30bG36U= X-Received: by 2002:a25:be09:: with SMTP id h9mr10467862ybk.239.1628961509358; Sat, 14 Aug 2021 10:18:29 -0700 (PDT) MIME-Version: 1.0 References: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> In-Reply-To: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> From: Giacomo Fiorin Date: Sat, 14 Aug 2021 13:17:53 -0400 Message-ID: Subject: Re: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling To: NAMD list , =?UTF-8?Q?Ren=C3=A9_Hafner_TUK?= Content-Type: multipart/alternative; boundary="0000000000001e413005c98828cc" X-Proofpoint-GUID: _fJl6yhFfG0HVjsAz4Ke2GUJ3SB-vOcT X-CLX-Response: 1TFkXGBoYEQpMehcZGBwRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHhwbEQpDWRcHHx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhhxGxkaEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3VMYEYcU0JsTG0aYnxAWWtQHmFPGG1/YBl5aAdcZUl+EQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc35wAWgRCk1cFxkZHxEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRwRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF25rbEFlchNjfAFaEQpCWBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXbXt deWsZGxhdc2YRCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdoH1NfYwFcblJbcxAZGhEKcGgXbxNOEk 1BbFNAXlMQGRoRCnBoF2FdSxxaW1lob3xQEBkaEQpwaBdibVxJTxoFcBJSbhAZGhEKcGgXenxCY Gtkcl8ZensQGRoRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGhEK WE0XSxEg X-Proofpoint-ORIG-GUID: _fJl6yhFfG0HVjsAz4Ke2GUJ3SB-vOcT X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 phishscore=0 malwarescore=0 mlxlogscore=648 suspectscore=0 priorityscore=326 adultscore=0 bulkscore=0 impostorscore=0 clxscore=202 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108140108 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --0000000000001e413005c98828cc Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Ren=C3=A9, can you confirm that you are using extended ABF, and more specifically what estimator you used? (CZAR or Zheng/Yang). Orthogonality between variables is only required for straight ABF, where the force on the variable is obtained by projecting the atomic total forces directly, rather than using the extended-mass trick. Giacomo On Sat, Aug 14, 2021 at 11:24 AM Ren=C3=A9 Hafner TUK wrote: > Hi, > > I am trying to use a distance like colvar to sample a surface with a > ligand using extended ABF. > > In order to speed up the surface sampling process I turned the abf line > into a 3D one where I also sample the X and Y direction. > > > My colvar file roughly looks like: > > colvar { name X; distanceZ ... } # Ligand distance from Membrane Center > in X direction > > colvar { name Y; distanceZ ... } # Ligand distance from Membrane Center > in Y direction > > colvar { name distanceFromMembrane} # Ligand local distance from Membran= e > Surface (selfdefined) > > abf { colvars X Y distanceFromMembrane; ... } > > > This means the third variable is not independent from/orthogonal to X and > Y but that shouldn't be and issue when using eABF. > > > Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get > PMF(distMembrane) ) > > > * When I did 1D sampling ( only distanceFromMembrane) I obtained rougly > 5.5kcal/mol as dG (difference from Minimum to a point far away from > Membrane) > > * When I do *3D sampling* using "subtractAppliedForce *on*" *in all 3 > colvars* I obtained dG ~ 4kcal/mol. (I used the term > "subtractAppliedForce" because I initially used metadynamics +eABF) > > * When I do *3D sampling* using "subtractAppliedForce *off*" *in all 3 > colvars* I obtained dG ~ 1-2kcal/mol. > > > *What is the correct way to sample non-independent variables with proper > guesses?* > > (I expect the 3D to reconstruct the 1D sampling case when done correctly > and just help improving the sampling of the whole surface) > > > Kind regards > > Ren=C3=A9 > > > -- > -- > Dipl.-Phys. Ren=C3=A9 Hafner > TU Kaiserslautern > Germany > > --0000000000001e413005c98828cc Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Ren=C3=A9, can you confirm=C2=A0that you are using e= xtended ABF, and more specifically what estimator you used?=C2=A0 (CZAR or = Zheng/Yang).

Orthogonality between variables is only req= uired for straight ABF, where the force on the variable is obtained by proj= ecting the atomic total forces directly, rather than using the extended-mas= s trick.

Giacomo

On Sat, Aug 14, 2021 at 11:2= 4 AM Ren=C3=A9 Hafner TUK <= hamburge@physik.uni-kl.de> wrote:
=20 =20 =20

Hi,

I am trying to use a distance like colvar to sample a surface with a ligand using extended ABF.

In order to speed up the surface sampling process I turned the abf line into a 3D one where I also sample the X and Y direction.


My colvar file roughly looks like:

colvar { name X; distanceZ ... } #=C2=A0 Ligand distance from Membrane Center in X direction

colvar { name Y; distanceZ ... }=C2=A0 # Ligand distance from Membrane Center in Y direction

colvar { name distanceFromMembrane}=C2=A0 # Ligand local distance from Membrane Surface (selfdefined)

abf { colvars X Y distanceFromMembrane;=C2=A0 ... }


This means the third variable is not independent from/orthogonal to X and Y but that shouldn't be and issue when using eABF.


Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get PMF(distMembrane) )


* When I did 1D sampling ( only distanceFromMembrane) I obtained rougly 5.5kcal/mol as dG (difference from Minimum to a point far away from Membrane)

* When I do 3D sampling using "subtractAppliedForce o= n" in all 3 colvars I obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" because I initially used metady= namics +eABF)

* When I do 3D sampling using "subtractAppliedForce o= ff" in all 3 colvars I obtained dG ~ 1-2kcal/mol.


What is the correct way to sample non-independent variables with proper guesses?

(I expect the 3D to reconstruct the 1D sampling case when done correctly and just help improving the sampling of the whole surface)


Kind regards

Ren=C3=A9


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--0000000000001e413005c98828cc-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 14 12:29:05 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EHT5Sm001052; Sat, 14 Aug 2021 12:29:05 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17EHT5Np001051; Sat, 14 Aug 2021 12:29:05 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EHT4d8001047; Sat, 14 Aug 2021 12:29:04 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17EHT4Do001046; Sat, 14 Aug 2021 12:29:04 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17EHSswV001037 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 14 Aug 2021 12:28:54 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 17EHEXNG031925 for ; Sat, 14 Aug 2021 17:28:54 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3ae5tbtvcq-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 14 Aug 2021 17:28:53 +0000 Received: from [IPv6:2a02:810c:300:6724:ade3:8eb6:93db:d706] ([IPv6:2a02:810c:300:6724:ade3:8eb6:93db:d706]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 17EHSjaO079608 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Sat, 14 Aug 2021 19:28:47 +0200 Subject: Re: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling To: Giacomo Fiorin , NAMD list References: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: Date: Sat, 14 Aug 2021 19:28:46 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.13.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------C709C7ED31FDEAAA41CE5BD3" Content-Language: de-DE X-Spam-Status: No, hits=0.002, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-0.001,URIBL_BLOCKED=0.001 X-Spam-Score: (0.002) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: sHXOzoEHiaeJRr-jE_oOWsn1ZMcj2-0B X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMaEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBx4TGhEKQ1kXBx8ZEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF1licmVQRW9iQ0tPYHhYB0BvdUVlfVlEG3BnSUAYBxpoEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3N+S2JdEQpNXBcYGB8RCkxaF3hha0FNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF25rbEFlchNjfAFaEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXGBEKeUMXbXtdeWsZGxhdc2YRCnBnF2AZRkV7TkcZbVxFEBkaEQpwaBdhEmZCG0loXmV PEhAeEhEKcGgXbG94RU0aSUd/fUkQGhEKcGgXbBlaeB54b0tsWU4QHhIRCnBoF3pFYkBfZWsSY3 pQEB4SEQpwaBduT0leYEJCRG8aGhAaEQpwZxdgGHJBQR59UFpzXBAaEQpwbBd6H3h5b3hMQ19wR BAeEhEKcEwXbWhlGUFSfXsYRVIQGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: sHXOzoEHiaeJRr-jE_oOWsn1ZMcj2-0B X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 phishscore=0 bulkscore=0 mlxlogscore=566 impostorscore=0 mlxscore=0 adultscore=0 clxscore=190 malwarescore=0 lowpriorityscore=0 spamscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108140108 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------C709C7ED31FDEAAA41CE5BD3 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Giacomo,     yes I can confirm from the writings in the logfile stating:     "Enabling the extended Lagrangian term for colvar .. " for every colvar.     I make use of the CZAR estimator. By the way: I am using NAMD 2.14. René On 8/14/2021 7:17 PM, Giacomo Fiorin wrote: > Hello René, can you confirm that you are using extended ABF, and more > specifically what estimator you used? (CZAR or Zheng/Yang). > > Orthogonality between variables is only required for straight ABF, > where the force on the variable is obtained by projecting the atomic > total forces directly, rather than using the extended-mass trick. > > Giacomo > > On Sat, Aug 14, 2021 at 11:24 AM René Hafner TUK > > wrote: > > Hi, > > I am trying to use a distance like colvar to sample a surface with > a ligand using extended ABF. > > In order to speed up the surface sampling process I turned the abf > line into a 3D one where I also sample the X and Y direction. > > > My colvar file roughly looks like: > > colvar { name X; distanceZ ... } #  Ligand distance from > Membrane Center in X direction > > colvar { name Y; distanceZ ... }  # Ligand distance from > Membrane Center in Y direction > > colvar { name distanceFromMembrane}  # Ligand local distance > from Membrane Surface (selfdefined) > > abf { colvars X Y distanceFromMembrane;  ... } > > > This means the third variable is not independent from/orthogonal > to X and Y but that shouldn't be and issue when using eABF. > > > Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get > PMF(distMembrane) ) > > > * When I did 1D sampling ( only distanceFromMembrane) I obtained > rougly 5.5kcal/mol as dG (difference from Minimum to a point far > away from Membrane) > > * When I do *3D sampling* using "subtractAppliedForce *on*" *in > all 3 colvars* I obtained dG ~ 4kcal/mol. (I used the term > "subtractAppliedForce" because I initially used metadynamics +eABF) > > * When I do *3D sampling* using "subtractAppliedForce *off*" *in > all 3 colvars* I obtained dG ~ 1-2kcal/mol. > > > *What is the correct way to sample non-independent variables with > proper guesses?* > > (I expect the 3D to reconstruct the 1D sampling case when done > correctly and just help improving the sampling of the whole surface) > > > Kind regards > > René > > > -- > -- > Dipl.-Phys. René Hafner > TU Kaiserslautern > Germany > -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------C709C7ED31FDEAAA41CE5BD3 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Giacomo,

    yes I can confirm from the writings in the logfile stating:

    "Enabling the extended Lagrangian term for colvar .. " for every colvar.

    I make use of the CZAR estimator.

By the way: I am using NAMD 2.14.

René

On 8/14/2021 7:17 PM, Giacomo Fiorin wrote:
Hello René, can you confirm that you are using extended ABF, and more specifically what estimator you used?  (CZAR or Zheng/Yang).

Orthogonality between variables is only required for straight ABF, where the force on the variable is obtained by projecting the atomic total forces directly, rather than using the extended-mass trick.

Giacomo

On Sat, Aug 14, 2021 at 11:24 AM René Hafner TUK <hamburge@physik.uni-kl.de> wrote:

Hi,

I am trying to use a distance like colvar to sample a surface with a ligand using extended ABF.

In order to speed up the surface sampling process I turned the abf line into a 3D one where I also sample the X and Y direction.


My colvar file roughly looks like:

colvar { name X; distanceZ ... } #  Ligand distance from Membrane Center in X direction

colvar { name Y; distanceZ ... }  # Ligand distance from Membrane Center in Y direction

colvar { name distanceFromMembrane}  # Ligand local distance from Membrane Surface (selfdefined)

abf { colvars X Y distanceFromMembrane;  ... }


This means the third variable is not independent from/orthogonal to X and Y but that shouldn't be and issue when using eABF.


Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get PMF(distMembrane) )


* When I did 1D sampling ( only distanceFromMembrane) I obtained rougly 5.5kcal/mol as dG (difference from Minimum to a point far away from Membrane)

* When I do 3D sampling using "subtractAppliedForce on" in all 3 colvars I obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" because I initially used metadynamics +eABF)

* When I do 3D sampling using "subtractAppliedForce off" in all 3 colvars I obtained dG ~ 1-2kcal/mol.


What is the correct way to sample non-independent variables with proper guesses?

(I expect the 3D to reconstruct the 1D sampling case when done correctly and just help improving the sampling of the whole surface)


Kind regards

René


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="_000_SN6PR11MB287844F6D4F739F89DBAFE43B0FE9SN6PR11MB2878namp_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SN6PR11MB2878.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 1bfd2c29-c9e9-44a4-e6f3-08d961bf508b X-MS-Exchange-CrossTenant-originalarrivaltime: 17 Aug 2021 20:40:56.6000 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: M5KiF3mSEur/i8Ezy1ldka4PGv2cInE5khGn0Ff1U476zy3MTvYZiF5/k3QoFZDtyhkW4dRcByLirx61Xp/QHw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SN6PR11MB2576 X-CLX-Shades: MLX X-CLX-Response: 1TFkXHx8SEQpMehcaEQpZRBdubXxreXl8TEJgeREKWFgXZ0IfGkhSaEAYRkI RCnhOF2hjAUx/RX9CQWVAEQp5TBd6b2tFcBgTG1JsWREKQ0gXBxkYHxEKQ1kXBxgZGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGx4ecR0GHht3BhgaGgYaBhoGGxoaBhsbH3EbGRAadwYaBhoGGgYaB hoGGnEaEBp3BhoRClleF2hueREKSUYXX0NfSXVCRVleT04RCkNOF3NGZ2x1e1xFfUJ9RkZhRAdv T2xMaxh7a15QYW5QXFhdEQpYXBcfBBoEGBkZBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3N/SWQ eEQpNXBcZHxoRCkxaF2hpTWtNEQpMRhdva2tra2trEQpCTxd6XnNBEk8baRxGcxEKQ1oXHhoEGx odBBgZHQQbGRsRCkJeFxsRCkReFxgRCkJFF25uUB5sYRhhcx8fEQpCThdoYwFMf0V/QkFlQBEKQ kwXZ0IfGkhSaEAYRkIRCkJsF2RiZgFncxNTRU9SEQpCQBdtfU1sZV1bBXtHWhEKQlgXZ3Nlc0Bu YWFMXWIRClpYFxgRCnlDF2lZYmdYaUFsGlNOEQpwaBdkf1BOR2dpaBNBbRAZGhEKcGgXbkZmG2l yc2lcXVwQGRoRCnBoF2UaGG56ZkN8e1NwEBkaEQpwaBdpeB5JEkd+aRhuRBAZGhEKcGgXaU1uU3 hTfkscRF4QGRoRCnBsF2ZNfWdrW2NJfkdJEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: YlMF_QvoWhWllKn-EeFfA2QAtzKDzvrw X-Proofpoint-GUID: YlMF_QvoWhWllKn-EeFfA2QAtzKDzvrw X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 bulkscore=0 mlxlogscore=999 clxscore=558 phishscore=0 priorityscore=0 adultscore=0 lowpriorityscore=0 suspectscore=0 malwarescore=0 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108170129 X-Spam-Score: 0 X-Spam-OrigSender: royi@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ishaan Roy --_000_SN6PR11MB287844F6D4F739F89DBAFE43B0FE9SN6PR11MB2878namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hello, I am using eABF on two membrane helices to find the binding energy. During = the separation runs, the upper boundary for the distance colvar is set to 4= 0, the distance value only reaches around 20, even when I increase the simu= lation time. This current maximum it reaches is an inadequate separation, s= ince parts of the proteins are still interacting at this point and the pmf = has not levelled off. When looking at the VMD window, there doesn=92t seem = to be anything obvious that would prevent the ABF from separating them furt= her. Any ideas on what might be going on? Thanks, Ishaan Here are my colvar settings: ############################################################# ## Collective Variables ## ############################################################# # Global parameters ColvarsTrajfrequency 20 Colvarsrestartfrequency 100 analysis on colvar { name dist width 0.05 extendedLagrangian on extendedFluctuation 0.02 outputTotalForce on lowerboundary 10.0 upperboundary 40.0 distance { forceNoPBC yes group1 { psfSegID PROA atomNameResidueRange { CA 32-52 } } group2 { psfSegID PROB atomNameResidueRange { CA 87-106 } } } } colvar { name sa1 outputValue off width 1.0 lowerboundary -180.0 upperboundary 180.0 spinAngle { atoms { psfSegID PROA atomNameResidueRange { CA 32-52} } refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb } } colvar { name sa2 outputValue off width 1.0 lowerboundary -180.0 upperboundary 180.0 spinAngle { atoms { psfSegID PROB atomNameResidueRange { CA 87-106} } refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb } } colvar { name t1 outputValue off width 1.0 lowerboundary -1.0 upperboundary 1.0 tilt { atoms { psfSegID PROA atomNameResidueRange { CA 32-52} } refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb } } colvar { name t2 outputValue off width 1.0 lowerboundary -1.0 upperboundary 1.0 tilt { atoms { psfSegID PROB atomNameResidueRange { CA 87-106} } refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb } } colvar { name RMSD width 1.0 outputValue off lowerboundary 0.0 upperboundary 5.0 rmsd { atoms { psfSegID PROA PROB atomNameResidueRange { CA 32-52 } atomNameResidueRange { CA 87-106} } refpositionsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb } } ############################################################# ## RESTRAINTS AND PMF ############################################################## abf { colvars dist FullSamples 5000 } harmonic { colvars sa1 forceConstant 0.1 centers 0.0 } harmonic { colvars sa2 forceConstant 0.1 centers 0.0 } harmonic { colvars t1 forceConstant 0.1 centers 1.0 } harmonic { colvars t2 forceConstant 0.1 centers 1.0 } harmonic { colvars RMSD forceConstant 10.0 centers 0.0 } ############################################################# ### Restraint on Monomer A ############################################################### colvar { name Omega outputValue off orientation { atoms { psfSegID PROB atomNameResidueRange { CA 87-106 } } refpositionsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb } } colvar { name Pin outputValue off width 1.0 lowerboundary 22.9 upperboundary 24.9 distance { group1 { dummyatom (0, 0, 0) } group2 { psfSegID PROB atomNameResidueRange { CA 87-106 } } } } harmonic { colvars Omega forceConstant 100.0 centers ( 1.0, 0.0, 0.0, 0.0 ) } harmonic { colvars Pin forceConstant 100.0 centers 23.9 } --_000_SN6PR11MB287844F6D4F739F89DBAFE43B0FE9SN6PR11MB2878namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Hello,

 

I am using eABF on two membrane helices to find the = binding energy. During the separation runs, the upper boundary for the dist= ance colvar is set to 40, the distance value only reaches around 20, even w= hen I increase the simulation time. This current maximum it reaches is an inadequate separation, since parts o= f the proteins are still interacting at this point and the pmf has not leve= lled off. When looking at the VMD window, there doesn=92t seem to be anythi= ng obvious that would prevent the ABF from separating them further. Any ideas on what might be going on?

 

Thanks,

Ishaan

 

Here are my colvar settings:

 

####################################################= #########

## Collective Variables     = ;            &n= bsp;            = ;      ##

####################################################= #########

 

# Global parameters

ColvarsTrajfrequency    20

Colvarsrestartfrequency 100

analysis        o= n

 

colvar {

    name dist

 

    width 0.05

 

    extendedLagrangian on

    extendedFluctuation 0.02

 

    outputTotalForce on

 

    lowerboundary 10.0

    upperboundary 40.0

 

    distance {

        forceNoPB= C     yes

        group1 {<= /p>

        &nbs= p;   psfSegID PROA

        &nbs= p;   atomNameResidueRange { CA 32-52 }

        }

        group2 {<= /p>

        &nbs= p;   psfSegID PROB

        &nbs= p;   atomNameResidueRange { CA 87-106 }

        }

    }

}

 

colvar {

    name sa1

    outputValue off

 

    width 1.0

 

 

    lowerboundary -180.0

    upperboundary 180.0

 

    spinAngle {

        atoms {

        &nbs= p;   psfSegID PROA

        &nbs= p;   atomNameResidueRange { CA 32-52}

        }

        refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

    }

}

 

colvar {

    name sa2

    outputValue off

 

    width 1.0

 

    lowerboundary -180.0

    upperboundary 180.0

 

    spinAngle {

        atoms {

        &nbs= p;   psfSegID PROB

        &nbs= p;   atomNameResidueRange { CA 87-106}

        }

        refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

    }

}

 

colvar {

    name t1

    outputValue off

 

    width 1.0

 

 

    lowerboundary -1.0

    upperboundary 1.0

 

    tilt {

        atoms {

        &nbs= p;   psfSegID PROA

        &nbs= p;   atomNameResidueRange { CA 32-52}

        }

        refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

    }

}

 

colvar {

    name t2

    outputValue off

 

    width 1.0

 

    lowerboundary -1.0

    upperboundary 1.0

 

    tilt {

        atoms {

        &nbs= p;   psfSegID PROB

        &nbs= p;   atomNameResidueRange { CA 87-106}

        }

        refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

    }

}

 

colvar {

    name RMSD

    width 1.0

    outputValue off

 

    lowerboundary 0.0

    upperboundary 5.0

 

    rmsd {

        atoms {

        &nbs= p;   psfSegID PROA PROB

        &nbs= p;   atomNameResidueRange { CA 32-52 }

        &nbs= p;   atomNameResidueRange { CA 87-106}

        }

        refpositi= onsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

    }

}

 

####################################################= #########

## RESTRAINTS AND PMF

####################################################= ##########

 

 

abf {

    colvars    &n= bsp;    dist

    FullSamples   &nbs= p; 5000

}

 

harmonic {

    colvars    &n= bsp;    sa1

    forceConstant   0.1

    centers    &n= bsp;    0.0

}

 

harmonic {

    colvars    &n= bsp;    sa2

    forceConstant   0.1

    centers    &n= bsp;    0.0

}

 

harmonic {

    colvars    &n= bsp;    t1

    forceConstant   0.1

    centers    &n= bsp;    1.0

}

 

harmonic {

    colvars    &n= bsp;    t2

    forceConstant   0.1

    centers    &n= bsp;    1.0

}

 

harmonic {

    colvars    &n= bsp;    RMSD

    forceConstant   10.0

    centers    &n= bsp;    0.0

}

 

 

####################################################= #########

### Restraint on Monomer A

####################################################= ###########

 

 

colvar {

    name Omega

    outputValue off

    orientation {

        atoms {

        &nbs= p;   psfSegID PROB

        &nbs= p;   atomNameResidueRange { CA 87-106 }

        }

        refpositi= onsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

    }

}

 

colvar {

   name Pin

    outputValue off

 

   width 1.0

   lowerboundary 22.9

   upperboundary 24.9

 

   distance {

      group1 {

        &nbs= p;  dummyatom  (0, 0, 0)

        &nbs= p;     }

       group2 {

        &nbs= p;    psfSegID PROB

        &nbs= p;   atomNameResidueRange { CA 87-106 }

        }

    }

}

 

harmonic {

   colvars     &n= bsp;   Omega

   forceConstant   100.0

   centers     &n= bsp;   ( 1.0, 0.0, 0.0, 0.0 )

}

 

 

harmonic {

   colvars     &n= bsp;   Pin

   forceConstant   100.0

   centers     &n= bsp;   23.9

}

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boundary="0000000000007c11b605c9dc0ee2" X-Proofpoint-ORIG-GUID: QOuQjl_oqfHCiAsmizlytchXj7pZz6Um X-Proofpoint-GUID: QOuQjl_oqfHCiAsmizlytchXj7pZz6Um X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcZHxIRCllEF2BkGmkeckh4Xx5gEQpYWBdhW3Noc28ZSWF yXBEKeE4XY1Nja3sTWH4aX14RCnlMF2YSfXlJX2BjQWNFEQpDSBcHHxkTEQpDWRcHGxkcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3tlX3tARnVFW0xiaUNrWUdDUEZTXklCckAdWnBQHH9HEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3N/UhJJEQpNXBcZGxoRCkxaF3hpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGx0YEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2R+c3x5cx1rS0xAEQpCThdjU2NrexNYfhpfXhEKQkwXYVtzaHNvGUlhclwRCkJs F3p7Yh9QekVnBUdoEQpCQBdnWUUTHmdNHlkFWBEKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF2F EGR9oU0JoeEtFEQpwaBdnZWwebU9rcBpzYxAZGhEKcGgXbnl4UwV4Eh1OAWUQGRoRCnBoF25eQn pwWUBLfXgfEBkaEQpwaBdgG2MfZl8TUhpuTRAZGhEKcGgXZRoYbnpmQ3x7U3AQGRoRCnB9F3pEb BloSBt4UlwZEBkaEQpwfRdjQWN6a2kFHmIaWRAZGhEKcH8XbFx/aRNNQUtnXxgQExIRCnBfF2ta em1YE1N+R0VIEBIfEQpwfxdjQWN6a2kFHmIaWRAZGhEKcGwXaEkbbx8TU0VOQlsQHhIRCm1+Fxo RClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=358 mlxlogscore=999 adultscore=0 malwarescore=0 phishscore=0 impostorscore=0 spamscore=0 clxscore=171 bulkscore=0 mlxscore=0 suspectscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108180132 X-Spam-Score: 0 X-Spam-OrigSender: jeffcomer@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeff Comer --0000000000007c11b605c9dc0ee2 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable How long is your simulation? Even when ABF is converged, the exploration of the collective variable is limited by free diffusion. Diffusion of helices in a membrane is very slow (lipid exchange happens on a 10=E2=80=93100 ns timescale). You=E2=80=99d li= kely have to run this for several microseconds to get a decent PMF. You might try find that meta-eABF ( https://urldefense.com/v3/__https://doi.org/10.1021/acs.jpclett.8b01994__;!= !DZ3fjg!p--rg2JmHjjsQn3zUlSqmiEYslML__94okujSZ56ZYWn9C22bL21i_Gg37X7O1R5ag$= ) or umbrella sampling will get you an answer faster, but it=E2=80=99s still going to take a long time to g= et a reliable answer because you need to sample many different lipid arrangements and, again, lipid exchange happens on the 10=E2=80=93100 ns ti= mescale. Jeff On Tue, Aug 17, 2021 at 15:44 Ishaan Roy wrote: > Hello, > > > > I am using eABF on two membrane helices to find the binding energy. During > the separation runs, the upper boundary for the distance colvar is set to > 40, the distance value only reaches around 20, even when I increase the > simulation time. This current maximum it reaches is an inadequate > separation, since parts of the proteins are still interacting at this poi= nt > and the pmf has not levelled off. When looking at the VMD window, there > doesn=E2=80=99t seem to be anything obvious that would prevent the ABF fr= om > separating them further. Any ideas on what might be going on? > > > > Thanks, > > Ishaan > > > > Here are my colvar settings: > > > > ############################################################# > > ## Collective Variables ## > > ############################################################# > > > > # Global parameters > > ColvarsTrajfrequency 20 > > Colvarsrestartfrequency 100 > > analysis on > > > > colvar { > > name dist > > > > width 0.05 > > > > extendedLagrangian on > > extendedFluctuation 0.02 > > > > outputTotalForce on > > > > lowerboundary 10.0 > > upperboundary 40.0 > > > > distance { > > forceNoPBC yes > > group1 { > > psfSegID PROA > > atomNameResidueRange { CA 32-52 } > > } > > group2 { > > psfSegID PROB > > atomNameResidueRange { CA 87-106 } > > } > > } > > } > > > > colvar { > > name sa1 > > outputValue off > > > > width 1.0 > > > > > > lowerboundary -180.0 > > upperboundary 180.0 > > > > spinAngle { > > atoms { > > psfSegID PROA > > atomNameResidueRange { CA 32-52} > > } > > refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.p= db > > } > > } > > > > colvar { > > name sa2 > > outputValue off > > > > width 1.0 > > > > lowerboundary -180.0 > > upperboundary 180.0 > > > > spinAngle { > > atoms { > > psfSegID PROB > > atomNameResidueRange { CA 87-106} > > } > > refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.p= db > > } > > } > > > > colvar { > > name t1 > > outputValue off > > > > width 1.0 > > > > > > lowerboundary -1.0 > > upperboundary 1.0 > > > > tilt { > > atoms { > > psfSegID PROA > > atomNameResidueRange { CA 32-52} > > } > > refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.p= db > > } > > } > > > > colvar { > > name t2 > > outputValue off > > > > width 1.0 > > > > lowerboundary -1.0 > > upperboundary 1.0 > > > > tilt { > > atoms { > > psfSegID PROB > > atomNameResidueRange { CA 87-106} > > } > > refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.p= db > > } > > } > > > > colvar { > > name RMSD > > width 1.0 > > outputValue off > > > > lowerboundary 0.0 > > upperboundary 5.0 > > > > rmsd { > > atoms { > > psfSegID PROA PROB > > atomNameResidueRange { CA 32-52 } > > atomNameResidueRange { CA 87-106} > > } > > refpositionsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.p= db > > } > > } > > > > ############################################################# > > ## RESTRAINTS AND PMF > > ############################################################## > > > > > > abf { > > colvars dist > > FullSamples 5000 > > } > > > > harmonic { > > colvars sa1 > > forceConstant 0.1 > > centers 0.0 > > } > > > > harmonic { > > colvars sa2 > > forceConstant 0.1 > > centers 0.0 > > } > > > > harmonic { > > colvars t1 > > forceConstant 0.1 > > centers 1.0 > > } > > > > harmonic { > > colvars t2 > > forceConstant 0.1 > > centers 1.0 > > } > > > > harmonic { > > colvars RMSD > > forceConstant 10.0 > > centers 0.0 > > } > > > > > > ############################################################# > > ### Restraint on Monomer A > > ############################################################### > > > > > > colvar { > > name Omega > > outputValue off > > orientation { > > atoms { > > psfSegID PROB > > atomNameResidueRange { CA 87-106 } > > } > > refpositionsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.p= db > > } > > } > > > > colvar { > > name Pin > > outputValue off > > > > width 1.0 > > lowerboundary 22.9 > > upperboundary 24.9 > > > > distance { > > group1 { > > dummyatom (0, 0, 0) > > } > > group2 { > > psfSegID PROB > > atomNameResidueRange { CA 87-106 } > > } > > } > > } > > > > harmonic { > > colvars Omega > > forceConstant 100.0 > > centers ( 1.0, 0.0, 0.0, 0.0 ) > > } > > > > > > harmonic { > > colvars Pin > > forceConstant 100.0 > > centers 23.9 > > } > --=20 =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!p--rg2J= mHjjsQn3zUlSqmiEYslML__94okujSZ56ZYWn9C22bL21i_Gg37W7Pflqww$=20 --0000000000007c11b605c9dc0ee2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
How long is your simulation?
=
Even when ABF is converged, the exploration of = the collective variable is limited by free diffusion. Diffusion of helices = in a membrane is very slow (lipid exchange happens on a 10=E2=80=93100 ns t= imescale). You=E2=80=99d likely have to run this for several microseconds t= o get a decent PMF.

You = might try find that meta-eABF (=C2=A0
https:/= /doi.org/10.1021/acs.jpclett.8b01994 ) or umbrella sampling will get yo= u an answer faster, but it=E2=80=99s still going to take a long time to get= a reliable answer because you need to sample many different lipid arrangem= ents and, again, lipid exchange happens on the 10=E2=80=93100 ns timescale.=

Jeff
<= div>

On Tue, Aug 17, 2021 at 15:44 Ishaan Roy <royi@uchicago.edu> wrote:

Hello,

=C2=A0

I am using eABF on two membrane helices to find the = binding energy. During the separation runs, the upper boundary for the dist= ance colvar is set to 40, the distance value only reaches around 20, even w= hen I increase the simulation time. This current maximum it reaches is an inadequate separation, since parts o= f the proteins are still interacting at this point and the pmf has not leve= lled off. When looking at the VMD window, there doesn=E2=80=99t seem to be = anything obvious that would prevent the ABF from separating them further. Any ideas on what might be going on?

=C2=A0

Thanks,

Ishaan

=C2=A0

Here are my colvar settings:

=C2=A0

####################################################= #########

## Collective Variables=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ##

####################################################= #########

=C2=A0

# Global parameters

ColvarsTrajfrequency=C2=A0=C2=A0=C2=A0 20

Colvarsrestartfrequency 100

analysis=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 o= n

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name dist

=C2=A0

=C2=A0=C2=A0=C2=A0 width 0.05

=C2=A0

=C2=A0=C2=A0=C2=A0 extendedLagrangian on

=C2=A0=C2=A0=C2=A0 extendedFluctuation 0.02

=C2=A0

=C2=A0=C2=A0=C2=A0 outputTotalForce on

=C2=A0

=C2=A0=C2=A0=C2=A0 lowerboundary 10.0

=C2=A0=C2=A0=C2=A0 upperboundary 40.0

=C2=A0

=C2=A0=C2=A0=C2=A0 distance {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 forceNoPB= C=C2=A0=C2=A0=C2=A0=C2=A0 yes

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group1 {<= /p>

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROA

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 32-52 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group2 {<= /p>

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROB

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 87-106 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name sa1

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0

=C2=A0=C2=A0=C2=A0 width 1.0

=C2=A0

=C2=A0

=C2=A0=C2=A0=C2=A0 lowerboundary -180.0

=C2=A0=C2=A0=C2=A0 upperboundary 180.0

=C2=A0

=C2=A0=C2=A0=C2=A0 spinAngle {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROA

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 32-52}

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name sa2

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0

=C2=A0=C2=A0=C2=A0 width 1.0

=C2=A0

=C2=A0=C2=A0=C2=A0 lowerboundary -180.0

=C2=A0=C2=A0=C2=A0 upperboundary 180.0

=C2=A0

=C2=A0=C2=A0=C2=A0 spinAngle {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 =C2=A0=C2=A0psfSegID PROB

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 87-106}

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name t1

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0

=C2=A0=C2=A0=C2=A0 width 1.0

=C2=A0

=C2=A0

=C2=A0=C2=A0=C2=A0 lowerboundary -1.0

=C2=A0=C2=A0=C2=A0 upperboundary 1.0

=C2=A0

=C2=A0=C2=A0=C2=A0 tilt {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROA

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 32-52}

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name t2

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0

=C2=A0 =C2=A0=C2=A0width 1.0

=C2=A0

=C2=A0=C2=A0=C2=A0 lowerboundary -1.0

=C2=A0=C2=A0=C2=A0 upperboundary 1.0

=C2=A0

=C2=A0=C2=A0=C2=A0 tilt {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROB

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 87-106}

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refPositi= onsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name RMSD

=C2=A0=C2=A0=C2=A0 width 1.0

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0

=C2=A0=C2=A0=C2=A0 lowerboundary 0.0

=C2=A0=C2=A0=C2=A0 upperboundary 5.0

=C2=A0

=C2=A0=C2=A0=C2=A0 rmsd {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROA PROB

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 32-52 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 87-106}

=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0}

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refpositi= onsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

####################################################= #########

## RESTRAINTS AND PMF

####################################################= ##########

=C2=A0

=C2=A0

abf {

=C2=A0=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 dist

=C2=A0=C2=A0=C2=A0 FullSamples=C2=A0=C2=A0=C2=A0=C2= =A0 5000

}

=C2=A0

harmonic {

=C2=A0=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 sa1

=C2=A0=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 0.1

=C2=A0=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 0.0

}

=C2=A0

harmonic {

=C2=A0=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 sa2

=C2=A0=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 0.1

=C2=A0=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 0.0

}

=C2=A0

harmonic {

=C2=A0=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 t1

=C2=A0=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 0.1

=C2=A0=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 1.0

}

=C2=A0

harmonic {

=C2=A0=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 t2

=C2=A0=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 0.1

=C2=A0=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 1.0

}

=C2=A0

harmonic {

=C2=A0=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 RMSD

=C2=A0=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 10.0

=C2=A0=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 0.0

}

=C2=A0

=C2=A0

####################################################= #########

### Restraint on Monomer A

####################################################= ###########

=C2=A0

=C2=A0

colvar {

=C2=A0=C2=A0=C2=A0 name Omega

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0=C2=A0=C2=A0 orientation {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 atoms {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 psfSegID PROB

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 87-106 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 refpositi= onsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

colvar {

=C2=A0=C2=A0 name Pin

=C2=A0=C2=A0=C2=A0 outputValue off

=C2=A0

=C2=A0=C2=A0 width 1.0

=C2=A0=C2=A0 lowerboundary 22.9

=C2=A0=C2=A0 upperboundary 24.9

=C2=A0

=C2=A0=C2=A0 distance {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group1 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 dummyatom=C2=A0 (0, 0, 0)

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 group2 {

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 psfSegID PROB

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 atomNameResidueRange { CA 87-106 }

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }

=C2=A0=C2=A0=C2=A0 }

}

=C2=A0

harmonic {

=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 Omega

=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 100.0

=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 ( 1.0, 0.0, 0.0, 0.0 )

}

=C2=A0

=C2=A0

harmonic {

=C2=A0=C2=A0 colvars=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 Pin

=C2=A0=C2=A0 forceConstant=C2=A0=C2=A0 100.0

=C2=A0=C2=A0 centers=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 23.9

}

--

=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2= =80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94
Jeffrey Comer, PhD
Associa= te Professor
Department of Anatomy and Physiology
Kansas State Univer= sity
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us
--0000000000007c11b605c9dc0ee2-- From owner-namd-l@halifax.ks.uiuc.edu Sat Aug 21 19:43:49 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17M0hnEx018848; Sat, 21 Aug 2021 19:43:49 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17M0hnll018847; Sat, 21 Aug 2021 19:43:49 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17M0hmX9018843; Sat, 21 Aug 2021 19:43:48 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17M0hmAF018842; Sat, 21 Aug 2021 19:43:48 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17M0hYfU018831 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000a74bbd05ca1b3047" X-CLX-Response: 1TFkXGxkfEQpMehcZGx0RCllEF2BCHUlaE0JdXWRaEQpYWBdhEkxfe1JbZ0Z kTBEKeE4XY1Nja3sTWH4aX14RCnlMF25QXwFwT15hS29+EQpDSBcHGRMZEQpDWRcHGBMYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxsfcRsZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxNwQnlDWk9TaUIbdUVyc29cHB9DRFlNf2Z1TUllH2dNEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc3waYHgRCk1cFxgYHBEKTFoXb2lNa2sRCkxGF29ra2t raxEKQk8XbHsYcF5FXmRCE0kRCkNaFxgaEwQSHwQYGx4EGx0TEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hMGH5MYQFlYXAYEQpCThdjU2Nre xNYfhpfXhEKQkwXYRJMX3tSW2dGZEwRCkJsF2lYbXpffRNGTG5mEQpCQBduR1xaElMbTkt4BREK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF29AaGhwf1traElDEQpwaBdgaEBZU1pzS3w SfRAZGhEKcGgXZ2Z7HER4aR5jGXMQGRoRCnBoF2tIH3lTEn1nX0R9EBkaEQpwaBdvbk8ccl9ZQk FlQRAZGhEKcGgXaUYZWUdfY0htYhwQGRoRCnB9F2ESQHJbf0xieFtcEBkaEQpwfRdoHwEaGH1JR H4YeRAZGhEKcH8XZGtAZx9CUloTE1IQHhIRCnBfF2dLGn5YYUcdGEUaEBkaEQpwfxdpGFlHSW0a XG1ZYhAZGhEKcF8XYkZoThpPeFlzUk0QGRoRCnBsF2ZtaRNvQB1OTmlhEBkaEQptfhcbEQpYTRd LESA= X-Proofpoint-GUID: 9ZhSipeyCh1_oXYEv65insgUL_gcO5Mg X-Proofpoint-ORIG-GUID: 9ZhSipeyCh1_oXYEv65insgUL_gcO5Mg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=135 mlxscore=0 spamscore=0 bulkscore=0 suspectscore=0 adultscore=0 malwarescore=0 priorityscore=317 mlxlogscore=609 phishscore=0 impostorscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108220002 X-Spam-Score: 0 X-Spam-OrigSender: mpdezfouli@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mohammad Mehdi Pirnia --000000000000a74bbd05ca1b3047 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello all, I'm simulating peptide interactions with a bacterial membrane. I used https://urldefense.com/v3/__http://www.charmm-gui.org__;!!DZ3fjg!sUHTw_ttSk= V751JXFMZIn6vCaaIjvm4ZuAOZekC-qEyR14duGO4yelVtnRtpgpvn0Q$ in order to get = my membrane and it includes LPSA, PMCL, PMPE, PMPG, PVPE, and PVPG. 1- Is it a way to create such membranes using VMD? I just saw POPC and POPE in the membrane builder. 2- After download, I modified all residues' res-number to be consecutive, they were repetitive. Now, I'm trying to create my membrane's PSF file. Some parts of the output are shown below. I have shared the line of the whole output (output.log), psf-creator (memb_psf.tcl), related stream files, and the pdb file (semi_final_membrane.pdb). Here is the link: https://urldefense.com/v3/__https://files.fm/u/bcvap3g8g__;!!DZ3fjg!sUHTw_t= tSkV751JXFMZIn6vCaaIjvm4ZuAOZekC-qEyR14duGO4yelVtnRuL4FhcWw$=20 my VMD version is 1.9.4a.51 Thank you all Sincerely Adam Pirnia *output (broken into parts by "..."):* psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<< psfgen) psfgen) Created by CHARMM version 32 1 psfgen) reading topology file ../temporary2/toppar_all36_lipid_lps.str psfgen) reading topology from stream file psfgen) Topology for lipidA from LPS psfgen) psfgen) duplicate bond C71 C72 in residue BCLIPA psfgen) ERROR! Failed to parse bond statement. Line 2010: BOND CB3 OB3 OB3 C71 C71 C72 CB1 OA6 CA6 OA6 psfgen) duplicate bond C71 C72 in residue BCLIPB psfgen) ERROR! Failed to parse bond statement. Line 2760: BOND CB3 OB3 OB3 C71 C71 C72 CB1 OA6 CA6 OA6 .. .. psfgen) reading topology file ../temporary2/toppar_all36_carb_imlab.str psfgen) reading topology from stream file psfgen) glycan chemical modification patches psfgen) psfgen) Created by CHARMM version 41 1 psfgen) duplicate bond C5 N5 in residue ANEU psfgen) ERROR! Failed to parse bond statement. Line 6293: BOND C5 N5 N5 HN51 N5 HN52 psfgen) duplicate bond CE3 O31 in residue AMU2AC psfgen) ERROR! Failed to parse bond statement. Line 8981: BOND CE3 O31 CE3 O32 .. .. psfgen) reading topology file ../temporary2/toppar_all36_lipid_bacterial.str psfgen) Toppar stream file for Branched and Cyclic Chained lipids. Following reading of psfgen) top_all36_lipid.rtf psfgen) and psfgen) par_all36_lipid.rtf psfgen) psfgen) ERROR! FAILED TO RECOGNIZE SET. Line 22: set nat ?NATC psfgen) ERROR! FAILED TO RECOGNIZE SET. Line 23: set app psfgen) ERROR! FAILED TO RECOGNIZE IF. Line 27: if "@NAT" ne "?NATC" if @nat ne 0 set app append psfgen) reading topology from stream file psfgen) cholesterol residues psfgen) psfgen) Created by CHARMM version 36 1 psfgen) skipping parameters in stream file psfgen) new parameters psfgen) psfgen) reading topology file ./temporary2/toppar_all36_lipid_cardiolipin.str psfgen) reading topology from stream file 2.0 psfgen) building segment M psfgen) reading residues from pdb file semi_final_membrane.pdb psfgen) extracted 582 residues from pdb file Info: generating structure... psfgen) unknown atom type H psfgen) add atom failed in residue ECLI:1 Segmentation fault (core dumped) All these errors are odd to me, I didn't see anything wrong with my stream files and atom type H is definitely defined! --000000000000a74bbd05ca1b3047 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello all,

I'm simulating peptide int= eractions with a bacterial membrane. I used=C2=A0www.charmm-g= ui.org=C2=A0in order to get my membrane and it includes LPSA, PMCL, PMP= E, PMPG, PVPE, and PVPG.

1- Is it a way to create such membranes using VMD? I= just saw POPC and POPE in the membrane builder.

2- After download, I modifie= d all residues' res-number to be consecutive, they were repetitive. Now= , I'm trying to create my membrane's PSF file. Some parts of the ou= tput are shown below. I have shared the line of the whole output (output.lo= g), psf-creator (memb_psf.tcl), related stream files, and the pdb file (sem= i_final_membrane.pdb).=C2=A0

Here is the link:


<= div class=3D"gmail_default">
psfgen) = >>>>>>>>>>>>>>> parameter set = discussion forum <<<<<<<<<<<<<<&l= t;<<<
psfgen)
psfgen) Created by CHARMM version 32 1
psfg= en) reading topology file ../temporary2/toppar_all36_lipid_lps.str

p= sfgen) reading topology from stream file
psfgen) =C2=A0Topology for lipi= dA from LPS
psfgen)
psfgen) duplicate bond C71 C72 in residue BCLIPA<= br>psfgen) ERROR!=C2=A0 Failed to parse bond statement.=C2=A0 Line 2010: BO= ND CB3 =C2=A0 OB3 =C2=A0 =C2=A0 =C2=A0OB3 =C2=A0 C71 =C2=A0 =C2=A0 =C2=A0C7= 1 =C2=A0 C72 =C2=A0 =C2=A0 CB1 =C2=A0 OA6 =C2=A0 =C2=A0 CA6 =C2=A0 OA6
<= br>psfgen) duplicate bond C71 C72 in residue BCLIPB
psfgen) ERROR!=C2=A0= Failed to parse bond statement.=C2=A0 Line 2760: BOND CB3 =C2=A0 OB3 =C2= =A0 =C2=A0 =C2=A0OB3 =C2=A0 C71 =C2=A0 =C2=A0 =C2=A0C71 =C2=A0 C72 =C2=A0 = =C2=A0 CB1 =C2=A0 OA6 =C2=A0 =C2=A0 CA6 =C2=A0 OA6
...
...
psfgen)= reading topology file ../temporary2/toppar_all36_carb_imlab.str

psf= gen) reading topology from stream file
psfgen) =C2=A0glycan chemical mod= ification patches
psfgen) =C2=A0
psfgen) Created by CHARMM version 41= 1
psfgen) duplicate bond C5 N5 in residue ANEU
psfgen) ERROR!=C2=A0 = Failed to parse bond statement.=C2=A0 Line 6293: BOND =C2=A0 C5 =C2=A0 N5 = =C2=A0 =C2=A0 =C2=A0N5 =C2=A0 HN51 =C2=A0 =C2=A0 N5 =C2=A0 HN52

psfg= en) duplicate bond CE3 O31 in residue AMU2AC
psfgen) ERROR!=C2=A0 Failed= to parse bond statement.=C2=A0 Line 8981: BOND =C2=A0 CE3 =C2=A0O31 =C2=A0= =C2=A0CE3 =C2=A0O32
...
...
psfgen) reading topology file ../temp= orary2/toppar_all36_lipid_bacterial.str

psfgen) =C2=A0Toppar stream = file for Branched and Cyclic Chained lipids.=C2=A0 Following reading of
= psfgen) =C2=A0top_all36_lipid.rtf
psfgen) =C2=A0and
psfgen) =C2=A0par= _all36_lipid.rtf
psfgen)
psfgen) ERROR!=C2=A0 FAILED TO RECOGNIZE SET= .=C2=A0 Line 22: set nat ?NATC

psfgen) ERROR!=C2=A0 FAILED TO RECOGN= IZE SET.=C2=A0 Line 23: set app

psfgen) ERROR!=C2=A0 FAILED TO RECOG= NIZE IF.=C2=A0 Line 27: if "@NAT" ne "?NATC" if @nat ne= 0 set app append

psfgen) reading topology from stream file
psfge= n) =C2=A0cholesterol residues
psfgen)
psfgen) Created by CHARMM versi= on 36 1
psfgen) skipping parameters in stream file
psfgen) =C2=A0new = parameters
psfgen)
psfgen) reading topology file ../temporary2/toppar= _all36_lipid_cardiolipin.str

psfgen) reading topology from stream fi= le
2.0
psfgen) building segment M
psfgen) reading residues from pd= b file semi_final_membrane.pdb
psfgen) extracted 582 residues from pdb f= ile
Info: generating structure...
psfgen) unknown atom type H
psfg= en) add atom failed in residue ECLI:1
Segmentation fault (core dumped)



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Mon, 23 Aug 2021 17:22:20 +0000 From: "Capponi, Sara" To: "namd-l@ks.uiuc.edu" Subject: namd-l: sphingosine topology and parameter files Thread-Topic: sphingosine topology and parameter files Thread-Index: AQHXmEIH1fFiGW3og0WncGcrRrKuXQ== Date: Mon, 23 Aug 2021 17:22:20 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=ucsf.edu; x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: f3ab29a6-192c-43c7-875e-08d9665a90a7 x-ms-traffictypediagnostic: MN2PR05MB5981: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:9508; x-ms-exchange-senderadcheck: 1 x-ms-exchange-antispam-relay: 0 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:MN2PR05MB6702.namprd05.prod.outlook.com;PTR:;CAT:NONE;SFS:(4636009)(396003)(39860400002)(346002)(136003)(366004)(376002)(66476007)(86362001)(66946007)(66556008)(66446008)(76116006)(8676002)(186003)(478600001)(8936002)(64756008)(26005)(75432002)(2906002)(19627405001)(9686003)(33656002)(786003)(71200400001)(6916009)(316002)(5660300002)(52536014)(7696005)(38070700005)(6506007)(122000001)(38100700002)(4744005)(55016002);DIR:OUT;SFP:1101; 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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I'd like to perform simulations of a viral capsid protomer associated with = the sphingosine pocket factor, but I am having troubles to find/generate th= e parameter and topology files of the sphingosine. I am trying to use Param= Chem to obtain those files, but it has been running for 3 days without prod= ucing any output file. I also tried CHARMM-GUI but it is giving me problems= too. Has anyone already carried out simulations of sphingosine? If so, I will be= very grateful if he/she is willing to share the files. Thanks, Sara --_000_MN2PR05MB6702C488F957D1AD7B66EEE9E6C49MN2PR05MB6702namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello, 

I'd like to perform simulations of a viral capsid protomer associated with = the sphingosine pocket factor, but I am having troubles to find/generate th= e parameter and topology files of the sphingosine. I am trying to use Param= Chem to obtain those files, but it has been running for 3 days without producing any output file. I also t= ried CHARMM-GUI but it is giving me problems too.

Has anyone already carried out simulations of sphingosine? If so, I will be= very grateful if he/she is willing to share the files. 

Thanks, 

Sara
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To: KS UIUC Message-ID: <0204DC8E-E025-4B7E-8BDC-2E41F6B23002@gmail.com> Thread-Topic: Asymmetric concentration gradient Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3712597699_772123455" X-CLX-Shades: MLX X-Proofpoint-GUID: f7oZyktz5deXd5CuLvNFhY2tKQp0_i3j X-Proofpoint-ORIG-GUID: f7oZyktz5deXd5CuLvNFhY2tKQp0_i3j X-CLX-Response: 1TFkXGxITEQpMehcZHxkRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHx8aEQpDWRcHGBkbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwTcR4SEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0wdRXBTQV5QH05Pck4faV9mXGRsQnMYXmF7Whp1QxlAEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3N9TEFdEQpNXBcZGB4RCkxaF2xpa01NEQpMRhdva2t ra2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBBsdExEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja 3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdjaVlvek8dckdPfxEKQkAXbG1jfmNiTVheGF8R CkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5QxdoQB0faXJPZXxIYREKcGgXaW5wBUZDHFpmXGEQGxk bEQpwaBdnEmtFRFBjb0lnYRAZGhEKcGgXekhzUGhEfl8eeGYQGRoRCnBoF2hOY0ZoWkR9WltdEB kaEQpwaBdtH05tHxNkUBlwUhAZGhEKcGwXekdAaxhZeX8eG0gQGRoRCnBMF2d+UH1Na1BPT0ZiE BkaEQpwQxdvaBNZZnxyRkkaXxAZGhEKbX4XGhEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 spamscore=0 malwarescore=0 bulkscore=0 suspectscore=0 clxscore=189 mlxscore=0 impostorscore=0 lowpriorityscore=0 priorityscore=353 mlxlogscore=593 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108240012 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3712597699_772123455 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear users, =20 I am trying to simulate a membrane protein system where it has a concentrat= ion difference on one side as well as the other, similar to the work of Prof= essor JC Gumbart =E2=80=9CMolecular dynamics simulations of membrane proteins unde= r asymmetric ionic concentrations=E2=80=9D =20 My question is, how do I ionize or how do I place the ions on both sides wi= th a difference in concentration? Could you please share a script to do this= ?. =20 Best,=20 =20 Geo.=20 =20 --B_3712597699_772123455 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable
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To: "Gumbart, JC" , NAMD list Message-ID: <4A2DF878-C7B6-4255-AAF0-735C910F23C6@gmail.com> Thread-Topic: namd-l: Asymmetric concentration gradient References: <0204DC8E-E025-4B7E-8BDC-2E41F6B23002@gmail.com> <2FD8174C-744D-4828-B4B9-BCB9D6EFB520@physics.gatech.edu> In-Reply-To: <2FD8174C-744D-4828-B4B9-BCB9D6EFB520@physics.gatech.edu> Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3712605054_244053060" X-Proofpoint-GUID: c58mi7xCgZVw07nJJ73tOA08gdNZd58Y X-Proofpoint-ORIG-GUID: c58mi7xCgZVw07nJJ73tOA08gdNZd58Y X-CLX-Response: 1TFkXGxwZEQpMehcZHBsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHBIYEQpDWRcHHxkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhlxHxgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XSR8SR0MdUmlNcHxdGh1EYGAdGV5laxoSTU5kcE4fEnMRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzfUJyWBEKTVwXGRgdEQpMWhd7aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBB sdHxEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdj aVlvek8dckdPfxEKQkAXbVIaeGZwe2gZS28RCkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5Qxdmf11 +TXMTGkNzGxEKcGcXb15Ccn9+TGd/cEEQGRoRCnBoF2BAbGlcXmhBUlx6EBsbHxEKcGgXYVl6YH BEfmBdbxMQGRoRCnBoF2VwGHhneE1tXWB+EBkaEQpwaBdmQR0dHhoeZF1jHhAZGhEKcGgXbhpoG lxffm1yTn4QGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwbBd6R0BrGFl5fx4bSBAcGhEKcEwXbWhl GUFSfXsYRVIQHhIRCnBDF29oE1lmfHJGSRpfEBMaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=163 suspectscore=0 impostorscore=0 adultscore=0 mlxlogscore=846 malwarescore=0 lowpriorityscore=0 phishscore=0 bulkscore=0 priorityscore=361 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108240025 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3712605054_244053060 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear Prof. Gumbart, =20 My question was on that side, how to do the solvation up and down independe= ntly, could you give me an example of the script, to be able to do it please= . I find it a bit unfamiliar as this is my first time doing this. =20 From: "Gumbart, JC" Date: Monday, August 23, 2021 at 11:05 PM To: NAMD list , "Ropon-Palacios G." Subject: Re: namd-l: Asymmetric concentration gradient =20 Hi Geo,=20 =20 It=E2=80=99s been a long time since I ran this. But one way I can think of would= be to solvate and ionize above and below separately and then combine them w= ith psfgen. I attach an example tclBC script and NAMD input file for runnin= g the actual simulation once you=E2=80=99ve built the system.=20 =20 Best, JC =20 On Aug 23, 2021, at 10:08 PM, Ropon-Palacios G. wro= te: =20 Dear users, =20 I am trying to simulate a membrane protein system where it has a concentrat= ion difference on one side as well as the other, similar to the work of Prof= essor JC Gumbart =E2=80=9CMolecular dynamics simulations of membrane proteins unde= r asymmetric ionic concentrations=E2=80=9D =20 My question is, how do I ionize or how do I place the ions on both sides wi= th a difference in concentration? Could you please share a script to do this= ?. =20 Best,=20 =20 Geo.=20 =20 --B_3712605054_244053060 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Dear Prof. Gumbart,

 

My question was on that side, how= to do the solvation up and down independently, could you give me an example= of the script, to be able to do it please. I find it a bit unfamiliar as th= is is my first time doing this.

 =

From: "Gumba= rt, JC" <gumbart@physics.gatech.edu>
Date: Monday, Augu= st 23, 2021 at 11:05 PM
To: NAMD list <namd-l@ks.uiuc.edu>, = "Ropon-Palacios G." <biodano.geo@gmail.com>
Subject: <= /b>Re: namd-l: Asymmetric concentration gradient

=

 

H= i Geo,

 

It=E2=80=99s been a long time since I ran this.  But one= way I can think of would be to solvate and ionize above and below separatel= y and then combine them with psfgen.  I attach an example tclBC script = and NAMD input file for running the actual simulation once you=E2=80=99ve built th= e system.

 

=

Best,

JC=

 


On Aug 23, 2021, at 10:08 PM, Ropon-Palacios= G. <biodano.geo@gmail.com>= wrote:

 

Dear users,

 

I am trying to simu= late a membrane protein system where it has a concentration difference on on= e side as well as the other, similar to the work of Professor JC Gumbart =E2=80=9CMolecular dynamics simulations of= membrane proteins under asymmetric ionic concentrations=E2=80=9D

 

My question is, how do I ionize or how do I plac= e the ions on both sides with a difference in concentration? Could you pleas= e share a script to do this?.

 

Best, <= /p>

 <= /o:p>

Geo. 

=  

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01:26:01 -0700 (PDT) MIME-Version: 1.0 References: <0204DC8E-E025-4B7E-8BDC-2E41F6B23002@gmail.com> <2FD8174C-744D-4828-B4B9-BCB9D6EFB520@physics.gatech.edu> <4A2DF878-C7B6-4255-AAF0-735C910F23C6@gmail.com> In-Reply-To: <4A2DF878-C7B6-4255-AAF0-735C910F23C6@gmail.com> From: Mohammad Mehdi Pirnia Date: Tue, 24 Aug 2021 12:55:50 +0430 Message-ID: Subject: Re: namd-l: Asymmetric concentration gradient To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." Content-Type: multipart/alternative; boundary="000000000000511ab805ca49e2b6" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: fqFHN1ehDYjI1Nd63yWPh5E-J9ZwcI_Q X-CLX-Response: 1TFkXGxwTEQpMehcZHh0RCllEF2BCHUlaE0JdXWRaEQpYWBdhEkxfe1JbZ0Z kTBEKeE4XY1Nja3sTWH4aX14RCnlMF25QXwFwT15hS29+EQpDSBcHHRgfEQpDWRcHHxkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhNxGRoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XTFtsYmQbT0Juc0BjG2ROHBlTfXpCH28HYBNwXUljdXsRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc31GbRgRCk1cFxkYGREKTFoXfGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdkflhPZm5zSXBbTxEKQ1oXGBoTBBIfBBgbHA QfGxEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdoTBh+TGEBZWFwGBEKQk4XY1Nja3sTWH4aX14RCkJMF2ESTF97UltnRmRMEQpCbBdp WG16X30TRkxuZhEKQkAXbVIaeGZwe2gZS28RCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxdmf11 +TXMTGkNzGxEKcGcXb15Ccn9+TGd/cEEQHhIRCnBoF2UbWmFzfExCUhNaEBkaEQpwaBdrZ0hCeh 4bHm5hRhAZGhEKcGgXZmdQbBt6fB5uYkcQGRoRCnBoF2BgZB1ee0BBemkeEBkaEQpwaBdiTGYYQ nppGAVobRAZGhEKcGcXaUNuUAFZc0cBHlMQHhIRCnBsF2ZtaRNvQB1OTmlhEBkaEQptfhcaEQpY TRdLESA= X-Proofpoint-GUID: fqFHN1ehDYjI1Nd63yWPh5E-J9ZwcI_Q X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 adultscore=0 mlxlogscore=825 clxscore=169 bulkscore=0 phishscore=0 suspectscore=0 impostorscore=0 priorityscore=347 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108240056 X-Spam-Score: 0 X-Spam-OrigSender: mpdezfouli@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mohammad Mehdi Pirnia --000000000000511ab805ca49e2b6 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Geo, You can simply solvate your system twice, once per each ion concentration you want. Then remove one side of each system using VMD and combine them using psfgen. Adam On Tue, Aug 24, 2021 at 8:42 AM Ropon-Palacios G. wrote: > Dear Prof. Gumbart, > > > > My question was on that side, how to do the solvation up and down > independently, could you give me an example of the script, to be able to = do > it please. I find it a bit unfamiliar as this is my first time doing this= --000000000000511ab805ca49e2b6-- From owner-namd-l@halifax.ks.uiuc.edu Tue Aug 24 10:59:23 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17OFxM7r008337; Tue, 24 Aug 2021 10:59:22 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17OFxMtB008336; Tue, 24 Aug 2021 10:59:22 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17OFxLqm008331; Tue, 24 Aug 2021 10:59:21 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17OFxLGH008330; Tue, 24 Aug 2021 10:59:21 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17OFxB0A008323 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 24 Aug 2021 10:59:11 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 17OFrZSJ023642 for ; Tue, 24 Aug 2021 15:59:11 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20161025 header.d=gmail.com Received: from mail-qk1-f171.google.com (mail-qk1-f171.google.com [209.85.222.171]) by mx0b-00007101.pphosted.com with ESMTP id 3amg337je5-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Tue, 24 Aug 2021 15:59:10 +0000 Received: by mail-qk1-f171.google.com with SMTP id c10so21139463qko.11 for ; Tue, 24 Aug 2021 08:59:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:date:subject:from:to:cc:message-id:thread-topic :references:in-reply-to:mime-version; bh=jtSMtvFX1Yo8cs4nyNPzD0mviVhY6jyYYFCIEbWCZ8I=; b=fc9OAfIvwXNjXanOfWZqmF3Jc58CBiVpD0jWi6nAlfgz+QR8Kugq+ANdiscDKA0NBC mew11riypBsKDmBM8L4AgS4npTdKONL2bt4w9/Yfgw6fqPLbHmOEc4oYaqu4FZiA0wHs qdpdqI6O7xYkhZqhnzi5DtFla1ssN0IgVBGDHSDk5VTqeMdfI6xlabZw3bXHoVgeGP7p Q7+l7gt30xrG3PK++WwORGMdbLRJ0NzIK1q/wWHw1kL4T0t4gTzGKAAwkXsLTxYcDDCh SH+vWlqhqR/3dRk+LEJBVdiRfWmpdPXuW41tJVVuMHB374J/dQl4MHoOBF0DVrSvhH6K vYSg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:date:subject:from:to:cc:message-id :thread-topic:references:in-reply-to:mime-version; bh=jtSMtvFX1Yo8cs4nyNPzD0mviVhY6jyYYFCIEbWCZ8I=; b=FiBZ8KUvnvKJdNW8QdC8z2aMseWtO92SiRLZsN1Fm8pAzdIuWprbYz669/wKcp9XI6 5XuiDkTaaBTS8KGzfU7sxV/ZaNn23YG+bRl3IgVGfeuJDZO1xkYZ8qsZk/oQADNGt5qx COuKICjW9dJ+ah3/6lhUsp27joE4ibe2IuC0LD/IP00mA2+ET+4OfN9xA/zyZ4hGSbjT TCaezjTD5inNTpfNN9XggvXqZaPTNy9i3GYzH2S9AB9NpHP9NnSJoPQ9YvYiXTRVm8RY GLtmXpKpNtuQlO7n/BHYqiBlX73M5p/+hnX7RStaSYSmpLm5nnP3bn/KCVLXVhE/07vc dPSQ== X-Gm-Message-State: AOAM533tk+VlvSrTn8vY3akfqcS3fHm/LsETSbmvofBfCIc0WCY8WO9R 1Po0PNoEt7Se3M1mpfNpaoY= X-Google-Smtp-Source: ABdhPJzAo6HXLgzHvKA0FSoVLVzunAvE+g9eTSowcH5Tm+EurWQWuDoZgoV61MGbzz20iUWPR050FQ== X-Received: by 2002:a37:6255:: with SMTP id w82mr26912646qkb.252.1629820750116; Tue, 24 Aug 2021 08:59:10 -0700 (PDT) Received: from [172.20.10.12] ([181.176.100.214]) by smtp.gmail.com with ESMTPSA id x25sm8650902qtj.77.2021.08.24.08.59.08 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Tue, 24 Aug 2021 08:59:09 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Tue, 24 Aug 2021 10:59:07 -0500 Subject: Re: namd-l: Asymmetric concentration gradient From: "Ropon-Palacios G." To: "Gumbart, JC" CC: NAMD list Message-ID: Thread-Topic: namd-l: Asymmetric concentration gradient References: <0204DC8E-E025-4B7E-8BDC-2E41F6B23002@gmail.com> <2FD8174C-744D-4828-B4B9-BCB9D6EFB520@physics.gatech.edu> <4A2DF878-C7B6-4255-AAF0-735C910F23C6@gmail.com> <0E81B071-1755-483F-BA79-0E172B4882CD@physics.gatech.edu> In-Reply-To: <0E81B071-1755-483F-BA79-0E172B4882CD@physics.gatech.edu> Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3712647549_332439376" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIfEQpMehcZHxIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHBoYEQpDWRcHHxwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB9xHh4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XckZZbhNmZBhPEkBNfnNZXmhjeXtSZ2RuWEBvX2NfTUIRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXc31YXFsRCk1cFx8eHBEKTFoXaXhpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGB gEGx0bEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2hPHWFFcFlwBU0aEQpCThdjU2NrexNYfhpfXhEKQkwXeh5jQR5eXBwfcksRCkJs F2NpWW96Tx1yR09/EQpCQBdtUhp4ZnB7aBlLbxEKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2Z /XX5NcxMaQ3MbEQpwZxdvXkJyf35MZ39wQRAZGhEKcGgXZ0lzfmh7RHB7bVMQGhEKcGgXenB9Rk hfS2lOSWIQGhEKcGgXegF8SUlhbgESQnAQGhEKcGgXbGRwUH4FWgVJSxIQGhEKcGgXbWVlaERPa H1+HF0QGhEKcGcXaUNuUAFZc0cBHlMQGhEKcGwXekdAaxhZeX8eG0gQHhIRCnBMF21oZRlBUn17 GEVSEBoRCnBDF2RwQVlmfUFOf3hcEBoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: XlsD9LN2e8jgTYstBISQxMNDrjEuIugh X-Proofpoint-ORIG-GUID: XlsD9LN2e8jgTYstBISQxMNDrjEuIugh X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 malwarescore=0 adultscore=0 mlxlogscore=991 priorityscore=358 clxscore=185 suspectscore=0 lowpriorityscore=0 mlxscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108240105 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3712647549_332439376 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable I understood how to solvate in two parts, now I have a question perhaps a b= it silly, but having a membrane and solvate for example {0 60} above the mem= brane, water molecules are found in the membrane, I eliminate them in a rang= e of z < 26 angstrom, so I do the ionization first with KCl and then with Na= Cl 10 and 100 mM respectively, checking a little how the autoinize works, I = realized that this is based on the volume on the number of molecular water, = so if I eliminate molecular water and ionize, am I placing the same concentr= ation ?, because I also checked that it could be an infinite type of solutio= n, where it would not affect much if I add more water, since the concentrati= on of the solute does not vary. =20 My questions are: How do I add more than one kind of ions like KCl and NaCl and if when I do = this the concentrations that I choose are correct? =20 From: "Gumbart, JC" Date: Tuesday, August 24, 2021 at 12:11 AM To: "Ropon-Palacios G." Cc: NAMD list Subject: Re: namd-l: Asymmetric concentration gradient =20 You can give solvate a minmax to only solvate a region above or below the m= embrane mid-plane (make sure to give them different segnames for both the wa= ter and ions). Then a few lines using psfgen (readpsf ___ pdb ___) will com= bine them. There=E2=80=99s no script though, but if you play around with the opti= ons, you should quickly get a sense of what to do.=20 =20 Best, JC On Aug 24, 2021, at 12:10 AM, Ropon-Palacios G. wro= te: =20 Dear Prof. Gumbart, =20 My question was on that side, how to do the solvation up and down independe= ntly, could you give me an example of the script, to be able to do it please= . I find it a bit unfamiliar as this is my first time doing this. =20 From: "Gumbart, JC" Date: Monday, August 23, 2021 at 11:05 PM To: NAMD list , "Ropon-Palacios G." Subject: Re: namd-l: Asymmetric concentration gradient =20 Hi Geo,=20 =20 It=E2=80=99s been a long time since I ran this. But one way I can think of would= be to solvate and ionize above and below separately and then combine them w= ith psfgen. I attach an example tclBC script and NAMD input file for runnin= g the actual simulation once you=E2=80=99ve built the system.=20 =20 Best, JC =20 On Aug 23, 2021, at 10:08 PM, Ropon-Palacios G. wro= te: =20 Dear users, =20 I am trying to simulate a membrane protein system where it has a concentrat= ion difference on one side as well as the other, similar to the work of Prof= essor JC Gumbart =E2=80=9CMolecular dynamics simulations of membrane proteins unde= r asymmetric ionic concentrations=E2=80=9D =20 My question is, how do I ionize or how do I place the ions on both sides wi= th a difference in concentration? Could you please share a script to do this= ?. =20 Best,=20 =20 Geo. =20 --B_3712647549_332439376 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

I understood how to solvate in two parts, now I ha= ve a question perhaps a bit silly, but having a membrane and solvate for exa= mple {0 60} above the membrane, water molecules are found in the membrane, I= eliminate them in a range of z < 26 angstrom, so I do the ionization fir= st with KCl and then with NaCl 10 and 100 mM respectively, checking a little= how the autoinize works, I realized that this is based on the volume on the= number of molecular water, so if I eliminate molecular water and ionize, am= I placing the same concentration ?, because I also checked that it could be= an infinite type of solution, where it would not affect much if I add more = water, since the concentration of the solute does not vary.

 

My questions are:

How do I add more than one kind of ions like= KCl and NaCl and if when I do this the concentrations that I choose are cor= rect?

 

From: "Gumbart, JC" <gumbart@p= hysics.gatech.edu>
Date: Tuesday, August 24, 2021 at 12:11 AMTo: "Ropon-Palacios G." <biodano.geo@gmail.com>
= Cc: NAMD list <namd-l@ks.uiuc.edu>
Subject: Re: namd-= l: Asymmetric concentration gradient

 

You can give solva= te a minmax to only solvate a region above or below the membrane mid-plane (= make sure to give them different segnames for both the water and ions). &nbs= p;Then a few lines using psfgen (readpsf ___ pdb ___) will combine them. &nb= sp;There=E2=80=99s no script though, but if you play around with the options, you = should quickly get a sense of what to do.

 

Best,

JC

=

On Aug 24, 2021, at 12:10 AM, Ropon-Palacios G. = <biodano.geo@gmail.com> wro= te:

 

Dear Prof. Gumbart,

 

My question was on t= hat side, how to do the solvation up and down independently, could you give = me an example of the script, to be able to do it please. I find it a bit unf= amiliar as this is my first time doing this.

 

From: "Gumbart, JC" <gumbart= @physics.gatech.edu>
Date: Monday, August 23, 2021 at 11:05 PM
To: NAMD list <namd-l@ks.uiuc.edu>,= "Ropon-Palacios G." <biodano.geo@gmail.com
>
Subject:=  Re: namd-l: Asymmetric co= ncentration gradient

 

Hi Geo,=  

 

It=E2=80=99s been a long time since I ran this.  But one way I can thi= nk of would be to solvate and ionize above and below separately and then com= bine them with psfgen.  I attach an example tclBC script and NAMD input= file for running the actual simulation once you=E2=80=99ve built the system. 

 

Best,

JC=

 




<= /o:p>

On Aug 23, 2021, at 10:08 PM, Ropon-Palacios G. <= ;biodano.g= eo@gmail.com> wrote:

 

D= ear users,

 

I am trying to simulate = a membrane protein system where it has a concentration difference on one sid= e as well as the other, similar to the work of Professor JC Gumbart =E2=80=9CMolecular dynamics simulations of memb= rane proteins under asymmetric ionic concentrations=E2=80=9D

 =

My question is, how do I ionize= or how do I place the ions on both sides with a difference in concentration= ? Could you please share a script to do this?.

 

Best, =

 

Geo.

Dear users,=

 

I = am trying to simulate a membrane protein system where it has a concentration= difference on one side as well as the other, similar to the work of Profess= or JC Gumbart =E2=80=9CMolecular dynamics simulations of membrane proteins under asymmetric ioni= c concentrations=E2=80=9D<= b>

 

My question is, how do I ionize or= how do I place the ions on both sides with a difference in concentration? C= ould you please share a script to do this?.

 

Best,

 

Geo. =

 

<= /div>

 

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boundary="_004_SN6PR11MB28782D0FE3225E95714684C6B0C59SN6PR11MB2878namp_"; type="multipart/alternative" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SN6PR11MB2878.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 0ef55ac0-a739-4ef8-cd57-08d9674dd2e3 X-MS-Exchange-CrossTenant-originalarrivaltime: 24 Aug 2021 22:23:39.6434 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: d7SYnleOZei5W/+O5nGuUHWS3qR0R/2k/G2JGC7fTyoaPBs4VAd5rPkIPpd1U0wZanR9DKLrNsG0GZ42TwB2Mg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SN6PR11MB3056 X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 6_Xk_atInCeHnbeqS1fF0tsqE3qs6NdY X-CLX-Response: 1TFkXGxsaEQpMehceEhEKWUQXbm18a3l5fExCYHkRClhYF2dCHxpIUmhAGEZ CEQp4ThdoYwFMf0V/QkFlQBEKeUwXem9rRXAYExtSbFkRCkNIFwcfHB8RCkNZFwcYHhsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYTGnEdEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxx1ckF1S15jRGlPYkRIT1t5G0xsGl5ZW28ZW1kcZE5zEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3N9UnNNEQpNXBcYHB8RCkxaF2hpTWtrEQpMRhdva2tra2t rEQpCTxdtcmlebk9ME1IfHBEKQ1oXHhoEGxodBBMeBBsaHBEKQl4XGxEKRF4XGBEKQkUXbm5QHm xhGGFzHx8RCkJOF2hjAUx/RX9CQWVAEQpCTBdnQh8aSFJoQBhGQhEKQmwXZGJmAWdzE1NFT1IRC kJAF2tsE0RwTVAcbnkBEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXZhhEZ0RZZWlH R2ERCnBnF2ttYl1nQlxmR2BjEBscHxEKcGgXaxp6GHxIZkQeXH0QGRoRCnBoF25Scx1MGE9aR1B 8EBkaEQpwaBduTX14GEVcflBpGRAZGhEKcGgXYx5GaFhvXlNcAQEQGRoRCnBoF214T0BlR2cFf2 BnEBkaEQpwYxdsa3pMEnpzZEwbfBAZGhEKcGwXZk19Z2tbY0l+R0kQGRoRCm1+FxsRClhNF0sRI A== X-Proofpoint-GUID: 6_Xk_atInCeHnbeqS1fF0tsqE3qs6NdY X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 adultscore=0 mlxlogscore=275 clxscore=110 bulkscore=0 phishscore=0 suspectscore=0 impostorscore=0 priorityscore=48 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108240139 X-Spam-Score: 0 X-Spam-OrigSender: royi@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ishaan Roy --_004_SN6PR11MB28782D0FE3225E95714684C6B0C59SN6PR11MB2878namp_ Content-Type: multipart/alternative; boundary="_000_SN6PR11MB28782D0FE3225E95714684C6B0C59SN6PR11MB2878namp_" --_000_SN6PR11MB28782D0FE3225E95714684C6B0C59SN6PR11MB2878namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hello, I am using eABF to separate two membrane proteins to find the free binding = energy. The PMF values produced in my runs seem to be incredibly high compa= red to consistently reaching the 100s order of magnitude. We haven=92t comp= leted a run that plateaus in free energy yet, but this is an example showin= g what the PMF looks like. [cid:image001.png@01D79905.BA65D100] A maximum PMF this high already produces a value for the binding constant t= hat is on an order beyond 10^100. Besides being high, it might be worth men= tioning that the nonbonded energies are very close to 0 near the end of thi= s run, but the PMF gradient doesn=92t level off at all. Any ideas on what m= ight be causing this? Or is such a value plausible? This only seems to be a= problem with the separation runs; my other colvars produce PMF plots that = are closer to what I=92ve seen. Thanks, Ishaan --_000_SN6PR11MB28782D0FE3225E95714684C6B0C59SN6PR11MB2878namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

 

Hello,

 

I am using eABF to separate two membrane proteins to= find the free binding energy. The PMF values produced in my runs seem to b= e incredibly high compared to consistently reaching the 100s order of magni= tude. We haven=92t completed a run that plateaus in free energy yet, but this is an example showing what the PMF l= ooks like.

A maximum PMF this high already produces a value for= the binding constant that is on an order beyond 10^100. Besides being high= , it might be worth mentioning that the nonbonded energies are very close t= o 0 near the end of this run, but the PMF gradient doesn=92t level off at all. Any ideas on what might be ca= using this? Or is such a value plausible? This only seems to be a problem w= ith the separation runs; my other colvars produce PMF plots that are closer= to what I=92ve seen.

 

Thanks,

Ishaan

 

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(version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Tue, 24 Aug 2021 17:45:31 -0700 (PDT) User-Agent: Microsoft-MacOutlook/10.10.1b.201012 Date: Tue, 24 Aug 2021 19:45:27 -0500 Subject: Re: namd-l: Asymmetric concentration gradient From: "Ropon-Palacios G." To: "Gumbart, JC" CC: NAMD list Message-ID: Thread-Topic: namd-l: Asymmetric concentration gradient References: <0204DC8E-E025-4B7E-8BDC-2E41F6B23002@gmail.com> <2FD8174C-744D-4828-B4B9-BCB9D6EFB520@physics.gatech.edu> <4A2DF878-C7B6-4255-AAF0-735C910F23C6@gmail.com> <0E81B071-1755-483F-BA79-0E172B4882CD@physics.gatech.edu> In-Reply-To: Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3712679130_1485913439" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: vIXmQHGlhyOa4jOYQDEiyQM8d_HqFaXX X-CLX-Response: 1TFkXGxwcEQpMehcZGB0RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF25cWlNBGGcSAUdbEQpDSBcHHh0SEQpDWRcHEhgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhxxHx0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XXGNyR3tibUZCU2VLHkBlc3tub0NTe2cSTnViW2xLcnIRClhcFx8EGgQYGRkF GxoEGxsaBB8aBBseGBAbHhofGhEKXlkXc31QTmIRCk1cFx8aHBEKTFoXf2lrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEw QfHhEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdoTx1hRXBZcAVNGhEKQk4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdj aVlvek8dckdPfxEKQkAXbVIaeGZwe2gZS28RCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxdmf11 +TXMTGkNzGxEKcGcXb15Ccn9+TGd/cEEQHhIRCnBoF2dJc35oe0Rwe21TEBkaEQpwaBdlWhJeGm 4eUFJzUxAZGhEKcGgXenB9RkhfS2lOSWIQGRoRCnBoF3oBfElJYW4BEkJwEBkaEQpwaBd6UEdcS H1DQl1kEhAZGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnBsF3pHQGsYWXl/HhtIEBwaEQpwTBdtaGUZ QVJ9exhFUhAZGhEKcEMXZHBBWWZ9QU5/eFwQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: vIXmQHGlhyOa4jOYQDEiyQM8d_HqFaXX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 adultscore=0 mlxlogscore=999 clxscore=166 bulkscore=0 phishscore=0 suspectscore=0 impostorscore=0 priorityscore=327 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108250002 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Ropon-Palacios G." > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3712679130_1485913439 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Thanks so much Prof. Gumbart,=20 =20 All is good now.=20 =20 Best,=20 =20 Geo.=20 =20 From: "Gumbart, JC" Date: Tuesday, August 24, 2021 at 5:34 PM To: "Ropon-Palacios G." Cc: NAMD list Subject: Re: namd-l: Asymmetric concentration gradient =20 You can always calculate the concentration according to the equation=20 =20 # ions *( 55.5 M / # water molecules ) =3D (ion conc.) M (55.5 M is the conc= entration of pure water) * be careful to count water *molecules* and not water *atoms* =20 As for adding more species of ions, autoionize can do this. =20 Best, JC On Aug 24, 2021, at 11:59 AM, Ropon-Palacios G. wro= te: =20 I understood how to solvate in two parts, now I have a question perhaps a b= it silly, but having a membrane and solvate for example {0 60} above the mem= brane, water molecules are found in the membrane, I eliminate them in a rang= e of z < 26 angstrom, so I do the ionization first with KCl and then with Na= Cl 10 and 100 mM respectively, checking a little how the autoinize works, I = realized that this is based on the volume on the number of molecular water, = so if I eliminate molecular water and ionize, am I placing the same concentr= ation ?, because I also checked that it could be an infinite type of solutio= n, where it would not affect much if I add more water, since the concentrati= on of the solute does not vary. =20 My questions are: How do I add more than one kind of ions like KCl and NaCl and if when I do = this the concentrations that I choose are correct? =20 From: "Gumbart, JC" Date: Tuesday, August 24, 2021 at 12:11 AM To: "Ropon-Palacios G." Cc: NAMD list Subject: Re: namd-l: Asymmetric concentration gradient =20 You can give solvate a minmax to only solvate a region above or below the m= embrane mid-plane (make sure to give them different segnames for both the wa= ter and ions). Then a few lines using psfgen (readpsf ___ pdb ___) will com= bine them. There=E2=80=99s no script though, but if you play around with the opti= ons, you should quickly get a sense of what to do.=20 =20 Best, JC On Aug 24, 2021, at 12:10 AM, Ropon-Palacios G. wro= te: =20 Dear Prof. Gumbart, =20 My question was on that side, how to do the solvation up and down independe= ntly, could you give me an example of the script, to be able to do it please= . I find it a bit unfamiliar as this is my first time doing this. =20 From: "Gumbart, JC" Date: Monday, August 23, 2021 at 11:05 PM To: NAMD list , "Ropon-Palacios G." Subject: Re: namd-l: Asymmetric concentration gradient =20 Hi Geo,=20 =20 It=E2=80=99s been a long time since I ran this. But one way I can think of would= be to solvate and ionize above and below separately and then combine them w= ith psfgen. I attach an example tclBC script and NAMD input file for runnin= g the actual simulation once you=E2=80=99ve built the system.=20 =20 Best, JC =20 On Aug 23, 2021, at 10:08 PM, Ropon-Palacios G. wro= te: =20 Dear users, =20 I am trying to simulate a membrane protein system where it has a concentrat= ion difference on one side as well as the other, similar to the work of Prof= essor JC Gumbart =E2=80=9CMolecular dynamics simulations of membrane proteins unde= r asymmetric ionic concentrations=E2=80=9D =20 My question is, how do I ionize or how do I place the ions on both sides wi= th a difference in concentration? Could you please share a script to do this= ?. =20 Best,=20 =20 Geo. =20 =20 --B_3712679130_1485913439 Content-type: text/html; charset="UTF-8" Content-transfer-encoding: quoted-printable

Thanks so much Prof. Gumbart,

 

All is good now. =

 

Best, <= o:p>

 

Geo= .

 

From: "Gumbart, JC" <gumbart@phys= ics.gatech.edu>
Date: Tuesday, August 24, 2021 at 5:34 PM
To:
"Ropon-Palacios G." <biodano.geo@gmail.com>
C= c: NAMD list <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: A= symmetric concentration gradient

 

You can always calcula= te the concentration according to the equation

 

# ions *( 55.5 = M / # water molecules ) =3D (ion conc.) M  (55.5 M is the concentration o= f pure water)

* be careful to co= unt water *molecules* and not water *atoms*

 

As for adding= more species of ions, autoionize can do this.

 

Best,=

JC



On Aug 24, 2021, at 11:59 AM, Ropon-Palacio= s G. <biodano.geo@gmail.com>= ; wrote:

 

I understood how to solvate in two parts, now I h= ave a question perhaps a bit silly, but having a membrane and solvate for ex= ample {0 60} above the membrane, water molecules are found in the membrane, = I eliminate them in a range of z < 26 angstrom, so I do the ionization fi= rst with KCl and then with NaCl 10 and 100 mM respectively, checking a littl= e how the autoinize works, I realized that this is based on the volume on th= e number of molecular water, so if I eliminate molecular water and ionize, a= m I placing the same concentration ?, because I also checked that it could b= e an infinite type of solution, where it would not affect much if I add more= water, since the concentration of the solute does not vary.

<= /div>

 

My questions are:

How do I a= dd more than one kind of ions like KCl and NaCl and if when I do this the co= ncentrations that I choose are correct?

 

From: "= ;Gumbart, JC" <gumbart@p= hysics.gatech.edu>
Date: Tuesday, August 24, 2021 at 12:11 = AM
To: "Ropon-Palacios G." <biodano.geo@gmail.com>
Cc: NAMD list <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: Asymmetric concentration gradient

<= /div>

 

You can give solvate a minmax to only solvate a region above = or below the membrane mid-plane (make sure to give them different segnames f= or both the water and ions).  Then a few lines using psfgen (readpsf __= _ pdb ___) will combine them.  There=E2=80=99s no script though, but if you p= lay around with the options, you should quickly get a sense of what to do. <= o:p>

 

=

Best,

JC




On Aug 24, 2021, at 12:10 AM, Ro= pon-Palacios G. <biodano.geo@gmail= .com> wrote:

 =

Dear Prof. Gumbart,

 

<= /div>

My question was on that side, how to= do the solvation up and down independently, could you give me an example of= the script, to be able to do it please. I find it a bit unfamiliar as this = is my first time doing this.

 

= From:&nb= sp;"Gumbart, JC" = <g= umbart@physics.gatech.edu>
Date: Monday, August 23, 2021 at 11:05 PM
To: 
NAMD list <namd-l@ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo@gmail.com>
Su= bject: Re: namd-l: Asymmet= ric concentration gradient

=

 

Hi Geo, <= o:p>

 

It=E2=80=99s been a long = time since I ran this.  But one way I can think of would be to solvate = and ionize above and below separately and then combine them with psfgen. &nb= sp;I attach an example tclBC script and NAMD input file for running the actu= al simulation once you=E2=80=99ve built the system. 

 

Be= st,

JC

 





On Aug = 23, 2021, at 10:08 PM, Ropon-Palacios G. <biodano.geo@gmail.com> wrot= e:

 <= /o:p>

Dear users,=

 

I am trying = to simulate a membrane protein system where it has a concentration differenc= e on one side as well as the other, similar to the work of Professor JC Gumb= art =E2=80=9CMolecular dynamics simulat= ions of membrane proteins under asymmetric ionic concentrations=E2=80=9D

<= b> 

My question is, how do I ionize or how do I place the ions on both sides = with a difference in concentration? Could you please share a script to do th= is?.

 = ;

Best, 

 

<= div>

Geo.

 

=

 

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boundary="00000000000005a45305ca6df489" X-Proofpoint-ORIG-GUID: SJxQ_uV1A5TXxnY3Rj3m1YdbEmnxhlwC X-CLX-Response: 1TFkXGBsSEQpMehcbHxIRCllEF2dMU0cZaBJoR0x7EQpYWBdjWGZBfmxIWGB SexEKeE4XYX5mSUN9fVxYHUARCnlMF29Pf24BGnlLH1NlEQpDSBcHHhMfEQpDWRcHGx8dEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxMScRsTGxAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThd5YFJ7dV98G2sffnJSRHMZeEAZRxtzTkhvR0RSQkZdaREKWFwXHwQaBBgZ GQUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzcmEdSxEKTVwXGB4YEQpMWhd4aU1NaxEKRVkXb2s RCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF20TYBMBYVprbUASEQpDWhcYGhMEEh8EGB sfBBsSGhEKQl4XGxEKRF4XGREKQlwXGxEKXk4XGxEKQksXYX5mSUN9fVxYHUARCkJJF2F+ZklDf X1cWB1AEQpCRRdmGB59bmBIS2ZFchEKQk4XYX5mSUN9fVxYHUARCkJMF2NYZkF+bEhYYFJ7EQpC bBdtb2YcXG9+X1tjXBEKQkAXbxNuW0JwW1pbTRwRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBc YEQp5QxdnfHp9bWQackdZchEKcGgXbUBrSWRfYGZeUxsQGRoRCnBoF2FYSRh5bFJOfHp5EBkaEQ pwaBdjTnBgE2dBY2BlbBAZGhEKcGgXbx0SX2VlG1tkckQQGRoRCnBoF2xkaHxoRhpHH31PEBkaE QpwYxdsa3pMEnpzZEwbfBAZGhEKcGwXZkxhGkh4cB98Ym8QGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: SJxQ_uV1A5TXxnY3Rj3m1YdbEmnxhlwC X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 mlxscore=0 lowpriorityscore=0 spamscore=0 malwarescore=0 adultscore=0 clxscore=218 bulkscore=0 priorityscore=158 mlxlogscore=908 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108260017 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --00000000000005a45305ca6df489 Content-Type: multipart/alternative; boundary="00000000000005a45105ca6df488" --00000000000005a45105ca6df488 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Ishaan, If your simulations haven't yet converged, there is really no sense in evaluating the energies completely yet. With that said, how is the sampling looking across the different values of your reaction coordinate? Is the reaction coordinate stuck somewhere or is the system diffusing freely along it? Have you visually inspected your system to make sure nothing weird is happening? Best, Peter On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy wrote: > > > Hello, > > > > I am using eABF to separate two membrane proteins to find the free bindin= g > energy. The PMF values produced in my runs seem to be incredibly high > compared to consistently reaching the 100s order of magnitude. We haven= =E2=80=99t > completed a run that plateaus in free energy yet, but this is an example > showing what the PMF looks like. > > A maximum PMF this high already produces a value for the binding constant > that is on an order beyond 10^100. Besides being high, it might be worth > mentioning that the nonbonded energies are very close to 0 near the end o= f > this run, but the PMF gradient doesn=E2=80=99t level off at all. Any idea= s on what > might be causing this? Or is such a value plausible? This only seems to b= e > a problem with the separation runs; my other colvars produce PMF plots th= at > are closer to what I=E2=80=99ve seen. > > > > Thanks, > > Ishaan > > > --00000000000005a45105ca6df488 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Ishaan,
If your simulations haven'= t yet converged, there is really no sense in evaluating the energies comple= tely yet. With that said, how is the sampling looking across the different = values of your reaction coordinate? Is the reaction coordinate stuck somewh= ere or is the system diffusing freely along it?
Have you visually= inspected your system to make sure nothing weird is happening?
B= est,
Peter

On Tue, Aug 24, 2021 at 7:08 PM Ishaan Ro= y <royi@uchicago.edu> wrote:=

=C2=A0

Hello,

=C2=A0

I am using eABF to separate two membrane proteins to= find the free binding energy. The PMF values produced in my runs seem to b= e incredibly high compared to consistently reaching the 100s order of magni= tude. We haven=E2=80=99t completed a run that plateaus in free energy yet, but this is an example showing what the PMF l= ooks like.

A maximum PMF this high already produces a value for= the binding constant that is on an order beyond 10^100. Besides being high= , it might be worth mentioning that the nonbonded energies are very close t= o 0 near the end of this run, but the PMF gradient doesn=E2=80=99t level off at all. Any ideas on what might= be causing this? Or is such a value plausible? This only seems to be a pro= blem with the separation runs; my other colvars produce PMF plots that are = closer to what I=E2=80=99ve seen.

=C2=A0

Thanks,

Ishaan

=C2=A0

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Ishaan Roy --_004_SN6PR11MB287871974FEFFC6368826F00B0C79SN6PR11MB2878namp_ Content-Type: multipart/alternative; boundary="_000_SN6PR11MB287871974FEFFC6368826F00B0C79SN6PR11MB2878namp_" --_000_SN6PR11MB287871974FEFFC6368826F00B0C79SN6PR11MB2878namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Peter, Nothing stands out as weird about the runs, visually or otherwise. The samp= ling distribution is, I believe, as one would expect, generally increasing = for higher values of the coordinate and the trajectory follows a square-roo= t diffusion trend. There=92s no sign of the protein getting stuck anywhere. Thanks, Ishaan From: Peter Freddolino Sent: Wednesday, August 25, 2021 10:34 PM To: ; Ishaan Roy Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation Dear Ishaan, If your simulations haven't yet converged, there is really no sense in eval= uating the energies completely yet. With that said, how is the sampling loo= king across the different values of your reaction coordinate? Is the reacti= on coordinate stuck somewhere or is the system diffusing freely along it? Have you visually inspected your system to make sure nothing weird is happe= ning? Best, Peter On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy > wrote: Hello, I am using eABF to separate two membrane proteins to find the free binding = energy. The PMF values produced in my runs seem to be incredibly high compa= red to consistently reaching the 100s order of magnitude. We haven=92t comp= leted a run that plateaus in free energy yet, but this is an example showin= g what the PMF looks like. [cid:17b807eaccd56cdf7d61] A maximum PMF this high already produces a value for the binding constant t= hat is on an order beyond 10^100. Besides being high, it might be worth men= tioning that the nonbonded energies are very close to 0 near the end of thi= s run, but the PMF gradient doesn=92t level off at all. Any ideas on what m= ight be causing this? Or is such a value plausible? This only seems to be a= problem with the separation runs; my other colvars produce PMF plots that = are closer to what I=92ve seen. Thanks, Ishaan --_000_SN6PR11MB287871974FEFFC6368826F00B0C79SN6PR11MB2878namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Hi Peter,

 

Nothing stands out as weird about the runs, visually= or otherwise. The sampling distribution is, I believe, as one would expect= , generally increasing for higher values of the coordinate and the trajecto= ry follows a square-root diffusion trend. There=92s no sign of the protein getting stuck anywhere.

 

Thanks,

Ishaan

 

From: Peter Freddolino
Sent: Wednesday, August 25, 2021 10:34 PM
To: <namd-l@ks.uiuc.edu>= ; Ishaan Roy
Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation

 

Dear Ishaan,

If your simulations haven't yet converged, there is = really no sense in evaluating the energies completely yet. With that said, = how is the sampling looking across the different values of your reaction co= ordinate? Is the reaction coordinate stuck somewhere or is the system diffusing freely along it?

Have you visually inspected your system to make sure= nothing weird is happening?

Best,

Peter

 

On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy <royi@uchicago.edu> wrote:=

 

Hello,

 

I am using eABF to separate two membrane proteins to find the free binding = energy. The PMF values produced in my runs seem to be incredibly high compa= red to consistently reaching the 100s order of magnitude. We haven=92t comp= leted a run that plateaus in free energy yet, but this is an example showing what the PMF looks like.

A maximum PMF this high already produces a value for the binding constant t= hat is on an order beyond 10^100. Besides being high, it might be worth men= tioning that the nonbonded energies are very close to 0 near the end of thi= s run, but the PMF gradient doesn=92t level off at all. Any ideas on what might be causing this? Or is such a va= lue plausible? This only seems to be a problem with the separation runs; my= other colvars produce PMF plots that are closer to what I=92ve seen.

 

Thanks,

Ishaan

 

 

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owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Chris Chipot --------------EA886E7C026C5D9DCFFC5F1C Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: Quoted-printable Ishaan, there are a number of quantities that you ought to look into. First, you=20 should histogram the difference between the extended variable and the=20 actual variable (from your *traj* file), and ascertain that it obeys a=20 normal law. Second, you should make sure that your bias is properly=20 applied, that is past a threshold (fullSamples) of accrued force samples=20 guaranteeing minimum non-equilibrium effects. Third, you should make=20 sure that your distanceXY component is correctly defined, with the=20 desired subsets of atoms. Regards, Chris On 8/26/21 12:28 AM, Ishaan Roy wrote: > > Hi Peter, > > Nothing stands out as weird about the runs, visually or otherwise. The=20 > sampling distribution is, I believe, as one would expect, generally=20 > increasing for higher values of the coordinate and the trajectory=20 > follows a square-root diffusion trend. There=92s no sign of the protein=20 > getting stuck anywhere. > > Thanks, > > Ishaan > > *From: *Peter Freddolino > *Sent: *Wednesday, August 25, 2021 10:34 PM > *To: * ; Ishaan Roy=20 > > *Subject: *Re: namd-l: Unrealistically High Keq in eABF Seperation > > Dear Ishaan, > > If your simulations haven't yet converged, there is really no sense in=20 > evaluating the energies completely yet. With that said, how is the=20 > sampling looking across the different values of your reaction=20 > coordinate? Is the reaction coordinate stuck somewhere or is the=20 > system diffusing freely along it? > > Have you visually inspected your system to make sure nothing weird is=20 > happening? > > Best, > > Peter > > On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy > wrote: > > Hello, > > I am using eABF to separate two membrane proteins to find the free > binding energy. The PMF values produced in my runs seem to be > incredibly high compared to consistently reaching the 100s order > of magnitude. We haven=92t completed a run that plateaus in free > energy yet, but this is an example showing what the PMF looks like. > > A maximum PMF this high already produces a value for the binding > constant that is on an order beyond 10^100. Besides being high, it > might be worth mentioning that the nonbonded energies are very > close to 0 near the end of this run, but the PMF gradient doesn=92t > level off at all. Any ideas on what might be causing this? Or is > such a value plausible? This only seems to be a problem with the > separation runs; my other colvars produce PMF plots that are > closer to what I=92ve seen. > > Thanks, > > Ishaan > --=20 Chris Chipot, Ph.D. CNRS research director, University of Lorraine Adjunct professor of physics, University of Illinois, Urbana-Champaign _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group 3161 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Urbana, Illinois 61801 Phone: (217) 244-4361 E-mail: chipot@illinois.edu Christophe.Chipot@Univ-Lorraine.fr Web: https://physics.illinois.edu https://urldefense.com/v3/__http://ww= w.lia-uiuc.cnrs.fr__;!!DZ3fjg!sg_GdAfoKSs-iZn3SbG9gjML3m0CX5iHxHS49Dpkprfd2= J9JKiyRNjWCn5lC-6KJPQ$=20 http://www.ks.uiuc.edu/~chipot Fiat justitia, et pereat mundus --Heinrich von Kleist _______________________________________________________________________ --------------EA886E7C026C5D9DCFFC5F1C Content-Type: multipart/related; boundary="------------29C3263BDBFEEA1DE5D54220" --------------29C3263BDBFEEA1DE5D54220 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: Quoted-printable
Ishaan,

there are a number of quantities that you ought to look into. First, you should histogram the difference between the extended variable and the actual variable (from your traj file), and ascertain that it obeys a normal law. Second, you should make sure that your bias is properly applied, that is past a threshold (= fullSamples) of accrued force samples guaranteeing minimum non-equilibrium effects. Third, you should make sure that your distanceXY component is correctly defined, with the desired subsets of atoms.

Regards,


Chris



On 8/26/21 12:28 AM, Ishaan Roy wrote:
=20=20=20=20=20=20

Hi Peter,

 

Nothing stands out as weird about the runs, visually or otherwise. The sampling distribution is, I believe, as one would expect, generally increasing for higher values of the coordinate and the trajectory follows a square-root diffusion trend. There=92s no sign of the protein getting stuck anywhere.

 

Thanks,

Ishaan

 

From: Peter Freddolino
Sent: Wednesday, August 25, 2021 10:34 PM
To: <namd-l@ks.uiuc.edu>; Ishaan Roy
Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation

 

Dear Ishaan,

If your simulations haven't yet converged, there is really no sense in evaluating the energies completely yet. With that said, how is the sampling looking across the different values of your reaction coordinate? Is the reaction coordinate stuck somewhere or is the system diffusing freely along it?

Have you visually inspected your system to make sure nothing weird is happening?

Best,

Peter

 

On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy <royi@uchicago.edu> wrote:

 

Hello,

 

I am using eABF to separate two membrane proteins to find the free binding energy. The PMF values produced in my runs seem to be incredibly high compared to consistently reaching the 100s order of magnitude. We haven=92t completed a run that plateaus in free energy yet, but this is an example showing what the PMF looks like.

A maximum PMF this high already produces a value for the binding constant that is on an order beyond 10^100. Besides being high, it might be worth mentioning that the nonbonded energies are very close to 0 near the end of this run, but the PMF gradient doesn=92t level off at all. Any ideas on what might be causing this? Or is such a value plausible? This only seems to be a problem with the separation runs; my other colvars produce PMF plots that are closer to what I=92ve seen.

 

Thanks,

Ishaan

 

 



--=20

Chris Chipot, Ph.D.
CNRS research director, University of Lorraine
Adjunct professor of physics, University of Illinois, Urbana-Champaign

_______________________________________________________________________

Chris Chipot, Ph.D.=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20
Theoretical and Computational Biophysics Group=20=20=20=20=20=20=20
3161 Beckman Institute for Advanced Science and Technology=20=20
University of Illinois at Urbana-Champaign=20=20=20=20=20=20=20=20
405 North Mathews=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=
=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20
Urbana, Illinois 61801                            Phone: (217) 244-4361

                             E-mail: chipot@illinois.edu
                                     Christophe.Chipot@Univ-L=
orraine.fr
                             Web:    https://physics.illinois.edu
                                     http://ww=
w.lia-uiuc.cnrs.fr
                                     http://www.ks.uiuc.edu/~chipot

                       			Fiat justitia, et pereat mundus
                                                  --Heinrich von Kleist=20
_______________________________________________________________________
  


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From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= 
To: NAMD list ,
        =?utf-8?B?UmVuw6k=?= Hafner TUK 
Cc: Giacomo Fiorin 
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References: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de>  
Subject: Re: namd-l: eABF 3D sampling using distance Colvars + X and Y:
 averaged PMF difference to 1D sampling
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Hi Ren=C3=A9,=20

> What is the correct way to sample non-independent variables with proper g=
uesses?

I'm not sure I can add much to answer this question. What you did seems cor=
rect, as far as I can tell.=20

The one concern I have is how you extract the "marginal" free energy profil=
es from the 3D profile. That is not very clear to me. A correct way would b=
e to compute the integral of the Boltzmann factor (exp(-A(x,y,z)/RT)) over =
coordinates x and y.=20

Best,=20
J=C3=A9r=C3=B4me=20

----- On Aug 14, 2021, at 7:28 PM, Ren=C3=A9 Hafner TUK  wrote:=20

> Hi Giacomo,

> yes I can confirm from the writings in the logfile stating:

> "Enabling the extended Lagrangian term for colvar .. " for every colvar.

> I make use of the CZAR estimator.

> By the way: I am using NAMD 2.14.

> Ren=C3=A9
> On 8/14/2021 7:17 PM, Giacomo Fiorin wrote:

>> Hello Ren=C3=A9, can you confirm that you are using extended ABF, and mo=
re
>> specifically what estimator you used? (CZAR or Zheng/Yang).

>> Orthogonality between variables is only required for straight ABF, where=
 the
>> force on the variable is obtained by projecting the atomic total forces
>> directly, rather than using the extended-mass trick.

>> Giacomo

>> On Sat, Aug 14, 2021 at 11:24 AM Ren=C3=A9 Hafner TUK < [
>> mailto:hamburge@physik.uni-kl.de | hamburge@physik.uni-kl.de ] > wrote:

>>> Hi,

>>> I am trying to use a distance like colvar to sample a surface with a li=
gand
>>> using extended ABF.

>>> In order to speed up the surface sampling process I turned the abf line=
 into a
>>> 3D one where I also sample the X and Y direction.

>>> My colvar file roughly looks like:

>>>> colvar { name X; distanceZ ... } # Ligand distance from Membrane Cente=
r in X
>>>> direction

>>>> colvar { name Y; distanceZ ... } # Ligand distance from Membrane Cente=
r in Y
>>>> direction

>>>> colvar { name distanceFromMembrane} # Ligand local distance from Membr=
ane
>>>> Surface (selfdefined)

>>>> abf { colvars X Y distanceFromMembrane; ... }
>>> This means the third variable is not independent from/orthogonal to X a=
nd Y but
>>> that shouldn't be and issue when using eABF.

>>> Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get
>>> PMF(distMembrane) )

>>> * When I did 1D sampling ( only distanceFromMembrane) I obtained rougly
>>> 5.5kcal/mol as dG (difference from Minimum to a point far away from Mem=
brane)

>>> * When I do 3D sampling using "subtractAppliedForce on " in all 3 colva=
rs I
>>> obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" becaus=
e I
>>> initially used metadynamics +eABF)

>>> * When I do 3D sampling using "subtractAppliedForce off " in all 3 colv=
ars I
>>> obtained dG ~ 1-2kcal/mol.

>>> What is the correct way to sample non-independent variables with proper=
 guesses?

>>> (I expect the 3D to reconstruct the 1D sampling case when done correctl=
y and
>>> just help improving the sampling of the whole surface)

>>> Kind regards

>>> Ren=C3=A9

>>> --
>>> --
>>> Dipl.-Phys. Ren=C3=A9 Hafner
>>> TU Kaiserslautern
>>> Germany

> --
> --
> Dipl.-Phys. Ren=C3=A9 Hafner
> TU Kaiserslautern
> Germany

--=_5e12490f-b858-4679-9e3e-36c4672464d6
Content-Type: text/html; charset=utf-8
Content-Transfer-Encoding: quoted-printable

Hi Ren=C3=A9,

What is the correct way to sample non-independent variables with = proper guesses?

I'm not sure= I can add much to answer this question. What you did seems correct, as far= as I can tell.

The one conce= rn I have is how you extract the "marginal" free energy profiles from the 3= D profile. That is not very clear to me. A correct way would be to compute = the integral of the Boltzmann factor (exp(-A(x,y,z)/RT)) over coordinates x= and y.

Best,
J=C3= =A9r=C3=B4me


<= span id=3D"zwchr" data-marker=3D"__DIVIDER__">----- On Aug 14, 2021, at 7:2= 8 PM, Ren=C3=A9 Hafner TUK <hamburge@physik.uni-kl.de> wrote:

Hi Giacomo,

    yes I can confirm from the writings in the logfil= e stating:

    "Enabling the extended Lagrangian term for colvar= .. " for every colvar.

    I make use of the CZAR estimator.

By the way: I am using NAMD 2.14.

Ren=C3=A9

On 8/14/2021 7:17 PM, Giacomo Fiorin wrote:
=20
Hello Ren=C3=A9, can you confirm that you are u= sing extended ABF, and more specifically what estimator you used?  (CZAR or Zheng/Yang).

Orthogonality between variables is only required for straight ABF, where the force on the variable is obtained by projecting the atomic total forces directly, rather than using the extended-mass trick.

Giacomo

On Sat, Aug 14, 2021 at 11:24 AM Ren=C3=A9 Hafner TUK <hamburge@phy= sik.uni-kl.de> wrote:

Hi,

I am trying to use a distance like colvar to sample a surface with a ligand using extended ABF.

In order to speed up the surface sampling process I turned the abf line into a 3D one where I also sample the X and Y direction.


My colvar file roughly looks like:

colvar { name X; distanceZ ... } #  Ligand distance from Membrane Center in X direction

colvar { name Y; distanceZ ... }  # Ligand distance from Membrane Center in Y direction

colvar { name distanceFromMembrane}  # Ligand local distance from Membrane Surface (selfdefined)

abf { colvars X Y distanceFromMembrane;  ... }


This means the third variable is not independent from/orthogonal to X and Y but that shouldn't be and issue when using eABF.


Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get PMF(distMembrane) )


* When I did 1D sampling ( only distanceFromMembrane) I obtained rougly 5.5kcal/mol as dG (difference from Minimum to a point far away from Membrane)

* When I do 3D sampling using "subtractAppliedForce on" in all 3 colvars I obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" because I initially used metadynamics +eABF)

* When I do 3D sampling using "subtractAppliedForce off" in all 3 colvars I obtained dG ~ 1-2kcal/mol.


What is the correct way to sample non-independent variables with proper guesses?

(I expect the 3D to reconstruct the 1D sampling case when done correctly and just help improving the sampling of the whole surface)


Kind regards

Ren=C3=A9


--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany
--=20
--
Dipl.-Phys. Ren=C3=A9 Hafner
TU Kaiserslautern
Germany

--=_5e12490f-b858-4679-9e3e-36c4672464d6-- From owner-namd-l@halifax.ks.uiuc.edu Thu Aug 26 13:53:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17QIrKel017519; Thu, 26 Aug 2021 13:53:20 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17QIrKgF017518; Thu, 26 Aug 2021 13:53:20 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17QIrJZx017514; Thu, 26 Aug 2021 13:53:19 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17QIrI1Q017513; Thu, 26 Aug 2021 13:53:18 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17QIr9Bo017505 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 26 Aug 2021 13:53:09 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 17QIit0K026124 for ; Thu, 26 Aug 2021 18:53:08 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=hamburge@physik.uni-kl.de Received: from mailgw1.uni-kl.de (mailgw1.uni-kl.de [131.246.120.220]) by mx0b-00007101.pphosted.com with ESMTP id 3apf2d0y4y-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Thu, 26 Aug 2021 18:53:08 +0000 Received: from [IPv6:2a02:810c:300:6724:11f2:cc1b:54bb:6737] ([IPv6:2a02:810c:300:6724:11f2:cc1b:54bb:6737]) (authenticated bits=0) by mailgw1.uni-kl.de (8.14.4/8.14.4/Debian-8+deb8u2) with ESMTP id 17QIqK6e025450 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Thu, 26 Aug 2021 20:52:24 +0200 Subject: Re: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling To: =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= , NAMD list References: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> <776238278.121985.1629979279975.JavaMail.zimbra@ibpc.fr> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: <75ed1df2-a28f-0d0c-336c-2ed26ad9d1b3@physik.uni-kl.de> Date: Thu, 26 Aug 2021 20:52:19 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.13.0 MIME-Version: 1.0 In-Reply-To: <776238278.121985.1629979279975.JavaMail.zimbra@ibpc.fr> Content-Type: multipart/alternative; boundary="------------16DEF3FD6371AE54D547D4A8" Content-Language: de-DE X-Spam-Status: No, hits=-2.138, tests=HELO_NO_DOMAIN=0.001,HTML_MESSAGE=0.001,NICE_REPLY_A=-2.24,SHORT_HELO_AND_INLINE_IMAGE=0.1 X-Spam-Score: (-2.138) X-Spam-Flag: NO X-Proofpoint-ORIG-GUID: 9X69lm8FQkEpnXo7uU7B3sEXo3afkd0Y X-CLX-Shades: MLX X-Proofpoint-GUID: 9X69lm8FQkEpnXo7uU7B3sEXo3afkd0Y X-CLX-Response: 1TFkXGxIbEQpMehcaEQpZRBdpUEETaEB8UhpPZhEKWFgXYGAbUhkdGBpScgU RCnhOF2QaSW56engaZH1cEQp5TBduYVxDTmhYRxJ+RxEKQ0gXBxwSHhEKQ1kXBx0ZEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwbcR4aEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxNyHBNGRxJse0FvWkRyRR1ffx1oGVlvckUZS0xBThpzEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3Nyc09cEQpNXBcZGBIRCkxaF3hha0FNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbF9sZl9wTEscUksRCkNaFxsZGwQYHhwEGxgaBBgYGh EKQl4XGxEKRF4XGBEKQkUXbB1YckUfHEdJBW4RCkJOF2QaSW56engaZH1cEQpCTBdgYBtSGR0YG lJyBREKQmwXZmtiZBhZYm1IfmwRCkJAF25rbEFlchNjfAFaEQpCWBdnc2VzQG5hYUxdYhEKWlgX GREKeUMXbXtdeWsZGxhdc2YRCnBnF2AZRkV7TkcZbVxFEB4SEQpwaBdiT0VzE3sbUkxuTxAdHxE KcGgXb3BBSBp4WxxJRHgQGRoRCnBoF2JyE24fWRtJBRlnEBkaEQpwaBdpRnhwXkgdc2VaZhAZGh EKcGgXZnNQaBNbQ28dfxwQGRoRCnBnF3p4GGR9HU9sYntdEBkaEQpwZxdmeRlAU2JhXlJ5ZxAZG hEKcGMXaxl7cF9IWWtGXlsQGRoRCnBsF3ofeHlveExDX3BEEBkaEQpwTBdtaGUZQVJ9exhFUhAZ GhEKbX4XGhEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 lowpriorityscore=0 bulkscore=0 clxscore=181 mlxscore=0 malwarescore=0 impostorscore=0 adultscore=0 mlxlogscore=907 priorityscore=0 spamscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108260103 X-Spam-Score: 0 X-Spam-OrigSender: hamburge@physik.uni-kl.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= This is a multi-part message in MIME format. --------------16DEF3FD6371AE54D547D4A8 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Jérôme! The way I extract it was to run second abf instance with only the distanceFromMembrane colvar that is **not** applied. Which turned out to be the same as when just weighting the zgrad(x,y,z) by the respective counts and average over X,Y. But we were wondering whether this is the correct way. I even tried an easier setup with an almost flat membrane surface where I can compare results to a simple distanceZ variable. Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol (same as distanceZ)                         the 3D case returns dG = 4.3 (+- 0.1) kcal/mol (with the above assumption) Though what you suggest is to calculate the marginal distribution via the following? What I additionally needed to do in order to gain a smooth curve here was to weight every grid point by its counts (such that "bad" guesses with low counts get suppressed). But I am not yet the sure the scale is correct. Best René On 8/26/2021 2:01 PM, Jérôme Hénin wrote: > Hi René, > > *What is the correct way to sample non-independent variables with > proper guesses?* > > * > * > I'm not sure I can add much to answer this question. What you did > seems correct, as far as I can tell. > > The one concern I have is how you extract the "marginal" free energy > profiles from the 3D profile. That is not very clear to me. A correct > way would be to compute the integral of the Boltzmann factor > (exp(-A(x,y,z)/RT)) over coordinates x and y. > > Best, > Jérôme > > > ----- On Aug 14, 2021, at 7:28 PM, René Hafner TUK > wrote: > > Hi Giacomo, > >     yes I can confirm from the writings in the logfile stating: > >     "Enabling the extended Lagrangian term for colvar .. " for > every colvar. > >     I make use of the CZAR estimator. > > By the way: I am using NAMD 2.14. > > René > > On 8/14/2021 7:17 PM, Giacomo Fiorin wrote: > > Hello René, can you confirm that you are using extended ABF, > and more specifically what estimator you used?  (CZAR or > Zheng/Yang). > > Orthogonality between variables is only required for straight > ABF, where the force on the variable is obtained by projecting > the atomic total forces directly, rather than using the > extended-mass trick. > > Giacomo > > On Sat, Aug 14, 2021 at 11:24 AM René Hafner TUK > > > wrote: > > Hi, > > I am trying to use a distance like colvar to sample a > surface with a ligand using extended ABF. > > In order to speed up the surface sampling process I turned > the abf line into a 3D one where I also sample the X and Y > direction. > > > My colvar file roughly looks like: > > colvar { name X; distanceZ ... } #  Ligand distance > from Membrane Center in X direction > > colvar { name Y; distanceZ ... }  # Ligand distance > from Membrane Center in Y direction > > colvar { name distanceFromMembrane}  # Ligand local > distance from Membrane Surface (selfdefined) > > abf { colvars X Y distanceFromMembrane;  ... } > > > This means the third variable is not independent > from/orthogonal to X and Y but that shouldn't be and issue > when using eABF. > > > Comparing 1D run and 3D run (averaged the 3D PMF over X,Y > to get PMF(distMembrane) ) > > > * When I did 1D sampling ( only distanceFromMembrane) I > obtained rougly 5.5kcal/mol as dG (difference from Minimum > to a point far away from Membrane) > > * When I do *3D sampling* using "subtractAppliedForce > *on*" *in all 3 colvars* I obtained dG ~ 4kcal/mol. (I > used the term "subtractAppliedForce" because I initially > used metadynamics +eABF) > > * When I do *3D sampling* using "subtractAppliedForce > *off*" *in all 3 colvars* I obtained dG ~ 1-2kcal/mol. > > > *What is the correct way to sample non-independent > variables with proper guesses?* > > (I expect the 3D to reconstruct the 1D sampling case when > done correctly and just help improving the sampling of the > whole surface) > > > Kind regards > > René > > > -- > -- > Dipl.-Phys. René Hafner > TU Kaiserslautern > Germany > > -- > -- > Dipl.-Phys. René Hafner > TU Kaiserslautern > Germany > > -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------16DEF3FD6371AE54D547D4A8 Content-Type: multipart/related; boundary="------------2FD9B7E2DDB470D57AD10A47" --------------2FD9B7E2DDB470D57AD10A47 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Jérôme!

The way I extract it was to run second abf instance with only the distanceFromMembrane colvar that is **not** applied.

Which turned out to be the same as when just weighting the zgrad(x,y,z) by the respective counts and average over X,Y.

But we were wondering whether this is the correct way.


I even tried an easier setup with an almost flat membrane surface where I can compare results to a simple distanceZ variable.

Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol (same as distanceZ)

                        the 3D case returns dG = 4.3 (+- 0.1) kcal/mol (with the above assumption)


Though what you suggest is to calculate the marginal distribution via the following?

What I additionally needed to do in order to gain a smooth curve here was to weight every grid point by its counts (such that "bad" guesses with low counts get suppressed). But I am not yet the sure the scale is correct.

Best

René


On 8/26/2021 2:01 PM, Jérôme Hénin wrote:
Hi René,

What is the correct way to sample non-independent variables with proper guesses?

I'm not sure I can add much to answer this question. What you did seems correct, as far as I can tell.

The one concern I have is how you extract the "marginal" free energy profiles from the 3D profile. That is not very clear to me. A correct way would be to compute the integral of the Boltzmann factor (exp(-A(x,y,z)/RT)) over coordinates x and y.

Best,
Jérôme


----- On Aug 14, 2021, at 7:28 PM, René Hafner TUK <hamburge@physik.uni-kl.de> wrote:

Hi Giacomo,

    yes I can confirm from the writings in the logfile stating:

    "Enabling the extended Lagrangian term for colvar .. " for every colvar.

    I make use of the CZAR estimator.

By the way: I am using NAMD 2.14.

René

On 8/14/2021 7:17 PM, Giacomo Fiorin wrote:
Hello René, can you confirm that you are using extended ABF, and more specifically what estimator you used?  (CZAR or Zheng/Yang).

Orthogonality between variables is only required for straight ABF, where the force on the variable is obtained by projecting the atomic total forces directly, rather than using the extended-mass trick.

Giacomo

On Sat, Aug 14, 2021 at 11:24 AM René Hafner TUK <hamburge@physik.uni-kl.de> wrote:

Hi,

I am trying to use a distance like colvar to sample a surface with a ligand using extended ABF.

In order to speed up the surface sampling process I turned the abf line into a 3D one where I also sample the X and Y direction.


My colvar file roughly looks like:

colvar { name X; distanceZ ... } #  Ligand distance from Membrane Center in X direction

colvar { name Y; distanceZ ... }  # Ligand distance from Membrane Center in Y direction

colvar { name distanceFromMembrane}  # Ligand local distance from Membrane Surface (selfdefined)

abf { colvars X Y distanceFromMembrane;  ... }


This means the third variable is not independent from/orthogonal to X and Y but that shouldn't be and issue when using eABF.


Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get PMF(distMembrane) )


* When I did 1D sampling ( only distanceFromMembrane) I obtained rougly 5.5kcal/mol as dG (difference from Minimum to a point far away from Membrane)

* When I do 3D sampling using "subtractAppliedForce on" in all 3 colvars I obtained dG ~ 4kcal/mol. (I used the term "subtractAppliedForce" because I initially used metadynamics +eABF)

* When I do 3D sampling using "subtractAppliedForce off" in all 3 colvars I obtained dG ~ 1-2kcal/mol.


What is the correct way to sample non-independent variables with proper guesses?

(I expect the 3D to reconstruct the 1D sampling case when done correctly and just help improving the sampling of the whole surface)


Kind regards

René


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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ABdhPJweVB/nHCuwAOiMr9JTGVUNFy9dLAxYlar2VrDFUetjGVFylSsV7inTPoCAA035wGc9jDE1u9BR4lUIDJL5Ays= X-Received: by 2002:a05:6a00:1716:b0:3f2:269e:76b with SMTP id h22-20020a056a00171600b003f2269e076bmr5675013pfc.77.1630026853711; Thu, 26 Aug 2021 18:14:13 -0700 (PDT) References: In-Reply-To: From: Mohammad Mehdi Pirnia Date: Fri, 27 Aug 2021 05:44:02 +0430 Message-ID: Subject: namd-l: Error: psfgen) unknown atom type H To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="00000000000097031f05ca8033a7" X-Proofpoint-GUID: -XwGksNIjW05G88mpYYQaPGqUafYduFD X-Proofpoint-ORIG-GUID: -XwGksNIjW05G88mpYYQaPGqUafYduFD X-CLX-Response: 1TFkXGxkSEQpMehcZGR4RCllEF2BCHUlaE0JdXWRaEQpYWBdhEkxfe1JbZ0Z kTBEKeE4XY1Nja3sTWH4aX14RCnlMF25QXwFwT15hS29+EQpDSBcHHx4fEQpDWRcHEhkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGxJxGx4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XB3JdbUFZZGNAfRofbRISR1pzc3tLem1bf0tMc05fbG4RClhcFx8EGgQYGRkF GxoEGxoaBB4SBBgYEBseGh8aEQpeWRdzck9vaREKTVwXGRweEQpMWhdoaU1raxEKTEYXb2trbGt rEQpCTxdtE2ATAWFaa21AEhEKQ1oXGBoTBBIfBBgbHwQbHRgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaEwYfkxhAWVhcBgRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdhEkxfe1JbZ0ZkTBEKQmwXaVhtel99E0ZMbmYRCkJAF2lPHk9oHlgZSEVNEQpC WBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXbXNOZ3h7eVBQHFARCnBoF2t9awFNSFtpTEBSEBkaEQp waBdoGQFDYk4TZGJveBAZGhEKcGgXY2IYcHtHAURHa2QQGRoRCnBoF2llWlN+R2VAWE1HEBkaEQ pwaBdhGXwSBUdBYV1HaBAZGhEKcH0XYRJAclt/TGJ4W1wQGRoRCnB9F2ZJYWcZGl9HYmNpEBkaE QpwfRdiRmhOGk94WXNSTRAZGhEKcH8XZGtAZx9CUloTE1IQHBoRCnBfF2dLGn5YYUcdGEUaEBka EQpwfxdnQ1t/EhhTZXNAbBAZGhEKcF8XZklhZxkaX0diY2kQGRoRCnB/F2kYWUdJbRpcbVliEBk aEQpwXxdiRmhOGk94WXNSTRAZGhEKcGwXZm1pE29AHU5OaWEQGRoRCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=138 adultscore=0 spamscore=0 impostorscore=0 mlxscore=0 suspectscore=0 bulkscore=0 phishscore=0 lowpriorityscore=0 priorityscore=334 mlxlogscore=999 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108270006 X-Spam-Score: 0 X-Spam-OrigSender: mpdezfouli@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mohammad Mehdi Pirnia --00000000000097031f05ca8033a7 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear users, Please see the output below and all my codes and files uploaded in the link at the bottom. psfgen) $Id: top_allxx_sugar.inp,v 1.106 2014/08/19 19:07:43 alex Exp $ psfgen) >>>>>>>>>>>> All-hydrogen topologies used in the <<<<<<<<<<<<<<<< psfgen) >>>>> development of the CHARMM carbohydrate force field<<<<<<<< psfgen) >>>>>>>>>>>>>>>>>>>>>>>>> June 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< psfgen) >>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< psfgen) >>>>>>>>>> via the CHARMM web site: https://urldefense.com/v3/__htt= p://www.charmm.org__;!!DZ3fjg!sN1ZQPHyGqtzMAVzV4NGwbp0DYwKNoHjDVsVHnWD_Bqbg= gqVptqiKvozjI3iSuOirQ$ <<<<<<<<<<<<<< psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<< psfgen) psfgen) Created by CHARMM version 32 1 psfgen) reading topology file ../temporary2/toppar_all36_lipid_lps.str psfgen) reading topology from stream file psfgen) Topology for lipidA from LPS psfgen) psfgen) skipping parameters in stream file psfgen) new parametes psfgen) psfgen) reading topology file ../temporary2/toppar_all36_carb_imlab.str psfgen) reading topology from stream file psfgen) glycan chemical modification patches psfgen) psfgen) Created by CHARMM version 41 1 psfgen) cross-term entries present in topology definitions psfgen) skipping parameters in stream file psfgen) glycan chemical modification patches psfgen) 2.0 psfgen) building segment L psfgen) reading residues from pdb file upper_leaflet.pdb psfgen) extracted 540 residues from pdb file Info: generating structure... psfgen) unknown atom type H psfgen) add atom failed in residue ECLI:1 Segmentation fault (core dumped) ---------------------------- I've been getting this error for days. I didn't see anything wrong with my stream files and atom type H is definitely defined! I'm simulating peptide interactions with a bacterial membrane. I used https://urldefense.com/v3/__http://www.charmm-gui.org__;!!DZ3fjg!sN1ZQPHyGq= tzMAVzV4NGwbp0DYwKNoHjDVsVHnWD_BqbggqVptqiKvozjI39vxcbvQ$ in order to buil= d my membrane and it includes LPSA, PMCL, PMPE, PMPG, PVPE, and PVPG. - Is there a way to create such membranes using VMD? I just saw POPC and POPE in the membrane builder. - After downloading, I modified all residues' res-numbers to be consecutive, they were repetitive. Now, I'm trying to create my membrane's PSF file. The output is shown below. my VMD version is 1.9.4a.51 Here is the link on which I've uploaded all my files: https://urldefense.com/v3/__https://files.fm/u/bcvap3g8g__;!!DZ3fjg!sN1ZQPH= yGqtzMAVzV4NGwbp0DYwKNoHjDVsVHnWD_BqbggqVptqiKvozjI2YfcU4HQ$=20 Thank you all Sincerely Adam --00000000000097031f05ca8033a7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear users,

Please see the output below and= all my codes and files uploaded in the link at the=C2=A0bottom.

<= /div>
=

psfgen) =C2=A0$Id: top_allxx_sugar.inp,v 1.106 20= 14/08/19 19:07:43 alex Exp $
psfgen) >>>>>>>>&= gt;>>> All-hydrogen topologies used in the <<<<<<= ;<<<<<<<<<<
psfgen) >>>>> d= evelopment of the CHARMM carbohydrate =C2=A0force field<<<<<= <<<
psfgen) >>>>>>>>>>>>>= ;>>>>>>>>>>>> June 2009 <<<<= ;<<<<<<<<<<<<<<<<<<&l= t;<<<<<<
psfgen) >>>>>>>> Dire= ct comments to Alexander D. MacKerell Jr. <<<<<<<<&= lt;<
psfgen) >>>>>>>>>> via the CHARMM = web site: www.charmm.org <<<<<<<<<<<<<<= ;
psfgen) >>>>>>>>>>>>>>> p= arameter set discussion forum <<<<<<<<<<<&= lt;<<<<<<
psfgen)
psfgen) Created by CHARMM versio= n 32 1
psfgen) reading topology file ../temporary2/toppar_all36_lipid_lp= s.str

psfgen) reading topology from stream file
psfgen) =C2=A0Top= ology for lipidA from LPS
psfgen)
psfgen) skipping parameters in str= eam file
psfgen) =C2=A0 =C2=A0 new parametes
psfgen)
psfgen) read= ing topology file ../temporary2/toppar_all36_carb_imlab.str

psfgen) = reading topology from stream file
psfgen) =C2=A0glycan chemical modifica= tion patches
psfgen) =C2=A0
psfgen) Created by CHARMM version 41 1psfgen) cross-term entries present in topology definitions
psfgen) skip= ping parameters in stream file
psfgen) =C2=A0glycan chemical modificatio= n patches
psfgen)
2.0
psfgen) building segment L
psfgen) readi= ng residues from pdb file upper_leaflet.pdb
psfgen) extracted 540 residu= es from pdb file
Info: generating structure...
psfgen) unknown atom t= ype H
psfgen) add atom failed in residue ECLI:1
Segmentation fault (core dumped= )

----------------------------

I've been getting this error for days. I didn= 't see anything wrong with my stream files and atom type H is definitel= y defined!

I'm simulating peptide interactions wi= th a bacterial membrane. I used=C2=A0www.charmm-gui.org=C2=A0in order to=C2= =A0build=C2=A0my membrane and it inclu= des LPSA, PMCL, PMPE, PMPG, PVPE, and PVPG.

- Is ther= e a way to create such membranes using VMD? I just saw POPC and POPE in the= membrane builder.

=
- After downloading, I modified al= l residues' res-numbers to be consecutive, they were repetitive. Now, I= 'm trying to create my membrane's PSF file.=C2=A0The output=C2=A0is= =C2=A0shown below.=C2=A0

=
my VMD version is 1.9.4a.51<= /div>

Here is the link o= n which I've uploaded all my files:

Thank you all
=
Sincerely
Adam=C2=A0


--00000000000097031f05ca8033a7-- From owner-namd-l@halifax.ks.uiuc.edu Fri Aug 27 07:05:44 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17RC5iCD000422; Fri, 27 Aug 2021 07:05:44 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17RC5ige000421; Fri, 27 Aug 2021 07:05:44 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17RC5hn9000417; Fri, 27 Aug 2021 07:05:43 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 17RC5h7P000416; Fri, 27 Aug 2021 07:05:43 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 17RC5T7E000403 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Fri, 27 Aug 2021 14:05:20 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id CE5621E40542; Fri, 27 Aug 2021 14:05:19 +0200 (CEST) Date: Fri, 27 Aug 2021 14:05:16 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: =?utf-8?B?UmVuw6k=?= Hafner TUK Cc: NAMD list Message-ID: <436085002.225603.1630065916919.JavaMail.zimbra@ibpc.fr> In-Reply-To: <75ed1df2-a28f-0d0c-336c-2ed26ad9d1b3@physik.uni-kl.de> References: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> <776238278.121985.1629979279975.JavaMail.zimbra@ibpc.fr> <75ed1df2-a28f-0d0c-336c-2ed26ad9d1b3@physik.uni-kl.de> Subject: Re: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_69f9a380-7663-4db4-af84-85a985bbaf90" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling Thread-Index: Od9tHOJ4dn4y1FD0zRldelJ2H2KMxw== X-Proofpoint-ORIG-GUID: SXEV-X2jZ-o2mShBFbbls8ZCa58mAfOz X-Proofpoint-GUID: SXEV-X2jZ-o2mShBFbbls8ZCa58mAfOz X-CLX-Response: 1TFkXGx0SEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBx4YGhEKQ1kXBx0bEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ScRkdEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF3lyb3wHchhAcAdFGEd5QmhsSEhGWRJwaUsfEkdrTGVQEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQYGBAbHhofGhEKXlkXc3JER0ERCk1cFxgeExEKTFoXeG1rTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdoQEVIGBh8a1t6GREKQ1oXGxMZBB4TBBgZHgQYGBsRCk JeFxsRCkRJFxsRCkJFF2RYXFxNflJJG2VJEQpCThdlT34SQ2lmWRwBaREKQkwXehJnaWBZeUZBT 2URCkJsF2ESEk9PTE1/Tx4FEQpCQBdua2xBZXITY3wBWhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsR ClpYFxkRCnlDF217XXlrGRsYXXNmEQpwZxdgGUZFe05HGW1cRRAeEhEKcGgXYBprcnpwf1JwZV4 QGxoaEQpwaBdoeVp8QEl8Wk1rfRAZGhEKcGgXZHhfXGR8QHAbR1MQGRoRCnBoF21HcwEYTlNufx lgEBkaEQpwaBduR0lnUmFEHmZNRxAZGhEKcGcXengYZH0dT2xie10QHhIRCnB9F2VYaHtebVtzW FN9EBkaEQpwfRdjbHtdck1vW1xyeRAZGhEKcGMXYkBbRkwfHRwYXUUQGRoRCnB/F2dNe218cmRF GFgBEBkaEQpwXxdnZ15ic1JfckZ7fBAZGhEKcH8XblJyHkRNZXkYc1gQGRoRCnBfF2RQTRtQS0s eQXlYEBkaEQpwbBdmYBNkXE0aZ096UBAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0 sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 adultscore=0 mlxscore=0 clxscore=178 lowpriorityscore=0 mlxlogscore=992 phishscore=0 suspectscore=0 spamscore=0 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2108270077 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_69f9a380-7663-4db4-af84-85a985bbaf90 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Ren=C3=A9,=20 ----- On Aug 26, 2021, at 8:52 PM, Ren=C3=A9 Hafner TUK wrote:=20 > Hi J=C3=A9r=C3=B4me! >> The way I extract it was to run second abf instance with only the >> distanceFromMembrane colvar that is **not** applied. >> Which turned out to be the same as when just weighting the zgrad(x,y,z) = by the >> respective counts and average over X,Y. >> But we were wondering whether this is the correct way. I don't think that is correct, because the simulation is biased in the dire= ctions X and Y, so you are not computing an unbiased average at each z valu= e.=20 >> I even tried an easier setup with an almost flat membrane surface where = I can >> compare results to a simple distanceZ variable. >> Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol (same as dist= anceZ) >> the 3D case returns dG =3D 4.3 (+- 0.1) kcal/mol (with the above assumpt= ion) >> Though what you suggest is to calculate the marginal distribution via th= e >> following? Just an integral instead of an average:=20 >> What I additionally needed to do in order to gain a smooth curve here wa= s to >> weight every grid point by its counts (such that "bad" guesses with low = counts >> get suppressed). But I am not yet the sure the scale is correct. With the expression above you won't need to worry about that.=20 J=C3=A9r=C3=B4me=20 --=_69f9a380-7663-4db4-af84-85a985bbaf90 Content-Type: multipart/related; boundary="=_89529963-d2dd-460b-aa96-3e35b42021f4" --=_89529963-d2dd-460b-aa96-3e35b42021f4 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Ren=C3=A9,

----- On A= ug 26, 2021, at 8:52 PM, Ren=C3=A9 Hafner TUK <hamburge@physik.uni-kl.de= > wrote:

Hi J=C3= =A9r=C3=B4me!

The way I extract it was to run second abf = instance with only the distanceFromMembrane colvar that is **not** applied.=

Which turned out to be the same as when just weighting the zgrad(x,y= ,z) by the respective counts and average over X,Y.

But we were wonder= ing whether this is the correct way.

I do= n't think that is correct, because the simulation is biased in the directio= ns X and Y, so you are not computing an unbiased average at each z value.


I even tried an easier setup with an almost fl= at membrane surface where I can compare results to a simple distanceZ varia= ble.

Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol (same= as distanceZ)

          =               the 3D case= returns dG =3D 4.3 (+- 0.1) kcal/mol (with the above assumption)


Though what you suggest is to calculate the marginal distributi= on via the following?

3D""

Just an integral instead of an ave= rage:

What I additionally needed to do in order to gain a smooth curve he= re was to weight every grid point by its counts (such that "bad" guesses wi= th low counts get suppressed). But I am not yet the sure the scale is corre= ct.

With the expression above you won't n= eed to worry about that.

J=C3=A9r=C3=B4me
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cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Fri, 27 Aug 2021 15:47:27 +0200 Subject: Re: namd-l: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling To: namd-l@ks.uiuc.edu, =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= References: <5d2f7873-25f5-fb14-5d0f-2c4f2717ef3a@physik.uni-kl.de> <776238278.121985.1629979279975.JavaMail.zimbra@ibpc.fr> <75ed1df2-a28f-0d0c-336c-2ed26ad9d1b3@physik.uni-kl.de> <436085002.225603.1630065916919.JavaMail.zimbra@ibpc.fr> From: =?UTF-8?Q?Ren=c3=a9_Hafner_TUK?= Message-ID: Date: Fri, 27 Aug 2021 15:47:26 +0200 User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:78.0) Gecko/20100101 Thunderbird/78.13.0 MIME-Version: 1.0 In-Reply-To: <436085002.225603.1630065916919.JavaMail.zimbra@ibpc.fr> Content-Type: multipart/alternative; boundary="------------21DB48BB979654BD85286CFA" Content-Language: de-DE X-Spam-Status: No, hits=-1.898, 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Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Jérôme,     alright, I'll try it like that! Best René On 8/27/2021 2:05 PM, Jérôme Hénin wrote: > Hi René, > > ----- On Aug 26, 2021, at 8:52 PM, René Hafner TUK > wrote: > > Hi Jérôme! > > The way I extract it was to run second abf instance with only > the distanceFromMembrane colvar that is **not** applied. > > Which turned out to be the same as when just weighting the > zgrad(x,y,z) by the respective counts and average over X,Y. > > But we were wondering whether this is the correct way. > > I don't think that is correct, because the simulation is biased in the > directions X and Y, so you are not computing an unbiased average at > each z value. > > > I even tried an easier setup with an almost flat membrane > surface where I can compare results to a simple distanceZ > variable. > > Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol > (same as distanceZ) > >                         the 3D case returns dG = 4.3 (+- 0.1) > kcal/mol (with the above assumption) > > > Though what you suggest is to calculate the marginal > distribution via the following? > > Just an integral instead of an average: > > What I additionally needed to do in order to gain a smooth > curve here was to weight every grid point by its counts (such > that "bad" guesses with low counts get suppressed). But I am > not yet the sure the scale is correct. > > With the expression above you won't need to worry about that. > > Jérôme -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany --------------21DB48BB979654BD85286CFA Content-Type: multipart/related; boundary="------------8C7A3399C414536E98500867" --------------8C7A3399C414536E98500867 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Jérôme,

    alright, I'll try it like that!

Best

René

On 8/27/2021 2:05 PM, Jérôme Hénin wrote:
Hi René,

----- On Aug 26, 2021, at 8:52 PM, René Hafner TUK <hamburge@physik.uni-kl.de> wrote:

Hi Jérôme!

The way I extract it was to run second abf instance with only the distanceFromMembrane colvar that is **not** applied.

Which turned out to be the same as when just weighting the zgrad(x,y,z) by the respective counts and average over X,Y.

But we were wondering whether this is the correct way.

I don't think that is correct, because the simulation is biased in the directions X and Y, so you are not computing an unbiased average at each z value.


I even tried an easier setup with an almost flat membrane surface where I can compare results to a simple distanceZ variable.

Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol (same as distanceZ)

                        the 3D case returns dG = 4.3 (+- 0.1) kcal/mol (with the above assumption)


Though what you suggest is to calculate the marginal distribution via the following?

Just an integral instead of an average:

What I additionally needed to do in order to gain a smooth curve here was to weight every grid point by its counts (such that "bad" guesses with low counts get suppressed). But I am not yet the sure the scale is correct.

With the expression above you won't need to worry about that.

Jérôme
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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b=ZU3y2z1dLG6FUhaOGdG+BCq+Srjj+4PtlceyoXXi1LkV5kIk8k35Ckzkb+dgBGi8uUejtO+PVmtHzj9+a0J/iWflqxcgg+a4Gzh+qfygpKzZFYxIEWOcsRT05ljeB+ufvfpoL7CfIR15vwWqsZKvrlYAFdPtYbyB7TnVA1MLcG4= Received: from BN7PR07MB4481.namprd07.prod.outlook.com (2603:10b6:406:b2::23) by BN8PR07MB6820.namprd07.prod.outlook.com (2603:10b6:408:b9::26) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.4457.23; Fri, 27 Aug 2021 15:27:52 +0000 Received: from BN7PR07MB4481.namprd07.prod.outlook.com ([fe80::a840:294d:7d17:8e87]) by BN7PR07MB4481.namprd07.prod.outlook.com ([fe80::a840:294d:7d17:8e87%7]) with mapi id 15.20.4457.023; Fri, 27 Aug 2021 15:27:52 +0000 From: "Gumbart, JC" To: NAMD list , Mohammad Mehdi Pirnia Subject: Re: namd-l: Error: psfgen) unknown atom type H Thread-Topic: namd-l: Error: psfgen) unknown atom type H Thread-Index: AQHXmueu0zP1iWYAbU+gTOPMU/VVcquHemKA Date: Fri, 27 Aug 2021 15:27:52 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US 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X-CLX-Response: 1TFkXGBoTEQpMehcaEQpZRBdie05gWEVmQ09tTREKWFgXZhlwY2FScgFYG3A RCnhOF2hpBUkaRWhhHWVvEQp5TBdnbmRSR2NCG25rehEKQ0gXBxkYHhEKQ1kXBx0eEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxITcRsfGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdHegd1aVxEQ3obbXxTS2NcHlpEWlAZSUhec0ZfW0sHZBEKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NyW0F8EQpNXBcZGx0RCkxaF3hpa01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29va2tsa2sRCkJPF3pec0ESTxtpHEZzEQpDWhceGgQbGh0EGBkcBB sbHREKQl4XGxEKRF4XGBEKQlwXGxEKQksXaBNPUBJ8YwF+c0cRCkJJF2hpBUkaRWhhHWVvEQpCR RdvbXxiTnNvTX1PfREKQk4XaGkFSRpFaGEdZW8RCkJMF2YZcGNhUnIBWBtwEQpCbBdsTUFFQE5b b1lLchEKQkAXbhkTQFgTHl0YQF4RCkJYF2dzZXNAbmFhTF1iEQpaWBccEQp5QxdlEmBDGWd8YGM SSREKcGgXYBJ6QnNpax9vfWYQGRoRCnBoF2liZAF6fmYaBR5IEBkaEQpwaBdpBR0ZTAVTf29sZR AZGhEKcGgXbFBEaFoee2xnTk8QGRoRCnBoF2FcfgVBUGxETmRNEBkaEQpwfRdkXxlDZBNlWHsbG xAbEhEKcH0XbEYYYH9/WlBjel0QGRoRCnB9F2V4E2sdehtaHktyEBkaEQpwfRdga31gemUZBXAb UxAbEhEKcH0XZkNvehxtBXoBQmYQGxIRCnB9F2ZAYgVGYx19XFtuEBkaEQpwfxdtRF9GRW19SHk 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challenging as you have found. Unfortunately, there=E2=80=99s no qu= ick solution. Ideally, you would find a way to avoid it altogether, just u= sing the output of CHARMM-GUI directly. We find this is sufficient for alm= ost all of our use cases. If all you need is to combine parts of your system, you can do this without= the trouble of rebuilding by using the =E2=80=9Creadpsf ___.psf pdb ___.p= db=E2=80=9D command in psfgen. This will just take the parameters and coor= dinates directly from the CHARMM-GUI output without modifying anything. Best, JC On Aug 26, 2021, at 9:14 PM, Mohammad Mehdi Pirnia > wrote: Dear users, Please see the output below and all my codes and files uploaded in the link= at the bottom. psfgen) $Id: top_allxx_sugar.inp,v 1.106 2014/08/19 19:07:43 alex Exp $ psfgen) >>>>>>>>>>>> All-hydrogen topologies used in the <<<<<<<<<<<<<<<< psfgen) >>>>> development of the CHARMM carbohydrate force field<<<<<<<< psfgen) >>>>>>>>>>>>>>>>>>>>>>>>> June 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< psfgen) >>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< psfgen) >>>>>>>>>> via the CHARMM web site: https://urldefense.com/v3/__htt= p://www.charmm.org__;!!DZ3fjg!vO0uc_anTOzmqkjSf2C59dllukgfC0GMxBt9EO-qGcmwD= XT6qKcK82D60kuBPnFWHA$ <<<<<<<<<<<<<< psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<< psfgen) psfgen) Created by CHARMM version 32 1 psfgen) reading topology file ../temporary2/toppar_all36_lipid_lps.str psfgen) reading topology from stream file psfgen) Topology for lipidA from LPS psfgen) psfgen) skipping parameters in stream file psfgen) new parametes psfgen) psfgen) reading topology file ../temporary2/toppar_all36_carb_imlab.str psfgen) reading topology from stream file psfgen) glycan chemical modification patches psfgen) psfgen) Created by CHARMM version 41 1 psfgen) cross-term entries present in topology definitions psfgen) skipping parameters in stream file psfgen) glycan chemical modification patches psfgen) 2.0 psfgen) building segment L psfgen) reading residues from pdb file upper_leaflet.pdb psfgen) extracted 540 residues from pdb file Info: generating structure... psfgen) unknown atom type H psfgen) add atom failed in residue ECLI:1 Segmentation fault (core dumped) ---------------------------- I've been getting this error for days. I didn't see anything wrong with my = stream files and atom type H is definitely defined! I'm simulating peptide interactions with a bacterial membrane. I used https= ://urldefense.com/v3/__http://www.charmm-gui.org__;!!DZ3fjg!vO0uc_anTOzmqkj= Sf2C59dllukgfC0GMxBt9EO-qGcmwDXT6qKcK82D60kvsyb-qHw$ in order to build my membrane and it = includes LPSA, PMCL, PMPE, PMPG, PVPE, and PVPG. - Is there a way to create such membranes using VMD? I just saw POPC and PO= PE in the membrane builder. - After downloading, I modified all residues' res-numbers to be consecutive= , they were repetitive. Now, I'm trying to create my membrane's PSF file. T= he output is shown below. my VMD version is 1.9.4a.51 Here is the link on which I've uploaded all my files: https://urldefense.com/v3/__https://files.fm/u/bcvap3g8g__;!!DZ3fjg!vO0uc_a= nTOzmqkjSf2C59dllukgfC0GMxBt9EO-qGcmwDXT6qKcK82D60ktIPKOTWA$ Thank you all Sincerely Adam --_000_DA02A6EFC90649BFBCD711EA9551E17Bphysicsgatechedu_ Content-Type: text/html; charset="utf-8" Content-ID: Content-Transfer-Encoding: base64 PGh0bWw+DQo8aGVhZD4NCjxtZXRhIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSIgY29udGVudD0i dGV4dC9odG1sOyBjaGFyc2V0PXV0Zi04Ij4NCjwvaGVhZD4NCjxib2R5IHN0eWxlPSJ3b3JkLXdy YXA6IGJyZWFrLXdvcmQ7IC13ZWJraXQtbmJzcC1tb2RlOiBzcGFjZTsgbGluZS1icmVhazogYWZ0 ZXItd2hpdGUtc3BhY2U7IiBjbGFzcz0iIj4NCkhpIEFkYW0sDQo8ZGl2IGNsYXNzPSIiPjxiciBj bGFzcz0iIj4NCjwvZGl2Pg0KPGRpdiBjbGFzcz0iIj5SZWJ1aWxkaW5nIGEgUFNGIGZyb20gQ0hB Uk1NLUdVSSBvdXRwdXQgaXMgY2VydGFpbmx5IHBvc3NpYmxlLCBidXQgaXMgb2Z0ZW4gcXVpdGUg Y2hhbGxlbmdpbmcgYXMgeW91IGhhdmUgZm91bmQuICZuYnNwO1VuZm9ydHVuYXRlbHksIHRoZXJl 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multipart/alternative; boundary="000000000000c0922a05cac73f90" X-Proofpoint-ORIG-GUID: wLJjkDsRll7moc7lI91mhpDxbrNgwITA X-CLX-Shades: MLX X-Proofpoint-GUID: wLJjkDsRll7moc7lI91mhpDxbrNgwITA X-CLX-Response: 1TFkXExIRCkx6FxkZHBEKWUQXbAFvYRsdTnN+ZlgRClhYF2dQTWxPUxpzGl9 PEQp4ThdjU2NrexNYfhpfXhEKeUwXYXBibXpbSEN6Q20RCkNIFwcSEhEKQ1kXBxsSGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3Bh0ScR8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XXWZgQEFuWXhGRh1HRUkdRmMTG0dCWm5SSFhkTV1jfmsRClhcFx8EGgQYGRkFGxoE GxsaBB8aBBseGBAbHhofGhEKXlkXc3NFQBMRCk1cFxsZHREKTFoXaGlNa2sRCkxGF29ra2traxE KQk8XbHsYcF5FXmRCE0kRCkNaFxgaEwQSHwQYGx4EGxIaEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2IdS3pbZExiYGZlEQpCThdjU2NrexNYf hpfXhEKQkwXZ1BNbE9TGnMaX08RCkJsF2lNeEAFenkfHltrEQpCQBduQGBcZUhtUmxueBEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2h4b0lFHG9tXmVvEQpwaBdoG04YYm9IUlhuYhA ZGhEKcGgXbhN8AWRpWF1uR2YQGRoRCnBoF2dTTFNleR5CeXpQEBkaEQpwaBdoRx9AGmJ5b1BiEh 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Now I want to calculate the binding free energy for my ligand and protein. I am new to using In NAMD so I don't have any idea how to approach it. In AMBER we can use MMPBSA.py for free energy calculation that I know. What is the alternative for this in NAMD? It will be really helpful if I can get any insight on this. Thank you Regards, Nancy --000000000000c0922a05cac73f90 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hii,
I have done simulations for my protein-ligand= complex for 20ns. Now I want to calculate the binding free energy for my l= igand and protein. I am new to using In=C2=A0 NAMD so I don't have any = idea how to approach it. In AMBER we can use=C2=A0MMPBSA.py for free energy= =C2=A0calculation that=C2=A0I=C2=A0know.
What is the alternative = for this in NAMD? It will be really helpful if I can get any insight on thi= s.
Thank you



Regards,
Nancy
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charset="UTF-8" Look for the Cafe plugin for VMD to use MMPBSA. there is also a new binding free energy estimator in the alpha versions of the latest VMD but it is not MMPBSA based. On Mon, 30 Aug, 2021, 7:32 pm Nancy Singh, wrote: > Hii, > I have done simulations for my protein-ligand complex for 20ns. Now I want > to calculate the binding free energy for my ligand and protein. I am new to > using In NAMD so I don't have any idea how to approach it. In AMBER we can > use MMPBSA.py for free energy calculation that I know. > What is the alternative for this in NAMD? It will be really helpful if I > can get any insight on this. > Thank you > > > > Regards, > Nancy > --0000000000006f418e05cac76075 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Look for the Cafe plugin for VMD to use MMPBSA. there is = also a new binding free energy estimator in the alpha versions of the lates= t VMD but it is not MMPBSA based.

On Mon, 30 Aug, 2021, 7:32 pm Nancy Singh,= <kapoornancy25@gmail.com= > wrote:
Hii,
I have done simulations for my protein-ligand complex for 20ns. Now = I want to calculate the binding free energy for my ligand and protein. I am= new to using In=C2=A0 NAMD so I don't have any idea how to approach it= . In AMBER we can use=C2=A0MMPBSA.py for free energy=C2=A0calculation that= =C2=A0I=C2=A0know.
What is the alternative for this in NAMD? It w= ill be really helpful if I can get any insight on this.
Thank you=



Regards,
= Nancy
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boundary="000000000000b4225d05caec7fd2" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0cEQpMehcYExkRCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHHh4bEQpDWRcHGxIdEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccRkfEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2lEXQdQRV5pW3V5GAdzWmBhbl9LRhlsHkJsBxNzWXJ9EQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NwekRcEQpNXBcZGxoRCkxaF2hpa01NEQpMRhdva2t ra2sRCkJPF2IZQmccRXNjW0FgEQpDWhcYGhMEEh8EGBsdBB8eEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF298TxtvXkVfchgYEQpCThdjU2Nre xNYfhpfXhEKQkwXaHp7YG5wUnNwWl8RCkJsF29QBX9PYWYZT0VyEQpCQBdvekR9Z0AZaW9AAREK QlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF21DGUgcHHBJUllfEQpwaBdmG3JAEhhPZkdHRhAZGhE KcGgXYWh4QXxga3IBWXgQGRoRCnBoF3pNeVJISWRGaEUdEBkaEQpwaBduU21Jc39ua2hTHRAZGh EKcGgXZ0JjZwFtAUloS10QGRoRCnB9F2MdcntzQksFfmVoEBkaEQpwfRdvWktpQRpHengTSBAZG hEKcH8XZVhyGB1JGF5GaXwQGxsSEQpwXxdoQHhpf29IQkIfaxAZGhEKcH8XZhISeRwTEm9jHB0Q EhgRCnBfF29aS2lBGkd6eBNIEBkaEQpwbBdsUh1baWZsXnJIYRAZGhEKcEwXbWhlGUFSfXsYRVI QGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: Cnw-zotCq_S2-YpJKDual3F4hF-9YsXW X-Proofpoint-ORIG-GUID: Cnw-zotCq_S2-YpJKDual3F4hF-9YsXW MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=293 spamscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 malwarescore=0 phishscore=0 impostorscore=0 clxscore=176 mlxlogscore=583 suspectscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2109010060 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --000000000000b4225d05caec7fd2 Content-Type: text/plain; charset="UTF-8" Dear All, I want to perform a replica-exchange umbrella sampling (reUS) on a system composed of a nanotube and an amino acid solvated in water using a polarizable force field (Drude). I did the standard MD of the system with no problem using NAMD 2.14. The collective variable for my system is the radial distance of the mass center of amino acid from the mass center of the carbon nanotube. Collective variable is divided by 10 windows. As soon as, I perform the reUS simulation I get the following error: colvars: Collective variables biases initialized, 2 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 344 atoms in total). colvars: updating grid object data (0 grid objects in total). colvars: Re-initialized atom group for variable "Translocation":0/0. 24 atoms: total mass = 154.105, total charge = -0.279001. colvars: Re-initialized atom group for variable "Translocation":0/1. 320 atoms: total mass = 1921.76, total charge = 5.91999. colvars: The final output state file will be "output/0/win-out.job0.0.colvars.state". colvars: Opening trajectory file "output/0/win-out.job0.0.colvars.traj". colvars: Redefining the Tcl "cv" command to the new script interface. Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use Info: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use Info: Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use Info: Finished startup at 26.3569 s, 67.6719 MB of memory in use colvars: # centers = { 6.7 } colvars: # forceConstant = 0.025 [default] TCL: Running for 1000 steps colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 344 atoms in total). colvars: updating grid object data (0 grid objects in total). colvars: Re-initialized atom group for variable "Translocation":0/0. 24 atoms: total mass = 154.105, total charge = -0.279001. colvars: Re-initialized atom group for variable "Translocation":0/1. 320 atoms: total mass = 1921.76, total charge = 5.91999. colvars: The final output state file will be "output/0/win-out.job0.0.colvars.state". FATAL ERROR: Bad global Thole count! (0 vs 707) FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html [Partition 0][Node 0] End of program I have to say that the collective variable is considered to be the mass center of a group of atoms with no lone-pair. Since the lone-pairs are massless. Here is the collective variable conformation file (US-base.in): colvarsTrajFrequency 100 colvar { name Translocation width 0.1 lowerboundary 4.5 upperboundary 18.8 lowerwall 6.5 upperwall 16.8 lowerwallconstant 100.0 upperwallconstant 100.0 distanceXY { main { atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 32 34 35 37 38 } } ref { atomnumbers { 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360} } axis ( 0.0, 0.0, 1.0 ) } } harmonic { name Z colvars Translocation centers 0.0 forceConstant 0.025;# 2.5 * 0.1^2 = 0.025 } Here is the NAMD configuration file to run the simulation: structure input/rm-bonds-modified.psf ###coordinates input/start%d.pdb paraTypeCharmm on parameters toppar_drude/toppar_drude_master_protein_2019g.str; parameters toppar_drude/toppar_drude_lipid_2017c.str; parameters toppar_drude/toppar_drude_model_2019g.str; parameters toppar_drude/toppar_drude_carbohydrate_2019a.str; parameters toppar_drude/toppar_drude_nucleic_acid_2017c.str; # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on ##vdwForceSwitching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 1.0 ;# 1fs/step (only if needed to finish quickly) #rigidBonds water nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 # Constant Temperature Control langevin on ;# do langevin dynamicsgmail.google.com langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions #cellBasisVector1 61.5 0. 0. #cellBasisVector2 0. 61.5 0. #cellBasisVector3 0. 0 71.5 #cellOrigin -16.06 -14.75 -12 #wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 # Constant Pressure Control (variable volume) useGroupPressure yes useConstantArea yes useFlexibleCell yes margin 5 Would be very much grateful if somebody could guide me.. All the best, Zeynab --000000000000b4225d05caec7fd2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear All,

I want to perform a replica-e= xchange umbrella sampling (reUS) on a system composed of a nanotube and an = amino acid solvated in water using a polarizable force field (Drude). I did= the standard MD of the system with no problem using NAMD 2.14. The collect= ive=C2=A0variable=C2=A0for my system is the radial distance of the mass cen= ter of amino acid from the mass center of the carbon nanotube. Collective v= ariable is divided=C2=A0by 10 windows. As soon as, I perform=C2=A0the reUS = simulation I get the following error:

colvars: Col= lective variables biases initialized, 2 in total.
colvars: -------------= ---------------------------------------------------------
colvars: Colle= ctive variables module (re)initialized.
colvars: -----------------------= -----------------------------------------------
colvars: Updating NAMD i= nterface:
colvars: updating atomic data (0 atoms).
colvars: updating = group data (2 scalable groups, 344 atoms in total).
colvars: updating gr= id object data (0 grid objects in total).
colvars: Re-initialized atom g= roup for variable "Translocation":0/0. 24 atoms: total mass =3D 1= 54.105, total charge =3D -0.279001.
colvars: Re-initialized atom group f= or variable "Translocation":0/1. 320 atoms: total mass =3D 1921.7= 6, total charge =3D 5.91999.
colvars: The final output state file will b= e "output/0/win-out.job0.0.colvars.state".
colvars: Opening tr= ajectory file "output/0/win-out.job0.0.colvars.traj".
colvars:= Redefining the Tcl "cv" command to the new script interface.
= Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use
In= fo: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use
Info= : Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use
Info: = Finished startup at 26.3569 s, 67.6719 MB of memory in use

colvars: = =C2=A0 # centers =3D { 6.7 }
colvars: =C2=A0 # forceConstant =3D 0.025 [= default]
TCL: Running for 1000 steps
colvars: Updating NAMD interface= :
colvars: updating atomic data (0 atoms).
colvars: updating group da= ta (2 scalable groups, 344 atoms in total).
colvars: updating grid objec= t data (0 grid objects in total).
colvars: Re-initialized atom group for= variable "Translocation":0/0. 24 atoms: total mass =3D 154.105, = total charge =3D -0.279001.
colvars: Re-initialized atom group for varia= ble "Translocation":0/1. 320 atoms: total mass =3D 1921.76, total= charge =3D 5.91999.
colvars: The final output state file will be "= output/0/win-out.job0.0.colvars.state".
FATAL ERROR: Bad global Tho= le count! (0 vs 707)

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugr= eport.html
[Partition 0][Node 0] End of program

I have to say that the collective variable is considered to be the= mass center of a group of atoms with no lone-pair. Since the lone-pairs ar= e massless.=C2=A0
Here is the collective variable conformation fi= le (US-base.in):
colvarsTrajFrequency =C2=A0 =C2=A0 =C2=A0 =C2=A0= 100

colvar {
=C2=A0 =C2=A0name Translocation
=C2=A0 =C2=A0widt= h 0.1
=C2=A0 =C2=A0lowerboundary =C2=A0 =C2=A04.5
=C2=A0 =C2=A0upperb= oundary =C2=A0 =C2=A018.8
=C2=A0 =C2=A0lowerwall =C2=A0 =C2=A06.5
= =C2=A0 =C2=A0upperwall =C2=A0 16.8
=C2=A0 =C2=A0lowerwallconstant 100.0<= br>=C2=A0 =C2=A0upperwallconstant 100.0

=C2=A0 =C2=A0distanceXY {=C2=A0 =C2=A0 =C2=A0 main {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbe= rs {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 32 34 35 37 38 }=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 ref =C2=A0{
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0atomnumbers {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64= 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89= 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 = 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129= 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 14= 8 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 1= 67 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 = 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204= 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 22= 3 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 2= 42 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 = 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279= 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 29= 8 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 3= 17 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 = 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354= 355 356 357 358 359 360}
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0= axis =C2=A0( 0.0, =C2=A00.0, 1.0 )
=C2=A0 =C2=A0}
}

harmonic = {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 name Z
colvars Translocation
=C2=A0= =C2=A0 =C2=A0 =C2=A0 centers 0.0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 forceConst= ant 0.025;# 2.5 * 0.1^2 =3D 0.025
}



=C2=A0Here is the NAMD configuration file to run the= simulation:
structure =C2=A0 =C2=A0 =C2=A0 =C2=A0 input/rm-bonds= -modified.psf
###coordinates =C2=A0 =C2=A0 =C2=A0 =C2=A0input/start%d.pd= b

paraTypeCharmm on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= toppar_drude/toppar_drude_master_protein_2019g.str;
parameters =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_lipid_2017c.str;
pa= rameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_model_= 2019g.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/top= par_drude_carbohydrate_2019a.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0toppar_drude/toppar_drude_nucleic_acid_2017c.str;


# Force= -Field Parameters
exclude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scal= ed1-4
1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
cutoff =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012.
switching =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 on
##vdwForceSwitching =C2=A0 on
switchdist =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A010.
pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A01= 3.5


# Integrator Parameters
timestep =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A01.0 =C2=A0;# 1fs/step (only if needed to finish quickly)#rigidBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0water =C2=A0
nonbondedFr= eq =C2=A0 =C2=A0 =C2=A0 2
fullElectFrequency =C2=A04 =C2=A0
stepsperc= ycle =C2=A0 =C2=A0 =C2=A0 20


# Constant Temperature Control
l= angevin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on =C2=A0 =C2=A0;# do lang= evin dynamicsgmail.google.com
langevinDamping =C2=A0 =C2=A0 1 =C2= =A0 =C2=A0 ;# damping coefficient (gamma) of 5/ps
langevinTemp =C2=A0 = =C2=A0 =C2=A0 =C2=A0$temperature
langevinHydrogen =C2=A0 =C2=A0off =C2= =A0 =C2=A0;# don't couple langevin bath to hydrogens

# Periodic = Boundary Conditions =C2=A0
#cellBasisVector1 =C2=A0 61.5 =C2=A0 =C2=A00.= =C2=A0 0.
#cellBasisVector2 =C2=A0 =C2=A0 0. =C2=A0 61.5 =C2=A0 0.
#= cellBasisVector3 =C2=A0 =C2=A0 0. =C2=A0 =C2=A00 =C2=A0 =C2=A071.5
#cell= Origin =C2=A0 =C2=A0 =C2=A0 =C2=A0-16.06 -14.75 -12

#wrapAll =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on

# PME (for full-system periodi= c electrostatics)
PME =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 yes
PMEGridSpacing =C2=A0 =C2=A0 =C2=A01.0

# Constant Pres= sure Control (variable volume)
useGroupPressure =C2=A0 =C2=A0 yes
use= ConstantArea =C2=A0 =C2=A0 =C2=A0yes
useFlexibleCell =C2=A0 =C2=A0 =C2= =A0yes
margin 5


Would be ver= y much grateful if somebody could guide me..

All t= he best,
Zeynab
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Wed, 1 Sep 2021 16:25:17 +0000 From: HANNAH MARIE BURTON To: "namd-l@ks.uiuc.edu" Subject: namd-l: Modifying a DRUDE pdb file and producing a new psf file Thread-Topic: Modifying a DRUDE pdb file and producing a new psf file Thread-Index: AQHXn02C4XXskqlHL0K0RXi2ULzszQ== Date: Wed, 1 Sep 2021 16:25:17 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=utah.edu; x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: c5f00b12-b252-4930-d001-08d96d6515e6 x-ms-traffictypediagnostic: MN2PR11MB4256: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:8882; x-ms-exchange-senderadcheck: 1 x-ms-exchange-antispam-relay: 0 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:MN2PR11MB4349.namprd11.prod.outlook.com;PTR:;CAT:NONE;SFS:(4636009)(376002)(39860400002)(366004)(396003)(346002)(136003)(52536014)(8676002)(7696005)(38070700005)(91956017)(76116006)(66946007)(122000001)(8936002)(66476007)(38100700002)(66556008)(66446008)(6916009)(4744005)(64756008)(478600001)(316002)(75432002)(19627405001)(2906002)(5660300002)(26005)(6506007)(86362001)(71200400001)(186003)(55016002)(9686003)(33656002);DIR:OUT;SFP:1101; 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boundary="_000_MN2PR11MB43490E22400CE040EA5EBD50E1CD9MN2PR11MB4349namp_" MIME-Version: 1.0 X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: MN2PR11MB4349.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: c5f00b12-b252-4930-d001-08d96d6515e6 X-MS-Exchange-CrossTenant-originalarrivaltime: 01 Sep 2021 16:25:17.4589 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 5217e0e7-539d-4563-b1bf-7c6dcf074f91 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: XlvrMKgWrFpEWKBjIo71avzKm8psvceiMRlHJe5HHI4ybA0GCs/FET7q1XDTEhlh5wT8wVG2Dh8BOVcG4NbBWQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: MN2PR11MB4256 X-OriginatorOrg: utah.edu X-CFilter-Loop: Reflected X-Proofpoint-GUID: b-fib7mbZISkxWLwiYbQ-B8xLDTTKVes X-Proofpoint-ORIG-GUID: b-fib7mbZISkxWLwiYbQ-B8xLDTTKVes X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBoSEQpMehceEhEKWUQXZlx8X15hBXoYWx4RClhYF2FpZ3hMe39Ie1l SEQp4Thd6fUtzRH9cU1xHGREKeUwXekFMUlwdUxpaBWMRCkNIFwcZGx0RCkNZFwcYGRsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhJxGx8aEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0gHTENIHUdIcGN5QVJ9Zl1Dc0h7B2gSUmZufn5hfE9ZEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc3B/Hn4RCk1cFxsdGhEKTFoXfGlNTWsRCkVZF28RCkx fF3oFBQUFBQUFBQVDEQpMRhdvb2tra2lrEQpCTxdmbVJ7RGgaSExYHxEKQ1oXGx8fBBMdBBseHg QfExEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXen1Lc0R/XFNcRxkRCkJJF3p9S3NEf1xTX EcZEQpCRRdhHExGc2ZpSUxvGhEKQk4Xen1Lc0R/XFNcRxkRCkJMF2FpZ3hMe39Ie1lSEQpCbBds TE4ceH8YHnhbUBEKQkAXbRNGaFB6U21iTm4RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdjeRNdG3J6cHNpcBEKWUsXGxgcHRIRCnBoF2J6SRtOQ28bTF1YEBkaEQpwaBdoQ0QSUGscY1 JCchAZGhEKcGgXZWRCR24Bbn9FZmYQGRoRCnBoF29QS2VwXEtjEx9mEBkaEQpwaBdvGUNNfWQaH FJPYRAZGhEKcGwXYF5aS2FNGXNicHMQGRoRCnBDF2ldHmYYQ2ZdTHN+EBsYHxEKbX4XGxEKWE0X SxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=48 mlxlogscore=444 lowpriorityscore=0 suspectscore=0 phishscore=0 bulkscore=0 mlxscore=0 spamscore=0 impostorscore=0 clxscore=208 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2107140000 definitions=main-2109010095 domainage_hfrom=12678 X-Spam-Score: 0 X-Spam-OrigSender: u1304129@utah.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, HANNAH MARIE BURTON --_000_MN2PR11MB43490E22400CE040EA5EBD50E1CD9MN2PR11MB4349namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hey All! I have an old drude simulation and its relevant xplor file. Everything in t= his simulation works as expected, I am implementing the correct topologies = and get good output files. However we want to add ions to this system and = cannot rebuild the system in charmm as we do not have the original pdb fil= es anymore used to generate that specific build. It is a membrane system wi= th 17 chloride ions in SWM4. How would I go about adding in new ions ,to th= is DRUDE system, and then export a new DRUDE psf file. I attempted to add ions and vmd told me that it wasnt solvated and does not= seem to be recognizing swm4 as a water molecule. Thanks, Hannah --_000_MN2PR11MB43490E22400CE040EA5EBD50E1CD9MN2PR11MB4349namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hey All!
I have an old drude simulation and its relevant xplor file. Everything in t= his simulation works as expected, I am implementing the correct topologies = and get good output files. However we want to add ions to this system and &= nbsp;cannot  rebuild the system in charmm as we do not have the original pdb files anymore used to generate that spe= cific build. It is a membrane system with 17 chloride ions in SWM4. How wou= ld I go about adding in new ions ,to this DRUDE system, and then export a n= ew DRUDE psf file. 

I attempted to add ions and vmd told me that it wasnt solvated and does not= seem to be recognizing swm4 as a water molecule. 

Thanks,
Hannah 
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boundary="00000000000008028c05cafdfe51" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwcEQpMehcZGRkRCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHHhIZEQpDWRcHGxwfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ccR8dEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1leTn5gGW5rQkhBSxscaGZJQFAcfkBlZ2l7WWVOaUVYEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc3BCE14RCk1cFx4cGhEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdgZGsfZ0QYcGYYWhEKQ1oXGBoTBBIfBBgYGA QfGhEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdvfE8bb15FX3IYGBEKQk4XY1Nja3sTWH4aX14RCkJMF2h6e2BucFJzcFpfEQpCbBdv UAV/T2FmGU9FchEKQkAXem9heV9FSHAeE2kRCkJYF2dzZXNAbmFhTF1iEQpaWBcdEQp5QxdhHV9 ORHBjQRweHBEKcGgXbhh4Z0xuUkZIZEEQGRoRCnBoF2FTWR8TE2cTQkJsEBkaEQpwaBd6TXlSSE lkRmhFHRAZGhEKcGgXZGtzWEVGZVgZXWYQGRoRCnBoF2dCY2cBbQFJaEtdEBkaEQpwfRdjHXJ7c 0JLBX5laBAZGhEKcH0XbmRHZ0kfYW1PbR0QGRoRCnB9F294WkRYTG5HSFgbEBkaEQpwfxdlWHIY HUkYXkZpfBAbGxIRCnBfF2hAeGl/b0hCQh9rEBkaEQpwfxdtRF9GRW19SHkZbhAbGBkRCnBfF2t GSxN5aGlufBN4EBMfEQpwfxdhZm9bGmdkQkgdWxAbGxwRCnBfF2NiElBIY3gffEJ9EBIfEQpwbB dsUh1baWZsXnJIYRAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: stdTJ3DAhbka16BLcjz6TjOMCQsOdCor X-Proofpoint-GUID: stdTJ3DAhbka16BLcjz6TjOMCQsOdCor X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=166 suspectscore=0 impostorscore=0 mlxscore=0 adultscore=0 spamscore=0 malwarescore=0 bulkscore=0 priorityscore=333 phishscore=0 lowpriorityscore=0 mlxlogscore=745 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109020047 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --00000000000008028c05cafdfe51 Content-Type: text/plain; charset="UTF-8" Hi Giacomo, Thank you so much for your reply. Sorry about that but unfortunately I couldn't completely understand your prescription. I made 10 windows centered at 6.7A, 6.8A, 6.9A, 7A, 8A, 9A, 11A, 13A, 15A and 17A. The output I already sent is related to window-0 centered at 6.7A. I understood to perform standard MD for each replica independently(short one)? but what do you mean by setting the centers of harmonic restraints to zero? You mean for example for the window-0 I put the center 0 instead of 6.7? That would't produce problem? All the best, Zeynab On Wed, Sep 1, 2021 at 10:01 AM Giacomo Fiorin wrote: > Hi Zeynab, I've not used yet polarizable models in NAMD, so I don't know > specifically where the error arises. Assuming that this is a symptom of an > unstable configuration, what I would try to do is doing for each replica a > short MD run of 100-1000 steps on your workstation or an interactive node. > Start with the centers of the harmonic restraints to zero as you have shown > (i.e. test the configuration of the first replica), and then do the same > for all other values that will be set by the REUS script, which will modify > that center for all other replicas. > > Giacomo > > On Wed, Sep 1, 2021 at 6:28 AM zeynab hosseini > wrote: > >> Dear All, >> >> I want to perform a replica-exchange umbrella sampling (reUS) on a system >> composed of a nanotube and an amino acid solvated in water using a >> polarizable force field (Drude). I did the standard MD of the system with >> no problem using NAMD 2.14. The collective variable for my system is the >> radial distance of the mass center of amino acid from the mass center of >> the carbon nanotube. Collective variable is divided by 10 windows. As soon >> as, I perform the reUS simulation I get the following error: >> >> colvars: Collective variables biases initialized, 2 in total. >> colvars: >> ---------------------------------------------------------------------- >> colvars: Collective variables module (re)initialized. >> colvars: >> ---------------------------------------------------------------------- >> colvars: Updating NAMD interface: >> colvars: updating atomic data (0 atoms). >> colvars: updating group data (2 scalable groups, 344 atoms in total). >> colvars: updating grid object data (0 grid objects in total). >> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >> atoms: total mass = 154.105, total charge = -0.279001. >> colvars: Re-initialized atom group for variable "Translocation":0/1. 320 >> atoms: total mass = 1921.76, total charge = 5.91999. >> colvars: The final output state file will be >> "output/0/win-out.job0.0.colvars.state". >> colvars: Opening trajectory file "output/0/win-out.job0.0.colvars.traj". >> colvars: Redefining the Tcl "cv" command to the new script interface. >> Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use >> Info: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use >> Info: Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use >> Info: Finished startup at 26.3569 s, 67.6719 MB of memory in use >> >> colvars: # centers = { 6.7 } >> colvars: # forceConstant = 0.025 [default] >> TCL: Running for 1000 steps >> colvars: Updating NAMD interface: >> colvars: updating atomic data (0 atoms). >> colvars: updating group data (2 scalable groups, 344 atoms in total). >> colvars: updating grid object data (0 grid objects in total). >> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >> atoms: total mass = 154.105, total charge = -0.279001. >> colvars: Re-initialized atom group for variable "Translocation":0/1. 320 >> atoms: total mass = 1921.76, total charge = 5.91999. >> colvars: The final output state file will be >> "output/0/win-out.job0.0.colvars.state". >> FATAL ERROR: Bad global Thole count! (0 vs 707) >> >> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html >> [Partition 0][Node 0] End of program >> >> I have to say that the collective variable is considered to be the mass >> center of a group of atoms with no lone-pair. Since the lone-pairs are >> massless. >> Here is the collective variable conformation file (US-base.in): >> colvarsTrajFrequency 100 >> >> colvar { >> name Translocation >> width 0.1 >> lowerboundary 4.5 >> upperboundary 18.8 >> lowerwall 6.5 >> upperwall 16.8 >> lowerwallconstant 100.0 >> upperwallconstant 100.0 >> >> distanceXY { >> main { >> atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 >> 32 34 35 37 38 } >> } >> ref { >> atomnumbers { >> >> 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 >> 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 >> 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 >> 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 >> 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 >> 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 >> 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 >> 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 >> 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 >> 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 >> 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 >> 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 >> 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 >> 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 >> 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 >> 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 >> 358 359 360} >> } >> axis ( 0.0, 0.0, 1.0 ) >> } >> } >> >> harmonic { >> name Z >> colvars Translocation >> centers 0.0 >> forceConstant 0.025;# 2.5 * 0.1^2 = 0.025 >> } >> >> >> >> Here is the NAMD configuration file to run the simulation: >> structure input/rm-bonds-modified.psf >> ###coordinates input/start%d.pdb >> >> paraTypeCharmm on >> parameters toppar_drude/toppar_drude_master_protein_2019g.str; >> parameters toppar_drude/toppar_drude_lipid_2017c.str; >> parameters toppar_drude/toppar_drude_model_2019g.str; >> parameters toppar_drude/toppar_drude_carbohydrate_2019a.str; >> parameters toppar_drude/toppar_drude_nucleic_acid_2017c.str; >> >> >> # Force-Field Parameters >> exclude scaled1-4 >> 1-4scaling 1.0 >> cutoff 12. >> switching on >> ##vdwForceSwitching on >> switchdist 10. >> pairlistdist 13.5 >> >> >> # Integrator Parameters >> timestep 1.0 ;# 1fs/step (only if needed to finish quickly) >> #rigidBonds water >> nonbondedFreq 2 >> fullElectFrequency 4 >> stepspercycle 20 >> >> >> # Constant Temperature Control >> langevin on ;# do langevin dynamicsgmail.google.com >> >> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps >> langevinTemp $temperature >> langevinHydrogen off ;# don't couple langevin bath to hydrogens >> >> # Periodic Boundary Conditions >> #cellBasisVector1 61.5 0. 0. >> #cellBasisVector2 0. 61.5 0. >> #cellBasisVector3 0. 0 71.5 >> #cellOrigin -16.06 -14.75 -12 >> >> #wrapAll on >> >> # PME (for full-system periodic electrostatics) >> PME yes >> PMEGridSpacing 1.0 >> >> # Constant Pressure Control (variable volume) >> useGroupPressure yes >> useConstantArea yes >> useFlexibleCell yes >> margin 5 >> >> >> Would be very much grateful if somebody could guide me.. >> >> All the best, >> Zeynab >> > --00000000000008028c05cafdfe51 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Giacomo,

Thank you so much for your = reply. Sorry about that but unfortunately I couldn't completely underst= and your prescription. I made 10 windows=C2=A0centered at 6.7A, 6.8A, 6.9A,= 7A, 8A, 9A, 11A, 13A, 15A and 17A. The output I already sent is related to= window-0 centered at 6.7A. I understood to perform=C2=A0standard MD for ea= ch replica independently(short one)? but what do you mean by setting the ce= nters of harmonic restraints to zero? You mean for example for the window-0= I put the center 0 instead of 6.7? That would't produce problem?

All the best,
Zeynab

On Wed, Sep 1, = 2021 at 10:01 AM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
Hi Zeynab, I've not used = yet polarizable models in NAMD, so I don't know specifically where the = error arises.=C2=A0 Assuming that this is a symptom=C2=A0of an unstable con= figuration, what I would try to do is doing for each replica a short MD run= of 100-1000 steps on your workstation or an interactive node.=C2=A0 Start = with the centers of the harmonic restraints to zero as you have shown (i.e.= test the configuration of the first replica), and then do the same for all= other values that will be set by the REUS script, which will modify that c= enter for all other replicas.

Giacomo

On Wed, Sep 1= , 2021 at 6:28 AM zeynab hosseini <hosseinizeynab93@gmail.com> wrote:
Dear = All,

I want to perform a replica-exchange umbrella sampl= ing (reUS) on a system composed of a nanotube and an amino acid solvated in= water using a polarizable force field (Drude). I did the standard MD of th= e system with no problem using NAMD 2.14. The collective=C2=A0variable=C2= =A0for my system is the radial distance of the mass center of amino acid fr= om the mass center of the carbon nanotube. Collective variable is divided= =C2=A0by 10 windows. As soon as, I perform=C2=A0the reUS simulation I get t= he following error:

colvars: Collective variables = biases initialized, 2 in total.
colvars: -------------------------------= ---------------------------------------
colvars: Collective variables mo= dule (re)initialized.
colvars: -----------------------------------------= -----------------------------
colvars: Updating NAMD interface:
colva= rs: updating atomic data (0 atoms).
colvars: updating group data (2 scal= able groups, 344 atoms in total).
colvars: updating grid object data (0 = grid objects in total).
colvars: Re-initialized atom group for variable = "Translocation":0/0. 24 atoms: total mass =3D 154.105, total char= ge =3D -0.279001.
colvars: Re-initialized atom group for variable "= Translocation":0/1. 320 atoms: total mass =3D 1921.76, total charge = =3D 5.91999.
colvars: The final output state file will be "output/0= /win-out.job0.0.colvars.state".
colvars: Opening trajectory file &q= uot;output/0/win-out.job0.0.colvars.traj".
colvars: Redefining the = Tcl "cv" command to the new script interface.
Info: Startup ph= ase 13 took 0.00555027 s, 66.3516 MB of memory in use
Info: Startup phas= e 14 took 5.4094e-05 s, 66.3516 MB of memory in use
Info: Startup phase = 15 took 4.1293e-05 s, 67.6719 MB of memory in use
Info: Finished startup= at 26.3569 s, 67.6719 MB of memory in use

colvars: =C2=A0 # centers= =3D { 6.7 }
colvars: =C2=A0 # forceConstant =3D 0.025 [default]
TCL:= Running for 1000 steps
colvars: Updating NAMD interface:
colvars: up= dating atomic data (0 atoms).
colvars: updating group data (2 scalable g= roups, 344 atoms in total).
colvars: updating grid object data (0 grid o= bjects in total).
colvars: Re-initialized atom group for variable "= Translocation":0/0. 24 atoms: total mass =3D 154.105, total charge =3D= -0.279001.
colvars: Re-initialized atom group for variable "Transl= ocation":0/1. 320 atoms: total mass =3D 1921.76, total charge =3D 5.91= 999.
colvars: The final output state file will be "output/0/win-out= .job0.0.colvars.state".
FATAL ERROR: Bad global Thole count! (0 vs = 707)

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bu= greport.html
[Partition 0][Node 0] End of program

=
I have to say that the collective variable is considered to be t= he mass center of a group of atoms with no lone-pair. Since the lone-pairs = are massless.=C2=A0
Here is the collective variable conformation = file (US-base.in):
colvarsTrajFrequency =C2=A0 =C2=A0 =C2=A0 =C2= =A0100

colvar {
=C2=A0 =C2=A0name Translocation
=C2=A0 =C2=A0w= idth 0.1
=C2=A0 =C2=A0lowerboundary =C2=A0 =C2=A04.5
=C2=A0 =C2=A0upp= erboundary =C2=A0 =C2=A018.8
=C2=A0 =C2=A0lowerwall =C2=A0 =C2=A06.5=C2=A0 =C2=A0upperwall =C2=A0 16.8
=C2=A0 =C2=A0lowerwallconstant 100.0=
=C2=A0 =C2=A0upperwallconstant 100.0

=C2=A0 =C2=A0distanceXY {=C2=A0 =C2=A0 =C2=A0 main {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumb= ers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 32 34 35 37 38 }=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 ref =C2=A0{
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0atomnumbers {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64= 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89= 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 = 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129= 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 14= 8 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 1= 67 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 = 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204= 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 22= 3 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 2= 42 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 = 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279= 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 29= 8 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 3= 17 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 = 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354= 355 356 357 358 359 360}
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0= axis =C2=A0( 0.0, =C2=A00.0, 1.0 )
=C2=A0 =C2=A0}
}

harmonic = {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 name Z
colvars Translocation
=C2=A0= =C2=A0 =C2=A0 =C2=A0 centers 0.0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 forceConst= ant 0.025;# 2.5 * 0.1^2 =3D 0.025
}



=C2=A0Here is the NAMD configuration file to run the= simulation:
structure =C2=A0 =C2=A0 =C2=A0 =C2=A0 input/rm-bonds= -modified.psf
###coordinates =C2=A0 =C2=A0 =C2=A0 =C2=A0input/start%d.pd= b

paraTypeCharmm on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= toppar_drude/toppar_drude_master_protein_2019g.str;
parameters =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_lipid_2017c.str;
pa= rameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_model_= 2019g.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/top= par_drude_carbohydrate_2019a.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0toppar_drude/toppar_drude_nucleic_acid_2017c.str;


# Force= -Field Parameters
exclude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scal= ed1-4
1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
cutoff =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012.
switching =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 on
##vdwForceSwitching =C2=A0 on
switchdist =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A010.
pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A01= 3.5


# Integrator Parameters
timestep =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A01.0 =C2=A0;# 1fs/step (only if needed to finish quickly)#rigidBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0water =C2=A0
nonbondedFr= eq =C2=A0 =C2=A0 =C2=A0 2
fullElectFrequency =C2=A04 =C2=A0
stepsperc= ycle =C2=A0 =C2=A0 =C2=A0 20


# Constant Temperature Control
l= angevin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on =C2=A0 =C2=A0;# do lang= evin dynamicsgmail.google.com
langevinDamping =C2= =A0 =C2=A0 1 =C2=A0 =C2=A0 ;# damping coefficient (gamma) of 5/ps
langev= inTemp =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature
langevinHydrogen =C2=A0 = =C2=A0off =C2=A0 =C2=A0;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions =C2=A0
#cellBasisVector1 =C2=A0 61.5 = =C2=A0 =C2=A00. =C2=A0 0.
#cellBasisVector2 =C2=A0 =C2=A0 0. =C2=A0 61.5= =C2=A0 0.
#cellBasisVector3 =C2=A0 =C2=A0 0. =C2=A0 =C2=A00 =C2=A0 =C2= =A071.5
#cellOrigin =C2=A0 =C2=A0 =C2=A0 =C2=A0-16.06 -14.75 -12

= #wrapAll =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on

# PME (for ful= l-system periodic electrostatics)
PME =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 yes
PMEGridSpacing =C2=A0 =C2=A0 =C2=A01.0

= # Constant Pressure Control (variable volume)
useGroupPressure =C2=A0 = =C2=A0 yes
useConstantArea =C2=A0 =C2=A0 =C2=A0yes
useFlexibleCell = =C2=A0 =C2=A0 =C2=A0yes
margin 5


=
Would be very much grateful if somebody could guide me..
All the best,
Zeynab
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Thu, 02 Sep 2021 02:40:46 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Hemanth Haridas Date: Thu, 2 Sep 2021 15:06:46 +0530 Message-ID: Subject: Re: namd-l: Problem with running replica-exchange umbrella sampling of polarizable system To: namd-l@ks.uiuc.edu, zeynab hosseini Content-Type: multipart/alternative; boundary="0000000000002f5f6205cafffacd" X-CLOUD-SEC-AV-Sent: true X-CLOUD-SEC-AV-Info: iitgn,google_mail,monitor X-Gm-Spam: 0 X-Gm-Phishy: 0 X-Proofpoint-GUID: wy-hnhok9slCCnqQnqPiXyWeFwUaxcuC X-Proofpoint-ORIG-GUID: wy-hnhok9slCCnqQnqPiXyWeFwUaxcuC X-CLX-Response: 1TFkXGxIZEQpMehcaEQpZRBd6TGFZQlJpY2BGHxEKWFgXaUVcWHhmZhsYXxk RCnhOF2dpW2ZtYl9AGwFjEQp5TBdkbEseZX4TYmxkfhEKQ0gXBx4TGREKQ1kXBxscHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGXESHxAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThddUwdCREJFQRNZRmlpRFt7RFt6Q3JTfU9sXX9LUklfaREKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzcEFpHBEKTVwXHx8TEQpMWhd7aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2ZMH01pbUFAHxNzEQpDWhcYGhMEEh8EGxwdBBsdEx EKQl4XGxEKRF4XGBEKQkUXYkdgb3IBXFpcHW0RCkJOF2dpW2ZtYl9AGwFjEQpCTBdpRVxYeGZmG xhfGREKQmwXZkdpBWV4Uh9sek4RCkJAF3pvYXlfRUhwHhNpEQpCWBdnc2VzQG5hYUxdYhEKWlgX HREKeUMXYR1fTkRwY0EcHhwRCllLFx4cHxIRCnBnF2xSZGBwAVoaYkV4EBkaEQpwaBduGHhnTG5 SRkhkQRAeEhEKcGgXYVNZHxMTZxNCQmwQHhIRCnBoF3pNeVJISWRGaEUdEB4SEQpwaBdka3NYRU ZlWBldZhAeEhEKcGgXb2lsclkaZ14fU1kQGRoRCnBnF25Be39+WUJGAWZmEBkaEQpwfRdjHXJ7c 0JLBX5laBAeEhEKcH0XbmRHZ0kfYW1PbR0QHhIRCnB9F294WkRYTG5HSFgbEB4SEQpwfxdlWHIY HUkYXkZpfBAbHhkRCnBfF2hAeGl/b0hCQh9rEB4SEQpwfxdtRF9GRW19SHkZbhAbGB4RCnBfF2t GSxN5aGlufBN4EBMZEQpwfxdhZm9bGmdkQkgdWxAbGxwRCnBfF2NiElBIY3gffEJ9EBIZEQpwbB dnZAVneBxIS29TcBAZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=898 bulkscore=0 mlxscore=0 priorityscore=0 adultscore=0 malwarescore=0 impostorscore=0 spamscore=0 lowpriorityscore=0 suspectscore=0 clxscore=183 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109020059 domainage_hfrom=4658 X-Spam-Score: 0 X-Spam-OrigSender: hemanth.h@iitgn.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hemanth Haridas --0000000000002f5f6205cafffacd Content-Type: text/plain; charset="UTF-8" Dear Zeynab, Can you please post the psf and the input file that you used. I have some experience in setting up and running umbrella sampling simulations using Drude FF. On Thu, Sep 2, 2021 at 12:51 PM zeynab hosseini wrote: > Hi Giacomo, > > Thank you so much for your reply. Sorry about that but unfortunately I > couldn't completely understand your prescription. I made 10 > windows centered at 6.7A, 6.8A, 6.9A, 7A, 8A, 9A, 11A, 13A, 15A and 17A. > The output I already sent is related to window-0 centered at 6.7A. I > understood to perform standard MD for each replica independently(short > one)? but what do you mean by setting the centers of harmonic restraints to > zero? You mean for example for the window-0 I put the center 0 instead of > 6.7? That would't produce problem? > > All the best, > Zeynab > > On Wed, Sep 1, 2021 at 10:01 AM Giacomo Fiorin > wrote: > >> Hi Zeynab, I've not used yet polarizable models in NAMD, so I don't know >> specifically where the error arises. Assuming that this is a symptom of an >> unstable configuration, what I would try to do is doing for each replica a >> short MD run of 100-1000 steps on your workstation or an interactive node. >> Start with the centers of the harmonic restraints to zero as you have shown >> (i.e. test the configuration of the first replica), and then do the same >> for all other values that will be set by the REUS script, which will modify >> that center for all other replicas. >> >> Giacomo >> >> On Wed, Sep 1, 2021 at 6:28 AM zeynab hosseini < >> hosseinizeynab93@gmail.com> wrote: >> >>> Dear All, >>> >>> I want to perform a replica-exchange umbrella sampling (reUS) on a >>> system composed of a nanotube and an amino acid solvated in water using a >>> polarizable force field (Drude). I did the standard MD of the system with >>> no problem using NAMD 2.14. The collective variable for my system is the >>> radial distance of the mass center of amino acid from the mass center of >>> the carbon nanotube. Collective variable is divided by 10 windows. As soon >>> as, I perform the reUS simulation I get the following error: >>> >>> colvars: Collective variables biases initialized, 2 in total. >>> colvars: >>> ---------------------------------------------------------------------- >>> colvars: Collective variables module (re)initialized. >>> colvars: >>> ---------------------------------------------------------------------- >>> colvars: Updating NAMD interface: >>> colvars: updating atomic data (0 atoms). >>> colvars: updating group data (2 scalable groups, 344 atoms in total). >>> colvars: updating grid object data (0 grid objects in total). >>> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >>> atoms: total mass = 154.105, total charge = -0.279001. >>> colvars: Re-initialized atom group for variable "Translocation":0/1. 320 >>> atoms: total mass = 1921.76, total charge = 5.91999. >>> colvars: The final output state file will be >>> "output/0/win-out.job0.0.colvars.state". >>> colvars: Opening trajectory file "output/0/win-out.job0.0.colvars.traj". >>> colvars: Redefining the Tcl "cv" command to the new script interface. >>> Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use >>> Info: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use >>> Info: Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use >>> Info: Finished startup at 26.3569 s, 67.6719 MB of memory in use >>> >>> colvars: # centers = { 6.7 } >>> colvars: # forceConstant = 0.025 [default] >>> TCL: Running for 1000 steps >>> colvars: Updating NAMD interface: >>> colvars: updating atomic data (0 atoms). >>> colvars: updating group data (2 scalable groups, 344 atoms in total). >>> colvars: updating grid object data (0 grid objects in total). >>> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >>> atoms: total mass = 154.105, total charge = -0.279001. >>> colvars: Re-initialized atom group for variable "Translocation":0/1. 320 >>> atoms: total mass = 1921.76, total charge = 5.91999. >>> colvars: The final output state file will be >>> "output/0/win-out.job0.0.colvars.state". >>> FATAL ERROR: Bad global Thole count! (0 vs 707) >>> >>> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html >>> [Partition 0][Node 0] End of program >>> >>> I have to say that the collective variable is considered to be the mass >>> center of a group of atoms with no lone-pair. Since the lone-pairs are >>> massless. >>> Here is the collective variable conformation file (US-base.in): >>> colvarsTrajFrequency 100 >>> >>> colvar { >>> name Translocation >>> width 0.1 >>> lowerboundary 4.5 >>> upperboundary 18.8 >>> lowerwall 6.5 >>> upperwall 16.8 >>> lowerwallconstant 100.0 >>> upperwallconstant 100.0 >>> >>> distanceXY { >>> main { >>> atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 >>> 31 32 34 35 37 38 } >>> } >>> ref { >>> atomnumbers { >>> >>> 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 >>> 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 >>> 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 >>> 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 >>> 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 >>> 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 >>> 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 >>> 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 >>> 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 >>> 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 >>> 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 >>> 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 >>> 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 >>> 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 >>> 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 >>> 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 >>> 358 359 360} >>> } >>> axis ( 0.0, 0.0, 1.0 ) >>> } >>> } >>> >>> harmonic { >>> name Z >>> colvars Translocation >>> centers 0.0 >>> forceConstant 0.025;# 2.5 * 0.1^2 = 0.025 >>> } >>> >>> >>> >>> Here is the NAMD configuration file to run the simulation: >>> structure input/rm-bonds-modified.psf >>> ###coordinates input/start%d.pdb >>> >>> paraTypeCharmm on >>> parameters toppar_drude/toppar_drude_master_protein_2019g.str; >>> parameters toppar_drude/toppar_drude_lipid_2017c.str; >>> parameters toppar_drude/toppar_drude_model_2019g.str; >>> parameters toppar_drude/toppar_drude_carbohydrate_2019a.str; >>> parameters toppar_drude/toppar_drude_nucleic_acid_2017c.str; >>> >>> >>> # Force-Field Parameters >>> exclude scaled1-4 >>> 1-4scaling 1.0 >>> cutoff 12. >>> switching on >>> ##vdwForceSwitching on >>> switchdist 10. >>> pairlistdist 13.5 >>> >>> >>> # Integrator Parameters >>> timestep 1.0 ;# 1fs/step (only if needed to finish quickly) >>> #rigidBonds water >>> nonbondedFreq 2 >>> fullElectFrequency 4 >>> stepspercycle 20 >>> >>> >>> # Constant Temperature Control >>> langevin on ;# do langevin dynamicsgmail.google.com >>> >>> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps >>> langevinTemp $temperature >>> langevinHydrogen off ;# don't couple langevin bath to hydrogens >>> >>> # Periodic Boundary Conditions >>> #cellBasisVector1 61.5 0. 0. >>> #cellBasisVector2 0. 61.5 0. >>> #cellBasisVector3 0. 0 71.5 >>> #cellOrigin -16.06 -14.75 -12 >>> >>> #wrapAll on >>> >>> # PME (for full-system periodic electrostatics) >>> PME yes >>> PMEGridSpacing 1.0 >>> >>> # Constant Pressure Control (variable volume) >>> useGroupPressure yes >>> useConstantArea yes >>> useFlexibleCell yes >>> margin 5 >>> >>> >>> Would be very much grateful if somebody could guide me.. >>> >>> All the best, >>> Zeynab >>> >> -- *Hemanth H 18310019* Research Scholar IIT Gandhinagar --0000000000002f5f6205cafffacd Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Zeynab,

Can you please = post the psf and the input file that you used. I have some experience in se= tting up and running umbrella sampling simulations using Drude FF.

On Thu, Sep 2, 2021 at 12:51 PM zeynab hosseini <hosseinizeynab93@gmail.com> wrote:
=
Hi Giaco= mo,

Thank you so much for your reply. Sorry about that b= ut unfortunately I couldn't completely understand your prescription. I = made 10 windows=C2=A0centered at 6.7A, 6.8A, 6.9A, 7A, 8A, 9A, 11A, 13A, 15= A and 17A. The output I already sent is related to window-0 centered at 6.7= A. I understood to perform=C2=A0standard MD for each replica independently(= short one)? but what do you mean by setting the centers of harmonic restrai= nts to zero? You mean for example for the window-0 I put the center 0 inste= ad of 6.7? That would't produce problem?

A= ll the best,
Zeynab

On Wed, Sep 1, 2021 at 10:01 AM Giacomo = Fiorin <gi= acomo.fiorin@gmail.com> wrote:
Hi Zeynab, I've not used yet pol= arizable models in NAMD, so I don't know specifically where the error a= rises.=C2=A0 Assuming that this is a symptom=C2=A0of an unstable configurat= ion, what I would try to do is doing for each replica a short MD run of 100= -1000 steps on your workstation or an interactive node.=C2=A0 Start with th= e centers of the harmonic restraints to zero as you have shown (i.e. test t= he configuration of the first replica), and then do the same for all other = values that will be set by the REUS script, which will modify that center f= or all other replicas.

Giacomo

On Wed, Sep 1, 2021 = at 6:28 AM zeynab hosseini <hosseinizeynab93@gmail.com> wrote:
Dear All,
I want to perform a replica-exchange umbrella sampling (re= US) on a system composed of a nanotube and an amino acid solvated in water = using a polarizable force field (Drude). I did the standard MD of the syste= m with no problem using NAMD 2.14. The collective=C2=A0variable=C2=A0for my= system is the radial distance of the mass center of amino acid from the ma= ss center of the carbon nanotube. Collective variable is divided=C2=A0by 10= windows. As soon as, I perform=C2=A0the reUS simulation I get the followin= g error:

colvars: Collective variables biases init= ialized, 2 in total.
colvars: ------------------------------------------= ----------------------------
colvars: Collective variables module (re)in= itialized.
colvars: ----------------------------------------------------= ------------------
colvars: Updating NAMD interface:
colvars: updatin= g atomic data (0 atoms).
colvars: updating group data (2 scalable groups= , 344 atoms in total).
colvars: updating grid object data (0 grid object= s in total).
colvars: Re-initialized atom group for variable "Trans= location":0/0. 24 atoms: total mass =3D 154.105, total charge =3D -0.2= 79001.
colvars: Re-initialized atom group for variable "Translocati= on":0/1. 320 atoms: total mass =3D 1921.76, total charge =3D 5.91999.<= br>colvars: The final output state file will be "output/0/win-out.job0= .0.colvars.state".
colvars: Opening trajectory file "output/0/= win-out.job0.0.colvars.traj".
colvars: Redefining the Tcl "cv&= quot; command to the new script interface.
Info: Startup phase 13 took 0= .00555027 s, 66.3516 MB of memory in use
Info: Startup phase 14 took 5.4= 094e-05 s, 66.3516 MB of memory in use
Info: Startup phase 15 took 4.129= 3e-05 s, 67.6719 MB of memory in use
Info: Finished startup at 26.3569 s= , 67.6719 MB of memory in use

colvars: =C2=A0 # centers =3D { 6.7 }<= br>colvars: =C2=A0 # forceConstant =3D 0.025 [default]
TCL: Running for = 1000 steps
colvars: Updating NAMD interface:
colvars: updating atomic= data (0 atoms).
colvars: updating group data (2 scalable groups, 344 at= oms in total).
colvars: updating grid object data (0 grid objects in tot= al).
colvars: Re-initialized atom group for variable "Translocation= ":0/0. 24 atoms: total mass =3D 154.105, total charge =3D -0.279001.colvars: Re-initialized atom group for variable "Translocation"= :0/1. 320 atoms: total mass =3D 1921.76, total charge =3D 5.91999.
colva= rs: The final output state file will be "output/0/win-out.job0.0.colva= rs.state".
FATAL ERROR: Bad global Thole count! (0 vs 707)

F= ATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html<= /a>
[Partition 0][Node 0] End of program

colvarsTrajFrequency =C2=A0 =C2=A0 =C2=A0 =C2=A0100

= colvar {
=C2=A0 =C2=A0name Translocation
=C2=A0 =C2=A0width 0.1
= =C2=A0 =C2=A0lowerboundary =C2=A0 =C2=A04.5
=C2=A0 =C2=A0upperboundary = =C2=A0 =C2=A018.8
=C2=A0 =C2=A0lowerwall =C2=A0 =C2=A06.5
=C2=A0 =C2= =A0upperwall =C2=A0 16.8
=C2=A0 =C2=A0lowerwallconstant 100.0
=C2=A0 = =C2=A0upperwallconstant 100.0

=C2=A0 =C2=A0distanceXY {
=C2=A0 = =C2=A0 =C2=A0 main {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers {1 2 = 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 32 34 35 37 38 }
=C2=A0 = =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 ref =C2=A0{
=C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0atomnumbers {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
41 42 = 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 = 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 = 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 11= 3 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 1= 32 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 = 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169= 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 18= 8 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 2= 07 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 = 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244= 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 26= 3 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 2= 82 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 = 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319= 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 33= 8 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 3= 57 358 359 360}
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 axis =C2= =A0( 0.0, =C2=A00.0, 1.0 )
=C2=A0 =C2=A0}
}

harmonic {
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 name Z
colvars Translocation
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 centers 0.0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 forceConstant 0.02= 5;# 2.5 * 0.1^2 =3D 0.025
}


structure =C2=A0 =C2=A0 =C2=A0 =C2=A0 input/rm-bonds-modifie= d.psf
###coordinates =C2=A0 =C2=A0 =C2=A0 =C2=A0input/start%d.pdb
paraTypeCharmm on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_d= rude/toppar_drude_master_protein_2019g.str;
parameters =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_lipid_2017c.str;
parameters = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_model_2019g.str= ;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude= _carbohydrate_2019a.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0to= ppar_drude/toppar_drude_nucleic_acid_2017c.str;


# Force-Field Pa= rameters
exclude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scaled1-4
= 1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
cutoff =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012.
switching =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 on
##vdwForceSwitching =C2=A0 on
switchdist =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A010.
pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A013.5
=

# Integrator Parameters
timestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A01.0 =C2=A0;# 1fs/step (only if needed to finish quickly)
#rigi= dBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0water =C2=A0
nonbondedFreq =C2= =A0 =C2=A0 =C2=A0 2
fullElectFrequency =C2=A04 =C2=A0
stepspercycle = =C2=A0 =C2=A0 =C2=A0 20


# Constant Temperature Control
langev= in =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on =C2=A0 =C2=A0;# do langevin =
dynamicsgmail.google.com
langevinDamping =C2=A0 = =C2=A0 1 =C2=A0 =C2=A0 ;# damping coefficient (gamma) of 5/ps
langevinTe= mp =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature
langevinHydrogen =C2=A0 =C2= =A0off =C2=A0 =C2=A0;# don't couple langevin bath to hydrogens

#= Periodic Boundary Conditions =C2=A0
#cellBasisVector1 =C2=A0 61.5 =C2= =A0 =C2=A00. =C2=A0 0.
#cellBasisVector2 =C2=A0 =C2=A0 0. =C2=A0 61.5 = =C2=A0 0.
#cellBasisVector3 =C2=A0 =C2=A0 0. =C2=A0 =C2=A00 =C2=A0 =C2= =A071.5
#cellOrigin =C2=A0 =C2=A0 =C2=A0 =C2=A0-16.06 -14.75 -12

= #wrapAll =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on

# PME (for ful= l-system periodic electrostatics)
PME =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 yes
PMEGridSpacing =C2=A0 =C2=A0 =C2=A01.0

= # Constant Pressure Control (variable volume)
useGroupPressure =C2=A0 = =C2=A0 yes
useConstantArea =C2=A0 =C2=A0 =C2=A0yes
useFlexibleCell = =C2=A0 =C2=A0 =C2=A0yes
margin 5


=
Would be very much grateful if somebody could guide me..
All the best,
Zeynab


--
Hemanth H 18310019
Research Scholar
IIT Gandhinagar
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boundary="0000000000005f5f3605cb00079d" X-CLX-Response: 1TFkXGxMZEQpMehcZGh4RCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHHxsbEQpDWRcHGxwfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0ZcR8ZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2YbB0FIU2FrYmh9RXt7XWxTHmtiH39jdWMYREIdWFt7EQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc3BBbXMRCk1cFxkTEhEKTFoXaXxpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYhlCZxxFc2NbQWARCkNaFxgaEwQSHwQYGx 0EHhIRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXb3xPG29eRV9yGBgRCkJOF2NTY2t7E1h+Gl9eEQpCTBdoentgbnBSc3BaXxEKQmwX b1AFf09hZhlPRXIRCkJAF3pvYXlfRUhwHhNpEQpCWBdnc2VzQG5hYUxdYhEKWlgXHREKeUMXYR1 fTkRwY0EcHhwRCnBoF2FTWR8TE2cTQkJsEBsSEQpwaBd6TXlSSElkRmhFHRAbEhEKcGgXZGtzWE VGZVgZXWYQGxIRCnBoF2caRGlwQ0RDfWlsEBoRCnBoF2dCY2cBbQFJaEtdEBkaEQpwfRdjHXJ7c 0JLBX5laBAbEhEKcH0XbmRHZ0kfYW1PbR0QGxIRCnB9F294WkRYTG5HSFgbEBsSEQpwfxdlWHIY HUkYXkZpfBAbGh0RCnBfF2hAeGl/b0hCQh9rEBsSEQpwfxdtRF9GRW19SHkZbhAbGh4RCnBfF2t GSxN5aGlufBN4EBIYEQpwfxdhZm9bGmdkQkgdWxASGBEKcF8XY2ISUEhjeB98Qn0QHx8RCnBsF2 xSHVtpZmxeckhhEBkaEQpwTBdtaGUZQVJ9exhFUhAaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: L1-kbyKAHBWoQQwFy4AH5UI_I2nh7rqQ X-Proofpoint-ORIG-GUID: L1-kbyKAHBWoQQwFy4AH5UI_I2nh7rqQ X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 clxscore=193 priorityscore=304 adultscore=0 impostorscore=0 mlxlogscore=830 phishscore=0 bulkscore=0 malwarescore=0 suspectscore=0 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109020060 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --0000000000005f5f3605cb00079d Content-Type: text/plain; charset="UTF-8" Hi Giacomo, Really sorry. I made such stupid mistake! when converting my MD configuration file to reUS conf file, I totally forgot to turn on the drude option in my conf file. It is working perfectly right now. So sorry to take your time and thank you for your prompt reply again. All the best, Zeynab On Wed, Sep 1, 2021 at 10:01 AM Giacomo Fiorin wrote: > Hi Zeynab, I've not used yet polarizable models in NAMD, so I don't know > specifically where the error arises. Assuming that this is a symptom of an > unstable configuration, what I would try to do is doing for each replica a > short MD run of 100-1000 steps on your workstation or an interactive node. > Start with the centers of the harmonic restraints to zero as you have shown > (i.e. test the configuration of the first replica), and then do the same > for all other values that will be set by the REUS script, which will modify > that center for all other replicas. > > Giacomo > > On Wed, Sep 1, 2021 at 6:28 AM zeynab hosseini > wrote: > >> Dear All, >> >> I want to perform a replica-exchange umbrella sampling (reUS) on a system >> composed of a nanotube and an amino acid solvated in water using a >> polarizable force field (Drude). I did the standard MD of the system with >> no problem using NAMD 2.14. The collective variable for my system is the >> radial distance of the mass center of amino acid from the mass center of >> the carbon nanotube. Collective variable is divided by 10 windows. As soon >> as, I perform the reUS simulation I get the following error: >> >> colvars: Collective variables biases initialized, 2 in total. >> colvars: >> ---------------------------------------------------------------------- >> colvars: Collective variables module (re)initialized. >> colvars: >> ---------------------------------------------------------------------- >> colvars: Updating NAMD interface: >> colvars: updating atomic data (0 atoms). >> colvars: updating group data (2 scalable groups, 344 atoms in total). >> colvars: updating grid object data (0 grid objects in total). >> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >> atoms: total mass = 154.105, total charge = -0.279001. >> colvars: Re-initialized atom group for variable "Translocation":0/1. 320 >> atoms: total mass = 1921.76, total charge = 5.91999. >> colvars: The final output state file will be >> "output/0/win-out.job0.0.colvars.state". >> colvars: Opening trajectory file "output/0/win-out.job0.0.colvars.traj". >> colvars: Redefining the Tcl "cv" command to the new script interface. >> Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use >> Info: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use >> Info: Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use >> Info: Finished startup at 26.3569 s, 67.6719 MB of memory in use >> >> colvars: # centers = { 6.7 } >> colvars: # forceConstant = 0.025 [default] >> TCL: Running for 1000 steps >> colvars: Updating NAMD interface: >> colvars: updating atomic data (0 atoms). >> colvars: updating group data (2 scalable groups, 344 atoms in total). >> colvars: updating grid object data (0 grid objects in total). >> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >> atoms: total mass = 154.105, total charge = -0.279001. >> colvars: Re-initialized atom group for variable "Translocation":0/1. 320 >> atoms: total mass = 1921.76, total charge = 5.91999. >> colvars: The final output state file will be >> "output/0/win-out.job0.0.colvars.state". >> FATAL ERROR: Bad global Thole count! (0 vs 707) >> >> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html >> [Partition 0][Node 0] End of program >> >> I have to say that the collective variable is considered to be the mass >> center of a group of atoms with no lone-pair. Since the lone-pairs are >> massless. >> Here is the collective variable conformation file (US-base.in): >> colvarsTrajFrequency 100 >> >> colvar { >> name Translocation >> width 0.1 >> lowerboundary 4.5 >> upperboundary 18.8 >> lowerwall 6.5 >> upperwall 16.8 >> lowerwallconstant 100.0 >> upperwallconstant 100.0 >> >> distanceXY { >> main { >> atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 >> 32 34 35 37 38 } >> } >> ref { >> atomnumbers { >> >> 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 >> 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 >> 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 >> 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 >> 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 >> 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 >> 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 >> 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 >> 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 >> 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 >> 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 >> 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 >> 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 >> 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 >> 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 >> 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 >> 358 359 360} >> } >> axis ( 0.0, 0.0, 1.0 ) >> } >> } >> >> harmonic { >> name Z >> colvars Translocation >> centers 0.0 >> forceConstant 0.025;# 2.5 * 0.1^2 = 0.025 >> } >> >> >> >> Here is the NAMD configuration file to run the simulation: >> structure input/rm-bonds-modified.psf >> ###coordinates input/start%d.pdb >> >> paraTypeCharmm on >> parameters toppar_drude/toppar_drude_master_protein_2019g.str; >> parameters toppar_drude/toppar_drude_lipid_2017c.str; >> parameters toppar_drude/toppar_drude_model_2019g.str; >> parameters toppar_drude/toppar_drude_carbohydrate_2019a.str; >> parameters toppar_drude/toppar_drude_nucleic_acid_2017c.str; >> >> >> # Force-Field Parameters >> exclude scaled1-4 >> 1-4scaling 1.0 >> cutoff 12. >> switching on >> ##vdwForceSwitching on >> switchdist 10. >> pairlistdist 13.5 >> >> >> # Integrator Parameters >> timestep 1.0 ;# 1fs/step (only if needed to finish quickly) >> #rigidBonds water >> nonbondedFreq 2 >> fullElectFrequency 4 >> stepspercycle 20 >> >> >> # Constant Temperature Control >> langevin on ;# do langevin dynamicsgmail.google.com >> >> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps >> langevinTemp $temperature >> langevinHydrogen off ;# don't couple langevin bath to hydrogens >> >> # Periodic Boundary Conditions >> #cellBasisVector1 61.5 0. 0. >> #cellBasisVector2 0. 61.5 0. >> #cellBasisVector3 0. 0 71.5 >> #cellOrigin -16.06 -14.75 -12 >> >> #wrapAll on >> >> # PME (for full-system periodic electrostatics) >> PME yes >> PMEGridSpacing 1.0 >> >> # Constant Pressure Control (variable volume) >> useGroupPressure yes >> useConstantArea yes >> useFlexibleCell yes >> margin 5 >> >> >> Would be very much grateful if somebody could guide me.. >> >> All the best, >> Zeynab >> > --0000000000005f5f3605cb00079d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Giacomo,

Really sorry. I made such s= tupid mistake! when converting my MD configuration file to reUS conf file, = I totally forgot to turn on the drude option in my conf file. It is working= perfectly right now. So sorry to take your time and thank you for your pro= mpt reply again.

All the best,
Zeynab

On Wed, Sep 1, 2021 at 10:01 AM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
Hi Zeynab, = I've not used yet polarizable models in NAMD, so I don't know speci= fically where the error arises.=C2=A0 Assuming that this is a symptom=C2=A0= of an unstable configuration, what I would try to do is doing for each repl= ica a short MD run of 100-1000 steps on your workstation or an interactive = node.=C2=A0 Start with the centers of the harmonic restraints to zero as yo= u have shown (i.e. test the configuration of the first replica), and then d= o the same for all other values that will be set by the REUS script, which = will modify that center for all other replicas.

Giacomo<= /div>

On Wed, Sep 1, 2021 at 6:28 AM zeynab hosseini <hosseinizeynab93@gmail.com= > wrote:
Dear All,

I want to perform a replica-excha= nge umbrella sampling (reUS) on a system composed of a nanotube and an amin= o acid solvated in water using a polarizable force field (Drude). I did the= standard MD of the system with no problem using NAMD 2.14. The collective= =C2=A0variable=C2=A0for my system is the radial distance of the mass center= of amino acid from the mass center of the carbon nanotube. Collective vari= able is divided=C2=A0by 10 windows. As soon as, I perform=C2=A0the reUS sim= ulation I get the following error:

colvars: Collec= tive variables biases initialized, 2 in total.
colvars: ----------------= ------------------------------------------------------
colvars: Collecti= ve variables module (re)initialized.
colvars: --------------------------= --------------------------------------------
colvars: Updating NAMD inte= rface:
colvars: updating atomic data (0 atoms).
colvars: updating gro= up data (2 scalable groups, 344 atoms in total).
colvars: updating grid = object data (0 grid objects in total).
colvars: Re-initialized atom grou= p for variable "Translocation":0/0. 24 atoms: total mass =3D 154.= 105, total charge =3D -0.279001.
colvars: Re-initialized atom group for = variable "Translocation":0/1. 320 atoms: total mass =3D 1921.76, = total charge =3D 5.91999.
colvars: The final output state file will be &= quot;output/0/win-out.job0.0.colvars.state".
colvars: Opening traje= ctory file "output/0/win-out.job0.0.colvars.traj".
colvars: Re= defining the Tcl "cv" command to the new script interface.
Inf= o: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use
Info:= Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use
Info: S= tartup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use
Info: Fin= ished startup at 26.3569 s, 67.6719 MB of memory in use

colvars: =C2= =A0 # centers =3D { 6.7 }
colvars: =C2=A0 # forceConstant =3D 0.025 [def= ault]
TCL: Running for 1000 steps
colvars: Updating NAMD interface:colvars: updating atomic data (0 atoms).
colvars: updating group data = (2 scalable groups, 344 atoms in total).
colvars: updating grid object d= ata (0 grid objects in total).
colvars: Re-initialized atom group for va= riable "Translocation":0/0. 24 atoms: total mass =3D 154.105, tot= al charge =3D -0.279001.
colvars: Re-initialized atom group for variable= "Translocation":0/1. 320 atoms: total mass =3D 1921.76, total ch= arge =3D 5.91999.
colvars: The final output state file will be "out= put/0/win-out.job0.0.colvars.state".
FATAL ERROR: Bad global Thole = count! (0 vs 707)

FATAL ERROR: See http://www.ks.uiuc.edu/Res= earch/namd/bugreport.html
[Partition 0][Node 0] End of program

I have to say that the collective variable is consi= dered to be the mass center of a group of atoms with no lone-pair. Since th= e lone-pairs are massless.=C2=A0
Here is the collective variable = conformation file (US-base.in):
colvarsTrajFrequency =C2=A0 =C2= =A0 =C2=A0 =C2=A0100

colvar {
=C2=A0 =C2=A0name Translocation
= =C2=A0 =C2=A0width 0.1
=C2=A0 =C2=A0lowerboundary =C2=A0 =C2=A04.5
= =C2=A0 =C2=A0upperboundary =C2=A0 =C2=A018.8
=C2=A0 =C2=A0lowerwall =C2= =A0 =C2=A06.5
=C2=A0 =C2=A0upperwall =C2=A0 16.8
=C2=A0 =C2=A0lowerwa= llconstant 100.0
=C2=A0 =C2=A0upperwallconstant 100.0

=C2=A0 =C2= =A0distanceXY {
=C2=A0 =C2=A0 =C2=A0 main {
=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 = 32 34 35 37 38 }
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 ref =C2= =A0{
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers {
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 = 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 = 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 = 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124= 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 14= 3 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 1= 62 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 = 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199= 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 21= 8 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 2= 37 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 = 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274= 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 29= 3 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 3= 12 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 = 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349= 350 351 352 353 354 355 356 357 358 359 360}
=C2=A0 =C2=A0 =C2=A0 }
= =C2=A0 =C2=A0 =C2=A0 axis =C2=A0( 0.0, =C2=A00.0, 1.0 )
=C2=A0 =C2=A0}}

harmonic {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 name Z
colvars Tra= nslocation
=C2=A0 =C2=A0 =C2=A0 =C2=A0 centers 0.0
=C2=A0 =C2=A0 =C2= =A0 =C2=A0 forceConstant 0.025;# 2.5 * 0.1^2 =3D 0.025
}
<= br>


=C2=A0Here is the NAMD configur= ation file to run the simulation:
structure =C2=A0 =C2=A0 =C2=A0 = =C2=A0 input/rm-bonds-modified.psf
###coordinates =C2=A0 =C2=A0 =C2=A0 = =C2=A0input/start%d.pdb

paraTypeCharmm on
parameters =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_master_protein_2019g.str;=
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_= lipid_2017c.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_dru= de/toppar_drude_model_2019g.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0toppar_drude/toppar_drude_carbohydrate_2019a.str;
parameters =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_nucleic_acid_2017c= .str;


# Force-Field Parameters
exclude =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 scaled1-4
1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A01.0
cutoff =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012.
= switching =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on
##vdwForceSwitching =C2= =A0 on
switchdist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A010.
pairlistdist = =C2=A0 =C2=A0 =C2=A0 =C2=A013.5


# Integrator Parameters
times= tep =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0 =C2=A0;# 1fs/step (only if= needed to finish quickly)
#rigidBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0water =C2=A0
nonbondedFreq =C2=A0 =C2=A0 =C2=A0 2
fullElectFrequen= cy =C2=A04 =C2=A0
stepspercycle =C2=A0 =C2=A0 =C2=A0 20


# Con= stant Temperature Control
langevin =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0on =C2=A0 =C2=A0;# do langevin dynamicsgmail.googl= e.com
langevinDamping =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 ;# damping coeff= icient (gamma) of 5/ps
langevinTemp =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperat= ure
langevinHydrogen =C2=A0 =C2=A0off =C2=A0 =C2=A0;# don't couple l= angevin bath to hydrogens

# Periodic Boundary Conditions =C2=A0
#= cellBasisVector1 =C2=A0 61.5 =C2=A0 =C2=A00. =C2=A0 0.
#cellBasisVector2= =C2=A0 =C2=A0 0. =C2=A0 61.5 =C2=A0 0.
#cellBasisVector3 =C2=A0 =C2=A0 = 0. =C2=A0 =C2=A00 =C2=A0 =C2=A071.5
#cellOrigin =C2=A0 =C2=A0 =C2=A0 =C2= =A0-16.06 -14.75 -12

#wrapAll =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 on

# PME (for full-system periodic electrostatics)
PME =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 yes
PMEGridSpacing =C2= =A0 =C2=A0 =C2=A01.0

# Constant Pressure Control (variable volume)useGroupPressure =C2=A0 =C2=A0 yes
useConstantArea =C2=A0 =C2=A0 =C2= =A0yes
useFlexibleCell =C2=A0 =C2=A0 =C2=A0yes
margin 5


Would be very much grateful if somebody coul= d guide me..

All the best,
Zeynab
<= /div>
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boundary="0000000000000ed84d05cb000d33" X-Proofpoint-GUID: fcKhC8ST10MZwBpQ7wfA0UXo3BIro5B8 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIaEQpMehcZGhwRCllEF2ViQXllXnJwYG9hEQpYWBdoentgbnBSc3B aXxEKeE4XY1Nja3sTWH4aX14RCnlMF2ZJUh1CfX9dQ3BNEQpDSBcHHxgaEQpDWRcHGxwfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwacRkTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0xJYUJpEnl+GxpncF1oWnsdXUxrGn9yRRloY1hFH2gSEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc3BBYhkRCk1cFx4fHhEKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdgZGsfZ0QYcGYYWhEKQ1oXGBoTBBIfBBgYGA QeHxEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdvfE8bb15FX3IYGBEKQk4XY1Nja3sTWH4aX14RCkJMF2h6e2BucFJzcFpfEQpCbBdv UAV/T2FmGU9FchEKQkAXem9heV9FSHAeE2kRCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp5QxdhHV9 ORHBjQRweHBEKcGcXZWRtBX5IR38SXR8QGRoRCnBoF24YeGdMblJGSGRBEBwaEQpwaBdhU1kfEx NnE0JCbBAcGhEKcGgXek15UkhJZEZoRR0QHBoRCnBoF2Rrc1hFRmVYGV1mEBwaEQpwaBd6flAdG kZbQHsBYBAZGhEKcGcXbkF7f35ZQkYBZmYQHBoRCnB9F2MdcntzQksFfmVoEBwaEQpwfRduZEdn SR9hbU9tHRAcGhEKcH8XZVhyGB1JGF5GaXwQGx4fEQpwXxdoQHhpf29IQkIfaxAcGhEKcH8XbUR fRkVtfUh5GW4QGxobEQpwXxdrRksTeWhpbnwTeBAdExEKcGwXbFIdW2lmbF5ySGEQGRoRCnBMF2 1oZRlBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: fcKhC8ST10MZwBpQ7wfA0UXo3BIro5B8 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=180 mlxscore=0 malwarescore=0 suspectscore=0 lowpriorityscore=0 bulkscore=0 adultscore=0 priorityscore=306 mlxlogscore=930 phishscore=0 spamscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109020060 X-Spam-Score: 0 X-Spam-OrigSender: hosseinizeynab93@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, zeynab hosseini --0000000000000ed84d05cb000d33 Content-Type: text/plain; charset="UTF-8" Dear Hemanth, Thank you for your answer. The problem is fixed now.. All the best, Zeynab On Thu, Sep 2, 2021 at 5:40 AM Hemanth Haridas wrote: > Dear Zeynab, > > Can you please post the psf and the input file that you used. I have some > experience in setting up and running umbrella sampling simulations using > Drude FF. > > On Thu, Sep 2, 2021 at 12:51 PM zeynab hosseini < > hosseinizeynab93@gmail.com> wrote: > >> Hi Giacomo, >> >> Thank you so much for your reply. Sorry about that but unfortunately I >> couldn't completely understand your prescription. I made 10 >> windows centered at 6.7A, 6.8A, 6.9A, 7A, 8A, 9A, 11A, 13A, 15A and 17A. >> The output I already sent is related to window-0 centered at 6.7A. I >> understood to perform standard MD for each replica independently(short >> one)? but what do you mean by setting the centers of harmonic restraints to >> zero? You mean for example for the window-0 I put the center 0 instead of >> 6.7? That would't produce problem? >> >> All the best, >> Zeynab >> >> On Wed, Sep 1, 2021 at 10:01 AM Giacomo Fiorin >> wrote: >> >>> Hi Zeynab, I've not used yet polarizable models in NAMD, so I don't know >>> specifically where the error arises. Assuming that this is a symptom of an >>> unstable configuration, what I would try to do is doing for each replica a >>> short MD run of 100-1000 steps on your workstation or an interactive node. >>> Start with the centers of the harmonic restraints to zero as you have shown >>> (i.e. test the configuration of the first replica), and then do the same >>> for all other values that will be set by the REUS script, which will modify >>> that center for all other replicas. >>> >>> Giacomo >>> >>> On Wed, Sep 1, 2021 at 6:28 AM zeynab hosseini < >>> hosseinizeynab93@gmail.com> wrote: >>> >>>> Dear All, >>>> >>>> I want to perform a replica-exchange umbrella sampling (reUS) on a >>>> system composed of a nanotube and an amino acid solvated in water using a >>>> polarizable force field (Drude). I did the standard MD of the system with >>>> no problem using NAMD 2.14. The collective variable for my system is the >>>> radial distance of the mass center of amino acid from the mass center of >>>> the carbon nanotube. Collective variable is divided by 10 windows. As soon >>>> as, I perform the reUS simulation I get the following error: >>>> >>>> colvars: Collective variables biases initialized, 2 in total. >>>> colvars: >>>> ---------------------------------------------------------------------- >>>> colvars: Collective variables module (re)initialized. >>>> colvars: >>>> ---------------------------------------------------------------------- >>>> colvars: Updating NAMD interface: >>>> colvars: updating atomic data (0 atoms). >>>> colvars: updating group data (2 scalable groups, 344 atoms in total). >>>> colvars: updating grid object data (0 grid objects in total). >>>> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >>>> atoms: total mass = 154.105, total charge = -0.279001. >>>> colvars: Re-initialized atom group for variable "Translocation":0/1. >>>> 320 atoms: total mass = 1921.76, total charge = 5.91999. >>>> colvars: The final output state file will be >>>> "output/0/win-out.job0.0.colvars.state". >>>> colvars: Opening trajectory file "output/0/win-out.job0.0.colvars.traj". >>>> colvars: Redefining the Tcl "cv" command to the new script interface. >>>> Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use >>>> Info: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use >>>> Info: Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use >>>> Info: Finished startup at 26.3569 s, 67.6719 MB of memory in use >>>> >>>> colvars: # centers = { 6.7 } >>>> colvars: # forceConstant = 0.025 [default] >>>> TCL: Running for 1000 steps >>>> colvars: Updating NAMD interface: >>>> colvars: updating atomic data (0 atoms). >>>> colvars: updating group data (2 scalable groups, 344 atoms in total). >>>> colvars: updating grid object data (0 grid objects in total). >>>> colvars: Re-initialized atom group for variable "Translocation":0/0. 24 >>>> atoms: total mass = 154.105, total charge = -0.279001. >>>> colvars: Re-initialized atom group for variable "Translocation":0/1. >>>> 320 atoms: total mass = 1921.76, total charge = 5.91999. >>>> colvars: The final output state file will be >>>> "output/0/win-out.job0.0.colvars.state". >>>> FATAL ERROR: Bad global Thole count! (0 vs 707) >>>> >>>> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html >>>> [Partition 0][Node 0] End of program >>>> >>>> I have to say that the collective variable is considered to be the mass >>>> center of a group of atoms with no lone-pair. Since the lone-pairs are >>>> massless. >>>> Here is the collective variable conformation file (US-base.in): >>>> colvarsTrajFrequency 100 >>>> >>>> colvar { >>>> name Translocation >>>> width 0.1 >>>> lowerboundary 4.5 >>>> upperboundary 18.8 >>>> lowerwall 6.5 >>>> upperwall 16.8 >>>> lowerwallconstant 100.0 >>>> upperwallconstant 100.0 >>>> >>>> distanceXY { >>>> main { >>>> atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 >>>> 31 32 34 35 37 38 } >>>> } >>>> ref { >>>> atomnumbers { >>>> >>>> 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 >>>> 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 >>>> 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 >>>> 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 >>>> 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 >>>> 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 >>>> 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 >>>> 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 >>>> 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 >>>> 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 >>>> 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 >>>> 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 >>>> 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 >>>> 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 >>>> 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 >>>> 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 >>>> 358 359 360} >>>> } >>>> axis ( 0.0, 0.0, 1.0 ) >>>> } >>>> } >>>> >>>> harmonic { >>>> name Z >>>> colvars Translocation >>>> centers 0.0 >>>> forceConstant 0.025;# 2.5 * 0.1^2 = 0.025 >>>> } >>>> >>>> >>>> >>>> Here is the NAMD configuration file to run the simulation: >>>> structure input/rm-bonds-modified.psf >>>> ###coordinates input/start%d.pdb >>>> >>>> paraTypeCharmm on >>>> parameters toppar_drude/toppar_drude_master_protein_2019g.str; >>>> parameters toppar_drude/toppar_drude_lipid_2017c.str; >>>> parameters toppar_drude/toppar_drude_model_2019g.str; >>>> parameters toppar_drude/toppar_drude_carbohydrate_2019a.str; >>>> parameters toppar_drude/toppar_drude_nucleic_acid_2017c.str; >>>> >>>> >>>> # Force-Field Parameters >>>> exclude scaled1-4 >>>> 1-4scaling 1.0 >>>> cutoff 12. >>>> switching on >>>> ##vdwForceSwitching on >>>> switchdist 10. >>>> pairlistdist 13.5 >>>> >>>> >>>> # Integrator Parameters >>>> timestep 1.0 ;# 1fs/step (only if needed to finish quickly) >>>> #rigidBonds water >>>> nonbondedFreq 2 >>>> fullElectFrequency 4 >>>> stepspercycle 20 >>>> >>>> >>>> # Constant Temperature Control >>>> langevin on ;# do langevin dynamicsgmail.google.com >>>> >>>> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps >>>> langevinTemp $temperature >>>> langevinHydrogen off ;# don't couple langevin bath to hydrogens >>>> >>>> # Periodic Boundary Conditions >>>> #cellBasisVector1 61.5 0. 0. >>>> #cellBasisVector2 0. 61.5 0. >>>> #cellBasisVector3 0. 0 71.5 >>>> #cellOrigin -16.06 -14.75 -12 >>>> >>>> #wrapAll on >>>> >>>> # PME (for full-system periodic electrostatics) >>>> PME yes >>>> PMEGridSpacing 1.0 >>>> >>>> # Constant Pressure Control (variable volume) >>>> useGroupPressure yes >>>> useConstantArea yes >>>> useFlexibleCell yes >>>> margin 5 >>>> >>>> >>>> Would be very much grateful if somebody could guide me.. >>>> >>>> All the best, >>>> Zeynab >>>> >>> > > -- > *Hemanth H 18310019* > Research Scholar > IIT Gandhinagar > --0000000000000ed84d05cb000d33 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Hemanth,

Thank you for your answer= . The problem is fixed now..

All the=C2=A0best,
Zeynab

On Thu, Sep 2, 2021 at 5:40 AM Hemanth Haridas <hemanth.h@iitgn.ac.in> wrote:
=
Dear Zeynab,

Can you please post the psf and = the input file that you used. I have some experience in setting up and runn= ing umbrella sampling simulations using Drude FF.

On Thu, Sep 2, 2= 021 at 12:51 PM zeynab hosseini <hosseinizeynab93@gmail.com> wrote:
Hi Giac= omo,

Thank you so much for your reply. Sorry about that = but unfortunately I couldn't completely understand your prescription. I= made 10 windows=C2=A0centered at 6.7A, 6.8A, 6.9A, 7A, 8A, 9A, 11A, 13A, 1= 5A and 17A. The output I already sent is related to window-0 centered at 6.= 7A. I understood to perform=C2=A0standard MD for each replica independently= (short one)? but what do you mean by setting the centers of harmonic restra= ints to zero? You mean for example for the window-0 I put the center 0 inst= ead of 6.7? That would't produce problem?

= All the best,
Zeynab

On Wed, Sep 1, 2021 at 10:01 AM Giacomo= Fiorin <g= iacomo.fiorin@gmail.com> wrote:
Hi Zeynab, I've not used yet po= larizable models in NAMD, so I don't know specifically where the error = arises.=C2=A0 Assuming that this is a symptom=C2=A0of an unstable configura= tion, what I would try to do is doing for each replica a short MD run of 10= 0-1000 steps on your workstation or an interactive node.=C2=A0 Start with t= he centers of the harmonic restraints to zero as you have shown (i.e. test = the configuration of the first replica), and then do the same for all other= values that will be set by the REUS script, which will modify that center = for all other replicas.

Giacomo

On Wed, Sep 1, 2021= at 6:28 AM zeynab hosseini <hosseinizeynab93@gmail.com> wrote:
Dear All,
I want to perform a replica-exchange umbrella sampling (r= eUS) on a system composed of a nanotube and an amino acid solvated in water= using a polarizable force field (Drude). I did the standard MD of the syst= em with no problem using NAMD 2.14. The collective=C2=A0variable=C2=A0for m= y system is the radial distance of the mass center of amino acid from the m= ass center of the carbon nanotube. Collective variable is divided=C2=A0by 1= 0 windows. As soon as, I perform=C2=A0the reUS simulation I get the followi= ng error:

colvars: Collective variables biases ini= tialized, 2 in total.
colvars: -----------------------------------------= -----------------------------
colvars: Collective variables module (re)i= nitialized.
colvars: ---------------------------------------------------= -------------------
colvars: Updating NAMD interface:
colvars: updati= ng atomic data (0 atoms).
colvars: updating group data (2 scalable group= s, 344 atoms in total).
colvars: updating grid object data (0 grid objec= ts in total).
colvars: Re-initialized atom group for variable "Tran= slocation":0/0. 24 atoms: total mass =3D 154.105, total charge =3D -0.= 279001.
colvars: Re-initialized atom group for variable "Translocat= ion":0/1. 320 atoms: total mass =3D 1921.76, total charge =3D 5.91999.=
colvars: The final output state file will be "output/0/win-out.job= 0.0.colvars.state".
colvars: Opening trajectory file "output/0= /win-out.job0.0.colvars.traj".
colvars: Redefining the Tcl "cv= " command to the new script interface.
Info: Startup phase 13 took = 0.00555027 s, 66.3516 MB of memory in use
Info: Startup phase 14 took 5.= 4094e-05 s, 66.3516 MB of memory in use
Info: Startup phase 15 took 4.12= 93e-05 s, 67.6719 MB of memory in use
Info: Finished startup at 26.3569 = s, 67.6719 MB of memory in use

colvars: =C2=A0 # centers =3D { 6.7 }=
colvars: =C2=A0 # forceConstant =3D 0.025 [default]
TCL: Running for= 1000 steps
colvars: Updating NAMD interface:
colvars: updating atomi= c data (0 atoms).
colvars: updating group data (2 scalable groups, 344 a= toms in total).
colvars: updating grid object data (0 grid objects in to= tal).
colvars: Re-initialized atom group for variable "Translocatio= n":0/0. 24 atoms: total mass =3D 154.105, total charge =3D -0.279001.<= br>colvars: Re-initialized atom group for variable "Translocation"= ;:0/1. 320 atoms: total mass =3D 1921.76, total charge =3D 5.91999.
colv= ars: The final output state file will be "output/0/win-out.job0.0.colv= ars.state".
FATAL ERROR: Bad global Thole count! (0 vs 707)

= FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html=
[Partition 0][Node 0] End of program

I= have to say that the collective variable is considered to be the mass cent= er of a group of atoms with no lone-pair. Since the lone-pairs are massless= .=C2=A0
Here is the collective variable conformation file (US-bas= e.in):
colvarsTrajFrequency =C2=A0 =C2=A0 =C2=A0 =C2=A0100
colvar {
=C2=A0 =C2=A0name Translocation
=C2=A0 =C2=A0width 0.1
= =C2=A0 =C2=A0lowerboundary =C2=A0 =C2=A04.5
=C2=A0 =C2=A0upperboundary = =C2=A0 =C2=A018.8
=C2=A0 =C2=A0lowerwall =C2=A0 =C2=A06.5
=C2=A0 =C2= =A0upperwall =C2=A0 16.8
=C2=A0 =C2=A0lowerwallconstant 100.0
=C2=A0 = =C2=A0upperwallconstant 100.0

=C2=A0 =C2=A0distanceXY {
=C2=A0 = =C2=A0 =C2=A0 main {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0atomnumbers {1 2 = 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31 32 34 35 37 38 }
=C2=A0 = =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 ref =C2=A0{
=C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0atomnumbers {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
41 42 = 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 = 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 = 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 11= 3 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 1= 32 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 = 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169= 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 18= 8 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 2= 07 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 = 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244= 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 26= 3 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 2= 82 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 = 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319= 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 33= 8 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 3= 57 358 359 360}
=C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 axis =C2= =A0( 0.0, =C2=A00.0, 1.0 )
=C2=A0 =C2=A0}
}

harmonic {
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 name Z
colvars Translocation
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 centers 0.0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 forceConstant 0.02= 5;# 2.5 * 0.1^2 =3D 0.025
}


=
=C2=A0Here is the NAMD configuration file to run the simulat= ion:
structure =C2=A0 =C2=A0 =C2=A0 =C2=A0 input/rm-bonds-modifie= d.psf
###coordinates =C2=A0 =C2=A0 =C2=A0 =C2=A0input/start%d.pdb
paraTypeCharmm on
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_d= rude/toppar_drude_master_protein_2019g.str;
parameters =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_lipid_2017c.str;
parameters = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude_model_2019g.str= ;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0toppar_drude/toppar_drude= _carbohydrate_2019a.str;
parameters =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0to= ppar_drude/toppar_drude_nucleic_acid_2017c.str;


# Force-Field Pa= rameters
exclude =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 scaled1-4
= 1-4scaling =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0
cutoff =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012.
switching =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 on
##vdwForceSwitching =C2=A0 on
switchdist =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A010.
pairlistdist =C2=A0 =C2=A0 =C2=A0 =C2=A013.5
=

# Integrator Parameters
timestep =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A01.0 =C2=A0;# 1fs/step (only if needed to finish quickly)
#rigi= dBonds =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0water =C2=A0
nonbondedFreq =C2= =A0 =C2=A0 =C2=A0 2
fullElectFrequency =C2=A04 =C2=A0
stepspercycle = =C2=A0 =C2=A0 =C2=A0 20


# Constant Temperature Control
langev= in =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0on =C2=A0 =C2=A0;# do langevin = dynamicsgmail.google.com
langevinDamping =C2=A0 = =C2=A0 1 =C2=A0 =C2=A0 ;# damping coefficient (gamma) of 5/ps
langevinTe= mp =C2=A0 =C2=A0 =C2=A0 =C2=A0$temperature
langevinHydrogen =C2=A0 =C2= =A0off =C2=A0 =C2=A0;# don't couple langevin bath to hydrogens

#= Periodic Boundary Conditions =C2=A0
#cellBasisVector1 =C2=A0 61.5 =C2= =A0 =C2=A00. =C2=A0 0.
#cellBasisVector2 =C2=A0 =C2=A0 0. =C2=A0 61.5 = =C2=A0 0.
#cellBasisVector3 =C2=A0 =C2=A0 0. =C2=A0 =C2=A00 =C2=A0 =C2= =A071.5
#cellOrigin =C2=A0 =C2=A0 =C2=A0 =C2=A0-16.06 -14.75 -12

= #wrapAll =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on

# PME (for ful= l-system periodic electrostatics)
PME =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 yes
PMEGridSpacing =C2=A0 =C2=A0 =C2=A01.0

= # Constant Pressure Control (variable volume)
useGroupPressure =C2=A0 = =C2=A0 yes
useConstantArea =C2=A0 =C2=A0 =C2=A0yes
useFlexibleCell = =C2=A0 =C2=A0 =C2=A0yes
margin 5


=
Would be very much grateful if somebody could guide me..
All the best,
Zeynab


--
Hemanth H 18310019
Research Scholar
IIT Gandhinagar
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boundary="0000000000007628ae05cb042b5f" X-CLX-Response: 1TFkXGxwbEQpMehcZHxMRCllEF2dsTFNucBIbRAUfEQpYWBdubEZva0x/WGh AGREKeE4XZ25bXUIZR1lnWEERCnlMF2lfYmFLQVtvGG1tEQpDSBcHGRwdEQpDWRcHGxgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFx4dcRsGEx53Bh8eBhoGBxgfQAYbGhoGGnEaEBp3BhoGGgYaBgcbH wYaBhpxGhAadwYaEQpZXhdobnkRCklGF19DX0l1QkVZXk9OEQpDThdMZRJmRGl7E2N/T3USZUBa U09nGwcaHX0dQH8ff01MQREKWFwXHwQaBBgZGQUbGgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3NwRUl 4EQpNXBcZEhsRCkxaF3tpTXhrEQpFWRdoEQpMXxd6BQUFBQUFBQUFUhEKTU4XaWsRCkJPF3pQeG RrWlJyWkZGEQpDWhcYGhMEEh8EGxwcBB8eEQpCXhcbEQpCRRdtenl4GUlzchgBcBEKQk4XZ25bX UIZR1lnWEERCkJMF25sRm9rTH9YaEAZEQpCbBdoBVtvS3lafxMfGBEKQlgXZ3Nlc0BuYWFMXWIR Ck1eFwcbEQpaWBcbEQpZSxcZEhkcEQpwaBdpUgVZb1JBaWNYaxAHGRoRCnBoF2JCQUkdZWB5WmB BEAcZGhEKcGgXZGwcE21MU014QGcQBxkaEQpwaBdoBWcBEkRoE2JHcBAHGRoRCnBoF2xeRGt8b0 hHW08aEAcZGhEKcH0XZRxlZnsaexx7RUcQBxkaEQpwfxdkGEZibE5ISH1kbhAHGRoRCnBfF2VgR gVaU2h/E25lEAcZGhEKcGwXbWF6RGVAfWNzRmAQBxkaEQptfhcHGxEKWE0XSxEg X-Proofpoint-GUID: fO8LnCQ9IUe_8OjpyeM1-07W7jU5Ugfk X-Proofpoint-ORIG-GUID: fO8LnCQ9IUe_8OjpyeM1-07W7jU5Ugfk X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 clxscore=161 priorityscore=359 adultscore=0 impostorscore=0 mlxlogscore=821 phishscore=0 bulkscore=0 malwarescore=0 suspectscore=0 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109020089 domainage_hfrom=3836 X-Spam-Score: 0 X-Spam-OrigSender: krithika17@students.cutn.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Krithika Unmesh --0000000000007628ae05cb042b5f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I was trying to simulate an ATP molecule using NAMD and VMD. I was following various tutorials on NAMD available on internet. All the tutorials are based on proteins. What I understood is, it is different from ATP. While I was performing the minimization and NAMD run, it was running without any error. But, the resulting dcd file is found to be empty. It does not having any molecule. In fact I am not able to understand the mistakes I am making. I will write in detail various steps and trials I did. I first loaded the pdb file in VMD. In fact, I collected three different pdb structures. I then generated the psf file using Automatic psf Builder from the extension menu in vmd. But, here also I was having doubts. ATP contains 31 atoms without hydrogen and 47 with hydrogen. But, even before generating psf files, the loaded molecule was found to contain 47 atoms and to my surprise, after generating psf file, the number of atoms was reduced to 43. I tried with all the 3 pdb files I collected and for all the three, the same thing happened. Then, for solvation, I typed the following command in Tk Console: package require solvate solvate atp.psf atp.pdb -t 30 -o atp_wb [And I could not get how we could provide solvent models such as tip3p, spce etc. But, here I could not find it in any step. Also, is it possible to set a desired number of water molecules(of our choice, say 800 molecules in a box with dimension 30A x 30A x 30A box). ] I, then, manually added Na+ ions, using Add ions from Modelling section of extensions. I then calculated the minimum and maximum value of x, y, and z coordinates of to find the center and the length of each coordinate of the water box, using libre calc. In namd graphical interface, I set the time step to 1fs. So, for minimisations, I gave 10^6 steps (0.1ns) and for dynamics 2*10^7 steps (2ns). I selected NPT ensemble (with desired temperature and pressure), and gave periodic boundary conditions (for which xsc file was generated using the calculations from libre calc); also provided particle Mesh Ewald for electrostatic interactions. In simulation space partitioning, I gave the cut off distance as 12 A. All other simulation parameters, I used the default itself. And gave NAMD Run.But then, the dcd file is found to be empty. --=20 Central University of Tamil Nadu is in not responsible for the contents of= =20 this email. The sender takes responsibility for the content of this email.= =20 This mail is also governed by the relevant disclaimer policies of=C2=A0Cent= ral=20 University of Tamil Nadu. --0000000000007628ae05cb042b5f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
I was trying to simulate an ATP molecule= using NAMD and=20 VMD. I was following various tutorials on NAMD available on internet.=20 All the tutorials are based on proteins. What I understood is, it is=20 different from ATP. While I was performing the minimization and NAMD=20 run, it was running without any error. But, the resulting dcd file is=20 found to be empty. It does not having any molecule. In fact I am not=20 able to understand the mistakes I am making.

I will write in detail various steps and trials I did.=

I first loaded the pdb file in VMD. In fact, I collected three different=20 pdb structures. I then generated the psf file using Automatic psf=20 Builder from the extension menu in vmd. But, here also I was having=20 doubts. ATP contains 31 atoms without hydrogen and 47 with hydrogen.=20 But, even before generating psf files, the loaded molecule was found to=20 contain 47 atoms and to my surprise, after generating psf file, the=20 number of atoms was reduced to 43. I tried with all the 3 pdb files I=20 collected and for all the three, the same thing happened.

Then, for solvation, I typed the followin= g command in Tk Console:
package require solvate
solvate atp.psf atp.pdb -t 30 -o atp_wb

[And I could not get how we could provide solvent models such as tip3p, spce etc. But, here I could not find it in any step. Also, is it possible to set a desired=20 number of water molecules(of our choice, say 800 molecules in a box with dimension 30A x 30A x 30A box). ]

I, then, manually added Na+ ions, using Add ions from Modelling = section of extensions.

I then calculated the minimum and maximum value of x, y, and z=20 coordinates of to find the center and the length of each coordinate of=20 the water box, using libre calc.
In namd graphical=20 interface, I set the time step to 1fs. So, for minimisations, I gave=20 10^6 steps (0.1ns) and for dynamics 2*10^7 steps (2ns). I selected NPT=20 ensemble (with desired temperature and pressure), and gave periodic=20 boundary conditions (for which xsc file was generated using the=20 calculations from libre calc); also provided particle Mesh Ewald for=20 electrostatic interactions. In simulation space partitioning, I gave the cut off distance as 12 A. All other simulation parameters, I used the=20 default itself. And gave NAMD Run.But then, the dcd file is found to be=20 empty.





Central University of Tamil Nadu is in not responsible for the cont= ents of this email. The sender takes responsibility for the content of this= email. This mail is also governed by the relevant disclaim= er policies of=C2=A0Central University of Tamil Nadu.
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charset=utf-8 Content-Transfer-Encoding: quoted-printable When you generate psf and pdb after ion add you view all system ?=20 Enviado desde mi iPhone > El 2 set. 2021, a la(s) 9:42 a. m., Krithika Unmesh escribi=C3=B3: >=20 > =EF=BB=BF > I was trying to simulate an ATP molecule using NAMD and VMD. I was followi= ng various tutorials on NAMD available on internet. All the tutorials are ba= sed on proteins. What I understood is, it is different from ATP. While I was= performing the minimization and NAMD run, it was running without any error.= But, the resulting dcd file is found to be empty. It does not having any mo= lecule. In fact I am not able to understand the mistakes I am making. >=20 > I will write in detail various steps and trials I did. >=20 > I first loaded the pdb file in VMD. In fact, I collected three different p= db structures. I then generated the psf file using Automatic psf Builder fro= m the extension menu in vmd. But, here also I was having doubts. ATP contain= s 31 atoms without hydrogen and 47 with hydrogen. But, even before generatin= g psf files, the loaded molecule was found to contain 47 atoms and to my sur= prise, after generating psf file, the number of atoms was reduced to 43. I t= ried with all the 3 pdb files I collected and for all the three, the same th= ing happened. >=20 > Then, for solvation, I typed the following command in Tk Console: > package require solvate > solvate atp.psf atp.pdb -t 30 -o atp_wb >=20 > [And I could not get how we could provide solvent models such as tip3p, sp= ce etc. But, here I could not find it in any step. Also, is it possible to s= et a desired number of water molecules(of our choice, say 800 molecules in a= box with dimension 30A x 30A x 30A box). ] >=20 > I, then, manually added Na+ ions, using Add ions from Modelling section of= extensions. >=20 > I then calculated the minimum and maximum value of x, y, and z coordinates= of to find the center and the length of each coordinate of the water box, u= sing libre calc. > In namd graphical interface, I set the time step to 1fs. So, for minimisat= ions, I gave 10^6 steps (0.1ns) and for dynamics 2*10^7 steps (2ns). I selec= ted NPT ensemble (with desired temperature and pressure), and gave periodic b= oundary conditions (for which xsc file was generated using the calculations f= rom libre calc); also provided particle Mesh Ewald for electrostatic interac= tions. In simulation space partitioning, I gave the cut off distance as 12 A= . All other simulation parameters, I used the default itself. And gave NAMD R= un.But then, the dcd file is found to be empty. >=20 >=20 >=20 >=20 > Central University of Tamil Nadu is in not responsible for the contents of= this email. The sender takes responsibility for the content of this email. T= his mail is also governed by the relevant disclaimer policies of Central Uni= versity of Tamil Nadu. --Apple-Mail-3A7A603C-2F92-4448-99A9-78BB2D18924C Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable When you generate psf and pdb after ion add= you view all system ? 


Enviado= desde mi iPhone

El 2 se= t. 2021, a la(s) 9:42 a. m., Krithika Unmesh <krithika17@students.cu= tn.ac.in> escribi=C3=B3:

=EF=BB=BF
I was tryin= g to simulate an ATP molecule using NAMD and=20 VMD. I was following various tutorials on NAMD available on internet.=20 All the tutorials are based on proteins. What I understood is, it is=20 different from ATP. While I was performing the minimization and NAMD=20 run, it was running without any error. But, the resulting dcd file is=20 found to be empty. It does not having any molecule. In fact I am not=20 able to understand the mistakes I am making.

I will write in detail various steps and trials I did.

I first loaded the pdb file in VMD. In fact, I collected three different=20 pdb structures. I then generated the psf file using Automatic psf=20 Builder from the extension menu in vmd. But, here also I was having=20 doubts. ATP contains 31 atoms without hydrogen and 47 with hydrogen.=20 But, even before generating psf files, the loaded molecule was found to=20 contain 47 atoms and to my surprise, after generating psf file, the=20 number of atoms was reduced to 43. I tried with all the 3 pdb files I=20 collected and for all the three, the same thing happened.

Then, for solvation, I typed the following c= ommand in Tk Console:
package require solvate
solvate atp.psf atp.pdb -t 30 -o atp_wb

[And I could not get how we could provide solvent models such as tip3p, spce etc. But, here I could not find it in any step. Also, is it possible to set a desired=20 number of water molecules(of our choice, say 800 molecules in a box with dimension 30A x 30A x 30A box). ]

I, then, manually added Na+ ions, using Add ions from Modelling se= ction of extensions.

I then calculated the minimum and maximum value of x, y, and z=20 coordinates of to find the center and the length of each coordinate of=20 the water box, using libre calc.
In namd graphical=20= interface, I set the time step to 1fs. So, for minimisations, I gave=20 10^6 steps (0.1ns) and for dynamics 2*10^7 steps (2ns). I selected NPT=20 ensemble (with desired temperature and pressure), and gave periodic=20 boundary conditions (for which xsc file was generated using the=20 calculations from libre calc); also provided particle Mesh Ewald for=20 electrostatic interactions. In simulation space partitioning, I gave the cut off distance as 12 A. All other simulation parameters, I used the=20 default itself. And gave NAMD Run.But then, the dcd file is found to be=20 empty.





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Fri, 3 Sep 2021 19:05:48 +0000 Date: Fri, 3 Sep 2021 19:05:39 +0000 (UTC) From: "oivalf_nix@yahoo.com" To: NAMD DISCUSSION LIST Message-ID: <2090202302.1394638.1630695939738@mail.yahoo.com> Subject: namd-l: Binary coordinates NAMD 2.14 Content-Type: multipart/alternative; boundary="----=_Part_1394637_113304454.1630695939736" References: <2090202302.1394638.1630695939738.ref@mail.yahoo.com> X-Mailer: WebService/1.1.18924 YahooMailAndroidMobile X-CLX-Response: 1TFkXGR0TEQpMehcZGxkRCllEF21rUB4ZSWBhfnxIEQpYWBdvH0R5W0FsGk1 5ehEKeE4XekQcHW9FbG1EQ2YRCnhLF28fRHlbQWwaTXl6EQp4TBdpAV1jE11HW29mRxEKeUwXaQ FdYxNdR1tvZkcRCkNIFwcYHh0RCkNZFwcbExsRCkNJFxoEGhoaEQpZTRdnZnIRCllJFxgbcRsGH hh3BhgaGgYbGhpCHQYaBh8SBhpxGhAadwYaBhoGGgYaBhoGGnEaEBp3BhoRClleF2xseREKSUYX X0NfSXVCRVleT04RCkNOF21SYWhkSEITUlAYYHViTXpzXmFCW1NPHkZlT0xLXXJGEQpYXBcfBBo EGBkZBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NLaEtaEQpNXBcbGxwRCkxaF2hta2trEQpMRh dva2tva2sRCkJPF2Z4Zh9pWWxhfl1rEQpDWhcdHgQcBBsZHwQeGBEKQl4XGxEKQlwXGxEKXk4XG xEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmEQpCRRdtfnhZXnt+QhwSHBEKQk4XekQc HW9FbG1EQ2YRCkJMF28fRHlbQWwaTXl6EQpCbBdvH0R5W0FsGk15ehEKQkAXYlp8bXBNXhNcaUU RCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXHBEKeUMXbVkZWmd+Qhtuc38RCllLFxMdGB8RCl pLFxMdGB8RCnBoF24Ba3tdE3NvYmYfEAcZGhEKcGgXYFNSGWJES1hbeGgQBxkaEQpwaBdoZ05YH 3NtS2tYThAHGRoRCnBoF2tIaVxyQ0ZeZwESEAcZGhEKcGgXZXB9ZEJoHV9dZB4QBxkaEQpwfRdg Z3B9aFNaGxt8ARAHGRoRCnB9F2t9RHwaGV5+HW1+EBweEQpwfxdlWHIYHUkYXkZpfBAbGR0RCnB fF2YFYVpsa05lWEkBEAcZGhEKcH8XaRpifm5HQBxFXG8QHB8RCnBfF258bBhOY05MUGMZEBwfEQ pwbBdhZF8bbnB9bkRkZxAHGRoRCnBMF2BOE1ATRENmaXhfEAcZGhEKbX4XBxsRClhNF0sRIA== X-Proofpoint-GUID: GxKBNbh9xz2J_HgPYtKhqye4lOefawXl X-Proofpoint-ORIG-GUID: GxKBNbh9xz2J_HgPYtKhqye4lOefawXl X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 spamscore=0 clxscore=379 phishscore=0 mlxscore=0 suspectscore=0 bulkscore=0 mlxlogscore=999 impostorscore=0 adultscore=0 priorityscore=313 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109030112 domainage_hfrom=9725 domainage_replyto=9725 X-Spam-Score: 0 X-Spam-OrigSender: oivalf_nix@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "oivalf_nix@yahoo.com" ------=_Part_1394637_113304454.1630695939736 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi. I upgrade to NAMD 2.14 and foind the following problem: Does v2.14 use only binary files??? Info: NAMD 2.14 for Linux-x86_64-MPI-memoptWarning:=C2=A0Warning:=C2=A0 =C2= =A0 =C2=A0 =C2=A0 ***=C2=A0 EXPERIMENTAL MEMORY OPTIMIZED VERSION=C2=A0 ***= Warning:=C2=A0Info:=C2=A0Info: Please visit http://www.ks.uiuc.edu/Research= /namd/Info: for updates, documentation, and support information.Info:=C2=A0= Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.= 1063/5.0014475Info: in all publications reporting results obtained with NAM= D.Info:=C2=A0Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpi= cxxInfo: Built Wed Aug 11 15:56:56 -03 2021 by root on headnode.ada.cenapad= .unicamp.brInfo: 1 NAMD=C2=A0 2.14=C2=A0 Linux-x86_64-MPI-memopt=C2=A0 128= =C2=A0 =C2=A0 adagp04=C2=A0 faseixasInfo: Running on 128 processors, 128 no= des, 1 physical nodes.Info: CPU topology information available.Info: Charm+= +/Converse parallel runtime startup completed at 4.18685 sInfo: 8740.82 MB = of memory in use based on /proc/self/statInfo: Configuration file is ./inpu= t.confInfo: Changed directory to .TCL: Suspending until startup complete.Wa= rning: The following variables were set in theWarning: configuration file b= ut will be ignored:Warning:=C2=A0 =C2=A0 fixedAtomsFile (fixedatoms)Warning= :=C2=A0 =C2=A0 fixedAtomsCol (fixedatoms)FATAL ERROR: bincoordinates not fo= und in the configuration file for the memory optimized version![Partition 0= ][Node 0] End of program Enviado do Yahoo Mail no Android ------=_Part_1394637_113304454.1630695939736 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable Hi.

I upgrade to NAMD 2.14 and fo= ind the following problem:

Do= es v2.14 use only binary files???

Info: NAMD 2.14 for Linux-x86_64-MPI-me= mopt
Warning:&nbs= p;
Warning: =       ***  EXPERIMENTAL MEMORY OPTIMIZED VERSION = ***
Warning:&nbs= p;
Info: 
Info: Please visit = http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support informat= ion.
Info: <= /div>
Info: Please cite= Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all public= ations reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 61002 for mpi-linux-= x86_64-mpicxx
Inf= o: Built Wed Aug 11 15:56:56 -03 2021 by root on headnode.ada.cenapad.unica= mp.br
Info: 1 NAM= D  2.14  Linux-x86_64-MPI-memopt  128    adagp04&n= bsp; faseixas
Inf= o: Running on 128 processors, 128 nodes, 1 physical nodes.
Info: CPU topology information av= ailable.
Info: Ch= arm++/Converse parallel runtime startup completed at 4.18685 s
Info: 8740.82 MB of memory in= use based on /proc/self/stat
Info: Configuration file is ./input.conf
Info: Changed directory to .
TCL: Suspending until star= tup complete.
War= ning: The following variables were set in the
Warning: configuration file but will be ignore= d:
Warning: =   fixedAtomsFile (fixedatoms)
Warning:    fixedAtomsCol (fixedatoms)
FATAL ERROR: bincoordina= tes not found in the configuration file for the memory optimized version!
[Partition 0][Node= 0] End of program


=


Enviado do Yahoo Mail no Android
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boundary="00000000000019b8a705cb1c35bb" X-CLX-Response: 1TFkXGxIaEQpMehcZHh4RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGRofEQpDWRcHGxsSEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwacRkTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxIcfVl8TVt8fF5eHR4YZEwTSAdAdWsSU3oSUl1+HnVhEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc0toWksRCk1cFx4TExEKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbEhgRCkJeFxsRCkReFxoRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4 YBEKQmwXYV96UxlDRBp6G34RCkJAF2MeHHBpQ3kBH29/EQpCWBdnc2VzQG5hYUxdYhEKWlgXGBE KeUMXZ0ABYQVNUkgYfG0RCnBoF2ByH2hTbVtwUER+EBkaEQpwaBdlUGxzfBNdZFNlbxAZGhEKcG gXa01LfWsYWxtaYkwQGRoRCnBoF20TZmhCUhldQAVTEBkaEQpwaBd6QVhHWEVaWwVzTRAZGhEKc GwXZh97WFxiBUtYZB8QGRoRCnBMF2BOE1ATRENmaXhfEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 86WsVgqVVtt742Nf9b-j_A8yP8xwT4_K X-Proofpoint-ORIG-GUID: 86WsVgqVVtt742Nf9b-j_A8yP8xwT4_K X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 clxscore=180 adultscore=0 spamscore=0 priorityscore=344 bulkscore=0 mlxlogscore=999 suspectscore=0 malwarescore=0 mlxscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109030113 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000019b8a705cb1c35bb Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable By switching to the memory optimized version you commit to using binary coordinates/velocities files. Using PDBs as restart files is never a good idea for systems of any size, but for large systems the chances that you run into the PDB format's range limitations become dangerously high. Giacomo On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix@REMOVE_yahoo.com < oivalf_nix@remove_yahoo.com> wrote: > Hi. > > I upgrade to NAMD 2.14 and foind the following problem: > > Does v2.14 use only binary files??? > > Info: NAMD 2.14 for Linux-x86_64-MPI-memopt > Warning: > Warning: *** EXPERIMENTAL MEMORY OPTIMIZED VERSION *** > Warning: > Info: > Info: Please visit http://www.ks.uiuc.edu/Research/namd/ > Info: for updates, documentation, and support information. > Info: > Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) > doi:10.1063/5.0014475 > Info: in all publications reporting results obtained with NAMD. > Info: > Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx > Info: Built Wed Aug 11 15:56:56 -03 2021 by root on > headnode.ada.cenapad.unicamp.br > Info: 1 NAMD 2.14 Linux-x86_64-MPI-memopt 128 adagp04 faseixas > Info: Running on 128 processors, 128 nodes, 1 physical nodes. > Info: CPU topology information available. > Info: Charm++/Converse parallel runtime startup completed at 4.18685 s > Info: 8740.82 MB of memory in use based on /proc/self/stat > Info: Configuration file is ./input.conf > Info: Changed directory to . > TCL: Suspending until startup complete. > Warning: The following variables were set in the > Warning: configuration file but will be ignored: > Warning: fixedAtomsFile (fixedatoms) > Warning: fixedAtomsCol (fixedatoms) > FATAL ERROR: bincoordinates not found in the configuration file for the > memory optimized version! > [Partition 0][Node 0] End of program > > > > > Enviado do Yahoo Mail no Android > > --00000000000019b8a705cb1c35bb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
By switching to the memory optimized version you commit to= using binary coordinates/velocities files.=C2=A0 Using PDBs as restart fil= es is never a good idea for systems of any size, but for large systems the = chances that you run into the PDB format's range limitations become dan= gerously high.

Giacomo

On Fri, Sep 3, 2021 at 3:08 = PM oivalf_nix@REMOVE_yahoo.com <oivalf_nix@remove_yahoo.com> wrote:
Hi.

I upgrade to NAMD 2.14 = and foind the following problem:

Does v2.14 use only binary files???

Info: NAMD 2.14= for Linux-x86_64-MPI-memopt
Warning:= =C2=A0
Warning:=C2=A0 =C2=A0 =C2=A0 =C2= =A0 ***=C2=A0 EXPERIMENTAL MEMORY OPTIMIZED VERSION=C2=A0 ***
Warning:=C2=A0
= Info:=C2=A0
Info: for u= pdates, documentation, and support information.
Info:=C2=A0
Info: Please cite = Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all publications reporting result= s obtained with NAMD.
Info:=C2=A0
=
Info: Based on Charm++/Converse 61002 for mp= i-linux-x86_64-mpicxx
Info: Built Wed A= ug 11 15:56:56 -03 2021 by root on headnode.ada.c= enapad.unicamp.br
Info: 1 NAMD=C2= =A0 2.14=C2=A0 Linux-x86_64-MPI-memopt=C2=A0 128=C2=A0 =C2=A0 adagp04=C2=A0= faseixas
Info: Running on 128 processo= rs, 128 nodes, 1 physical nodes.
Info: = CPU topology information available.
Inf= o: Charm++/Converse parallel runtime startup completed at 4.18685 s
Info: 8740.82 MB of memory in use based on /pr= oc/self/stat
Info: Configuration file i= s ./input.conf
Info: Changed directory = to .
TCL: Suspending until startup comp= lete.
Warning: The following variables = were set in the
Warning: configuration = file but will be ignored:
Warning:=C2= =A0 =C2=A0 fixedAtomsFile (fixedatoms)
= Warning:=C2=A0 =C2=A0 fixedAtomsCol (fixedatoms)
FATAL ERROR: bincoordinates not found in the configuration file f= or the memory optimized version!
[Parti= tion 0][Node 0] End of program


<= br>

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Fri, 3 Sep 2021 19:58:59 +0000 Date: Fri, 3 Sep 2021 19:58:55 +0000 (UTC) From: "oivalf_nix@yahoo.com" To: "namd-l@ks.uiuc.edu" , Giacomo Fiorin Message-ID: <584673318.1399504.1630699135701@mail.yahoo.com> In-Reply-To: References: <2090202302.1394638.1630695939738.ref@mail.yahoo.com> <2090202302.1394638.1630695939738@mail.yahoo.com> Subject: Re: namd-l: Binary coordinates NAMD 2.14 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1399503_1991682264.1630699135699" X-Mailer: WebService/1.1.18924 YMailNorrin X-CLX-Response: 1TFkXGBofEQpMehcZGRMRCllEF21rUB4ZSWBhfnxIEQpYWBdvH0R5W0FsGk1 5ehEKeE4XekQcHW9FbG1EQ2YRCnlMF2kBXWMTXUdbb2ZHEQpDSBcHHhkZEQpDWRcHGxsSEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcZH3EbBh0adwYYGhoGGRpABhoGGxoaBhpxGhAadwYaBgcbGhoGG gYHHBoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XQGdlQUNvcHV6Tkxa aWUefk9NYUFfH1xOSR5FR15TZEARClhcFx8EGgQYGRkFGxoEGxoaBB4SBBgZEBseGh8aEQpeWRd zS2lnTBEKTVwXGBkYEQpMWhd/bU1raxEKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQpMRhdva2tsa2 sRCkJPF2hGeUdMAUwcW3JuEQpDWhcdHgQcBBsYEwQSGxEKQl4XGxEKRF4XGREKQlwXGxEKXk4XG xEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmEQpCRRdtfnhZXnt+QhwSHBEKQk4XekQc HW9FbG1EQ2YRCkJMF28fRHlbQWwaTXl6EQpCbBdvH0R5W0FsGk15ehEKQkAXYx4ccGlDeQEfb38 RCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGBEKeUMXZ0ABYQVNUkgYfG0RCllLFxMdGB8RCn BnF2lTQEJCUnxkcHNaEAcZGhEKcGgXaEFdH21eGE0cc0IQBxkaEQpwaBdtT0NnW2RPS21SfhAHG RoRCnBoF2tcWUBARmRrWGJnEAcZGhEKcGgXen4Ff21fREIFU0cQBxkaEQpwaBdtfhpOQk9nQEZH aRAHGRoRCnBsF2FkXxtucH1uRGRnEAcZGhEKbX4XBxsRClhNF0sRIA== X-Proofpoint-GUID: jMOkiEZ_PdfpCO4TegKku5vdc4omtyNj X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: jMOkiEZ_PdfpCO4TegKku5vdc4omtyNj X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 spamscore=0 lowpriorityscore=0 adultscore=0 priorityscore=339 mlxscore=0 impostorscore=0 clxscore=205 mlxlogscore=999 phishscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109030116 domainage_hfrom=9725 X-Spam-Score: 0 X-Spam-OrigSender: oivalf_nix@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "oivalf_nix@yahoo.com" ------=_Part_1399503_1991682264.1630699135699 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you Giacomo. However, I am using the CharmmGui output *.pdb and *.psf which are in text = format.Is there a way to convert them to binary, in order to use it as inpu= t for namd 2.14?? Regards, Flavio Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Giacomo Fiorin escreveu: =20 =20 By switching to the memory optimized version you commit to using binary co= ordinates/velocities files.=C2=A0 Using PDBs as restart files is never a go= od idea for systems of any size, but for large systems the chances that you= run into the PDB format's range limitations become dangerously high. Giacomo On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix@REMOVE_yahoo.com wrote: Hi. I upgrade to NAMD 2.14 and foind the following problem: Does v2.14 use only binary files??? Info: NAMD 2.14 for Linux-x86_64-MPI-memoptWarning:=C2=A0Warning:=C2=A0 =C2= =A0 =C2=A0 =C2=A0 ***=C2=A0 EXPERIMENTAL MEMORY OPTIMIZED VERSION=C2=A0 ***= Warning:=C2=A0Info:=C2=A0Info: Please visit http://www.ks.uiuc.edu/Research= /namd/Info: for updates, documentation, and support information.Info:=C2=A0= Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.= 1063/5.0014475Info: in all publications reporting results obtained with NAM= D.Info:=C2=A0Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpi= cxxInfo: Built Wed Aug 11 15:56:56 -03 2021 by root on headnode.ada.cenapad= .unicamp.brInfo: 1 NAMD=C2=A0 2.14=C2=A0 Linux-x86_64-MPI-memopt=C2=A0 128= =C2=A0 =C2=A0 adagp04=C2=A0 faseixasInfo: Running on 128 processors, 128 no= des, 1 physical nodes.Info: CPU topology information available.Info: Charm+= +/Converse parallel runtime startup completed at 4.18685 sInfo: 8740.82 MB = of memory in use based on /proc/self/statInfo: Configuration file is ./inpu= t.confInfo: Changed directory to .TCL: Suspending until startup complete.Wa= rning: The following variables were set in theWarning: configuration file b= ut will be ignored:Warning:=C2=A0 =C2=A0 fixedAtomsFile (fixedatoms)Warning= :=C2=A0 =C2=A0 fixedAtomsCol (fixedatoms)FATAL ERROR: bincoordinates not fo= und in the configuration file for the memory optimized version![Partition 0= ][Node 0] End of program Enviado do Yahoo Mail no Android =20 ------=_Part_1399503_1991682264.1630699135699 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thank you Giacomo.

However, I am using the CharmmGui output *.pdb and *.psf which a= re in text format.
Is there a w= ay to convert them to binary, in order to use it as input for namd 2.14??

Regards,

<= /div>
Flavio



=20
=20
Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Gia= como Fiorin <giacomo.fiorin@gmail.com> escreveu:


By swi= tching to the memory optimized version you commit to using binary coordinat= es/velocities files.  Using PDBs as restart files is never a good idea= for systems of any size, but for large systems the chances that you run in= to the PDB format's range limitations become dangerously high.

Giacomo

On = Fri, Sep 3, 2021 at 3:08 PM oivalf_nix@REMOVE_yahoo.com <o= ivalf_nix@remove_yahoo.com> wrote:
Hi.

I upgrade to NAMD 2.14 and foind the following problem= :

Does v2.14 use only binary fil= es???

<= /div>
Info: NAMD 2.= 14 for Linux-x86_64-MPI-memopt
Warning: 
Warnin= g:        ***  EXPERIMENTAL MEMORY OPTIMIZED VERSI= ON  ***
Warning: = ;
Info: 
Info: for updates, documentation,= and support information.
= Info: 
Info: Please c= ite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475=
Info: in all publications= reporting results obtained with NAMD.
Info: 
I= nfo: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx
Info: Built Wed Aug 11 15:56:56 -03 = 2021 by root on headnode.ada.cenapad.unicamp.br
Info: 1 NAMD  2.14  Linux-x86_64-MPI= -memopt  128    adagp04  faseixas
Info: Running on 128 processors, 128 nodes, 1 p= hysical nodes.
Info: CPU t= opology information available.
Info: Charm++/Converse parallel runtime startup completed at 4.18685 s=
Info: 8740.82 MB of memor= y in use based on /proc/self/stat
Info: Configuration file is ./input.conf
Info: Changed directory to .
TCL: Suspending until startup complete.
Warning: The following variables we= re set in the
Warning: con= figuration file but will be ignored:
Warning:    fixedAtomsFile (fixedatoms)
Warning:    fixedAtomsCol (f= ixedatoms)
FATAL ERROR: bi= ncoordinates not found in the configuration file for the memory optimized v= ersion!
[Partition 0][Node= 0] End of program



=

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dkim=none (message not signed) header.d=none;gmail.com; dmarc=none action=none header.from=msu.edu; Received: from CH2PR12MB4892.namprd12.prod.outlook.com (2603:10b6:610:65::9) by CH2PR12MB4807.namprd12.prod.outlook.com (2603:10b6:610:a::23) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.4478.17; Fri, 3 Sep 2021 20:42:45 +0000 Received: from CH2PR12MB4892.namprd12.prod.outlook.com ([fe80::bc47:de4d:2ec8:f1bb]) by CH2PR12MB4892.namprd12.prod.outlook.com ([fe80::bc47:de4d:2ec8:f1bb%9]) with mapi id 15.20.4478.022; Fri, 3 Sep 2021 20:42:45 +0000 Subject: Re: namd-l: Binary coordinates NAMD 2.14 To: namd-l@ks.uiuc.edu, "oivalf_nix@yahoo.com" , Giacomo Fiorin References: <2090202302.1394638.1630695939738.ref@mail.yahoo.com> <2090202302.1394638.1630695939738@mail.yahoo.com> <584673318.1399504.1630699135701@mail.yahoo.com> From: Josh Vermaas Message-ID: <488dd835-f35c-05b4-afc6-1c8862bc5390@msu.edu> Date: Fri, 3 Sep 2021 16:42:44 -0400 User-Agent: Mozilla/5.0 (X11; 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charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Flavio, Is there a reason you are using the memopt version of NAMD? As Giacomo=20 said, the memopt version requires bincoordinates files. However, if you=20 are using CHARMM-GUI to build your system, I'm inclined to believe that=20 your system is smaller than the multiple-millions of atoms that might=20 make a memopt version of NAMD mandatory. -Josh On 9/3/21 3:58 PM, oivalf_nix@REMOVE_yahoo.com wrote: > Thank you Giacomo. > > However, I am using the CharmmGui output *.pdb and *.psf which are in=20 > text format. > Is there a way to convert them to binary, in order to use it as input=20 > for namd 2.14?? > > Regards, > > Flavio > > > > Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Giacomo Fiorin=20 > escreveu: > > > By switching to the memory optimized version you commit to using=20 > binary coordinates/velocities files.=C2=A0 Using PDBs as restart files is= =20 > never a good idea for systems of any size, but for large systems the=20 > chances that you run into the PDB format's range limitations become=20 > dangerously high. > > Giacomo > > On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix@REMOVE_yahoo.com=20 > > wrote: > > Hi. > > I upgrade to NAMD 2.14 and foind the following problem: > > Does v2.14 use only binary files??? > > Info: NAMD 2.14 for Linux-x86_64-MPI-memopt > Warning: > Warning: =C2=A0 =C2=A0 =C2=A0 ***=C2=A0 EXPERIMENTAL MEMORY OPTIMIZED= VERSION=C2=A0 *** > Warning: > Info: > Info: Please visit http://www.ks.uiuc.edu/Research/namd/ > > Info: for updates, documentation, and support information. > Info: > Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 > (2020) doi:10.1063/5.0014475 > Info: in all publications reporting results obtained with NAMD. > Info: > Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx > Info: Built Wed Aug 11 15:56:56 -03 2021 by root on > headnode.ada.cenapad.unicamp.br > > Info: 1 NAMD=C2=A0 2.14=C2=A0 Linux-x86_64-MPI-memopt=C2=A0 128 =C2= =A0 adagp04=C2=A0 faseixas > Info: Running on 128 processors, 128 nodes, 1 physical nodes. > Info: CPU topology information available. > Info: Charm++/Converse parallel runtime startup completed at 4.18685 s > Info: 8740.82 MB of memory in use based on /proc/self/stat > Info: Configuration file is ./input.conf > Info: Changed directory to . > TCL: Suspending until startup complete. > Warning: The following variables were set in the > Warning: configuration file but will be ignored: > Warning: =C2=A0 fixedAtomsFile (fixedatoms) > Warning: =C2=A0 fixedAtomsCol (fixedatoms) > FATAL ERROR: bincoordinates not found in the configuration file > for the memory optimized version! > [Partition 0][Node 0] End of program > > > > > Enviado do Yahoo Mail no Android > > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!pLTmlRIWBK4k1zRwhYeeLura8z-OkuSvoPXFFCrs4EEKD85HLSwuFFg= cFXRWrECidA$=20 --------------DE089FAC3265507A713215F7 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Flavio,

Is there a reason you are using the memopt version of NAMD? As Giacomo said, the memopt version requires bincoordinates files. However, if you are using CHARMM-GUI to build your system, I'm inclined to believe that your system is smaller than the multiple-millions of atoms that might make a memopt version of NAMD mandatory.

-Josh

On 9/3/21 3:58 PM, oivalf_nix@REMOVE_yahoo.com wrote:
=20=20=20=20=20=20
Thank you Giacomo.

However, I am using the CharmmGui output *.pdb and *.psf which are in text format.
Is there a way to convert them to binary, in order to use it as input for namd 2.14??

Regards,

Flavio



Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Giacomo Fiorin <giacomo.fiorin@gmail.com> escreveu: =


By switching to the memory optimized version you commit to using binary coordinates/velocities files.  Using PDBs as restart files is never a good idea for systems of any size, but for large systems the chances that you run into the PDB format's range limitations become dangerously high.

Giacomo

On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix@REMOVE_yahoo.com <oivalf_nix@remove_yahoo.com= > wrote:
Hi.

I upgrade to NAMD 2.14 and foind the following problem:

Does v2.14 use only binary files???

Info: NAMD 2.14 for Linux-x86_64-MPI-memopt
Warni= ng: 
Warni= ng:        ***  EXPERIMENTAL MEM= ORY OPTIMIZED VERSION  ***
Warni= ng: 
Info:=  
Info: for updates, documentation, and support information.
Info:=  
Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all publications reporting results obtained with NAMD.
Info:=  
Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx
Info: Built Wed Aug 11 15:56:56 -03 2021 by root on headnode.ada.cen= apad.unicamp.br
Info: 1 NAMD  2.14  Linux-x86_64-MPI-memopt=   128    adagp04  faseixas
Info: Running on 128 processors, 128 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 4.18685 s
Info: 8740.82 MB of memory in use based on /proc/self/stat
Info: Configuration file is ./input.conf
Info: Changed directory to .
TCL: Suspending until startup complete.
Warni= ng: The following variables were set in the
Warni= ng: configuration file but will be ignored:
Warni= ng:    fixedAtomsFile (fixedatoms)
Warni= ng:    fixedAtomsCol (fixedatoms)
FATAL ERROR: bincoordinates not found in the configuration file for the memory optimized version!
[Part= ition 0][Node 0] End of program





--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="_000_016865263EA24EAF95656C3D16744606msuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 0825e37c-ae85-43c1-0eed-08d96f37bd43 X-MS-Exchange-CrossTenant-originalarrivaltime: 04 Sep 2021 00:05:43.7703 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: ba2zhpa9cIOpU4DObdHH/kfiQdmo6bHRsFmUlOAjXO+2mhQsaTH86deBRofp9tCATDu5nY0A3tsMAYqP0lvSGw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB4246 X-CLX-Response: 1TFkXGBobEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxkaExEKQ1kXBxMdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIbcRsYEhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThd/T3JJHBNDEkRQHX8eS2FTWVloGl9+EmYbQFMSR2geWBEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4YEBseGh8aEQpeWRdzS2xQGhEKTVwXHBobEQpMWhd8aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxd6XnNBEk8baRxGcxEKQ1oXHhoEGxodBBgZHQ QfGxEKQl4XGxEKRF4XGBEKREkXGBEKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCT BdvYVgTGktdG0NBZREKQmwXYXkcHxJce09aaUIRCkJAF2NfRm1NcF1jQUNJEQpCWBdnc2VzQG5h YUxdYhEKWlgXHxEKeUMXZGFuGBtcGENefE8RCllLFxsYHx4aEQpwZxdhU3JnTFl7Tl99YhAZGhE KcGgXYHIfaFNtW3BQRH4QGRoRCnBoF2xbfxNzUGNsbVtNEBkaEQpwaBdic2FeEnlrQ05kSRAZGh EKcGgXZVlPfB1PX0BnYHIQGRoRCnBoF2laQGV8WXMBTEAeEBkaEQpwfRdvS098YBoTSQUcbRAZG hEKcH0XZkFyZgVAeW1tYk0QGRoRCnB/F2sdax5Te2djS216EBsbGhEKcF8XbkREfEF4GmReb3sQ GRoRCnB/F2Fmb1saZ2RCSB1bEBsbHREKcF8XZHNkR0sFYkVIY1sQExkRCnBsF2d4GkBiGEkafnl NEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: UeXc69i8nz7U4aKyssB0uT8L1jy8mB4r X-Proofpoint-ORIG-GUID: UeXc69i8nz7U4aKyssB0uT8L1jy8mB4r X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 spamscore=0 clxscore=201 phishscore=0 mlxscore=0 suspectscore=0 bulkscore=0 mlxlogscore=999 impostorscore=0 adultscore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109030138 domainage_hfrom=12540 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_016865263EA24EAF95656C3D16744606msuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Flavio, I think you misunderstand. NAMD 2.14 can be compiled with memopt turned eit= her on or off. For 99% of users, memopt off is the correct version. Whoever= compiled the module you are using needs to recompile it for turning memopt= off (the default), or you can compile 2.14 yourself. I have streamlined in= structions I keep handy for myself that lays out the process, https://urlde= fense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/b= lob/main/NAMD.md__;!!DZ3fjg!pc5iD9KMmOEOj0jB1WuKWx7HjCF6dMv8cj7L2dUbzVUnO6Q= 64CTmwSDWinFkHOb3BA$ . 2.14 is fine, but it=E2=80=99s the memopt part that = is unneeded for your use case. -Josh From: "oivalf_nix@yahoo.com" Reply-To: "oivalf_nix@yahoo.com" Date: Friday, September 3, 2021 at 4:57 PM To: "Vermaas, Josh" Subject: Assunto: Re: namd-l: Binary coordinates NAMD 2.14 Thank you Josh Our national computing laboratory aways uses the lastest version of the pro= grams. So, I will ask them to instal v2.12 Regards Flavio Enviado do Yahoo Mail no Android Em sex., 3 3e set. 3e 2021 =C3=A0s 17:42, Josh Vermaas escreveu: Hi Flavio, Is there a reason you are using the memopt version of NAMD? As Giacomo said= , the memopt version requires bincoordinates files. However, if you are usi= ng CHARMM-GUI to build your system, I'm inclined to believe that your syste= m is smaller than the multiple-millions of atoms that might make a memopt v= ersion of NAMD mandatory. -Josh On 9/3/21 3:58 PM, oivalf_nix@REMOVE_yahoo.com wrote: Thank you Giacomo. However, I am using the CharmmGui output *.pdb and *.psf which are in text = format. Is there a way to convert them to binary, in order to use it as input for n= amd 2.14?? Regards, Flavio Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Giacomo Fiorin escreveu: By switching to the memory optimized version you commit to using binary coo= rdinates/velocities files. Using PDBs as restart files is never a good ide= a for systems of any size, but for large systems the chances that you run i= nto the PDB format's range limitations become dangerously high. Giacomo On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix@REMOVE_yahoo.com > wrote: Hi. I upgrade to NAMD 2.14 and foind the following problem: Does v2.14 use only binary files??? Info: NAMD 2.14 for Linux-x86_64-MPI-memopt Warning: Warning: *** EXPERIMENTAL MEMORY OPTIMIZED VERSION *** Warning: Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: for updates, documentation, and support information. Info: Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.= 1063/5.0014475 Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx Info: Built Wed Aug 11 15:56:56 -03 2021 by root on headnode.ada.cenapad.un= icamp.br Info: 1 NAMD 2.14 Linux-x86_64-MPI-memopt 128 adagp04 faseixas Info: Running on 128 processors, 128 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 4.18685 s Info: 8740.82 MB of memory in use based on /proc/self/stat Info: Configuration file is ./input.conf Info: Changed directory to . TCL: Suspending until startup complete. Warning: The following variables were set in the Warning: configuration file but will be ignored: Warning: fixedAtomsFile (fixedatoms) Warning: fixedAtomsCol (fixedatoms) FATAL ERROR: bincoordinates not found in the configuration file for the mem= ory optimized version! [Partition 0][Node 0] End of program Enviado do Yahoo Mail no Android -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!pc5iD9KMmOEOj0jB1WuKWx7HjCF6dMv8cj7L2dUbzVUnO6Q64CTmwSD= WinFp7cGv0w$=20 --_000_016865263EA24EAF95656C3D16744606msuedu_ Content-Type: text/html; charset="utf-8" Content-ID: Content-Transfer-Encoding: Quoted-printable

Hi Flavio,

 

I think you misunderstand. NAMD 2.14 can be compiled= with memopt turned either on or off. For 99% of users, memopt off is the c= orrect version. Whoever compiled the module you are using needs to recompil= e it for turning memopt off (the default), or you can compile 2.14 yourself. I have streamlined instructions I keep h= andy for myself that lays out the process, https://github.com/jvermaas/Software-Building-Instructions/bl= ob/main/NAMD.md. 2.14 is fine, but it=E2=80=99s the memopt part that is= unneeded for your use case.

 

-Josh

 

From= : "oivalf_nix@= yahoo.com" <oivalf_nix@yahoo.com>
Reply-To: "oivalf_nix@yahoo.com" <oivalf_nix@yahoo.com&= gt;
Date: Friday, September 3, 2021 at 4:57 PM
To: "Vermaas, Josh" <vermaasj@msu.edu>
Subject: Assunto: Re: namd-l: Binary coordinates NAMD 2.14

 

Thank you Josh 

 

Our national computing laboratory aways uses the las= test version of the programs. 

 

So, I will ask them to instal v2.12

 

Regards

 

Flavio 

 

 

 

Em = sex., 3 3e set. 3e 2021 =C3=A0s 17:42, Josh Vermaas

<= ;vermaasj@msu.edu> escreveu:

Hi Flavio,

Is there a reason you are using the memopt version of NAMD? As Giacomo said= , the memopt version requires bincoordinates files. However, if you are usi= ng CHARMM-GUI to build your system, I'm inclined to believe that your syste= m is smaller than the multiple-millions of atoms that might make a memopt version of NAMD mandatory.

-Josh

On 9/3/21 3:58 PM, oivalf_nix@REMOVE_yahoo.com wrote:

Thank you Giacomo.

 

However, I am using the CharmmGui output *.pdb and *.ps= f which are in text format.

Is there a way to convert them to binary, in order to u= se it as input for namd 2.14??

 

Regards,

 

Flavio

 

 

 

Em sexta-feira, 3 de setembro de 2021 16:= 43:02 BRT, Giacomo Fiorin <giacomo.f= iorin@gmail.com> escreveu:

 

 

By switching to the memory optimized vers= ion you commit to using binary coordinates/velocities files.  Using PD= Bs as restart files is never a good idea for systems of any size, but for large systems the chances that you run into the PDB f= ormat's range limitations become dangerously high.

 

Giacomo

 

On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix= @REMOVE_yahoo.com <oivalf_nix@remove_yahoo.com> wrote:

Hi.

 

I upgrade to NAMD 2.14 and foind the foll= owing problem:

 

Does v2.14 use only binary files???<= /o:p>

 

Info: NAMD 2.14 for Linux-x86_64-MPI-memo= pt

Warning: 

Warning:        ***&n= bsp; EXPERIMENTAL MEMORY OPTIMIZED VERSION  ***

Warning: 

Info: 

Info: for updates, documentation, and sup= port information.

Info: 

Info: Please cite Phillips et al., J. Che= m. Phys. 153:044130 (2020) doi:10.1063/5.0014475

Info: in all publications reporting resul= ts obtained with NAMD.

Info: 

Info: Based on Charm++/Converse 61002 for= mpi-linux-x86_64-mpicxx

Info: Built Wed Aug 11 15:56:56 -03 2021 = by root on headnode.ada.cenapad.unicamp.br

Info: 1 NAMD  2.14  Linux-x86_6= 4-MPI-memopt  128    adagp04  faseixas

Info: Running on 128 processors, 128 node= s, 1 physical nodes.

Info: CPU topology information available.=

Info: Charm++/Converse parallel runtime s= tartup completed at 4.18685 s

Info: 8740.82 MB of memory in use based o= n /proc/self/stat

Info: Configuration file is ./input.conf<= o:p>

Info: Changed directory to .

TCL: Suspending until startup complete.

Warning: The following variables were set= in the

Warning: configuration file but will be i= gnored:

Warning:    fixedAtomsFile (fix= edatoms)

Warning:    fixedAtomsCol (fixe= datoms)

FATAL ERROR: bincoordinates not found in = the configuration file for the memory optimized version!<= /p>

[Partition 0][Node 0] End of program=

 

 

 

 

 

-- 
Josh Vermaas
 
vermaasj@msu.edu=
Assistant Professor, Plant Research Laboratory and Biochemistry and Mo=
lecular Biology
Michigan State University
https://prl.natsci.msu.edu/=
people/faculty/josh-vermaas/
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boundary="_000_MA1PR01MB413288706742F9E4B4446C1FE3D29MA1PR01MB4132INDP_" X-OriginatorOrg: iisc.ac.in X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: MA1PR01MB4132.INDPRD01.PROD.OUTLOOK.COM X-MS-Exchange-CrossTenant-Network-Message-Id: 740373eb-1594-4153-4f8a-08d9715179fc X-MS-Exchange-CrossTenant-originalarrivaltime: 06 Sep 2021 16:15:00.1149 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 6f15cd97-f6a7-41e3-b2c5-ad4193976476 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: hPhNB+ShrjECoyUSL44WMfdfLdsNNBTFfpjuJPEjZ0AblwxnRrxAM/HBt9F/QPoJxaAS1TfzRq002s5BTMEeNw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: MAXPR01MB4213 X-Proofpoint-ORIG-GUID: t327H3qO8b2xokSmRJxUhop86hMoTyJj X-CLX-Shades: MLX X-Proofpoint-GUID: t327H3qO8b2xokSmRJxUhop86hMoTyJj X-CLX-Response: 1TFkXGRgZEQpMehcaEQpZRBdkARt5HGBoeUBZWREKWFgXbUVNQnMSfVNeXX8 RCnhOF2hMRU1yQHBcXXNjEQp5TBdnXmtiZnlAUmBpGxEKQ0gXBx4bHBEKQ1kXBxgcHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGxJxGwYZH3cGGBoaBhoGGgYdHwYZGnEbEBp3BhoGGgYaBhoGGgYac RoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XXhkYHWIZW2USSBhSRUF5R3hgUn9C RVoSHEJnRX5TYEARClhcFx8EGgQYGRkFGxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc0sBZ0ERCk1 cFxsfGhEKTFoXaGlNa2sRCkxGF29va2tra2sRCkJPF2x5U0NoWF1mS0hPEQpDWhceGgQbGh0EGx kTBB0TEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdoTEVNckBwXF1zYxEKQkkXaExFTXJAc Fxdc2MRCkJFF2QbT25BYxhwSX8TEQpCThdoTEVNckBwXF1zYxEKQkwXbUVNQnMSfVNeXX8RCkJs F21/X2UZQ31gaB9OEQpCQBdsUkhuTnISYlsZRhEKQlgXZGR4e34cYxkbBU0RCk1eFxsRClpYFxk RCnlDF3pIS3oFQ2hDUxl4EQpZSxcYGBgeEQpwaBdieQFibW5ka19lEhAZGhEKcGgXZRtSBUVGWk NGQHgQGRoRCnBoF2tIZHloaGRTfmBDEBkaEQpwaBdsGBNlYn1MZlwTTRAZGhEKcGgXZhxfa1pdZ 3hkExoQGRoRCnB9F2ZOQ15LXmFgeX9vEBkaEQpwfxdlS01Hb3AfeBNGBRAbGh0RCnBfF2lTQ2ls G2ljRhJ5EBkaEQpwbBdkSE9FUB5jQGhCXhAZGhEKbX4XGxEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 priorityscore=0 malwarescore=0 mlxlogscore=776 phishscore=0 lowpriorityscore=0 clxscore=323 suspectscore=0 impostorscore=0 adultscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2108310000 definitions=main-2109060104 domainage_hfrom=2224 X-Spam-Score: 0 X-Spam-OrigSender: venkatareddy@iisc.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Venkatareddy Dadireddy --_000_MA1PR01MB413288706742F9E4B4446C1FE3D29MA1PR01MB4132INDP_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Hi, I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9. I am following the protocol: https://urldefense.com/v3/__https://miaolab.ku= .edu/GaMD/tutorial_namd.html__;!!DZ3fjg!uR1u8UbK1TFiJzQDS6AOXJL5n-T_Ix3kl2O= 2GXTKg3JCKqO2SpouKhK1oiwSvSAUeGI_SzA$=20 I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. When I run conventional MD (cMD) on my test system, it runs quite faster (160ns/day) on single GPU. But when I use the same system for GaMD, it takes >3days with the following preparatory steps. accelMDGcMDPrepSteps 200000 accelMDGcMDSteps 1000000 accelMDGEquiPrepSteps 200000 accelMDGEquiSteps 25000000 timestep 2.0 # fs What I found is that 'CUDASOAintegrate on' accelerates the simulations but in case of GaMD equilibration and production steps the 'CUDASOAintegrate on' is not supported. In case of cMD, >90% GPU is used but in case of GaMD , only 13% of GPU is utilized. Please help me solving this problem. Thank you, Venkat --_000_MA1PR01MB413288706742F9E4B4446C1FE3D29MA1PR01MB4132INDP_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable
Hi,

I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
I am using some tutorial test file (pdb) to get hands on GaMD/NAMD.
When I run conventional MD (cMD) on my test system, it runs quite faster
(160ns/day) on single GPU. But when I use the same system for GaMD,
it takes >3days with the following preparatory steps.

accelMDGcMDPrepSteps      200= 000
accelMDGcMDSteps  1000000
accelMDGEquiPrepSteps      &nb= sp;200000
accelMDGEquiSteps   25000000
timestep 2.0 # fs

What I found is that 'CUDASOAintegrate on' accelerates the simulations
but in case of GaMD equilibration and production steps the
'CUDASOAintegrate on' is not supported.
In case of cMD, >90% GPU is used but in case of GaMD , only 13% of
GPU is utilized.
Please help me solving this problem.

Thank you,
Venkat




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dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=msu.edu; Received: from CH2PR12MB4892.namprd12.prod.outlook.com (2603:10b6:610:65::9) by CH2PR12MB4053.namprd12.prod.outlook.com (2603:10b6:610:7c::10) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.4478.22; Tue, 7 Sep 2021 14:08:01 +0000 Received: from CH2PR12MB4892.namprd12.prod.outlook.com ([fe80::bc47:de4d:2ec8:f1bb]) by CH2PR12MB4892.namprd12.prod.outlook.com ([fe80::bc47:de4d:2ec8:f1bb%9]) with mapi id 15.20.4478.024; Tue, 7 Sep 2021 14:08:01 +0000 Subject: Re: namd-l: GaMD is slower on GPU compared to cMD To: namd-l@ks.uiuc.edu, Venkatareddy Dadireddy , "namd-l-digest@ks.uiuc.edu" References: From: Josh Vermaas Message-ID: <52521c81-87c2-6f35-6b0a-2b2ee39f952e@msu.edu> Date: Tue, 7 Sep 2021 10:08:00 -0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 In-Reply-To: Content-Type: multipart/alternative; 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charset=windows-1252; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Venkat, Welcome to the wonderful world of alpha software. :D The performance you=20 see for conventional MD on normal GPUs is because it follows a new code=20 path that has been GPU optimized, and the simulation data doesn't leave=20 the GPU. Not everything in NAMD works that way, and so sometimes you get=20 to use the old code path, where the GPU computes only some of the terms=20 needed, and timestep integration has to happen on the CPU. Even if you=20 use more than 1 CPU to help accelerate the integration steps, shuffling=20 data back and forth still limits simulation performance on modern=20 hardware. So you aren't doing anything wrong per se (you are using more=20 than 1 CPU, right?), but your performance is going to be much worse=20 unless you fit your algorithm to fit the CUDASOAIntegrate codepath. -Josh On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote: > Hi, > > I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9. > I am following the protocol:=20 > https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutorial_namd.htm= l__;!!DZ3fjg!t0ZMZB01ovvii2oVGNN5oZSjFtMB-IYViaahbs6O8LRj8wWMPyinb8Afl0AIeD= qQf4KzyNg$=20=20 > > I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. > When I run conventional MD (cMD) on my test system, it runs quite faster > (160ns/day) on single GPU. But when I use the same system for GaMD, > it takes >3days with the following preparatory steps. > > accelMDGcMDPrepSteps=A0 =A0 =A0 200000 > accelMDGcMDSteps=A0 1000000 > accelMDGEquiPrepSteps=A0 =A0 =A0 =A0200000 > accelMDGEquiSteps=A0 =A025000000 > timestep 2.0 # fs > > What I found is that 'CUDASOAintegrate on' accelerates the simulations > but in case of GaMD equilibration and production steps the > 'CUDASOAintegrate on' is not supported. > In case of cMD, >90% GPU is used but in case of GaMD , only 13% of > GPU is utilized. > Please help me solving this problem. > > Thank you, > Venkat > > > > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!t0ZMZB01ovvii2oVGNN5oZSjFtMB-IYViaahbs6O8LRj8wWMPyinb8A= fl0AIeDqQvDlskOA$=20 --------------D9A239D2D9DF4AF50F62A3BB Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: Quoted-printable Hi Venkat,

Welcome to the wonderful world of alpha software. :D The performance you see for conventional MD on normal GPUs is because it follows a new code path that has been GPU optimized, and the simulation data doesn't leave the GPU. Not everything in NAMD works that way, and so sometimes you get to use the old code path, where the GPU computes only some of the terms needed, and timestep integration has to happen on the CPU. Even if you use more than 1 CPU to help accelerate the integration steps, shuffling data back and forth still limits simulation performance on modern hardware. So you aren't doing anything wrong per se (you are using more than 1 CPU, right?), but your performance is going to be much worse unless you fit your algorithm to fit the CUDASOAIntegrate codepath.

-Josh

On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote:
=20=20=20=20=20=20
Hi,

I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
I am using some tutorial test file (pdb) to get hands on GaMD/NAMD.
When I run conventional MD (cMD) on my test system, it runs quite faster
(160ns/day) on single GPU. But when I use the same system for GaMD,
it takes >3days with the following preparatory steps.

accelMDGcMDPrepSteps    &n= bsp; 200000
accelMDGcMDSteps  1000000
accelMDGEquiPrepSteps    &n= bsp;  200000
accelMDGEquiSteps   2500000= 0
timestep 2.0 # fs

What I found is that 'CUDASOAintegrate on' accelerates the simulations
but in case of GaMD equilibration and production steps the
'CUDASOAintegrate on' is not supported.
In case of cMD, >90% GPU is used but in case of GaMD , only 13% of
GPU is utilized.
Please help me solving this problem.

Thank you,
Venkat





--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.n=
atsci.msu.edu/people/faculty/josh-vermaas/
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Tue, 7 Sep 2021 14:08:01 +0000 Subject: Re: namd-l: GaMD is slower on GPU compared to cMD To: namd-l@ks.uiuc.edu, Venkatareddy Dadireddy , "namd-l-digest@ks.uiuc.edu" References: From: Josh Vermaas Message-ID: <52521c81-87c2-6f35-6b0a-2b2ee39f952e@msu.edu> Date: Tue, 7 Sep 2021 10:08:00 -0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.11.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------D9A239D2D9DF4AF50F62A3BB" Content-Language: en-US X-ClientProxiedBy: CH0PR04CA0109.namprd04.prod.outlook.com (2603:10b6:610:75::24) To CH2PR12MB4892.namprd12.prod.outlook.com (2603:10b6:610:65::9) Received: from [35.8.203.76] (35.8.203.76) by CH0PR04CA0109.namprd04.prod.outlook.com (2603:10b6:610:75::24) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.4500.14 via Frontend Transport; Tue, 7 Sep 2021 14:08:01 +0000 X-MS-PublicTrafficType: Email X-MS-Office365-Filtering-Correlation-Id: 51f0d2d7-e781-4023-04a8-08d97208e74c X-MS-TrafficTypeDiagnostic: CH2PR12MB4053: X-Microsoft-Antispam-PRVS: X-MS-Oob-TLC-OOBClassifiers: OLM:9508; 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charset=windows-1252; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Venkat, Welcome to the wonderful world of alpha software. :D The performance you=20 see for conventional MD on normal GPUs is because it follows a new code=20 path that has been GPU optimized, and the simulation data doesn't leave=20 the GPU. Not everything in NAMD works that way, and so sometimes you get=20 to use the old code path, where the GPU computes only some of the terms=20 needed, and timestep integration has to happen on the CPU. Even if you=20 use more than 1 CPU to help accelerate the integration steps, shuffling=20 data back and forth still limits simulation performance on modern=20 hardware. So you aren't doing anything wrong per se (you are using more=20 than 1 CPU, right?), but your performance is going to be much worse=20 unless you fit your algorithm to fit the CUDASOAIntegrate codepath. -Josh On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote: > Hi, > > I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9. > I am following the protocol:=20 > https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutorial_namd.htm= l__;!!DZ3fjg!uQcYvHNzuskaTzDCEXYY3I_ehMnzBgqURKRtox1v-A4cfy9NjLgNwgwj7UgAQ1= MVUA$=20=20 > > I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. > When I run conventional MD (cMD) on my test system, it runs quite faster > (160ns/day) on single GPU. But when I use the same system for GaMD, > it takes >3days with the following preparatory steps. > > accelMDGcMDPrepSteps=A0 =A0 =A0 200000 > accelMDGcMDSteps=A0 1000000 > accelMDGEquiPrepSteps=A0 =A0 =A0 =A0200000 > accelMDGEquiSteps=A0 =A025000000 > timestep 2.0 # fs > > What I found is that 'CUDASOAintegrate on' accelerates the simulations > but in case of GaMD equilibration and production steps the > 'CUDASOAintegrate on' is not supported. > In case of cMD, >90% GPU is used but in case of GaMD , only 13% of > GPU is utilized. > Please help me solving this problem. > > Thank you, > Venkat > > > > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!uQcYvHNzuskaTzDCEXYY3I_ehMnzBgqURKRtox1v-A4cfy9NjLgNwgw= j7UhBg2FMbw$=20 --------------D9A239D2D9DF4AF50F62A3BB Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: Quoted-printable Hi Venkat,

Welcome to the wonderful world of alpha software. :D The performance you see for conventional MD on normal GPUs is because it follows a new code path that has been GPU optimized, and the simulation data doesn't leave the GPU. Not everything in NAMD works that way, and so sometimes you get to use the old code path, where the GPU computes only some of the terms needed, and timestep integration has to happen on the CPU. Even if you use more than 1 CPU to help accelerate the integration steps, shuffling data back and forth still limits simulation performance on modern hardware. So you aren't doing anything wrong per se (you are using more than 1 CPU, right?), but your performance is going to be much worse unless you fit your algorithm to fit the CUDASOAIntegrate codepath.

-Josh

On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote:
=20=20=20=20=20=20
Hi,

I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
I am using some tutorial test file (pdb) to get hands on GaMD/NAMD.
When I run conventional MD (cMD) on my test system, it runs quite faster
(160ns/day) on single GPU. But when I use the same system for GaMD,
it takes >3days with the following preparatory steps.

accelMDGcMDPrepSteps    &n= bsp; 200000
accelMDGcMDSteps  1000000
accelMDGEquiPrepSteps    &n= bsp;  200000
accelMDGEquiSteps   2500000= 0
timestep 2.0 # fs

What I found is that 'CUDASOAintegrate on' accelerates the simulations
but in case of GaMD equilibration and production steps the
'CUDASOAintegrate on' is not supported.
In case of cMD, >90% GPU is used but in case of GaMD , only 13% of
GPU is utilized.
Please help me solving this problem.

Thank you,
Venkat





--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="000000000000663aa205cb7658fa" X-CLX-Response: 1TFkXGxkdEQpMehcZHhIRCllEF256fmtgR1lrfnBsEQpYWBd6WGZNaxJnGhp EYBEKeE4XY1Nja3sTWH4aX14RCnlMF2h7ekgdEmABa2QdEQpDSBcHGBMcEQpDWRcHHB0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsacRsGGBp3BhwZBhsaGkISBhoGBxkcBhpxGhAadwYaBhoGGgYaB hoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF2xrQ0F1YnlYE1lAUB9gZRhZ cE9DX2NJQmlNdWh8UwcTEQpYXBcfBBoEGBkZBRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc0hNYU8 RCk1cFwcdGBEKTFoXaGlNa2sRCkxGF29ra2traxEKQk8XaH1BYENafXNHQRMRCkNaFxgaEwQSHw QbGBIEHxgRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXYmtEeG9cbwFAb2sRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6WGZNaxJnGhpEYBEKQmwXbG9J fV1ORx5NE0ERCkJAF2Bgc2USG1MBeWMeEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxkRCnl DF2hPRlBaSEROYFtcEQpwaBdvXXJjHElzeUEYehAHGRoRCnBoF2FFbmhpfkhvT015EAcZGhEKcG gXZ35tSRNLXUkbT2QQBxkaEQpwaBdhY14dbhtdRVtYTRAHGRoRCnBoF2RCWnxYQUQbbFx5EAcZG hEKcH0XZ2Acc2tDZn1ZRkkQBxkaEQpwfRdgc2ZpYRltRmljEhAHGRoRCnB9F2l6Yh1vE2lvTW5/ EAcZGhEKcH8XZVhyGB1JGF5GaXwQEh0RCnBfF25rGGdDbmtQfU14EAcZGhEKcH8XZRl5Zl5HaRt kT3MQHx4RCnBfF2taWHJYYmNCaUVCEAcZGhEKcGwXbn5zElpEGB17HWQQBxkaEQptfhcHGxEKWE 0XSxEg X-Proofpoint-GUID: FAik_HSr9sjz5JO2sZeiuIchCg_BVy-9 X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: FAik_HSr9sjz5JO2sZeiuIchCg_BVy-9 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxlogscore=820 bulkscore=0 mlxscore=0 malwarescore=0 suspectscore=0 clxscore=137 phishscore=0 spamscore=0 lowpriorityscore=0 impostorscore=0 priorityscore=348 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109080043 X-Spam-Score: 0 X-Spam-OrigSender: sebastien.hoyas.pro@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?S=C3=A9bastien_Hoyas?= --000000000000663aa205cb7658fa Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear NAMD users, I am running ABF calculations. My reaction coordinate is split into multiple windows that I need to merge. I followed the instructions in the tutorials and in the colvar manual ( http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf, https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION0001262000= 00000000000 ) I added all the *.grad, *.count files in the same directory, adapted the colvar file with the full range of boundaries and added the "inputPrefix" (followed by the windows names) in the abf section and run 0 steps). I do not get any errors, but it does not produce the merged .pmf, .count and .grad (I am running calculations with NAMD 2.14). However, it works perfectly with NAMD 2.13. Is this a bug, or is there some additional keywords that must be added when using NAMD 2.14? Thank you in advance. Regards, S=C3=A9bastien --000000000000663aa205cb7658fa Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD users,

I am running ABF calcu= lations. My reaction coordinate is split into multiple windows that I need = to merge.

I added all the *.grad, *.count files in the same dir= ectory, adapted the colvar file with the full range of boundaries and added= the "inputPrefix" (followed by the windows names) in the abf sec= tion and run 0 steps). I do not get any errors, but it does not produce the= merged .pmf, .count and .grad (I am running calculations with NAMD 2.14).<= br>
However, it works perfectly with NAMD 2.13.

Is this a bug, or= is there some additional keywords that must be added when using NAMD 2.14?=

Thank you in advance.

Re= gards,

S=C3=A9bastien=C2=A0
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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Prof. Josh, Thank you for your explanation. It seems CUDASOAIntegrate is not for GaMD and some advance features in v3.0 are in development phase. When I use more cpu cores (>1), the GPU load goes down from ~13% to ~2%. With CUDASOAIntegrate disabled in v3.0, the performance of v3.0 is like v2.14 for cMD. v3.0 is many folds faster with CUDASOAIntegration. Thank you, Venkat ________________________________ From: owner-namd-l-digest@ks.uiuc.edu on = behalf of namd-l digest Sent: Wednesday, September 8, 2021 11:37 AM To: namd-l-digest@ks.uiuc.edu Subject: namd-l digest V1 #3135 External Email namd-l digest Wednesday, September 8 2021 Volume 01 : Number 3135 In this issue: namd-l: GaMD is slower on GPU compared to cMD Re: namd-l: GaMD is slower on GPU compared to cMD Re: namd-l: GaMD is slower on GPU compared to cMD ---------------------------------------------------------------------- Date: Mon, 6 Sep 2021 16:15:00 +0000 From: Venkatareddy Dadireddy Subject: namd-l: GaMD is slower on GPU compared to cMD Hi, I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9. I am following the protocol: https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutorial_namd.html_= _; !!DZ3fjg!uR1u8UbK1TFiJzQDS6AOXJL5n-T_Ix3kl2O2GXTKg3JCKqO2SpouKhK1oiwSvSAUeG= I_ SzA$ I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. When I run conventional MD (cMD) on my test system, it runs quite faster (160ns/day) on single GPU. But when I use the same system for GaMD, it takes >3days with the following preparatory steps. accelMDGcMDPrepSteps 200000 accelMDGcMDSteps 1000000 accelMDGEquiPrepSteps 200000 accelMDGEquiSteps 25000000 timestep 2.0 # fs What I found is that 'CUDASOAintegrate on' accelerates the simulations but in case of GaMD equilibration and production steps the 'CUDASOAintegrate on' is not supported. In case of cMD, >90% GPU is used but in case of GaMD , only 13% of GPU is utilized. Please help me solving this problem. Thank you, Venkat ------------------------------ Date: Tue, 7 Sep 2021 10:08:00 -0400 From: Josh Vermaas Subject: Re: namd-l: GaMD is slower on GPU compared to cMD Hi Venkat, Welcome to the wonderful world of alpha software. :D The performance you see for conventional MD on normal GPUs is because it follows a new code path that has been GPU optimized, and the simulation data doesn't leave the GPU. Not everything in NAMD works that way, and so sometimes you get to use the old code path, where the GPU computes only some of the terms needed, and timestep integration has to happen on the CPU. Even if you use more than 1 CPU to help accelerate the integration steps, shuffling data back and forth still limits simulation performance on modern hardware. So you aren't doing anything wrong per se (you are using more than 1 CPU, right?), but your performance is going to be much worse unless you fit your algorithm to fit the CUDASOAIntegrate codepath. - -Josh On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote: > Hi, > > I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9. > I am following the protocol: > https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutorial_namd.html_= _; !!DZ3fjg!t0ZMZB01ovvii2oVGNN5oZSjFtMB-IYViaahbs6O8LRj8wWMPyinb8Afl0AIeDqQf4= Kz yNg$ > > I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. > When I run conventional MD (cMD) on my test system, it runs quite faster > (160ns/day) on single GPU. But when I use the same system for GaMD, > it takes >3days with the following preparatory steps. > > accelMDGcMDPrepSteps 200000 > accelMDGcMDSteps 1000000 > accelMDGEquiPrepSteps 200000 > accelMDGEquiSteps 25000000 > timestep 2.0 # fs > > What I found is that 'CUDASOAintegrate on' accelerates the simulations > but in case of GaMD equilibration and production steps the > 'CUDASOAintegrate on' is not supported. > In case of cMD, >90% GPU is used but in case of GaMD , only 13% of > GPU is utilized. > Please help me solving this problem. > > Thank you, > Venkat > > > > - -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= ve rmaas/__;!!DZ3fjg!t0ZMZB01ovvii2oVGNN5oZSjFtMB-IYViaahbs6O8LRj8wWMPyinb8Afl= 0A IeDqQvDlskOA$ ------------------------------ Date: Tue, 7 Sep 2021 10:08:00 -0400 From: Josh Vermaas Subject: Re: namd-l: GaMD is slower on GPU compared to cMD Hi Venkat, Welcome to the wonderful world of alpha software. :D The performance you see for conventional MD on normal GPUs is because it follows a new code path that has been GPU optimized, and the simulation data doesn't leave the GPU. Not everything in NAMD works that way, and so sometimes you get to use the old code path, where the GPU computes only some of the terms needed, and timestep integration has to happen on the CPU. Even if you use more than 1 CPU to help accelerate the integration steps, shuffling data back and forth still limits simulation performance on modern hardware. So you aren't doing anything wrong per se (you are using more than 1 CPU, right?), but your performance is going to be much worse unless you fit your algorithm to fit the CUDASOAIntegrate codepath. - -Josh On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote: > Hi, > > I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9. > I am following the protocol: > https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutorial_namd.html_= _; !!DZ3fjg!uQcYvHNzuskaTzDCEXYY3I_ehMnzBgqURKRtox1v-A4cfy9NjLgNwgwj7UgAQ1MVUA= $ > > I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. > When I run conventional MD (cMD) on my test system, it runs quite faster > (160ns/day) on single GPU. But when I use the same system for GaMD, > it takes >3days with the following preparatory steps. > > accelMDGcMDPrepSteps 200000 > accelMDGcMDSteps 1000000 > accelMDGEquiPrepSteps 200000 > accelMDGEquiSteps 25000000 > timestep 2.0 # fs > > What I found is that 'CUDASOAintegrate on' accelerates the simulations > but in case of GaMD equilibration and production steps the > 'CUDASOAintegrate on' is not supported. > In case of cMD, >90% GPU is used but in case of GaMD , only 13% of > GPU is utilized. > Please help me solving this problem. > > Thank you, > Venkat > > > > - -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= ve rmaas/__;!!DZ3fjg!uQcYvHNzuskaTzDCEXYY3I_ehMnzBgqURKRtox1v-A4cfy9NjLgNwgwj7= Uh Bg2FMbw$ ------------------------------ End of namd-l digest V1 #3135 ***************************** --_000_MA1PR01MB4132A804984BBAC0AC24948EE3D49MA1PR01MB4132INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Dear Prof. Josh,

Thank you for your explanation.
It seems CUDASOAIntegrate is not for GaMD
and some advance features in v3.0 are in development phase.
When I use more cpu cores (>1), the GPU load
goes down from ~13% to ~2%.
With CUDASOAIntegrate disabled in v3.0,
the performance of v3.0 is like v2.14 for cMD.
v3.0 is many folds faster with CUDASOAIntegration.

Thank you,
Venkat


From: owner-namd-l-digest@k= s.uiuc.edu <owner-namd-l-digest@ks.uiuc.edu> on behalf of namd-l dige= st <owner-namd-l-digest@ks.uiuc.edu>
Sent: Wednesday, September 8, 2021 11:37 AM
To: namd-l-digest@ks.uiuc.edu <namd-l-digest@ks.uiuc.edu>
Subject: namd-l digest V1 #3135
 
External Email


namd-l digest      Wednesday, September 8 2021&nbs= p;     Volume 01 : Number 3135



In this issue:

    namd-l: GaMD is slower on GPU compared to cMD
    Re: namd-l: GaMD is slower on GPU compared to cMD
    Re: namd-l: GaMD is slower on GPU compared to cMD

----------------------------------------------------------------------

Date: Mon, 6 Sep 2021 16:15:00 +0000
From: Venkatareddy Dadireddy <venkatareddy@iisc.ac.in>
Subject: namd-l: GaMD is slower on GPU compared to cMD

Hi,

I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
I am following the protocol:
https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutor= ial_namd.html__;
!!DZ3fjg!uR1u8UbK1TFiJzQDS6AOXJL5n-T_Ix3kl2O2GXTKg3JCKqO2SpouKhK1oiwSvSAUeG= I_
SzA$
I am using some tutorial test file (pdb) to get hands on GaMD/NAMD.
When I run conventional MD (cMD) on my test system, it runs quite faster (160ns/day) on single GPU. But when I use the same system for GaMD,
it takes >3days with the following preparatory steps.

accelMDGcMDPrepSteps      200000
accelMDGcMDSteps  1000000
accelMDGEquiPrepSteps       200000
accelMDGEquiSteps   25000000
timestep 2.0 # fs

What I found is that 'CUDASOAintegrate on' accelerates the simulations
but in case of GaMD equilibration and production steps the
'CUDASOAintegrate on' is not supported.
In case of cMD, >90% GPU is used but in case of GaMD , only 13% of
GPU is utilized.
Please help me solving this problem.

Thank you,
Venkat

------------------------------

Date: Tue, 7 Sep 2021 10:08:00 -0400
From: Josh Vermaas <vermaasj@msu.edu>
Subject: Re: namd-l: GaMD is slower on GPU compared to cMD

Hi Venkat,

Welcome to the wonderful world of alpha software. :D The performance you see for conventional MD on normal GPUs is because it follows a new code
path that has been GPU optimized, and the simulation data doesn't leave
the GPU. Not everything in NAMD works that way, and so sometimes you get to use the old code path, where the GPU computes only some of the terms
needed, and timestep integration has to happen on the CPU. Even if you
use more than 1 CPU to help accelerate the integration steps, shuffling
data back and forth still limits simulation performance on modern
hardware. So you aren't doing anything wrong per se (you are using more
than 1 CPU, right?), but your performance is going to be much worse
unless you fit your algorithm to fit the CUDASOAIntegrate codepath.

- -Josh

On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote:
> Hi,
>
> I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
> I am following the protocol:
>
https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutor= ial_namd.html__;
!!DZ3fjg!t0ZMZB01ovvii2oVGNN5oZSjFtMB-IYViaahbs6O8LRj8wWMPyinb8Afl0AIeDqQf4= Kz
yNg$
>
<https://urldefense.com/v3/__https://miaolab.ku.edu/GaM= D/tutorial_namd.html__
;!!DZ3fjg!uR1u8UbK1TFiJzQDS6AOXJL5n-T_Ix3kl2O2GXTKg3JCKqO2SpouKhK1oiwSvSAUe= GI
_SzA$>
> I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. > When I run conventional MD (cMD) on my test system, it runs quite fast= er
> (160ns/day) on single GPU. But when I use the same system for GaMD, > it takes >3days with the following preparatory steps.
>
> accelMDGcMDPrepSteps      200000
> accelMDGcMDSteps  1000000
> accelMDGEquiPrepSteps       200000
> accelMDGEquiSteps   25000000
> timestep 2.0 # fs
>
> What I found is that 'CUDASOAintegrate on' accelerates the simulations=
> but in case of GaMD equilibration and production steps the
> 'CUDASOAintegrate on' is not supported.
> In case of cMD, >90% GPU is used but in case of GaMD , only 13% of<= br> > GPU is utilized.
> Please help me solving this problem.
>
> Thank you,
> Venkat
>
>
>
>

- --
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar
Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.edu/peopl= e/faculty/josh-ve
rmaas/__;!!DZ3fjg!t0ZMZB01ovvii2oVGNN5oZSjFtMB-IYViaahbs6O8LRj8wWMPyinb8Afl= 0A
IeDqQvDlskOA$

------------------------------

Date: Tue, 7 Sep 2021 10:08:00 -0400
From: Josh Vermaas <vermaasj@msu.edu>
Subject: Re: namd-l: GaMD is slower on GPU compared to cMD

Hi Venkat,

Welcome to the wonderful world of alpha software. :D The performance you see for conventional MD on normal GPUs is because it follows a new code
path that has been GPU optimized, and the simulation data doesn't leave
the GPU. Not everything in NAMD works that way, and so sometimes you get to use the old code path, where the GPU computes only some of the terms
needed, and timestep integration has to happen on the CPU. Even if you
use more than 1 CPU to help accelerate the integration steps, shuffling
data back and forth still limits simulation performance on modern
hardware. So you aren't doing anything wrong per se (you are using more
than 1 CPU, right?), but your performance is going to be much worse
unless you fit your algorithm to fit the CUDASOAIntegrate codepath.

- -Josh

On 9/6/21 12:15 PM, Venkatareddy Dadireddy wrote:
> Hi,
>
> I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
> I am following the protocol:
>
https://urldefense.com/v3/__https://miaolab.ku.edu/GaMD/tutor= ial_namd.html__;
!!DZ3fjg!uQcYvHNzuskaTzDCEXYY3I_ehMnzBgqURKRtox1v-A4cfy9NjLgNwgwj7UgAQ1MVUA= $
>
<https://urldefense.com/v3/__https://miaolab.ku.edu/GaM= D/tutorial_namd.html__
;!!DZ3fjg!uR1u8UbK1TFiJzQDS6AOXJL5n-T_Ix3kl2O2GXTKg3JCKqO2SpouKhK1oiwSvSAUe= GI
_SzA$>
> I am using some tutorial test file (pdb) to get hands on GaMD/NAMD. > When I run conventional MD (cMD) on my test system, it runs quite fast= er
> (160ns/day) on single GPU. But when I use the same system for GaMD, > it takes >3days with the following preparatory steps.
>
> accelMDGcMDPrepSteps      200000
> accelMDGcMDSteps  1000000
> accelMDGEquiPrepSteps       200000
> accelMDGEquiSteps   25000000
> timestep 2.0 # fs
>
> What I found is that 'CUDASOAintegrate on' accelerates the simulations=
> but in case of GaMD equilibration and production steps the
> 'CUDASOAintegrate on' is not supported.
> In case of cMD, >90% GPU is used but in case of GaMD , only 13% of<= br> > GPU is utilized.
> Please help me solving this problem.
>
> Thank you,
> Venkat
>
>
>
>

- --
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar
Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.edu/peopl= e/faculty/josh-ve
rmaas/__;!!DZ3fjg!uQcYvHNzuskaTzDCEXYY3I_ehMnzBgqURKRtox1v-A4cfy9NjLgNwgwj7= Uh
Bg2FMbw$

------------------------------

End of namd-l digest V1 #3135
*****************************

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Thanks Franvesco Pietra --0000000000000b270105cb786379 Content-Type: text/html; charset="UTF-8"
Does charmm36 provide a patch for non protonated lysine?
Thanks
Franvesco Pietra
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charset="UTF-8" X-Proofpoint-ORIG-GUID: -RUMQsarBy2nZBOvHHAsAiBO2TtqljdF X-CLX-Response: 1TFkXGx0TEQpMehcYExMRCllEF2BkGmkeckh4Xx5gEQpYWBdhW3Noc28ZSWF yXBEKeE4XY1Nja3sTWH4aX14RCnlMF2YSfXlJX2BjQWNFEQpDSBcHHRMRCkNZFwcbHh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxNxGRIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XB3h/Z3tZS1hoUxhEcGhlXGJia1lrQ2hlGH5eW0ZATmwRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzSEVGTxEKTVwXGxwYEQpMWhd4YWtBaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pAWn9aWEtwH3BdEQpDWhcYGhMEEh8EGBgbBB sdHREKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdkfnN8eXMda0tMQBEKQk4XY1Nja3sTWH4aX14RCkJMF2Fbc2hzbxlJYXJcEQpCbBd6 e2IfUHpFZwVHaBEKQkAXY2IYR1sdTl9QBWsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdiEhsYZR96YEJYbREKcGgXZGlBcFlFZV9GGR8QGRoRCnBoF29Bck9QAX5QH298EBkaEQpwaB dmRVlgZkR9bmloZBAZGhEKcGgXblpwX1NOAR56UGUQGRoRCnB9F2NBY3praQUeYhpZEBkaEQpwf xdjQWN6a2kFHmIaWRAZGhEKcGwXaEkbbx8TU0VOQlsQGRoRCnBMF21oZRlBUn17GEVSEBkaEQpt fhcbEQpYTRdLESA= X-Proofpoint-GUID: -RUMQsarBy2nZBOvHHAsAiBO2TtqljdF X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=179 phishscore=0 priorityscore=299 mlxlogscore=523 mlxscore=0 malwarescore=0 impostorscore=0 bulkscore=0 lowpriorityscore=0 spamscore=0 adultscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109080102 X-Spam-Score: 0 X-Spam-OrigSender: jeffcomer@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 188GSqHY013376 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeff Comer Yes, it does. There is a patch "LSN" in the "top_all36_prot.rtf". Jeff –––––––––––––––––––––––––––––––––––——————— Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!sNB4GvFOa-Ng__7iYL2BTGlSKKXs9k59iIjcDxgEKCHHSuAh_ypb-KcNAG_PC_t7Vw$ On Wed, Sep 8, 2021 at 4:21 AM Francesco Pietra wrote: > > Does charmm36 provide a patch for non protonated lysine? > Thanks > Franvesco Pietra From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 8 12:01:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 188H1el5015388; Wed, 8 Sep 2021 12:01:40 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 188H1em6015387; Wed, 8 Sep 2021 12:01:40 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 188H1deI015383; 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Wed, 08 Sep 2021 10:01:29 -0700 (PDT) References: In-Reply-To: From: Francesco Pietra Date: Wed, 8 Sep 2021 19:01:17 +0200 Message-ID: Subject: Re: namd-l: Patch for non protonated lysine To: Jeff Comer Cc: NAMD list Content-Type: multipart/alternative; boundary="0000000000005f74fd05cb7ed572" X-CLX-Response: 1TFkXGx0eEQpMehcZHxgRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHGxkTEQpDWRcHGx4eEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ecRkeEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1BfB3pDHWkHHh8acBlcQxJGR3hAQFtNXxIec2NQWhlLEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NIWm9sEQpNXBcTHBEKTFoXaXhpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGx MEHxoRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwX ZRhFRWJHS2FoS2wRCkJAF2NiGEdbHU5fUAVrEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXYhIbGGUfemBCWG0RCnBoF25lc2loUmMfGxJTEBoRCnBoF2tvQn1cfHsdUHNCEBoRCnBoF2 sfQkVaQ2FHZkRoEBoRCnBoF25+HVt8bkBlZ2xAEBoRCnBoF2ASXlphXnB/e2BsEBoRCnB9F2NBY 3praQUeYhpZEBoRCnB/F2NBY3praQUeYhpZEBoRCnBsF2R5fmRZZx5TU2lvEBoRCnBMF21oZRlB Un17GEVSEBoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: zu-Pi7C-450Z3vi8lmRjjqgu84YIzp3a X-CLX-Shades: MLX X-Proofpoint-GUID: zu-Pi7C-450Z3vi8lmRjjqgu84YIzp3a MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=428 adultscore=0 priorityscore=352 lowpriorityscore=0 mlxscore=0 suspectscore=0 bulkscore=0 impostorscore=0 malwarescore=0 clxscore=174 spamscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109080106 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000005f74fd05cb7ed572 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Jeff thanks a lot francesco On Wed, Sep 8, 2021 at 6:28 PM Jeff Comer wrote: > Yes, it does. There is a patch "LSN" in the "top_all36_prot.rtf". > > Jeff > > =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2= =80=94 > Jeffrey Comer, PhD > Associate Professor > Department of Anatomy and Physiology > Kansas State University > Office: P-213 Mosier Hall > Phone: 785-532-6311 > Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!ti8oY= 9-M13V3KKOAEf8IvWWgvryJJksw89wBMGW0CuWmUtQtP3DtC_kU-XGZtqC-dg$=20 > > On Wed, Sep 8, 2021 at 4:21 AM Francesco Pietra > wrote: > > > > Does charmm36 provide a patch for non protonated lysine? > > Thanks > > Franvesco Pietra > --0000000000005f74fd05cb7ed572 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Jeff
thanks a lot
francesco

On Wed, Sep 8, 2021 at 6:28 PM Jeff Comer <jeffcomer@gmail.com> wrote:
Yes, it does. There is a patch "LS= N" in the "top_all36_prot.rtf".

Jeff

=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Wed, Sep 8, 2021 at 4:21 AM Francesco Pietra <chiendarret@gmail.com> wrote:
>
> Does charmm36 provide a patch for non protonated lysine?
> Thanks
> Franvesco Pietra
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boundary="_000_SN6PR11MB28781744B09879344ECFB8CCB0D49SN6PR11MB2878namp_" --_000_SN6PR11MB28781744B09879344ECFB8CCB0D49SN6PR11MB2878namp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable Hello, Thanks to your help, Chris, I found that the sampling was indeed not adequa= te, and the PMF values were being inflated. However, the root problem still= stands; the PMF (and the PMF gradient) continues to heighten to an unreali= stic value, even long after the proteins should not be interacting anymore.= I am beginning to suspect that something is hindering the separation. Is t= here any way to help narrow down what this might be? Thanks, Ishaan From: Chris Chipot Sent: Thursday, August 26, 2021 1:16:14 PM To: Ishaan Roy Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation Hi, Ishaan, hard to say without specific detail. Still, please, check https://urldefens= e.com/v3/__https://doi.org/10.1080/08927022.2020.1775222__;!!DZ3fjg!r7ZuUmG= fAnbBUxIgFbhBlrgDXTBDIMVRIuI9iAy7EthweALME3PgIn6sn1ZKEg-jJw$ , which might = give you some pointers. Best regards, Chris On 8/26/21 11:08 AM, Ishaan Roy wrote: Hi Chris, I checked over the first and third points you mentioned (they appear fine),= but could you elaborate on the second point? Currently fullSamples is set = to 5000, would this be considered sufficient in a lipid membrane setting? Thanks, Ishaan From: Chris Chipot Sent: Thursday, August 26, 2021 2:42 AM To: namd-l@ks.uiuc.edu; Ishaan Roy; Peter Freddolino Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation Ishaan, there are a number of quantities that you ought to look into. First, you sh= ould histogram the difference between the extended variable and the actual = variable (from your traj file), and ascertain that it obeys a normal law. S= econd, you should make sure that your bias is properly applied, that is pas= t a threshold (fullSamples) of accrued force samples guaranteeing minimum n= on-equilibrium effects. Third, you should make sure that your distanceXY co= mponent is correctly defined, with the desired subsets of atoms. Regards, Chris On 8/26/21 12:28 AM, Ishaan Roy wrote: Hi Peter, Nothing stands out as weird about the runs, visually or otherwise. The samp= ling distribution is, I believe, as one would expect, generally increasing = for higher values of the coordinate and the trajectory follows a square-roo= t diffusion trend. There=92s no sign of the protein getting stuck anywhere. Thanks, Ishaan From: Peter Freddolino Sent: Wednesday, August 25, 2021 10:34 PM To: ; Ishaan Roy Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation Dear Ishaan, If your simulations haven't yet converged, there is really no sense in eval= uating the energies completely yet. With that said, how is the sampling loo= king across the different values of your reaction coordinate? Is the reacti= on coordinate stuck somewhere or is the system diffusing freely along it? Have you visually inspected your system to make sure nothing weird is happe= ning? Best, Peter On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy > wrote: Hello, I am using eABF to separate two membrane proteins to find the free binding = energy. The PMF values produced in my runs seem to be incredibly high compa= red to consistently reaching the 100s order of magnitude. We haven=92t comp= leted a run that plateaus in free energy yet, but this is an example showin= g what the PMF looks like. [cid:part9.F225B075.9737D567@illinois.edu] A maximum PMF this high already produces a value for the binding constant t= hat is on an order beyond 10^100. Besides being high, it might be worth men= tioning that the nonbonded energies are very close to 0 near the end of thi= s run, but the PMF gradient doesn=92t level off at all. Any ideas on what m= ight be causing this? Or is such a value plausible? This only seems to be a= problem with the separation runs; my other colvars produce PMF plots that = are closer to what I=92ve seen. Thanks, Ishaan -- Chris Chipot, Ph.D. CNRS research director, University of Lorraine Adjunct professor of physics, University of Illinois, Urbana-Champaign _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group 3161 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Urbana, Illinois 61801 Phone: (217) 244-4361 E-mail: chipot@illinois.edu Christophe.Chipot@Univ-Lorraine.fr Web: https://physics.illinois.edu https://urldefense.com/v3/__http://www= .lia-uiuc.cnrs.fr__;!!DZ3fjg!r7ZuUmGfAnbBUxIgFbhBlrgDXTBDIMVRIuI9iAy7EthweA= LME3PgIn6sn1blMUtJlw$ http://www.ks.uiuc.edu/~chipot Fiat justitia, et pereat mund= us --Heinrich von Kleist _______________________________________________________________________ -- Chris Chipot, Ph.D. CNRS research director, University of Lorraine Adjunct professor of physics, University of Illinois, Urbana-Champaign _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group 3161 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Urbana, Illinois 61801 Phone: (217) 244-4361 E-mail: chipot@illinois.edu Christophe.Chipot@Univ-Lorraine.fr Web: https://physics.illinois.edu https://urldefense.com/v3/__http://www= .lia-uiuc.cnrs.fr__;!!DZ3fjg!r7ZuUmGfAnbBUxIgFbhBlrgDXTBDIMVRIuI9iAy7EthweA= LME3PgIn6sn1blMUtJlw$=20 http://www.ks.uiuc.edu/~chipot Fiat justitia, et pereat mund= us --Heinrich von Kleist _______________________________________________________________________ --_000_SN6PR11MB28781744B09879344ECFB8CCB0D49SN6PR11MB2878namp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable

Hello,

 

Thanks to your help, Chris, I found that the samplin= g was indeed not adequate, and the PMF values were being inflated. However,= the root problem still stands; the PMF (and the PMF gradient) continues to= heighten to an unrealistic value, even long after the proteins should not be interacting anymore. I am begin= ning to suspect that something is hindering the separation. Is there any wa= y to help narrow down what this might be?

 

Thanks,

Ishaan

 

 

From: Chris Chipot <chipot@illinois.edu>
Sent: Thursday, August 26, 2021 1:16:14 PM
To: Ishaan Roy <royi@uchicago.edu>
Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation

 

Hi, Ishaan,

hard to say without specific detail. Still, please, check https://doi.org/10.1080/08927022.2020.1775222, which might give you som= e pointers.

Best regards,

Chris


On 8/26/21 11:08 AM, Ishaan Roy wrote:

Hi Chris,

 

I checked over the first and third points you mentioned (they appear fi= ne), but could you elaborate on the second point? Currently fullSamples is = set to 5000, would this be considered sufficient in a lipid membrane setting?

 

Thanks,

Ishaan

 

From: Chris Chipot
Sent: Thursday, August 26, 2021 2:42 AM
To: namd-l@ks.uiuc.edu; Ishaan Roy; Peter Freddolino<= br> Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation

 

Ishaan,

there are a number of quantities that you ought to look into. First, you sh= ould histogram the difference between the extended variable and the actual = variable (from your traj file), and ascertain that it obeys a normal law. Second, you sh= ould make sure that your bias is properly applied, that is past a threshold= (
fu= llSamples) of accrued force samples guaranteeing minimum non-equilibrium effects. Thi= rd, you should make sure that your distanceXY component is correctly define= d, with the desired subsets of atoms.

Regards,


Chris



On 8/26/21 12:28 AM, Ishaan Roy wrote:

Hi Peter,

 

Nothing stands out as weird about the runs, visually or otherwise. The = sampling distribution is, I believe, as one would expect, generally increas= ing for higher values of the coordinate and the trajectory follows a square-root diffusion trend. There=92s no sig= n of the protein getting stuck anywhere.

 

Thanks,

Ishaan

 

From: Peter Freddolino
Sent: Wednesday, August 25, 2021 10:34 PM
To: <namd-l@ks.uiuc.edu>= ; Ishaan Roy
Subject: Re: namd-l: Unrealistically High Keq in eABF Seperation

 

Dear Ishaan,

If your simulations haven't yet converged, there is really no sense in = evaluating the energies completely yet. With that said, how is the sampling= looking across the different values of your reaction coordinate? Is the reaction coordinate stuck somewhere or is= the system diffusing freely along it?

Have you visually inspected your system to make sure nothing weird is h= appening?

Best,

Peter

 

On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy <royi@uchicago.edu> wrote:

 

Hello,

 

I am using eABF to separate two membrane proteins to= find the free binding energy. The PMF values produced in my runs seem to b= e incredibly high compared to consistently reaching the 100s order of magnitude. We haven=92t completed a run that pl= ateaus in free energy yet, but this is an example showing what the PMF look= s like.

A maximum PMF this high already produces a value for= the binding constant that is on an order beyond 10^100. Besides being high= , it might be worth mentioning that the nonbonded energies are very close to 0 near the end of this run, but the P= MF gradient doesn=92t level off at all. Any ideas on what might be causing = this? Or is such a value plausible? This only seems to be a problem with th= e separation runs; my other colvars produce PMF plots that are closer to what I=92ve seen.

 

Thanks,

Ishaan

 

 



-- 
 
Chris Chipot, Ph.D.
CNRS research director, University of Lorra=
ine
Adjunct professor of physics, University of=
 Illinois, Urbana-Champaign
 
___________________________________________=
____________________________
 
Chris Chipot, Ph.D.    =
            &nb=
sp;   
Theoretical and Computational Biophysics Gr=
oup       
3161 Beckman Institute for Advanced Science=
 and Technology  
University of Illinois at Urbana-Champaign&=
nbsp;       
405 North Mathews    &n=
bsp;            =
;            &n=
bsp;    
Urbana, Illinois 61801   &nb=
sp;            =
            Phone: (=
217) 244-4361
 
       &=
nbsp;           &nbs=
p;         E-mail: chipot@illinois.edu
       &=
nbsp;           &nbs=
p;            &=
nbsp;    Christophe.Chipot@Univ-Lorraine.fr
       &=
nbsp;            &nb=
sp;        Web:    <=
a href=3D"https://physics.illinois.edu">https://physics.illinois.edu
       &=
nbsp;           &nbs=
p;            &=
nbsp;    http://www.lia-uiuc.cnrs.fr
       &=
nbsp;           &nbs=
p;            &=
nbsp;    http://w=
ww.ks.uiuc.edu/~chipot
 
       &=
nbsp;           &nbs=
p;             =
             Fi=
at justitia, et pereat mundus
       &=
nbsp;           &nbs=
p;            &=
nbsp;           &nbs=
p;     --Heinrich von Kleist 
___________________________________________=
____________________________

 




-- 
 
Chris Chipot, Ph.D.
CNRS research director, University of Lorra=
ine
Adjunct professor of physics, University of=
 Illinois, Urbana-Champaign
 
___________________________________________=
____________________________
 
Chris Chipot, Ph.D.    =
            &nb=
sp;   
Theoretical and Computational Biophysics Gr=
oup       
3161 Beckman Institute for Advanced Science=
 and Technology  
University of Illinois at Urbana-Champaign&=
nbsp;       
405 North Mathews    &n=
bsp;            =
;            &n=
bsp;    
Urbana, Illinois 61801   &nb=
sp;            =
            Phone: (=
217) 244-4361
 
       &=
nbsp;           &nbs=
p;         E-mail: chipot@illinois.edu
        =
            &nb=
sp;            =
    Christophe.Chipot@Univ-Lorraine.fr
       &=
nbsp;           &nbs=
p;         Web:    <=
a href=3D"https://physics.illinois.edu">https://physics.illinois.edu
       &=
nbsp;           &nbs=
p;             =
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       &=
nbsp;           &nbs=
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Thu, 09 Sep 2021 03:51:25 -0700 (PDT) MIME-Version: 1.0 From: Herald Delis Date: Thu, 9 Sep 2021 19:51:14 +0900 Message-ID: Subject: namd-l: Problem with speed of QMMM (namd2-ORCA) To: namd-l@ks.uiuc.edu Content-Type: multipart/related; boundary="000000000000bbf19405cb8dc71c" X-Proofpoint-ORIG-GUID: 236gN7mYEYnK9KxNjl4TPAO99YWvQ94S X-CLX-Response: 1TFkXEhwRCkx6FxkeGREKWUQXaXNAXXJHU3taGB0RClhYF3prUB56Em4SWl0 YEQp4ThdjU2NrexNYfhpfXhEKeUwXa1xbbxNdRx1NXRgRCkNIFwcYHB8RCkNZFwcbHhIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsdcRsGGR53Bh8cBhoGGgYZGQYZGnEbEBp3BhoGBx8aBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThcYGRxNZB1Hc29zRGETYVJkQEYe fnprZRMTc31cexMeeREKWFwXHwQaBBgZGQUbGgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NIHlxmEQp NXBccHREKTFoXbGlNa2sRCkxGF29ra2traxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGh IEGx0cEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RC kJFF2xBGBhrBRpzEkwSEQpCThdjU2NrexNYfhpfXhEKQkwXemtQHnoSbhJaXRgRCkJsF2VYe1tP elhjR3lDEQpCQBdjQlBnXU9eRxhdcxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnlDF2N cf11wHW9dZFBdEQpwaBd6Z3tjH0lvEnhMbhAZGhEKcGgXb2BQfFIBfR1/bBsQGRoRCnBoF2RCQx NhbVMTGktYEBkaEQpwaBdjQ1lOXFJnTBteUBAZGhEKcGgXenleaXBJBRJYfkMQGRoRCnB9F2N+G WhAXVxdRVgZEBkaEQpwYxdtXh5JHERsfltkbhAcHBEKcGMXYmB6RhppSx9SeFgQHB4RCnB/F2NT T25MZnAYTB56EBsaGREKcF8XaR1ERx5HYG5NaR8QGxobEQpwbBdsQXNkHVJTYVhoRxAZGhEKbX4 XGxEKWE0XSxEg X-Proofpoint-GUID: 236gN7mYEYnK9KxNjl4TPAO99YWvQ94S X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=86 phishscore=0 priorityscore=343 mlxlogscore=535 mlxscore=0 malwarescore=0 impostorscore=0 bulkscore=0 lowpriorityscore=0 spamscore=0 adultscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109090066 X-Spam-Score: 0 X-Spam-OrigSender: bioinfo2021great@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Herald Delis --000000000000bbf19405cb8dc71c Content-Type: multipart/alternative; boundary="000000000000bbf19205cb8dc71b" --000000000000bbf19205cb8dc71b Content-Type: text/plain; charset="UTF-8" [image: image.gif]Dear All, I am trying to run QMMM-MD using orca-namd2. But it happens to be too slow, I wanted to know if I am doing something wrong or is there a better way. I have a CPU node with 40 cores (and 4 unused GPU), my calculations of 75,000 atoms QMMM-Minimization takes 4 days. NAMD2 -> namd2 +p22 Min.conf ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf) # Number of simultaneous QM simulations per node QMSimsPerNode 20 Thanks and regards, Herald --000000000000bbf19205cb8dc71b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
3D"image.gif"Dear All,

I am trying to run QMMM-MD=C2= =A0using orca-namd2.
But it happens to be too slow, I wanted to k= now if I am doing something wrong or is there a better way.
I hav= e a CPU node with 40 cores (and 4 unused GPU), my calculations of 75,000 at= oms QMMM-Minimization=C2=A0takes 4 days.

NAMD2= -> namd2=C2=A0+p22 Min.conf
ORCA ->=C2=A0qmConfigLine &quo= t;% PAL NPROCS 20 END" (from Min.conf)

# = Number of simultaneous QM simulations per node
QMSimsPerNode 20

Thanks and=C2=A0regards,
Herald


3D""
--000000000000bbf19205cb8dc71b-- --000000000000bbf19405cb8dc71c Content-Type: image/gif; name="image.gif" Content-Disposition: inline; filename="image.gif" Content-Transfer-Encoding: base64 Content-ID: X-Attachment-Id: ii_ktcsqtfb0 R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7 --000000000000bbf19405cb8dc71c-- From owner-namd-l@halifax.ks.uiuc.edu Thu Sep 9 12:09:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 189H9jZu003344; Thu, 9 Sep 2021 12:09:45 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 189H9jUv003343; Thu, 9 Sep 2021 12:09:45 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 189H9iGE003339; Thu, 9 Sep 2021 12:09:44 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 189H9i3n003338; Thu, 9 Sep 2021 12:09:44 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 189H9UM0003330 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 9 Sep 2021 12:09:30 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 189H44Qv020061 for ; Thu, 9 Sep 2021 17:09:30 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=melomcr@gmail.com; dkim=pass header.d=gmail.com header.s=20210112 Received: from mail-lj1-f170.google.com (mail-lj1-f170.google.com [209.85.208.170]) by mx0a-00007101.pphosted.com with ESMTP id 3ay1ww8fmj-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 09 Sep 2021 17:09:29 +0000 Received: by mail-lj1-f170.google.com with SMTP id p15so4115257ljn.3 for ; Thu, 09 Sep 2021 10:09:29 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=lkJ0yvv61MMUDpZ2BX/E4q7WiKauOpRkgiMaHvN1jlc=; b=jvWiygC04PXCoNTeSDyNPw3RKbvM/EE9QglFh1avPsD7+I3odNfV6CuLakOo/F0Ge4 u3KSbhEaTicTXzF2fo24JKMdcEbv5qr0vPfzvZek5vfQPxW/Kdl+EJXRGUEVOipEkt4u 5QnPxufbpE6iHEFJdwErjH492rDApRdTftn2CoNsM82aTpDAkIWgdOBukkTMJsZihCb0 k9T9K7JEgeOfumP7tyuG4Y80dW4pjOa/lNh3GuOWDkwMV+fkfbdz6DGAVNxfiG8WD12R idIYFPgasRFd/ej10kW3GiIg7TvokTnnarSbcsndkffsjj0dsVq9kUkoaSmRzDPmB9bm qNEA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=lkJ0yvv61MMUDpZ2BX/E4q7WiKauOpRkgiMaHvN1jlc=; b=0SOWUoRWsXF+09eMmYRLEj8g9s5WEV04GuQbSr9V70dCDuzDk1a6cNbuaNzWID7Mgt hjN0hUnsZncWBqtrdEqHhZQqri+kDroPFhL8hV7cUCXoLWuSa/RuzyVCJpHPdujIHLKL GPpZw1s/Zzw/6ztzFNja54Wil5L/19gXgRTYSMh7jvrglQ8GJlH0ffbt42nyEVWNlkwK gAYnIW/cXYbhbp7bOXepFVhpMuXNrO+8YcoltL6FI024DgmSHZrj7A3cSmR1s/OD95W1 r5BbthO8xTpYkiiQAvI4CT0nvq1Lyw6FED3j+PZVWLvnKHVtxqJDI9OrRehD2cr4dpfi 41Eg== X-Gm-Message-State: AOAM532LqsR+ljOdrrEe7Cvnsnf1CO4UCXAzHS00qFFVCU1fztphTSx4 xFsmCX0rBbb6xW72yj8xyB9TWQMN0NQ3JPtyaY9G4x0EG7E= X-Google-Smtp-Source: ABdhPJwqZcprnA1sbTeX+GfGmncwe3ji4kXOqUIsOn5jI82qUXkCMb7HGaSApxV4z7CyAfQXiXG2cPvshYAgeMmEgtc= X-Received: by 2002:a2e:555:: with SMTP id 82mr703923ljf.245.1631207367065; Thu, 09 Sep 2021 10:09:27 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: "Marcelo C. R. Melo" Date: Thu, 9 Sep 2021 13:09:00 -0400 Message-ID: Subject: Re: namd-l: Problem with speed of QMMM (namd2-ORCA) To: NAMD , Herald Delis Content-Type: multipart/related; boundary="000000000000ac2dad05cb930fab" X-CLX-Shades: MLX X-Proofpoint-GUID: bpaQoMX_jq6880-sUqPErzrS4acYeIyL X-CLX-Response: 1TFkXGBoSEQpMehcZGx0RCllEF21ta2xYEn9bT2ZFEQpYWBdsekNpUlJ7QlN lTBEKeE4XY1Nja3sTWH4aX14RCnlMF28bTHN9E0ZMW0FFEQpDSBcHGBwbEQpDWRcHGxsYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIScRseExAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdIWkt7RWdydUBbHBISGgdZf1t6b1hQWHkeS0lzT2NTZhEKWFwXHwQaBBgZ GQUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3NIAXhBEQpNXBcHGBoRCkxaF3hhTUFrEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGh IEGx0aEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2RrWlhuXgFzRU9/EQpCThdjU2NrexNYfhpfXhEKQkwXbHpDaVJSe0JTZUwRCkJs F2ZzaEYYTRNaEh5bEQpCQBd6aFpNclwBT2MabhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxw RCnlDF2EdX05EcGNBHB4cEQpwZxdoHGtde24bHllZXxAZGhEKcGgXa29DEkFgc1hoRE8QGRoRCn BoF29gUHxSAX0df2wbEB4SEQpwaBdhX0NEUl5PBU98ThAZGhEKcGgXb0l5eVhAc0sYfhMQGRoRC nBoF2F/GENfHXBLGHlTEBkaEQpwfRdjfhloQF1cXUVYGRAZGhEKcGMXbV4eSRxEbH5bZG4QHB8R CnBjF2JgekYaaUsfUnhYEBwfEQpwfxdjU09uTGZwGEweehAbGh4RCnBfF2kdREceR2BuTWkfEBs aHREKcGwXaFt4TnpnWkBTUGYQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: bpaQoMX_jq6880-sUqPErzrS4acYeIyL X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 priorityscore=317 suspectscore=0 bulkscore=0 mlxscore=0 mlxlogscore=616 malwarescore=0 clxscore=208 lowpriorityscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109090106 X-Spam-Score: 0 X-Spam-OrigSender: melomcr@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Marcelo C. R. Melo" --000000000000ac2dad05cb930fab Content-Type: multipart/alternative; boundary="000000000000ac2da705cb930faa" --000000000000ac2da705cb930faa Content-Type: text/plain; charset="UTF-8" Hi Herald, I may have a couple of suggestions and questions for you. 1. Is 75.000 the total number of atoms in your entire system, or in your QM regions? How large is the QM region itself? If you have more than a few hundred atoms in your QM region, I would expect ORCA to take a while to calculate it. 2. In your NAMD execution line, you could ask for fewer nodes, like 5 or 10, and leave the rest for ORCA. For example: NAMD2 -> namd2 +p10 Min.conf ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) 3. If you only have one QM region in your system, you only need to ask for 1 QM simulations per node. This won't change your calculation. 4. What kind of QM calculation are you running? semi empirical? HF? Best, Marcelo On Thu, 9 Sept 2021 at 06:53, Herald Delis wrote: > [image: image.gif]Dear All, > > I am trying to run QMMM-MD using orca-namd2. > But it happens to be too slow, I wanted to know if I am doing something > wrong or is there a better way. > I have a CPU node with 40 cores (and 4 unused GPU), my calculations of > 75,000 atoms QMMM-Minimization takes 4 days. > > NAMD2 -> namd2 +p22 Min.conf > ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf) > > # Number of simultaneous QM simulations per node > QMSimsPerNode 20 > > Thanks and regards, > Herald > > > > --000000000000ac2da705cb930faa Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Herald,

I may have a couple of sugge= stions and questions for you.

1. Is 75.000 the tot= al number of atoms in your entire system, or in your QM regions? How large = is the QM region itself?=C2=A0
If you have more than a few hundre= d atoms in your QM region, I would expect ORCA to take a while to calculate= it.

2. In your NAMD execution line, you could ask= for fewer nodes, like 5 or 10, and leave the rest for ORCA.
For = example:
NAMD2 -> namd2=C2=A0+p10 Min.conf
ORCA= ->=C2=A0qmConfigLine "% PAL NPROCS 30 END" (from Min.conf)

3. If you only have one QM region in your syst= em, you only need to ask for 1 QM simulations per node. This won't chan= ge your calculation.

4. What kind of QM calculatio= n are you running? semi empirical? HF?

Best,
=
Marcelo

On Thu, 9 Sept 2021 at 06:53, Herald Delis <bioinfo2021great@gmail.com> wrot= e:
3D"image.gif"Dear All,

I am trying to run QMMM-MD=C2=A0using orca-n= amd2.
But it happens to be too slow, I wanted to know if I am doi= ng something wrong or is there a better way.
I have a CPU node wi= th 40 cores (and 4 unused GPU), my calculations of 75,000 atoms QMMM-Minimi= zation=C2=A0takes 4 days.

NAMD2 -> namd2=C2= =A0+p22 Min.conf
ORCA ->=C2=A0qmConfigLine "% PAL NPROCS = 20 END" (from Min.conf)

# Number of simul= taneous QM simulations per node
QMSimsPerNode 20

Thanks and=C2=A0regards,
Herald



=
3D""
--000000000000ac2da705cb930faa-- --000000000000ac2dad05cb930fab Content-Type: image/gif; name="image.gif" Content-Disposition: inline; filename="image.gif" Content-Transfer-Encoding: base64 Content-ID: X-Attachment-Id: ii_ktcsqtfb0 R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7 --000000000000ac2dad05cb930fab-- From owner-namd-l@halifax.ks.uiuc.edu Thu Sep 9 20:00:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18A10H5t009741; Thu, 9 Sep 2021 20:00:17 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18A10Hbp009740; Thu, 9 Sep 2021 20:00:17 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18A10GEU009736; Thu, 9 Sep 2021 20:00:16 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18A10GAA009735; Thu, 9 Sep 2021 20:00:16 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18A109aA009728 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 9 Sep 2021 20:00:09 -0500 (CDT) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 18A103eh016718 for ; Fri, 10 Sep 2021 01:00:09 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=bioinfo2021great@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-lf1-f41.google.com (mail-lf1-f41.google.com [209.85.167.41]) by mx0b-00007101.pphosted.com with ESMTP id 3ayteu90v1-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 10 Sep 2021 01:00:09 +0000 Received: by mail-lf1-f41.google.com with SMTP id a4so599888lfg.8 for ; Thu, 09 Sep 2021 18:00:08 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=mnYySXuJ2PevwHenWvlUImAHye9Q6611u7ZpAs6TncE=; b=dYfG/UrLUO3fV5anOrsyApjcMz5PWWyR+dCVFk9T+xihKfhXxc62ZLn4OqdtohXN0q WCS+yz+NGTYTiDP93HYJNdUDWGNCrvA8BgdtlwNaML5GwIX3qIuq+0Hs4lve/s7edZ9K 6Z7wUdgPylr46Z0jnH0mEcIRNo2/nhjTVjkku343MJO87VnpPvwHIaLr03sTRnyRKHf3 IDJgo0UnIvEritOQoGg/nFa/TTn73fqIqvGHviktGji5bvl+kpXTFHJleoyVovV136cB P2YOYUv3PrpJeV1aN1zVs0CiH4/HUwYTO3swSwK93SFT+9I1ttdET99S4dKOIPH4N5iA 9mEQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=mnYySXuJ2PevwHenWvlUImAHye9Q6611u7ZpAs6TncE=; b=wMhDCXsBozc/TnZgtApT+fWtzh/NXwoxtDPoi4FzhaPhRgkp9WXALPVJEcfTkPNuTX UMN56digMvKBjZqhQYGgG4tpsf7QnHiqBMztT75z9RR/iadMeqzUjTj3BHGhywxxGpCT EQbm8o31lKUGhGZepvqg4sAAGIsG1jfMsxoQIj4DAWCkQakwREysQYZJnPDE5L5Ub1Tf tluraFWp0HGEAsl4u+fHF6IfqZ5cPPkXyXyhP6yyPCAE33q1nBGfVQARhV88pW8Jmcjv 2CvTI4aTbP8w4gg4xtGl5O8gVJh8rkW6adWApknlvzjPIUMKLRvxV2IhDPEWs9cKQrOn KBlw== X-Gm-Message-State: AOAM53333P8mk2Hyq2ucgNcuOR2k9AE5HJGjCa5AogKY519G+wM/aYqR oN92YMm+ThZ8yr4xG2+JpqLMGbJvV8eO/o/inzA= X-Google-Smtp-Source: ABdhPJz86mHP2ibqHZTtClWjHJbNFUbY6eLHJSkpyNW8/47qiCQMA7mGLRM16uPoyx7mnGWKxALjxrD38nBhKZpymJA= X-Received: by 2002:a19:4910:: with SMTP id w16mr1942501lfa.540.1631235607151; Thu, 09 Sep 2021 18:00:07 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Herald Delis Date: Fri, 10 Sep 2021 09:59:56 +0900 Message-ID: Subject: Re: namd-l: Problem with speed of QMMM (namd2-ORCA) To: "Marcelo C. R. Melo" Cc: NAMD Content-Type: multipart/related; boundary="000000000000e8f94d05cb99a2ff" X-Proofpoint-ORIG-GUID: _l446F1H4dLcK-j_x53KwzTIlKWbNfcv X-CLX-Response: 1TFkXGx4bEQpMehcZGhkRCllEF2lzQF1yR1N7WhgdEQpYWBd6a1AeehJuElp dGBEKeE4XY1Nja3sTWH4aX14RCnlMF2tcW28TXUcdTV0YEQpDSBcHGRodEQpDWRcHGxoZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcYGHEYBhgYdwYSGwYaBhoGGxoaBh4ScRgQGncGGgYHHxoGGgYHH BoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XdUYeHhxsG2IeTmZJYQdA dVIfGWFdUH5jRmF9SGRMSVwRClhcFx8EGgQYGRkFGxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc0l sYRoRCk1cFx4aGhEKTFoXfGlNa2sRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQ pCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQQeGxEKQl4XGxEKREkXGxEKQlwXGxEKXk4XG xEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdsQRgYawUacxJMEhEKQk4XY1Nj a3sTWH4aX14RCkJMF3prUB56Em4SWl0YEQpCbBdlWHtbT3pYY0d5QxEKQkAXemhaTXJcAU9jGm4 RCkJYF2dzZXNAbmFhTF1iEQpaWBccEQp5QxdhHV9ORHBjQRweHBEKcGgXZ2FrTGZ5BUkfX24QGR oRCnBoF25FAUt/ZXt9GAVkEBkaEQpwaBdgW3NYZBllT1hcWhAZGhEKcGgXb0l5eVhAc0sYfhMQG RoRCnBoF21tQRJCGE9Ab0sFEBkaEQpwfRdjfhloQF1cXUVYGRAZGhEKcGMXbV4eSRxEbH5bZG4Q HBIRCnBjF2JgekYaaUsfUnhYEBwcEQpwfxdjU09uTGZwGEweehAbGxgRCnBfF2kdREceR2BuTWk fEBMaEQpwbBdsQXNkHVJTYVhoRxAZGhEKbX4XGhEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-GUID: _l446F1H4dLcK-j_x53KwzTIlKWbNfcv X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=141 bulkscore=0 priorityscore=303 mlxscore=0 spamscore=0 mlxlogscore=796 adultscore=0 phishscore=0 lowpriorityscore=0 impostorscore=0 suspectscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109100004 X-Spam-Score: 0 X-Spam-OrigSender: bioinfo2021great@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Herald Delis --000000000000e8f94d05cb99a2ff Content-Type: multipart/alternative; boundary="000000000000e8f94c05cb99a2fe" --000000000000e8f94c05cb99a2fe Content-Type: text/plain; charset="UTF-8" Hello Marcelo, Thank you for reply, Q: 1. Is 75.000 the total number of atoms in your entire system, or in your QM regions? How large is the QM region itself? If you have more than a few hundred atoms in your QM region, I would expect ORCA to take a while to calculate it. A1: 75,000 is the total atoms, 113 atoms in QM region. Q: 2. In your NAMD execution line, you could ask for fewer nodes, like 5 or 10, and leave the rest for ORCA. For example: NAMD2 -> namd2 +p10 Min.conf ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) A2: This works and speeds up. But it is still showing 52 hours remaining. QMENERGY: 16 1.0000 -3517431.7765 -3517172.7403 (From Step 16) Info: Writing QM charge output at step 16 Info: Writing QM position output at step 16 PRESSURE: 16 -3304.93 308.224 -262.003 312.544 -2742.12 -82.5491 -261.689 -85.8746 -2603.54 GPRESSURE: 16 -7758.39 303.504 -166.053 239.227 -6827.13 -132.006 -216.514 120.539 -6983.22 TIMING: 16 CPU: 4.09771, 0.11225/step Wall: 40290.3, 2258.54/step, 52.6993 hours remaining, 532.187500 MB of memory in use. ENERGY: 16 8544.0808 5371.1756 4389.7518 47.8456 -255440.1271 20369.6414 1.7922 -3517172.7403 0.0000 -3733888.5801 0.0000 -3733888.5801 -3733888.5801 0.0000 -2883.5306 -7189.5819 806859.3967 -2883.5306 -7189.5819 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 16 LINE MINIMIZER BRACKET: DX 0.000456178 0.000121109 DU -1281.69 90.8142 DUDX -5.59903e+06 2423.13 1.49124e+06 MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM LINE MINIMIZER REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7 WRITING COORDINATES TO DCD FILE QMMM-MinX.dcd AT STEP 16 WRITING COORDINATES TO RESTART FILE AT STEP 16 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 16 FINISHED WRITING RESTART VELOCITIES Q:3. If you only have one QM region in your system, you only need to ask for 1 QM simulations per node. This won't change your calculation. A: This works too. But please check the above answer. 4. What kind of QM calculation are you running? semi empirical? HF? A: QM Calculation: ! uks BP86 def2-TZVP def2/J EnGrad TightSCF %maxcore 3000 % PAL NPROCS 30 END % basis newgto C "DEF2-SVP" end newgto H "DEF2-SVP" end end % scf MaxIter 500 end %pointcharges "qmmm_exec/QMMM-Min/0/qmmm_0.input.pntchrg" %coords CTyp xyz Charge 3.000000 Mult 1.000000 Units Angs coords Additionationlly, I am using extrabonds for keeping my metal ion in place. Will it affect the speed or the calculation in any way? Thanks and regards, Herald On Fri, Sep 10, 2021 at 2:09 AM Marcelo C. R. Melo wrote: > Hi Herald, > > I may have a couple of suggestions and questions for you. > > 1. Is 75.000 the total number of atoms in your entire system, or in your > QM regions? How large is the QM region itself? > If you have more than a few hundred atoms in your QM region, I would > expect ORCA to take a while to calculate it. > > 2. In your NAMD execution line, you could ask for fewer nodes, like 5 or > 10, and leave the rest for ORCA. > For example: > NAMD2 -> namd2 +p10 Min.conf > ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) > > 3. If you only have one QM region in your system, you only need to ask for > 1 QM simulations per node. This won't change your calculation. > > 4. What kind of QM calculation are you running? semi empirical? HF? > > Best, > Marcelo > > On Thu, 9 Sept 2021 at 06:53, Herald Delis > wrote: > >> [image: image.gif]Dear All, >> >> I am trying to run QMMM-MD using orca-namd2. >> But it happens to be too slow, I wanted to know if I am doing something >> wrong or is there a better way. >> I have a CPU node with 40 cores (and 4 unused GPU), my calculations of >> 75,000 atoms QMMM-Minimization takes 4 days. >> >> NAMD2 -> namd2 +p22 Min.conf >> ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf) >> >> # Number of simultaneous QM simulations per node >> QMSimsPerNode 20 >> >> Thanks and regards, >> Herald >> >> >> >> --000000000000e8f94c05cb99a2fe Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello=C2=A0Marcelo,

Thank you for reply= ,

Q: 1. Is 75.000 the total number of atoms i= n your entire system, or in your QM regions? How large is the QM region its= elf?=C2=A0
= If you have more than a few hundred atoms in your QM region, I would expect= ORCA to take a while to calculate it.

A1: = 75,000 is the total atoms, 113 atoms in QM region.


Q: 2. In your NAMD execution line, you could ask for fewer = nodes, like 5 or 10, and leave the rest for ORCA.
For example:
NAMD2 -&= gt; namd2=C2=A0+p10 Min.conf
ORCA ->=C2=A0qmConfigLine "%= PAL NPROCS 30 END" (from Min.conf)

<= div>A2: This works and speeds up. But it is still showing 52 hours remainin= g.

QMENERGY: =C2=A0 =C2=A0 =C2=A016 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 1.0000 =C2=A0-3517431.7765 =C2=A0-3517172.7403

(From S= tep 16)
Info: Writing QM charge output at step 16
Info: Writing QM po= sition output at step 16
PRESSURE: 16 -3304.93 308.224 -262.003 312.544 = -2742.12 -82.5491 -261.689 -85.8746 -2603.54
GPRESSURE: 16 -7758.39 303.= 504 -166.053 239.227 -6827.13 -132.006 -216.514 120.539 -6983.22
TIMING:= 16 =C2=A0CPU: 4.09771, 0.11225/step =C2=A0Wall: 40290.3, 2258.54/step, 52.= 6993 hours remaining, 532.187500 MB of memory in use.
ENERGY: =C2=A0 =C2= =A0 =C2=A016 =C2=A0 =C2=A0 =C2=A08544.0808 =C2=A0 =C2=A0 =C2=A05371.1756 = =C2=A0 =C2=A0 =C2=A04389.7518 =C2=A0 =C2=A0 =C2=A0 =C2=A047.8456 =C2=A0 =C2= =A0 =C2=A0 =C2=A0-255440.1271 =C2=A0 =C2=A0 20369.6414 =C2=A0 =C2=A0 =C2=A0= =C2=A0 1.7922 =C2=A0-3517172.7403 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2= =A0 =C2=A0 =C2=A0 -3733888.5801 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0-3= 733888.5801 =C2=A0-3733888.5801 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0-2883.5306 =C2=A0 =C2=A0 -7189.5819 =C2=A0 =C2= =A0806859.3967 =C2=A0 =C2=A0 -2883.5306 =C2=A0 =C2=A0 -7189.5819

WRI= TING EXTENDED SYSTEM TO RESTART FILE AT STEP 16
LINE MINIMIZER BRACKET: = DX 0.000456178 0.000121109 DU -1281.69 90.8142 DUDX -5.59903e+06 2423.13 1.= 49124e+06
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINI= MIZER REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7
WRITING COORDINATES = TO DCD FILE QMMM-MinX.dcd AT STEP 16
WRITING COORDINATES TO RESTART FILE= AT STEP 16
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES T= O RESTART FILE AT STEP 16
FINISHED WRITING RESTART VELOCITIES
<= div>
Q:3. If you only have one QM region in your system, you = only need to ask for 1 QM simulations per node. This won't change your = calculation.

A: This works too. But please check t= he above answer.

4. What kind of QM calculation are you running? semi e= mpirical? HF?

A: QM Calculation:

! uks BP86 def2-TZVP def2/J EnGrad TightSCF
%maxcor= e 3000
% PAL NPROC= S 30 END
% basis
newgto C "DEF2-SVP" end
newgto H= "DEF2-SVP" end
end
% scf
MaxIter 500
end
%pointch= arges "qmmm_exec/QMMM-Min/0/qmmm_0.input.pntchrg"


%coo= rds
=C2=A0 CTyp xyz
=C2=A0 Charge 3.000000
=C2=A0 Mult 1.000000=C2=A0 Units Angs
=C2=A0 coords


=
Additionationlly, I am using extrabonds=C2=A0for keeping my metal ion = in place. Will it affect the speed or the calculation in any way?

Thanks and regards,
Herald

On Fri, Sep 10, 2= 021 at 2:09 AM Marcelo C. R. Melo <= melomcr@gmail.com> wrote:
Hi Herald,

I may have = a couple of suggestions and questions for you.

1. = Is 75.000 the total number of atoms in your entire system, or in your QM re= gions? How large is the QM region itself?=C2=A0
If you have more = than a few hundred atoms in your QM region, I would expect ORCA to take a w= hile to calculate it.

2. In your NAMD execution li= ne, you could ask for fewer nodes, like 5 or 10, and leave the rest for ORC= A.
For example:
NAMD2 -> namd2=C2=A0+p10 Min.co= nf
ORCA ->=C2=A0qmConfigLine "% PAL NPROCS 30 END" (= from Min.conf)

3. If you only have one QM re= gion in your system, you only need to ask for 1 QM simulations per node. Th= is won't change your calculation.

4. What kind= of QM calculation are you running? semi empirical? HF?

Best,
Marcelo

On Thu, 9 Sept 2021 at 06:53, Herald Del= is <bioi= nfo2021great@gmail.com> wrote:
3D=Dear All,

I am tryi= ng to run QMMM-MD=C2=A0using orca-namd2.
But it happens to be too= slow, I wanted to know if I am doing something wrong or is there a better = way.
I have a CPU node with 40 cores (and 4 unused GPU), my calcu= lations of 75,000 atoms QMMM-Minimization=C2=A0takes 4 days.
=
NAMD2 -> namd2=C2=A0+p22 Min.conf
ORCA ->=C2= =A0qmConfigLine "% PAL NPROCS 20 END" (from Min.conf)

# Number of simultaneous QM simulations per node
QMSim= sPerNode 20

Thanks and=C2=A0regards,
Herald



3D""
--000000000000e8f94c05cb99a2fe-- --000000000000e8f94d05cb99a2ff Content-Type: image/gif; name="image.gif" Content-Disposition: inline; filename="image.gif" Content-Transfer-Encoding: base64 Content-ID: X-Attachment-Id: ii_ktcsqtfb0 R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7 --000000000000e8f94d05cb99a2ff-- From owner-namd-l@halifax.ks.uiuc.edu Sat Sep 11 00:28:24 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18B5SOhL024376; Sat, 11 Sep 2021 00:28:24 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18B5SOev024375; Sat, 11 Sep 2021 00:28:24 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18B5SNEI024371; Sat, 11 Sep 2021 00:28:23 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18B5SNSD024370; Sat, 11 Sep 2021 00:28:23 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18B5SG4P024363 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 11 Sep 2021 00:28:16 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.0.43/8.16.0.43) with SMTP id 18B5PWFw025219 for ; Sat, 11 Sep 2021 05:28:15 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=melomcr@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-lf1-f47.google.com (mail-lf1-f47.google.com [209.85.167.47]) by mx0a-00007101.pphosted.com with ESMTP id 3b0hj097nx-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Sat, 11 Sep 2021 05:28:15 +0000 Received: by mail-lf1-f47.google.com with SMTP id l10so8542249lfg.4 for ; Fri, 10 Sep 2021 22:28:14 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=RIgnHyAXsZrMbbQNeMgRbFg1ENws3LTenEzMLc5t7Lw=; b=H74RGSk1kceTq646oZY/cVdgANfauyYwbNptNiaCzjGGxSdy3ijVUT3kxnawkACKbo ukDOj8qKoT5tsBtT1HRtfnZLVrKjS7Enf6awINzNZXyQ7KQoK5NEKklqwO/Yj5ogM7Ds EIsP5t8gMJHyYccSpAULCALUSJePqdHqz7zB1rxt4AUnoVY7khhHx41lpYVoUK0J4DWU J3CdUPodBmRM1GCJwq/A45H9zjBA5y94fUBYCEg6sOH7z5qrRxX+azRlYKpUWBe2Z/aR ydvJJVDq7eLsZsdKGTXxCpOKrpD9YNKXRHxqD0o0ND4xVlbU1WvHjhV9IPhg+hgJWzuS BXIg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=RIgnHyAXsZrMbbQNeMgRbFg1ENws3LTenEzMLc5t7Lw=; b=kV69rOxVTCQf8DoZ9DwUJcz0Qaq3hmwS9eVouz71rhczlJ6AhqXUITBPNjbwsLPrT3 zNLJxT+86G4EByQyUfBo12EDgcYzA9fKowOYYgYeCuPeJxpPVajHXAwvjcfn321Ev299 BsGfpCLb0E6E+ZYzl+KukGBz8gbyXua6G6gh96D2aaued/nH50zbsT4rE8MR8kFVnTol J4VIyttfZ0UYHbm5hgPSxxlLWfRPpkq09GYAIXOUu6nnA7FS4WM/meP5Dh2/Un6yhA/A mmVvy4pBIWCvaE0CT0IcwNZ4dmKeVQDX47JewljBkYqEupJC4ze80oZr+Ad80ql/qnsq HKFA== X-Gm-Message-State: AOAM533uzftchXaHMPbCTvTzth9s9Gm/6Ioh9fw9v1esJLUuCV48VcbE lYp1t/7IMZk8ueLqJXwkhE9lLTzcettDSHPY3PI= X-Google-Smtp-Source: ABdhPJxhUaE89CLmRFVDeVXcyfzArLK4uN9hZ3UkfBIK03vwmKfTEV0CSYTzhjO7VSxY/DnZTIvdM+jpJ0QRwVWqxGQ= X-Received: by 2002:a05:6512:3d94:: with SMTP id k20mr902366lfv.633.1631338092792; Fri, 10 Sep 2021 22:28:12 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: "Marcelo C. R. Melo" Date: Sat, 11 Sep 2021 01:27:46 -0400 Message-ID: Subject: Re: namd-l: Problem with speed of QMMM (namd2-ORCA) To: Herald Delis Cc: NAMD Content-Type: multipart/related; boundary="00000000000087df1e05cbb17fd9" X-Proofpoint-ORIG-GUID: 5FHdUC2NhuXI__PL3MV0HKYOedQl6WNo X-CLX-Response: 1TFkXGx0TEQpMehcZHhsRCllEF21ta2xYEn9bT2ZFEQpYWBdsekNpUlJ7QlN lTBEKeE4XY1Nja3sTWH4aX14RCnlMF28bTHN9E0ZMW0FFEQpDSBcHHhoZEQpDWRcHExwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxNxHRwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XH2xiTn9pGGRCX3JjdXV6ZhlnfBpiYXNlT057Rhx9ZEURClhcFx8EGgQYGRkF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzSU9nYREKTVwXGBwcEQpMWhd4aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB 4dEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2RrWlhuXgFzRU9/EQpCThdjU2NrexNYfhpfXhEKQkwXbHpDaVJSe0JTZUwRCkJsF2Zz aEYYTRNaEh5bEQpCQBd6aFpNclwBT2MabhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxwRCnl DF2EdX05EcGNBHB4cEQpwZxdoHGtde24bHllZXxAZGhEKcGgXbkUBS39le30YBWQQGRoRCnBoF2 ljX11kGWR6bGweEBkaEQpwaBdgW3NYZBllT1hcWhAZGhEKcGgXYh5HZ21QfmcYX1kQGRoRCnBoF 2NsUFNNYVhCWFlIEBkaEQpwfRdjfhloQF1cXUVYGRAZGhEKcGMXbV4eSRxEbH5bZG4QHR0RCnBj F2JgekYaaUsfUnhYEB0fEQpwfxdjU09uTGZwGEweehAbGxoRCnBfF2kdREceR2BuTWkfEBMaEQp wbBdoW3hOemdaQFNQZhAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: 5FHdUC2NhuXI__PL3MV0HKYOedQl6WNo X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 suspectscore=0 malwarescore=0 impostorscore=0 adultscore=0 mlxlogscore=999 priorityscore=341 mlxscore=0 spamscore=0 bulkscore=0 phishscore=0 clxscore=179 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109110032 X-Spam-Score: 0 X-Spam-OrigSender: melomcr@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Marcelo C. R. Melo" --00000000000087df1e05cbb17fd9 Content-Type: multipart/alternative; boundary="00000000000087df1d05cbb17fd8" --00000000000087df1d05cbb17fd8 Content-Type: text/plain; charset="UTF-8" Hi Herald, It looks like you are requesting a relatively expensive calculation from a ~110 atom system, and this is taking ~35minutes to calculate each SCF (52 hours is the time remaining to run ALL steps in your simulation). I don't think this is terrible, and improving this time will depend on how much parallelism you can achieve and what your hardware may look like. You can test the ratio NAMD/ORCA to find the optimal spot, maybe having as few as 2 or 3 cores for NAMD, and 37 cores for ORCA is the best balance for you. Do you have 40 cores or 40 threads on your system (as in 20 dual-thread cores)? NAMD and ORCA will likely use all the CPU, and using multithreading will decrease the performance. Best, Marcelo On Thu, 9 Sept 2021 at 21:00, Herald Delis wrote: > Hello Marcelo, > > Thank you for reply, > > Q: 1. Is 75.000 the total number of atoms in your entire system, or in > your QM regions? How large is the QM region itself? > If you have more than a few hundred atoms in your QM region, I would > expect ORCA to take a while to calculate it. > > A1: 75,000 is the total atoms, 113 atoms in QM region. > > > Q: 2. In your NAMD execution line, you could ask for fewer nodes, like 5 > or 10, and leave the rest for ORCA. > For example: > NAMD2 -> namd2 +p10 Min.conf > ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) > > A2: This works and speeds up. But it is still showing 52 hours remaining. > > QMENERGY: 16 1.0000 -3517431.7765 -3517172.7403 > > (From Step 16) > Info: Writing QM charge output at step 16 > Info: Writing QM position output at step 16 > PRESSURE: 16 -3304.93 308.224 -262.003 312.544 -2742.12 -82.5491 -261.689 > -85.8746 -2603.54 > GPRESSURE: 16 -7758.39 303.504 -166.053 239.227 -6827.13 -132.006 -216.514 > 120.539 -6983.22 > TIMING: 16 CPU: 4.09771, 0.11225/step Wall: 40290.3, 2258.54/step, > 52.6993 hours remaining, 532.187500 MB of memory in use. > ENERGY: 16 8544.0808 5371.1756 4389.7518 > 47.8456 -255440.1271 20369.6414 1.7922 -3517172.7403 > 0.0000 -3733888.5801 0.0000 -3733888.5801 > -3733888.5801 0.0000 -2883.5306 -7189.5819 > 806859.3967 -2883.5306 -7189.5819 > > WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 16 > LINE MINIMIZER BRACKET: DX 0.000456178 0.000121109 DU -1281.69 90.8142 > DUDX -5.59903e+06 2423.13 1.49124e+06 > MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM > LINE MINIMIZER REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7 > WRITING COORDINATES TO DCD FILE QMMM-MinX.dcd AT STEP 16 > WRITING COORDINATES TO RESTART FILE AT STEP 16 > FINISHED WRITING RESTART COORDINATES > WRITING VELOCITIES TO RESTART FILE AT STEP 16 > FINISHED WRITING RESTART VELOCITIES > > Q:3. If you only have one QM region in your system, you only need to ask > for 1 QM simulations per node. This won't change your calculation. > > A: This works too. But please check the above answer. > > 4. What kind of QM calculation are you running? semi empirical? HF? > > A: QM Calculation: > > ! uks BP86 def2-TZVP def2/J EnGrad TightSCF > %maxcore 3000 > % PAL NPROCS 30 END > % basis > newgto C "DEF2-SVP" end > newgto H "DEF2-SVP" end > end > % scf > MaxIter 500 > end > %pointcharges "qmmm_exec/QMMM-Min/0/qmmm_0.input.pntchrg" > > > %coords > CTyp xyz > Charge 3.000000 > Mult 1.000000 > Units Angs > coords > > > Additionationlly, I am using extrabonds for keeping my metal ion in place. > Will it affect the speed or the calculation in any way? > > Thanks and regards, > Herald > > On Fri, Sep 10, 2021 at 2:09 AM Marcelo C. R. Melo > wrote: > >> Hi Herald, >> >> I may have a couple of suggestions and questions for you. >> >> 1. Is 75.000 the total number of atoms in your entire system, or in your >> QM regions? How large is the QM region itself? >> If you have more than a few hundred atoms in your QM region, I would >> expect ORCA to take a while to calculate it. >> >> 2. In your NAMD execution line, you could ask for fewer nodes, like 5 or >> 10, and leave the rest for ORCA. >> For example: >> NAMD2 -> namd2 +p10 Min.conf >> ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) >> >> 3. If you only have one QM region in your system, you only need to ask >> for 1 QM simulations per node. This won't change your calculation. >> >> 4. What kind of QM calculation are you running? semi empirical? HF? >> >> Best, >> Marcelo >> >> On Thu, 9 Sept 2021 at 06:53, Herald Delis >> wrote: >> >>> [image: image.gif]Dear All, >>> >>> I am trying to run QMMM-MD using orca-namd2. >>> But it happens to be too slow, I wanted to know if I am doing something >>> wrong or is there a better way. >>> I have a CPU node with 40 cores (and 4 unused GPU), my calculations of >>> 75,000 atoms QMMM-Minimization takes 4 days. >>> >>> NAMD2 -> namd2 +p22 Min.conf >>> ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf) >>> >>> # Number of simultaneous QM simulations per node >>> QMSimsPerNode 20 >>> >>> Thanks and regards, >>> Herald >>> >>> >>> >>> --00000000000087df1d05cbb17fd8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi=C2=A0Herald,

It looks like you are r= equesting a relatively expensive calculation from a ~110 atom system, and t= his is taking ~35minutes to calculate each SCF (52 hours is the time remain= ing to run ALL steps in your simulation). I don't think this is terribl= e, and improving this time will depend on how much parallelism=C2=A0you can= achieve and what your hardware may look like.=C2=A0

You can test the ratio NAMD/ORCA to find the optimal spot, maybe having = as few as 2 or 3 cores for NAMD, and 37 cores for ORCA is the best balance = for you.

Do you have 40 cores or 40 threads on you= r system (as in 20 dual-thread cores)? NAMD and ORCA will likely use all th= e CPU, and using multithreading will decrease the performance.

Best,
Marcelo

On Thu, 9 Sept 2021 at 21:00,= Herald Delis <bioinfo2021great@gmail.com> wrote:
Hello=C2=A0Marcelo,
<= br>
Thank you for reply,

Q: 1. Is 7= 5.000 the total number of atoms in your entire system, or in your QM region= s? How large is the QM region itself?=C2=A0
If you have more than a few hundred atoms in your QM region, = I would expect ORCA to take a while to calculate it.

A1: 75,000 is the total atoms, 113 atoms in QM region.
=

Q: 2. In your NAMD execution line, you could = ask for fewer nodes, like 5 or 10, and leave the rest for ORCA.
For example:
NAMD2 -> n= amd2=C2=A0+p10 Min.conf
ORCA ->=C2=A0qmConfigLine "% PAL = NPROCS 30 END" (from Min.conf)

A= 2: This works and speeds up. But it is still showing 52 hours remaining.

QMENERGY: =C2=A0 =C2=A0 =C2=A016 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 1.0000 =C2=A0-3517431.7765 =C2=A0-3517172.7403

(From Step= 16)
Info: Writing QM charge output at step 16
Info: Writing QM posit= ion output at step 16
PRESSURE: 16 -3304.93 308.224 -262.003 312.544 -27= 42.12 -82.5491 -261.689 -85.8746 -2603.54
GPRESSURE: 16 -7758.39 303.504= -166.053 239.227 -6827.13 -132.006 -216.514 120.539 -6983.22
TIMING: 16= =C2=A0CPU: 4.09771, 0.11225/step =C2=A0Wall: 40290.3, 2258.54/step, 52.699= 3 hours remaining, 532.187500 MB of memory in use.
ENERGY: =C2=A0 =C2=A0= =C2=A016 =C2=A0 =C2=A0 =C2=A08544.0808 =C2=A0 =C2=A0 =C2=A05371.1756 =C2= =A0 =C2=A0 =C2=A04389.7518 =C2=A0 =C2=A0 =C2=A0 =C2=A047.8456 =C2=A0 =C2=A0= =C2=A0 =C2=A0-255440.1271 =C2=A0 =C2=A0 20369.6414 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 1.7922 =C2=A0-3517172.7403 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0= =C2=A0 =C2=A0 -3733888.5801 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0-3733= 888.5801 =C2=A0-3733888.5801 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0-2883.5306 =C2=A0 =C2=A0 -7189.5819 =C2=A0 =C2=A080= 6859.3967 =C2=A0 =C2=A0 -2883.5306 =C2=A0 =C2=A0 -7189.5819

WRITING = EXTENDED SYSTEM TO RESTART FILE AT STEP 16
LINE MINIMIZER BRACKET: DX 0.= 000456178 0.000121109 DU -1281.69 90.8142 DUDX -5.59903e+06 2423.13 1.49124= e+06
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER= REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7
WRITING COORDINATES TO DC= D FILE QMMM-MinX.dcd AT STEP 16
WRITING COORDINATES TO RESTART FILE AT S= TEP 16
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RES= TART FILE AT STEP 16
FINISHED WRITING RESTART VELOCITIES
<= br>
Q:3. If you only have one QM region in your system, you only = need to ask for 1 QM simulations per node. This won't change your calcu= lation.

A: This works too. But please check the ab= ove answer.

4. = What kind of QM calculation are you running? semi empirical? HF?
=
A: QM Calculation:

! u= ks BP86 def2-TZVP def2/J EnGrad TightSCF
%maxcore 3000
% PAL NPROCS 30 END
% basis
newgto C &quo= t;DEF2-SVP" end
newgto H "DEF2-SVP" end
end
% scfMaxIter 500
end
%pointcharges "qmmm_exec/QMMM-Min/0/qmmm_0.inp= ut.pntchrg"


%coords
=C2=A0 CTyp xyz
=C2=A0 Charge 3.0= 00000
=C2=A0 Mult 1.000000
=C2=A0 Units Angs
=C2=A0 coords


Additionationlly, I am using extrabond= s=C2=A0for keeping my metal ion in place. Will it affect the speed or the c= alculation in any way?

Thanks and regards,
Herald

On Fri, Sep 10, 2021 at 2:09 AM Marcelo C. R. Melo <melomcr@gmail.com>= ; wrote:
Hi Herald,

I may have a couple of suggestions = and questions for you.

1. Is 75.000 the total numb= er of atoms in your entire system, or in your QM regions? How large is the = QM region itself?=C2=A0
If you have more than a few hundred atoms= in your QM region, I would expect ORCA to take a while to calculate it.

2. In your NAMD execution line, you could ask for fe= wer nodes, like 5 or 10, and leave the rest for ORCA.
For example= :
NAMD2 -> namd2=C2=A0+p10 Min.conf
ORCA ->= =C2=A0qmConfigLine "% PAL NPROCS 30 END" (from Min.conf)

3. If you only have one QM region in your system, yo= u only need to ask for 1 QM simulations per node. This won't change you= r calculation.

4. What kind of QM calculation are = you running? semi empirical? HF?

Best,
M= arcelo

3D""
--00000000000087df1d05cbb17fd8-- --00000000000087df1e05cbb17fd9 Content-Type: image/gif; name="image.gif" Content-Disposition: inline; filename="image.gif" Content-Transfer-Encoding: base64 Content-ID: X-Attachment-Id: ii_ktcsqtfb0 R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7 --00000000000087df1e05cbb17fd9-- From owner-namd-l@halifax.ks.uiuc.edu Sun Sep 12 00:22:35 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18C5MZdf004955; Sun, 12 Sep 2021 00:22:35 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18C5MZqq004954; Sun, 12 Sep 2021 00:22:35 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18C5MYXX004950; Sun, 12 Sep 2021 00:22:34 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18C5MYHM004949; Sun, 12 Sep 2021 00:22:34 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18C5MMEf004940 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sun, 12 Sep 2021 00:22:22 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18C1xgMQ014907 for ; Sun, 12 Sep 2021 05:22:21 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=bioinfo2021great@gmail.com; dkim=pass header.d=gmail.com header.s=20210112 Received: from mail-lf1-f52.google.com (mail-lf1-f52.google.com [209.85.167.52]) by mx0a-00007101.pphosted.com with ESMTP id 3b0pqtmj75-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Sun, 12 Sep 2021 05:22:21 +0000 Received: by mail-lf1-f52.google.com with SMTP id t19so13387358lfe.13 for ; Sat, 11 Sep 2021 22:22:20 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=TKnE+zRctUSFnhLktY1EgaA9vOrn5Up4L4yUNF4BuR8=; b=UEJ3IQ+BkR4lhrbMCUYifRnkKO+OfNT/uywVp6oVNfngo/f4kjFtV0zpNg1IS+Gx/y 7BFJpEH/7ENIo6N4Gt+Jslah8XWlDvfc46Vt3jme4Ptf3E/jTWTIuqZpqq6HeOhor+rb nski7HlmQOCP7F2hY9OXLQLADH+SbUkTmr0jNllDAa4ww5M0MXy2WIvJ/WKQlP0Nnn3I EcVXpVR76L9DFGt4g8Suu5sZX7Mfbz3S8PFBB9CLD7QRnG/hb+DfUv268ozAnU5Ezksb Alae2XRUtxddxlVU7iU5f6ipbeAr0epSdcmg2GKJjf3n6l67WdqvnpyhrX5QrYyp2y0R 0/dQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=TKnE+zRctUSFnhLktY1EgaA9vOrn5Up4L4yUNF4BuR8=; b=gAiDhOcZdpKgeIZgV0eUHJzYb0QqN+dxZhipPXDO8++3p8oNoAuhdG4v/KOb/Yil6P AkApzX791IMv4+m/cwozROHEZ4FxHChGp79KHBYFclUmZiw+vKJoWkl+hJjQH3+ZwCpX Oy5qjBj10iLTq+09Vg6BcIc0f++DrXVv1oUN46aqw+88wRg1jOSeWTD/SHGy5duJ++a2 IbNUBsV/anJaA1dFegm5P494S88lQLVsuj/SENYqGd3XO/CE5ekNj4hQXAkh5RpB6URU /UyE9iOyq0w2lq4YWPT+ls8VcGBCumJkvxGD8wPecSP57QuhkC6aHCzwAGuywyVpBoOd gxmA== X-Gm-Message-State: AOAM533trqa/xzugBGV5LG1fGp+PvC5Hj6il54Lu3tUHTFLP4fWvfkmq 0hprzymxnvutDwvIZORO8ddTf3SJjopBP/tNUgY= X-Google-Smtp-Source: ABdhPJxfnf3ZWOX8g9Eq0sAj9k7eTHd8svkOj9LAwkoJHCFts+CI0m/mr4gCc1E7uX1fJFGx8dsiOaX9HoZO490DFXQ= X-Received: by 2002:a19:6510:: with SMTP id z16mr4158816lfb.566.1631424138966; Sat, 11 Sep 2021 22:22:18 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Herald Delis Date: Sun, 12 Sep 2021 14:22:07 +0900 Message-ID: Subject: Re: namd-l: Problem with speed of QMMM (namd2-ORCA) To: "Marcelo C. R. Melo" Cc: NAMD Content-Type: multipart/related; boundary="00000000000048721705cbc5882c" X-Proofpoint-ORIG-GUID: h3Os6YSUAhTEoPdjszCu19gSxJlgd4MP X-Proofpoint-GUID: h3Os6YSUAhTEoPdjszCu19gSxJlgd4MP X-CLX-Response: 1TFkXGxkbEQpMehcZGxIRCllEF2lzQF1yR1N7WhgdEQpYWBd6a1AeehJuElp dGBEKeE4XY1Nja3sTWH4aX14RCnlMF2tcW28TXUcdTV0YEQpDSBcHHhoYEQpDWRcHExwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGxtxGxgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XQhllWRxzeX9rQn5vRXpOQFlQaV8bE015UmBGTU4eZ3oRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzSVBnRREKTVwXGRsSEQpMWhd7aU1rTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB 8YEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2xBGBhrBRpzEkwSEQpCThdjU2NrexNYfhpfXhEKQkwXemtQHnoSbhJaXRgRCkJsF2VY e1tPelhjR3lDEQpCQBd6aFpNclwBT2MabhEKQlgXZ3Nlc0BuYWFMXWIRClpYFxwRCnlDF2EdX05 EcGNBHB4cEQpwaBd6Y0RdbmIBYXBtbxAZGhEKcGgXYFtzWGQZZU9YXFoQGRoRCnBoF2IeR2dtUH 5nGF9ZEBkaEQpwaBdgaW9zH2hSGWdeaxAZGhEKcGgXY2xQU01hWEJYWUgQGRoRCnB9F2N+GWhAX VxdRVgZEBkaEQpwYxdtXh5JHERsfltkbhAdHBEKcGMXYmB6RhppSx9SeFgQHRwRCnB/F2NTT25M ZnAYTB56EBsaGBEKcF8XaR1ERx5HYG5NaR8QEhwRCnBsF2xBc2QdUlNhWGhHEBkaEQptfhcaEQp YTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 spamscore=0 priorityscore=318 mlxscore=0 malwarescore=0 mlxlogscore=999 bulkscore=0 clxscore=131 suspectscore=0 adultscore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109120042 X-Spam-Score: 0 X-Spam-OrigSender: bioinfo2021great@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Herald Delis --00000000000048721705cbc5882c Content-Type: multipart/alternative; boundary="00000000000048721405cbc5882b" --00000000000048721405cbc5882b Content-Type: text/plain; charset="UTF-8" Hello Marcelo, Thanks, I will try different combinations for NAMD2 and ORCA. My CPU (on lscpu command except flags) Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 44 On-line CPU(s) list: 0-43 Thread(s) per core: 1 Core(s) per socket: 22 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz Stepping: 4 CPU MHz: 1000.012 CPU max MHz: 3700.0000 CPU min MHz: 1000.0000 BogoMIPS: 4200.00 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 30976K NUMA node0 CPU(s): 0-21 NUMA node1 CPU(s): 22-43 I have couple more question, 1.Does "extrabond" affect the speed? or the results? I have 2 Iron atoms in the active site. 2. In QMMM-Min/QMMM-Ann/QMMM-Equi can we use SQM/HF and then tight calculation in production QMMM? Thanks and regards, Herald On Sat, Sep 11, 2021 at 2:28 PM Marcelo C. R. Melo wrote: > Hi Herald, > > It looks like you are requesting a relatively expensive calculation from a > ~110 atom system, and this is taking ~35minutes to calculate each SCF (52 > hours is the time remaining to run ALL steps in your simulation). I don't > think this is terrible, and improving this time will depend on how much > parallelism you can achieve and what your hardware may look like. > > You can test the ratio NAMD/ORCA to find the optimal spot, maybe having as > few as 2 or 3 cores for NAMD, and 37 cores for ORCA is the best balance for > you. > > Do you have 40 cores or 40 threads on your system (as in 20 dual-thread > cores)? NAMD and ORCA will likely use all the CPU, and using multithreading > will decrease the performance. > > Best, > Marcelo > > On Thu, 9 Sept 2021 at 21:00, Herald Delis > wrote: > >> Hello Marcelo, >> >> Thank you for reply, >> >> Q: 1. Is 75.000 the total number of atoms in your entire system, or in >> your QM regions? How large is the QM region itself? >> If you have more than a few hundred atoms in your QM region, I would >> expect ORCA to take a while to calculate it. >> >> A1: 75,000 is the total atoms, 113 atoms in QM region. >> >> >> Q: 2. In your NAMD execution line, you could ask for fewer nodes, like 5 >> or 10, and leave the rest for ORCA. >> For example: >> NAMD2 -> namd2 +p10 Min.conf >> ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) >> >> A2: This works and speeds up. But it is still showing 52 hours remaining. >> >> QMENERGY: 16 1.0000 -3517431.7765 -3517172.7403 >> >> (From Step 16) >> Info: Writing QM charge output at step 16 >> Info: Writing QM position output at step 16 >> PRESSURE: 16 -3304.93 308.224 -262.003 312.544 -2742.12 -82.5491 -261.689 >> -85.8746 -2603.54 >> GPRESSURE: 16 -7758.39 303.504 -166.053 239.227 -6827.13 -132.006 >> -216.514 120.539 -6983.22 >> TIMING: 16 CPU: 4.09771, 0.11225/step Wall: 40290.3, 2258.54/step, >> 52.6993 hours remaining, 532.187500 MB of memory in use. >> ENERGY: 16 8544.0808 5371.1756 4389.7518 >> 47.8456 -255440.1271 20369.6414 1.7922 -3517172.7403 >> 0.0000 -3733888.5801 0.0000 -3733888.5801 >> -3733888.5801 0.0000 -2883.5306 -7189.5819 >> 806859.3967 -2883.5306 -7189.5819 >> >> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 16 >> LINE MINIMIZER BRACKET: DX 0.000456178 0.000121109 DU -1281.69 90.8142 >> DUDX -5.59903e+06 2423.13 1.49124e+06 >> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM >> LINE MINIMIZER REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7 >> WRITING COORDINATES TO DCD FILE QMMM-MinX.dcd AT STEP 16 >> WRITING COORDINATES TO RESTART FILE AT STEP 16 >> FINISHED WRITING RESTART COORDINATES >> WRITING VELOCITIES TO RESTART FILE AT STEP 16 >> FINISHED WRITING RESTART VELOCITIES >> >> Q:3. If you only have one QM region in your system, you only need to ask >> for 1 QM simulations per node. This won't change your calculation. >> >> A: This works too. But please check the above answer. >> >> 4. What kind of QM calculation are you running? semi empirical? HF? >> >> A: QM Calculation: >> >> ! uks BP86 def2-TZVP def2/J EnGrad TightSCF >> %maxcore 3000 >> % PAL NPROCS 30 END >> % basis >> newgto C "DEF2-SVP" end >> newgto H "DEF2-SVP" end >> end >> % scf >> MaxIter 500 >> end >> %pointcharges "qmmm_exec/QMMM-Min/0/qmmm_0.input.pntchrg" >> >> >> %coords >> CTyp xyz >> Charge 3.000000 >> Mult 1.000000 >> Units Angs >> coords >> >> >> Additionationlly, I am using extrabonds for keeping my metal ion in >> place. Will it affect the speed or the calculation in any way? >> >> Thanks and regards, >> Herald >> >> On Fri, Sep 10, 2021 at 2:09 AM Marcelo C. R. Melo >> wrote: >> >>> Hi Herald, >>> >>> I may have a couple of suggestions and questions for you. >>> >>> 1. Is 75.000 the total number of atoms in your entire system, or in your >>> QM regions? How large is the QM region itself? >>> If you have more than a few hundred atoms in your QM region, I would >>> expect ORCA to take a while to calculate it. >>> >>> 2. In your NAMD execution line, you could ask for fewer nodes, like 5 or >>> 10, and leave the rest for ORCA. >>> For example: >>> NAMD2 -> namd2 +p10 Min.conf >>> ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf) >>> >>> 3. If you only have one QM region in your system, you only need to ask >>> for 1 QM simulations per node. This won't change your calculation. >>> >>> 4. What kind of QM calculation are you running? semi empirical? HF? >>> >>> Best, >>> Marcelo >>> >>> On Thu, 9 Sept 2021 at 06:53, Herald Delis >>> wrote: >>> >>>> [image: image.gif]Dear All, >>>> >>>> I am trying to run QMMM-MD using orca-namd2. >>>> But it happens to be too slow, I wanted to know if I am doing something >>>> wrong or is there a better way. >>>> I have a CPU node with 40 cores (and 4 unused GPU), my calculations of >>>> 75,000 atoms QMMM-Minimization takes 4 days. >>>> >>>> NAMD2 -> namd2 +p22 Min.conf >>>> ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf) >>>> >>>> # Number of simultaneous QM simulations per node >>>> QMSimsPerNode 20 >>>> >>>> Thanks and regards, >>>> Herald >>>> >>>> >>>> >>>> --00000000000048721405cbc5882b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Marcelo,

Thanks, I will try diffe= rent combinations for NAMD2 and ORCA.

My CPU (on l= scpu command except flags)

Architecture: =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0x86_64
CPU op-mode(s): =C2=A0 =C2=A0 =C2=A0 = =C2=A032-bit, 64-bit
Byte Order: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0Little Endian
CPU(s): =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A044
On-line CPU(s) list: =C2=A0 0-43
Thread(s) per core: =C2= =A0 =C2=A01
Core(s) per socket: =C2=A0 =C2=A022
Socket(s): =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 2
NUMA node(s): =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A02
Vendor ID: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Genuine= Intel
CPU family: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A06
Model: = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 85
Model name: = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Intel(R) Xeon(R) Gold 6152 CPU @ 2= .10GHz
Stepping: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A04
CP= U MHz: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1000.012
CPU max= MHz: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3700.0000
CPU min MHz: =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 1000.0000
BogoMIPS: =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A04200.00
Virtualization: =C2=A0 =C2=A0 =C2=A0 =C2= =A0VT-x
L1d cache: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 32K
L1i = cache: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 32K
L2 cache: =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01024K
L3 cache: =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A030976K
NUMA node0 CPU(s): =C2=A0 =C2= =A0 0-21
NUMA node1 CPU(s): =C2=A0 =C2=A0 22-43

=
I have couple more question,=C2=A0

1.Does &qu= ot;extrabond" affect the speed? or the results? I have 2 Iron atoms in= the active site.
2. In QMMM-Min/QMMM-Ann/QMMM-Equi can we use SQ= M/HF and then tight calculation=C2=A0in production QMMM?

Thanks and regards,
Herald


<= div class=3D"gmail_quote">
Hi=C2=A0Herald,

= It looks like you are requesting a relatively expensive calculation from a = ~110 atom system, and this is taking ~35minutes to calculate each SCF (52 h= ours is the time remaining to run ALL steps in your simulation). I don'= t think this is terrible, and improving this time will depend on how much p= arallelism=C2=A0you can achieve and what your hardware may look like.=C2=A0=

You can test the ratio NAMD/ORCA to find the opti= mal spot, maybe having as few as 2 or 3 cores for NAMD, and 37 cores for OR= CA is the best balance for you.

Do you have 40 cor= es or 40 threads on your system (as in 20 dual-thread cores)? NAMD and ORCA= will likely use all the CPU, and using multithreading will decrease the pe= rformance.

Best,
Marcelo
=
On Thu= , 9 Sept 2021 at 21:00, Herald Delis <bioinfo2021great@gmail.com> wrote:
=
He= llo=C2=A0Marcelo,

Thank you for reply,

Q: 1. Is 75.000 the total number of atoms in your entire syste= m, or in your QM regions? How large is the QM region itself?=C2=A0
If you have more than a few hundred at= oms in your QM region, I would expect ORCA to take a while to calculate it.=

A1: 75,000 is the total atoms, 113 atoms i= n QM region.


Q: 2. In your NAMD exe= cution line, you could ask for fewer nodes, like 5 or 10, and leave the res= t for ORCA.
For example:
=
NAMD2 -> namd2=C2=A0+p10 Min.conf
ORCA ->=C2=A0qm= ConfigLine "% PAL NPROCS 30 END" (from Min.conf)
=
A2: This works and speeds up. But it is still showing= 52 hours remaining.

QMENERGY: =C2=A0 =C2=A0 =C2= =A016 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0000 =C2=A0-3517431.7765 =C2=A0-3517172= .7403

(From Step 16)
Info: Writing QM charge output at step 16Info: Writing QM position output at step 16
PRESSURE: 16 -3304.93 308.2= 24 -262.003 312.544 -2742.12 -82.5491 -261.689 -85.8746 -2603.54
GPRESSU= RE: 16 -7758.39 303.504 -166.053 239.227 -6827.13 -132.006 -216.514 120.539= -6983.22
TIMING: 16 =C2=A0CPU: 4.09771, 0.11225/step =C2=A0Wall: 40290.= 3, 2258.54/step, 52.6993 hours remaining, 532.187500 MB of memory in use.ENERGY: =C2=A0 =C2=A0 =C2=A016 =C2=A0 =C2=A0 =C2=A08544.0808 =C2=A0 =C2= =A0 =C2=A05371.1756 =C2=A0 =C2=A0 =C2=A04389.7518 =C2=A0 =C2=A0 =C2=A0 =C2= =A047.8456 =C2=A0 =C2=A0 =C2=A0 =C2=A0-255440.1271 =C2=A0 =C2=A0 20369.6414= =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.7922 =C2=A0-3517172.7403 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -3733888.5801 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0.0000 =C2=A0-3733888.5801 =C2=A0-3733888.5801 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0-2883.5306 =C2=A0 =C2=A0 -7= 189.5819 =C2=A0 =C2=A0806859.3967 =C2=A0 =C2=A0 -2883.5306 =C2=A0 =C2=A0 -7= 189.5819

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 16
LINE = MINIMIZER BRACKET: DX 0.000456178 0.000121109 DU -1281.69 90.8142 DUDX -5.5= 9903e+06 2423.13 1.49124e+06
MINIMIZER RESTARTING CONJUGATE GRADIENT ALG= ORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7
W= RITING COORDINATES TO DCD FILE QMMM-MinX.dcd AT STEP 16
WRITING COORDINA= TES TO RESTART FILE AT STEP 16
FINISHED WRITING RESTART COORDINATES
W= RITING VELOCITIES TO RESTART FILE AT STEP 16
FINISHED WRITING RESTART VE= LOCITIES

Q:3. If you only have one QM region i= n your system, you only need to ask for 1 QM simulations per node. This won= 't change your calculation.

A: This works too.= But please check the above answer.

4. What kind of QM calculation are you running? semi e= mpirical? HF?

A: QM Calculation:

! uks BP86 def2-TZVP def2/J EnGrad TightSCF
%maxcor= e 3000
% PAL NPROCS 30 END
= % basis
newgto C "DEF2-SVP" end
newgto H "DEF2-SVP&quo= t; end
end
% scf
MaxIter 500
end
%pointcharges "qmmm_ex= ec/QMMM-Min/0/qmmm_0.input.pntchrg"


%coords
=C2=A0 CTyp = xyz
=C2=A0 Charge 3.000000
=C2=A0 Mult 1.000000
=C2=A0 Units Angs<= br>=C2=A0 coords


Additionationl= ly, I am using extrabonds=C2=A0for keeping my metal ion in place. Will it a= ffect the speed or the calculation in any way?

Tha= nks and regards,
Herald

On Fri, Sep 10, 2021 at 2:09 AM Marc= elo C. R. Melo <m= elomcr@gmail.com> wrote:
Hi Herald,

I may have a= couple of suggestions and questions for you.

1. I= s 75.000 the total number of atoms in your entire system, or in your QM reg= ions? How large is the QM region itself?=C2=A0
If you have more t= han a few hundred atoms in your QM region, I would expect ORCA to take a wh= ile to calculate it.

2. In your NAMD execution lin= e, you could ask for fewer nodes, like 5 or 10, and leave the rest for ORCA= .
For example:
NAMD2 -> namd2=C2=A0+p10 Min.con= f
ORCA ->=C2=A0qmConfigLine "% PAL NPROCS 30 END" (f= rom Min.conf)

3. If you only have one QM reg= ion in your system, you only need to ask for 1 QM simulations per node. Thi= s won't change your calculation.

4. What kind = of QM calculation are you running? semi empirical? HF?

=
Best,
Marcelo

On Thu, 9 Sept 2021 at 06:53, Herald Deli= s <bioin= fo2021great@gmail.com> wrote:
3D"=Dear All,

I am tryin= g to run QMMM-MD=C2=A0using orca-namd2.
But it happens to be too = slow, I wanted to know if I am doing something wrong or is there a better w= ay.
I have a CPU node with 40 cores (and 4 unused GPU), my calcul= ations of 75,000 atoms QMMM-Minimization=C2=A0takes 4 days.
<= br>
NAMD2 -> namd2=C2=A0+p22 Min.conf
ORCA ->=C2= =A0qmConfigLine "% PAL NPROCS 20 END" (from Min.conf)

# Number of simultaneous QM simulations per node
QMSim= sPerNode 20

Thanks and=C2=A0regards,
Herald



3D""
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Tue, 14 Sep 2021 04:27:43 -0700 (PDT) MIME-Version: 1.0 From: Nancy Singh Date: Tue, 14 Sep 2021 13:27:32 +0200 Message-ID: Subject: namd-l: MMPBSA calculation using CAFE plugin vmd To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000c4afeb05cbf2de10" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxsfEQpMehcZGR0RCllEF2wBb2EbHU5zfmZYEQpYWBdnUE1sT1Macxp fTxEKeE4XY1Nja3sTWH4aX14RCnlMF2FwYm16W0hDekNtEQpDSBcHGxwTEQpDWRcHGxIcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGEx9xEhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdfYGBcYlJkfF5EQ0d/UhheHV9mbWFucm1JbHNSZXVzUhEKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NOQ1xmEQpNXBcYHhoRCkxaF2xpTWtrEQpMRhdva2tra2s RCkJPF2x7GHBeRV5kQhNJEQpDWhcYGhMEEh8EGBseBBsdGBEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdiHUt6W2RMYmBmZREKQk4XY1Nja3sTW H4aX14RCkJMF2dQTWxPUxpzGl9PEQpCbBdpTXhABXp5Hx5baxEKQkAXZ1xkel1wBR1tTE0RCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5Qxdgc2ccRk0fYHlHGxEKcGgXa0YBHlxaQGl9fmE QGRoRCnBoF2VjHHBafkFjHGlfEBkaEQpwaBdnX1NhaW5mH01TUBAZGhEKcGgXb2lAU2xgSH1ye0 YQGRoRCnBoF25rbV5ocl9CGFppEBkaEQpwbBdpek4TRWN+aBlObRAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: uJJvHxNVtnimUx2t7uLGKDXGcFYxO_Yx X-Proofpoint-GUID: uJJvHxNVtnimUx2t7uLGKDXGcFYxO_Yx X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 phishscore=0 malwarescore=0 suspectscore=0 adultscore=0 bulkscore=0 spamscore=0 priorityscore=337 impostorscore=0 clxscore=115 mlxlogscore=697 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109140070 X-Spam-Score: 0 X-Spam-OrigSender: kapoornancy25@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nancy Singh --000000000000c4afeb05cbf2de10 Content-Type: text/plain; charset="UTF-8" Hii, I did MMPBSA calculation using cafe plugin from VMD. I run the calculations for my 20ns trajectory file. Problem is it's taking a long time like almost 5 days for one calculation. Is there another way to make calculations faster? I run the calculation on NAMD 2.14 linux multicore. When I tried to run it with CUDA I got the error "Pair interaction calculation is not supported in CUDA version". Is there any way that I can run it on CUDA version? Any input on this will be really helpful. Thank you Regards, Nancy --000000000000c4afeb05cbf2de10 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hii,
I did MMPBSA=C2=A0calculation using cafe plugin f= rom VMD. I run the calculations for my 20ns trajectory=C2=A0file. Problem i= s it's taking a long time=C2=A0like almost 5 days for one calculation. = Is there another way to make calculations faster?=C2=A0 I run the calculati= on on NAMD 2.14 linux multicore. When I tried to run it with CUDA I got the= error "Pair interaction calculation is not supported i= n CUDA version".=C2=A0
Is there any way that I can ru= n it on CUDA version? Any input on this will be really=C2=A0helpful.=C2=A0<= /div>

Thank you


=


Regards,
Nancy
=
--000000000000c4afeb05cbf2de10-- From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 14 07:04:12 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18EC4CeJ005789; Tue, 14 Sep 2021 07:04:12 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18EC4BDM005788; Tue, 14 Sep 2021 07:04:11 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18EC4Aoj005775; Tue, 14 Sep 2021 07:04:10 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18EC4AnU005774; Tue, 14 Sep 2021 07:04:10 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18EC3tA0005683 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000000c617905cbf36074" X-CLX-Response: 1TFkXGxwbEQpMehcZHh4RCllEF2tpHmZvE1gFHxt/EQpYWBdtZAFsR3hcZmh SaBEKeE4XY1Nja3sTWH4aX14RCnlMF2FjZGhBRRtJQk1sEQpDSBcHGxscEQpDWRcHGRkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhtxHxsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XbmxLQlNfTRNCQHgeZF9wHBNtWURtRm1jWWdrfUdwTHgRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdzTkB4bBEKTVwXGRkRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XaH1BYENafXNHQRMRCkNaFxgaEwQSHwQbGBIEHh 4RCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXeh9/HHldXnxYHBoRCkJOF2NTY2t7E1h+Gl9eEQpCTBdtZAFsR3hcZmhSaBEKQmwXYml8 RmdQT25pHAURCkJAF2xBeFlTHB9mGGd5EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUM XaBl/U20cH29iHBkRCnBnF2VbAUJ5c2l6Qm8ZEBkaEQpwaBdgXnNkemt8fQETTRAZGhEKcGgXZ1 9TYWluZh9NU1AQHBoRCnBoF2J9chxfRUsbaUlIEBkaEQpwaBdgS29aXmtSb1JPQxAZGhEKcGgXb G5cE3kSc1BcXH8QGRoRCnBsF2ZsHhMZGG1YYlNZEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: DFahyug9hjR4NuZ69GsnGlGIsMAWmZfR X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: DFahyug9hjR4NuZ69GsnGlGIsMAWmZfR X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 suspectscore=0 adultscore=0 malwarescore=0 mlxlogscore=999 impostorscore=0 lowpriorityscore=0 phishscore=0 priorityscore=344 bulkscore=0 clxscore=161 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109140075 X-Spam-Score: 0 X-Spam-OrigSender: pratik.narain@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Pratik Narain Srivastava --0000000000000c617905cbf36074 Content-Type: text/plain; charset="UTF-8" There are a lot of technicalities here. First of all, do you really need to calculate BFE for the entire 20 ns? I usually use the last frames of my trajectory after checking that the simulation has converged sufficiently. Or, as an alternative, you should put a stride of 10. You will sacrifice some data but the global average BFE calculation should be fine. On Tue, 14 Sep, 2021, 4:59 pm Nancy Singh, wrote: > Hii, > I did MMPBSA calculation using cafe plugin from VMD. I run the > calculations for my 20ns trajectory file. Problem is it's taking a long > time like almost 5 days for one calculation. Is there another way to make > calculations faster? I run the calculation on NAMD 2.14 linux multicore. > When I tried to run it with CUDA I got the error "Pair interaction > calculation is not supported in CUDA version". > Is there any way that I can run it on CUDA version? Any input on this will > be really helpful. > > Thank you > > > > > > Regards, > Nancy > --0000000000000c617905cbf36074 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
There are a lot of technicalities here. First of all, do = you really need to calculate BFE for the entire 20 ns? I usually use the la= st frames of my trajectory after checking that the simulation has converged= sufficiently. Or, as an alternative, you should put a stride of 10. You wi= ll sacrifice some data but the global average BFE calculation should be fin= e.

On Tue, 14 Sep, 2021, 4:59 pm Nancy Singh, <kapoornancy25@gmail.com> wrote:
Hii,
I did MMPBSA=C2=A0calculatio= n using cafe plugin from VMD. I run the calculations for my 20ns trajectory= =C2=A0file. Problem is it's taking a long time=C2=A0like almost 5 days = for one calculation. Is there another way to make calculations faster?=C2= =A0 I run the calculation on NAMD 2.14 linux multicore. When I tried to run= it with CUDA I got the error "Pair interaction calcula= tion is not supported in CUDA version".=C2=A0
Is ther= e any way that I can run it on CUDA version? Any input on this will be real= ly=C2=A0helpful.=C2=A0

Thank you





Regards= ,
Nancy
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charset="UTF-8" Hello CHARMM36 file toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str contains nonbonded for atom NRN1, as shown below > NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - > cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 > !adm jr., 5/08/91, suggested cutoff scheme > !methylguanidine parameters > HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 > HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged > systems > HRM1 0.0 -0.0090 0.8750 ! aliphatic amines > HRM2 0.0 -0.0100 0.8750 ! aliphatic amines > ! > CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 > CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), > 4/98, yin, adm jr > ! > NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base > NRN1 0.0 -0.4500 2.0000 ! aliphatic amines > NRN2 0.0 -0.0600 1.9900 ! aliphatic amines > !end methylguanidine > Nonetheless, when running minimization for a system containing neutral ARG (which includes atom NRN1), namd reports error for lacking vdW for atom NRN1 Thanks for advice on this issue francesco pietra --000000000000df1e1005cbf48f2a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello
CHARMM36 file=C2=A0 toppar_c36_2016_m= ass_orig/stream/prot/toppar_all36_prot_arg0.str contains nonbonded for atom= NRN1, as shown below
NONBONDED nbxmod =C2=A05 atom cdiel fshift vatom vdistance vfswi= tch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 !adm jr., 5/08/91, = suggested cutoff scheme
!methylguanidine parameters
HRA3 =C2=A0 =C2=A0 0.0= =C2=A0 =C2=A0 =C2=A0 -0.0240 =C2=A0 =C2=A0 1.3400 ! alkane, yin and macker= ell, 4/98
HRP2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0460 =C2=A0 =C2= =A0 0.2245 ! small polar Hydrogen, charged systems
HRM1 =C2=A0 =C2=A0 0.= 0 =C2=A0 =C2=A0 =C2=A0 -0.0090 =C2=A0 =C2=A0 0.8750 ! aliphatic amines
H= RM2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0100 =C2=A0 =C2=A0 0.8750 ! a= liphatic amines
!
CRN1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.1100= =C2=A0 =C2=A0 2.0000 ! NMA pure solvent, adm jr., 3/3/93
CR33 =C2=A0 = =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0780 =C2=A0 =C2=A0 2.0500 =C2=A0 0.0 -0.= 01 1.9 ! alkane (CT3), 4/98, yin, adm jr
!
NRC4 =C2=A0 =C2=A0 0.0 =C2= =A0 =C2=A0 =C2=A0 -0.2000 =C2=A0 =C2=A0 1.8500 ! deprotonated Schiff's = base
NRN1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.4500 =C2=A0 =C2=A0 2= .0000 ! aliphatic amines
NRN2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.= 0600 =C2=A0 =C2=A0 1.9900 ! aliphatic amines
!end methylguanidine
<= /blockquote>

Nonetheless, when running minimization for = a system containing neutral ARG (which includes atom NRN1), namd reports er= ror for lacking vdW for atom NRN1

Thanks for advic= e on this issue

francesco pietra
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charset="UTF-8" I notice now from the terminal window that the stream file toppar_all36_prot_arg0.str , although present, was not read Info: PARAMETER file: CHARMM format! > Info: PARAMETERS ./par_all36_lipid.prm > Info: PARAMETERS ./par_all36_prot.prm > Info: PARAMETERS ./par_all36_na.prm > Info: PARAMETERS ./par_all36_cgenff.prm > Info: PARAMETERS ./ligand.str > Info: PARAMETERS ./par_water_ions.prm > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > Info: SKIPPING rtf SECTION IN STREAM FILE > No warning was reported about the params for the ligand, but it might be that namd halted at the first issue, before the stream file for the ligand was read Again, thanks for advice francesco pietra ---------- Forwarded message --------- From: Francesco Pietra Date: Tue, Sep 14, 2021 at 3:28 PM Subject: vdW for atom NRN1 To: NAMD Hello CHARMM36 file toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str contains nonbonded for atom NRN1, as shown below > NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - > cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 > !adm jr., 5/08/91, suggested cutoff scheme > !methylguanidine parameters > HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 > HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged > systems > HRM1 0.0 -0.0090 0.8750 ! aliphatic amines > HRM2 0.0 -0.0100 0.8750 ! aliphatic amines > ! > CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 > CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), > 4/98, yin, adm jr > ! > NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base > NRN1 0.0 -0.4500 2.0000 ! aliphatic amines > NRN2 0.0 -0.0600 1.9900 ! aliphatic amines > !end methylguanidine > Nonetheless, when running minimization for a system containing neutral ARG (which includes atom NRN1), namd reports error for lacking vdW for atom NRN1 Thanks for advice on this issue francesco pietra --0000000000003a704c05cbf4cef4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I notice now from the terminal window that the stream= file toppar_all36_prot_arg0.str , although present, was not read

Info: PAR= AMETER file: CHARMM format!
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 ./par_all36_lipid.prm
Info: PARAMETERS =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_prot.prm
Info: PARAMETERS =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_na.prm
Info: PARAMETERS = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_cgenff.prm
Info: P= ARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./ligand.str
Info: P= ARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_water_ions.prm
=C2= =A0Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKI= PPING rtf SECTION IN STREAM FILE

= No warning was reported about the params for the ligand, but it might be th= at namd halted at the first issue, before the stream file for the ligand wa= s read

Again, thanks for advice
francesc= o pietra

---------- Forwarded message ---------
From: Francesco Pietra = <chiendarret@gmail.com><= /span>
Date: Tue, Sep 14, 2021 at 3:28 PM
Subject: vdW for atom NRN1<= br>To: NAMD <namd-l@ks.uiuc.edu>


Hello
CHARMM36 file= =C2=A0 toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str con= tains nonbonded for atom NRN1, as shown below
NONBONDED nbxmod =C2=A05 atom cdiel fshi= ft vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0= e14fac 1.0 wmin 1.5
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 !adm jr., 5/08/91, suggested cutoff scheme
!methylguanidine parameters=
HRA3 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0240 =C2=A0 =C2=A0 1.340= 0 ! alkane, yin and mackerell, 4/98
HRP2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0= =C2=A0 -0.0460 =C2=A0 =C2=A0 0.2245 ! small polar Hydrogen, charged system= s
HRM1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0090 =C2=A0 =C2=A0 0.87= 50 ! aliphatic amines
HRM2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.010= 0 =C2=A0 =C2=A0 0.8750 ! aliphatic amines
!
CRN1 =C2=A0 =C2=A0 0.0 = =C2=A0 =C2=A0 =C2=A0 -0.1100 =C2=A0 =C2=A0 2.0000 ! NMA pure solvent, adm j= r., 3/3/93
CR33 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0780 =C2=A0 = =C2=A0 2.0500 =C2=A0 0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr
!NRC4 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.2000 =C2=A0 =C2=A0 1.8500 = ! deprotonated Schiff's base
NRN1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 = =C2=A0 -0.4500 =C2=A0 =C2=A0 2.0000 ! aliphatic amines
NRN2 =C2=A0 =C2= =A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0600 =C2=A0 =C2=A0 1.9900 ! aliphatic amine= s
!end methylguanidine

Nonetheless= , when running minimization for a system containing neutral ARG (which incl= udes atom NRN1), namd reports error for lacking vdW for atom NRN1

Thanks for advice on this issue

fr= ancesco pietra
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boundary="=_0d3688a5-1a44-4b96-8ced-a6c062e9c97a" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC76 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: vdW for atom NRN1 Thread-Index: rFxqkIcyZ9OBNFfgL4K8QLelDyjFIQ== X-CLX-Response: 1TFkXGxIZEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxsYHBEKQ1kXBxgfEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwZcR4YEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF0t+UFN/b0hlXW9eRVlFY2VFQlhJY0FGbFhhbxtCcE1ZEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXc05BGVkRCk1cFx4aHxEKTFoXfGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGx sRCkJeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXY R0eZmtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8 a3gRCkJAF2lCE31sUHByRntJEQpCWBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXbX5mGh0FXGYeRFo RCllLFwcZEQpwZxdjGmNHQX9hRngZfBAZGhEKcGgXYEBhY0tISxJTGXAQGRoRCnBoF2ZkYW9iHm dOc2JmEBkaEQpwaBdoQF94cEFeAUdMGRAZGhEKcGgXYUYTa0RycEBjX1oQGRoRCnBoF2d9EnB9U l16WxJ+EBkaEQpwfRdjc3tNBV0dAXhBcBAZGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnB9F2kaZU5c SBNgR3lGEBkaEQpwfxdvRGFQEhN/GxwSfhAbGhsRCnBfF2IYGhgfeEdMe3t7EBsaHhEKcGwXb2B /bXlMQURrTk4QGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: aTzyUEbOwEtosoIOohrcIklFrKE1hZgs X-Proofpoint-ORIG-GUID: aTzyUEbOwEtosoIOohrcIklFrKE1hZgs X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 adultscore=0 impostorscore=0 mlxlogscore=999 malwarescore=0 spamscore=0 lowpriorityscore=0 clxscore=183 priorityscore=0 suspectscore=0 phishscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109140086 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_0d3688a5-1a44-4b96-8ced-a6c062e9c97a Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear friend,=20 This is because=20 * you have not correctly added the path of toppar_all36_prot_arg0.str i= n your input file; or=20 * you have not added the path of toppar_all36_prot_arg0.str in your inp= ut file; or=20 * the file toppar_all36_prot_arg0.str is not a readable ASCII file.=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!otVH2KFC0w-5BSzWV3DfSN3DpH80KjI6gtfb7R70CExjmuQfu8hAFb0L= W0ochqhjSg$ ]=20 From: "Francesco Pietra" =20 To: "namd-l" =20 Sent: Tuesday, September 14, 2021 5:58:38 PM=20 Subject: namd-l: vdW for atom NRN1=20 Hello=20 CHARMM36 file toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.= str contains nonbonded for atom NRN1, as shown below=20 NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -=20 cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5=20 !adm jr., 5/08/91, suggested cutoff scheme=20 BQ_BEGIN !methylguanidine parameters=20 HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98=20 HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged systems=20 HRM1 0.0 -0.0090 0.8750 ! aliphatic amines=20 HRM2 0.0 -0.0100 0.8750 ! aliphatic amines=20 !=20 CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93=20 CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr=20 !=20 NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base=20 NRN1 0.0 -0.4500 2.0000 ! aliphatic amines=20 NRN2 0.0 -0.0600 1.9900 ! aliphatic amines=20 !end methylguanidine=20 BQ_END Nonetheless, when running minimization for a system containing neutral ARG = (which includes atom NRN1), namd reports error for lacking vdW for atom NRN= 1=20 Thanks for advice on this issue=20 francesco pietra=20 --=_0d3688a5-1a44-4b96-8ced-a6c062e9c97a Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear friend, 
This is becaus= e
  • you have not correctly added the path of toppar_all36_prot_arg0.str in your input file; o= r
  • = you have not added the path of toppar_all36_prot_arg= 0.str in your input file; or
  • th= e file toppar_all36_prot_arg0.str is not a readable ASCII file.=
    <= br>





Nonetheless, when running minimization for a system con= taining neutral ARG (which includes atom NRN1), namd reports error for lack= ing vdW for atom NRN1

Thanks for advice on this issue
francesco pietra

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charset="UTF-8" Hi Francesco, Once I faced a rather similar error. My source of forcefield files was my output from a source other than the CHARMM-download page. So, I downloaded the whole version from the CHARMM-download page and copied my str file in the right directory from which the vmd was reading toppar files. Hope this helps your problem gets addressed. Bests, Adam On Tue, Sep 14, 2021 at 6:17 PM Francesco Pietra wrote: > I notice now from the terminal window that the stream file > toppar_all36_prot_arg0.str , although present, was not read > > Info: PARAMETER file: CHARMM format! >> Info: PARAMETERS ./par_all36_lipid.prm >> Info: PARAMETERS ./par_all36_prot.prm >> Info: PARAMETERS ./par_all36_na.prm >> Info: PARAMETERS ./par_all36_cgenff.prm >> Info: PARAMETERS ./ligand.str >> Info: PARAMETERS ./par_water_ions.prm >> > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS >> Info: SKIPPING rtf SECTION IN STREAM FILE >> > > No warning was reported about the params for the ligand, but it might be > that namd halted at the first issue, before the stream file for the ligand > was read > > Again, thanks for advice > francesco pietra > > ---------- Forwarded message --------- > From: Francesco Pietra > Date: Tue, Sep 14, 2021 at 3:28 PM > Subject: vdW for atom NRN1 > To: NAMD > > > Hello > CHARMM36 file > toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str contains > nonbonded for atom NRN1, as shown below > >> NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - >> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 >> !adm jr., 5/08/91, suggested cutoff scheme >> > !methylguanidine parameters >> HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 >> HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged >> systems >> HRM1 0.0 -0.0090 0.8750 ! aliphatic amines >> HRM2 0.0 -0.0100 0.8750 ! aliphatic amines >> ! >> CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 >> CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), >> 4/98, yin, adm jr >> ! >> NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base >> NRN1 0.0 -0.4500 2.0000 ! aliphatic amines >> NRN2 0.0 -0.0600 1.9900 ! aliphatic amines >> !end methylguanidine >> > > Nonetheless, when running minimization for a system containing neutral ARG > (which includes atom NRN1), namd reports error for lacking vdW for atom NRN1 > > Thanks for advice on this issue > > francesco pietra > --000000000000bc9a0405cbf55cad Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Francesco,

Once I faced a rather similar error. My source of forcefiel= d=C2=A0files was my output from a source other than the CHARMM-download pag= e. So, I downloaded the whole version from the CHARMM-download page and cop= ied my str file in the right directory from which the vmd was reading toppa= r files. Hope this helps your problem gets addressed.

Bests,
Adam

I notice now from the termi= nal window that the stream file toppar_all36_prot_arg0.str , although prese= nt, was not read

Info: PARAMETER file: CHARMM format!
Info: PARAMETERS = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_lipid.prm
Info: PA= RAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_prot.prm
= Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_na.p= rm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all3= 6_cgenff.prm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = ./ligand.str
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = ./par_water_ions.prm
=C2=A0Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA P= ARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE

No warning was reported about the params for the liga= nd, but it might be that namd halted at the first issue, before the stream = file for the ligand was read

Again, thanks for adv= ice
francesco pietra

---------- Forwarded message -------= --
From: Francesco Pietra= <chiendarret@gmail.com>
Date: Tue, Sep 14, 2021 at = 3:28 PM
Subject: vdW for atom NRN1
To: NAMD <namd-l@ks.uiuc.edu>

=
Hello
CHARMM36 file=C2=A0 toppar_c36_20= 16_mass_orig/stream/prot/toppar_all36_prot_arg0.str contains nonbonded for = atom NRN1, as shown below
NONBONDED nbxmod =C2=A05 atom cdiel fshift vatom vdistance = vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.= 5
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 !adm jr., 5/08= /91, suggested cutoff scheme
!methylguanidine parameters
HRA3 =C2=A0 =C2= =A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0240 =C2=A0 =C2=A0 1.3400 ! alkane, yin and= mackerell, 4/98
HRP2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0460 =C2= =A0 =C2=A0 0.2245 ! small polar Hydrogen, charged systems
HRM1 =C2=A0 = =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0090 =C2=A0 =C2=A0 0.8750 ! aliphatic am= ines
HRM2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0100 =C2=A0 =C2=A0 0= .8750 ! aliphatic amines
!
CRN1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2= =A0 -0.1100 =C2=A0 =C2=A0 2.0000 ! NMA pure solvent, adm jr., 3/3/93
CR3= 3 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0780 =C2=A0 =C2=A0 2.0500 =C2= =A0 0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr
!
NRC4 =C2=A0 =C2= =A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.2000 =C2=A0 =C2=A0 1.8500 ! deprotonated Sc= hiff's base
NRN1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.4500 =C2= =A0 =C2=A0 2.0000 ! aliphatic amines
NRN2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2= =A0 =C2=A0 -0.0600 =C2=A0 =C2=A0 1.9900 ! aliphatic amines
!end methylgu= anidine

Nonetheless, when running min= imization for a system containing neutral ARG (which includes atom NRN1), n= amd reports error for lacking vdW for atom NRN1

Th= anks for advice on this issue

francesco pietra
=
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boundary="0000000000003b948205cbf55d1d" X-CLX-Response: 1TFkXGx0ZEQpMehcZGBIRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHx8RCkNZFwcYHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGXEZGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdaSGRTWERNX29cSE8ZaRxdTFptWGweUnJFa0RQbxgbbxEKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NORn1AEQpNXBcbEhgRCkxaF3tpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHBoEGx 0SEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2ZpGF1seG1jYVAdEQpCThdjU2NrexNYfhpfXhEKQkwXZHtPUn8TSVp6cxwRCkJsF2UY RUViR0thaEtsEQpCQBdpQhN9bFBwckZ7SREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx4RCnl DF21+ZhodBVxmHkRaEQpwZxdjGmNHQX9hRngZfBAeEhEKcGgXaVBrYBxLG3wbTkEQGhEKcGgXaF tTUH9zU0BZclkQGhEKcGgXYVoYG2gTG3gFYR4QHBoRCnBoF2JmWFJjGkZSQUh7EBoRCnBoF28Yf EATbRsFS1MBEBoRCnB9F2Nze00FXR0BeEFwEBkaEQpwZxdpQ25QAVlzRwEeUxAcGhEKcH0XaRpl TlxIE2BHeUYQGRoRCnB/F29EYVASE38bHBJ+EBMSEQpwXxdiGBoYH3hHTHt7exAbGhkRCnBsF2R 5fmRZZx5TU2lvEB0aEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: pbNyrnguEvbe3C6wfpGrF4xXoAnzE21E X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: pbNyrnguEvbe3C6wfpGrF4xXoAnzE21E MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 suspectscore=0 adultscore=0 malwarescore=0 mlxlogscore=950 impostorscore=0 lowpriorityscore=0 phishscore=0 priorityscore=328 bulkscore=0 clxscore=173 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109140089 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000003b948205cbf55d1d Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable You are rigth, but, to make the story short, I extracted the parameters from the stream file and now namd is happy thanks francesco On Tue, Sep 14, 2021 at 3:53 PM Ashkan Shekaari wrote: > Dear friend, > This is because > > - you have not correctly added the path of toppar_all36_prot_arg0.str > in your input file; or > - you have not added the path of toppar_all36_prot_arg0.str in your > input file; or > - the file toppar_all36_prot_arg0.str is not a readable ASCII file. > > > > --- > ,Best > Ashkan Shekaari > PhD Candidate in Solid State Physics > Department of Physics > K. N. Toosi University of Technology, Tehran, 15875-4416, Iran > > > > ------------------------------ > *From: *"Francesco Pietra" > *To: *"namd-l" > *Sent: *Tuesday, September 14, 2021 5:58:38 PM > *Subject: *namd-l: vdW for atom NRN1 > > Hello > CHARMM36 file > toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str contains > nonbonded for atom NRN1, as shown below > >> NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - >> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 >> !adm jr., 5/08/91, suggested cutoff scheme >> > !methylguanidine parameters >> HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 >> HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged >> systems >> HRM1 0.0 -0.0090 0.8750 ! aliphatic amines >> HRM2 0.0 -0.0100 0.8750 ! aliphatic amines >> ! >> CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 >> CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), >> 4/98, yin, adm jr >> ! >> NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base >> NRN1 0.0 -0.4500 2.0000 ! aliphatic amines >> NRN2 0.0 -0.0600 1.9900 ! aliphatic amines >> !end methylguanidine >> > > Nonetheless, when running minimization for a system containing neutral ARG > (which includes atom NRN1), namd reports error for lacking vdW for atom N= RN1 > > Thanks for advice on this issue > > francesco pietra > > --0000000000003b948205cbf55d1d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
You are rigth, but, to make the story short, I extrac= ted the parameters from the stream file and now namd is happy
tha= nks
francesco

On Tue, Sep 14, 2021 at 3:53 PM Ashkan She= kaari <shekaari@email.kntu.= ac.ir> wrote:
Dear friend,=C2=A0
This is because
  • you have not correctly added the p= ath of=C2=A0toppar_all36_prot= _arg0.str in your input file; or
  • you have not added=C2=A0the path of=C2=A0toppar_all36_prot_arg0.str in your input file; or
  • the file=C2=A0toppar_all36_prot_arg0.str is not a readable ASCII file.


<= div dir=3D"ltr">
---
,Best
<= /div>
<= /div>
Ashkan Shekaari
PhD= Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology,=C2=A0Tehran,= =C2=A015875-4416, Iran
<= /div>


From: "Francesco Pietra" <chiendarret@gmail.com>
To: "namd-l" <namd-l@ks.uiuc.edu>
Sent: Tuesday, September = 14, 2021 5:58:38 PM
Subject: namd-l: vdW for atom NRN1
<= div>
Hello
CHARMM36 file=C2= =A0 toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str contai= ns nonbonded for atom NRN1, as shown below
NONBONDED nbxmod =C2=A05 atom cdiel fshift = vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e1= 4fac 1.0 wmin 1.5
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 !adm jr., 5/08/91, suggested cutoff scheme
!methylguanidine parametersHRA3 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0240 =C2=A0 =C2=A0 1.3400 != alkane, yin and mackerell, 4/98
HRP2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 = =C2=A0 -0.0460 =C2=A0 =C2=A0 0.2245 ! small polar Hydrogen, charged systems=
HRM1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0090 =C2=A0 =C2=A0 0.875= 0 ! aliphatic amines
HRM2 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0100= =C2=A0 =C2=A0 0.8750 ! aliphatic amines
!
CRN1 =C2=A0 =C2=A0 0.0 =C2= =A0 =C2=A0 =C2=A0 -0.1100 =C2=A0 =C2=A0 2.0000 ! NMA pure solvent, adm jr.,= 3/3/93
CR33 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.0780 =C2=A0 =C2= =A0 2.0500 =C2=A0 0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr
!
N= RC4 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2=A0 -0.2000 =C2=A0 =C2=A0 1.8500 ! d= eprotonated Schiff's base
NRN1 =C2=A0 =C2=A0 0.0 =C2=A0 =C2=A0 =C2= =A0 -0.4500 =C2=A0 =C2=A0 2.0000 ! aliphatic amines
NRN2 =C2=A0 =C2=A0 0= .0 =C2=A0 =C2=A0 =C2=A0 -0.0600 =C2=A0 =C2=A0 1.9900 ! aliphatic amines
= !end methylguanidine

Nonetheless, when running m= inimization for a system containing neutral ARG (which includes atom NRN1),= namd reports error for lacking vdW for atom NRN1

Thanks for = advice on this issue

francesco pietra

--0000000000003b948205cbf55d1d-- From owner-namd-l@halifax.ks.uiuc.edu Fri Sep 17 05:12:22 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HACMWX017414; Fri, 17 Sep 2021 05:12:22 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18HACLCZ017413; Fri, 17 Sep 2021 05:12:21 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HACIsw017366; Fri, 17 Sep 2021 05:12:19 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18HACHxl017365; Fri, 17 Sep 2021 05:12:17 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HAC0hV017117 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 17 Sep 2021 05:12:01 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18H60Zvn007405 for ; Fri, 17 Sep 2021 10:11:59 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=vlad.cojocaru@mpi-muenster.mpg.de Received: from gmailer.gwdg.de (gmailer.gwdg.de [134.76.11.17]) by mx0a-00007101.pphosted.com with ESMTP id 3b3vqmb6xe-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 17 Sep 2021 10:11:59 +0000 Received: from excmbx-24.um.gwdg.de ([134.76.9.234] helo=email.gwdg.de) by mailer.gwdg.de with esmtp (GWDG Mailer) (envelope-from ) id 1mRAqa-0006lM-GM for namd-l@ks.uiuc.edu; Fri, 17 Sep 2021 12:11:57 +0200 Received: from [192.168.178.22] (10.250.9.200) by excmbx-24.um.gwdg.de (134.76.9.234) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P521) id 15.1.2308.14; Fri, 17 Sep 2021 12:11:56 +0200 Message-ID: <4752fff5-e485-2d33-4f54-7ecf4a878ba4@mpi-muenster.mpg.de> Date: Fri, 17 Sep 2021 12:11:56 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.0.3 Content-Language: en-US From: Vlad Cojocaru Subject: namd-l: performance scaling of CUDA accelerated NAMD over multiple nodes Organization: MPI Muenster To: NAMD Content-Type: text/plain; charset="UTF-8"; format=flowed X-Originating-IP: [10.250.9.200] X-ClientProxiedBy: excmbx-21.um.gwdg.de (134.76.9.231) To excmbx-24.um.gwdg.de (134.76.9.234) X-Virus-Scanned: (clean) by clamav X-CLX-Response: 1TFkXGx0cEQpMehcaEQpZRBdobGYFR1kZcgVJQxEKWFgXYk1gcnlNSRNPWWU RCnhOF2BfRF14RXlbcGZrEQp5TBdncHlGcFplZUVdTxEKQ0gXBxkaGBEKQ1kXBxseExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfHHEZHxAadwYYGgYaEQpZXhdoY3kRCklGF19DX0l1Q kVZXk9OEQpDThduT2FgWnAYTEhLE0BzYRJ6b2JOSHVwHmx+GkV/RRIHHBEKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3NPTRxhEQpNXBcZHx4RCkxaF2loaU1NTREKQk8XYwUdRhM bcxx/Qn8RCkNaFxsZHgQdHAQbGwQbHREKQl4XGxEKQkUXZ0diQGBjZ01QcGkRCkJOF2BfRF14RX lbcGZrEQpCTBdiTWByeU1JE09ZZREKQmwXaUt6G2QeX2dNQX4RCkJAF2wTEmVJWxN5HlxcEQpCW Bdnc2VzQG5hYUxdYhEKWlgXGREKeUMXYHxgfx9pUF99c0ERCnBoF25+aWF6Eltda09nEBoRCnBo F24TG2F6cHxBGl5fEBoRCnBoF3pacl5NX3l4a09cEBoRCnBoF2QFbkd9G2xEbB9rEBoRCnBoF2B NHGJsGwFDGkB5EBoRCnB9F2AaUntjYE9dT09kEBoRCnB/F2RQBVhJbX5JTUxsEBsaGhEKcF8Xek AeRV1PfkhabXgQGhEKcGwXZFl8eh8SeH5IQW0QGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: DeKJpZ2fba9jYK8PEHdb_Z4FT0oUo8-6 X-Proofpoint-ORIG-GUID: DeKJpZ2fba9jYK8PEHdb_Z4FT0oUo8-6 X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 lowpriorityscore=0 adultscore=0 clxscore=176 impostorscore=0 mlxlogscore=992 priorityscore=0 malwarescore=0 mlxscore=0 spamscore=0 phishscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109170066 X-Spam-Score: 0 X-Spam-OrigSender: vlad.cojocaru@mpi-muenster.mpg.de X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 18HAC2hU017145 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vlad Cojocaru Dear all, We have been doing some tests with the CUDA (11 I believe) accelerated version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads, 4 GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14. There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs almost no scaling. The simulation (classical MD) time per day for 500K atoms is similar to what expected (comparable to what is published on the NAMD website). However, for a large scale project, the supercomputer site requires scaling up to at least 10 nodes. And we are not able to get any scaling to more than 1 node. In fact, as soon as running on 2 nodes (with 4 GPUs each), the performance is getting worse than on a single node. I know that lots of details are needed to actually pinpoint the issue(s), many of these are architecture dependent and we do not have all these details. However, I would still like to ask in general if any of you has routinely managed to scale up the performance of the CUDA accelerated NAMD 2.14 with the number of nodes. And if yes, are there any general tips and tricks that could be tried ? Thank you for any insights ! Vlad -- Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM2F0_C7PXf-jew$ From owner-namd-l@halifax.ks.uiuc.edu Fri Sep 17 07:32:08 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HCW7YE018079; Fri, 17 Sep 2021 07:32:07 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18HCW63q018057; Fri, 17 Sep 2021 07:32:06 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HCW1Vp017963; 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Fri, 17 Sep 2021 12:31:45 +0000 From: "Vermaas, Josh" To: "namd-l@ks.uiuc.edu" , Vlad Cojocaru Subject: Re: namd-l: performance scaling of CUDA accelerated NAMD over multiple nodes Thread-Topic: namd-l: performance scaling of CUDA accelerated NAMD over multiple nodes Thread-Index: AQHXq7D4oY3szcYrskGkJv5oeDNmD6un5YIA Date: Fri, 17 Sep 2021 12:31:45 +0000 Message-ID: <2AC71BC2-518A-4B1E-BE87-FBACE7CA8855@msu.edu> References: <4752fff5-e485-2d33-4f54-7ecf4a878ba4@mpi-muenster.mpg.de> In-Reply-To: <4752fff5-e485-2d33-4f54-7ecf4a878ba4@mpi-muenster.mpg.de> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/16.53.21091200 authentication-results: ks.uiuc.edu; dkim=none (message not signed) header.d=none;ks.uiuc.edu; dmarc=none action=none header.from=msu.edu; x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: f132c910-ec03-421e-b61c-08d979d71c9e x-ms-traffictypediagnostic: CH2PR12MB3944: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:10000; 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charset="utf-8" Content-ID: <8F3A1D297E6C4B44B3D29FD4FF7D1B9D@namprd12.prod.outlook.com> MIME-Version: 1.0 X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: f132c910-ec03-421e-b61c-08d979d71c9e X-MS-Exchange-CrossTenant-originalarrivaltime: 17 Sep 2021 12:31:45.2926 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: z2+vBn/XJ8u1VyDLOhzaAMmclFBPNobszk5OtBUUqh0h/u6AbsylqOy2CkYclnOemGGbOQWQsiyTVQFBZK3Psg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB3944 X-CLX-Response: 1TFkXGBoYEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxgTGhEKQ1kXBxIfEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIYcRsZGxAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdTWGx7ZkFgfX5+TWscH2BMElxzf08ZTnxhZV0aHF9DGxEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdzT0MTehEKTVwXHhsbEQpMWhd4aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxdtcmlebk9ME1IfHBEKQ1oXHhoEGxodBBgeHg QeGxEKQl4XGxEKRF4XGREKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCTBdvYVgTG ktdG0NBZREKQmwXYXkcHxJce09aaUIRCkJAF254XVxZWmgSTn1mEQpCWBdnc2VzQG5hYUxdYhEK WlgXHhEKeUMXYkFIQXx9e1pgE34RCllLFxsYHx8ZEQpwZxdtR2FrTWMZTFNpbhAZGhEKcGgXYEs dWxpcEm5kaB4QGRoRCnBoF2FIcltOcGMcHRlfEBkaEQpwaBdkR2hLUExiRB9EeRAZGhEKcGgXbA V4cB1FQUVoHwEQGRoRCnBoF2USeW9GchgaHVpjEBkaEQpwZxdnU35SQ2NOSBkdWBAZGhEKcH0XY 3JvbUdCeWMeUGgQGRoRCnB/F21EX0ZFbX1IeRluEBseExEKcF8Xa0ZLE3loaW58E3gQGxodEQpw bBdneBpAYhhJGn55TRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: yrFQLkJWTTgA65Jf8vYUe3dVKOw06ui1 X-Proofpoint-ORIG-GUID: yrFQLkJWTTgA65Jf8vYUe3dVKOw06ui1 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 spamscore=0 clxscore=202 malwarescore=0 impostorscore=0 mlxscore=0 phishscore=0 bulkscore=0 mlxlogscore=999 priorityscore=0 adultscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109170080 domainage_hfrom=12553 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by halifax.ks.uiuc.edu id 18HCVpdR017734 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Hi Vlad, I've run NAMD on 4000 nodes, and it'll scale just fine (although the system was much larger than 500k atoms!). There are a few gotchas involved with multinode GPU NAMD. In no particular order: 1. This is an SMP build, yeah? Straight MPI builds with CUDA support are *possible* to build, but perform terribly relative to their SMP bretheren 2. I've found that each node performs best when a GPU gets its own rank/task that command dedicated CPUs. On the local resources here at MSU, that looks something like this: #!/bin/bash #SBATCH --gres=gpu:4 #4 GPUs per node #SBATCH --nodes=2 #SBATCH --ntasks-per-node=4 #Number of tasks per node should match the number of GPUs #SBATCH --cpus-per-task=12 #48 CPUs total, means each task gets 12 #SBATCH --gpu-bind=single:1 #Bind the GPU to a single task. Prevents a CPU from trying to distribute work over multiple GPUs, and lowers PCIE contention cd $SLURM_SUBMIT_DIR module use /mnt/home/vermaasj/modules module load NAMD/2.14-gpu #other modules are loaded automatically by the NAMD module. srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log #With this setup, NAMD sees 8 logical nodes, 4 from each physical node. 3. Set expectations appropriately. 10 nodes with 4 GPUs each = 40 GPUs. If the only thing you were doing is simulating 500k atoms (no replicas or anything), each GPU is responsible for ~10k atoms. There are two layers of communication for NAMD 2.14 on GPUs, transfers across the PCIe bus between GPU and CPU every timestep, and communication between logical nodes whenever pairlists get recomputed. If there isn't enough work for each GPU to do, those extra communication steps are going to murder performance. TLDR, at some point the scaling will break down, and for a system that small, it might happen before you think it will. 4. If the simulations you are planning are going to be regular equilibrium simulations, NAMD3 will likely be faster on modern hardware, as it eliminates CPU-GPU communication at most timesteps. -Josh On 9/17/21, 6:44 AM, "owner-namd-l@ks.uiuc.edu on behalf of Vlad Cojocaru" wrote: Dear all, We have been doing some tests with the CUDA (11 I believe) accelerated version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads, 4 GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14. There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs almost no scaling. The simulation (classical MD) time per day for 500K atoms is similar to what expected (comparable to what is published on the NAMD website). However, for a large scale project, the supercomputer site requires scaling up to at least 10 nodes. And we are not able to get any scaling to more than 1 node. In fact, as soon as running on 2 nodes (with 4 GPUs each), the performance is getting worse than on a single node. I know that lots of details are needed to actually pinpoint the issue(s), many of these are architecture dependent and we do not have all these details. However, I would still like to ask in general if any of you has routinely managed to scale up the performance of the CUDA accelerated NAMD 2.14 with the number of nodes. And if yes, are there any general tips and tricks that could be tried ? Thank you for any insights ! Vlad -- Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM2F0_C7PXf-jew$ From owner-namd-l@halifax.ks.uiuc.edu Fri Sep 17 08:06:07 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HD65qt001930; Fri, 17 Sep 2021 08:06:06 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18HD64DF001914; Fri, 17 Sep 2021 08:06:04 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HD63wh001875; 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Fri, 17 Sep 2021 15:05:41 +0200 Received: from [192.168.178.22] (10.250.9.200) by excmbx-24.um.gwdg.de (134.76.9.234) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P521) id 15.1.2308.14; Fri, 17 Sep 2021 15:05:40 +0200 Content-Type: multipart/alternative; boundary="------------Io8QGHVV2YSPbwsxxWL9rfmx" Message-ID: <78c910b7-8b21-73dd-198f-4f10d84bc35c@mpi-muenster.mpg.de> Date: Fri, 17 Sep 2021 15:05:40 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.0.3 Subject: Re: namd-l: performance scaling of CUDA accelerated NAMD over multiple nodes Content-Language: en-US To: "Vermaas, Josh" , "namd-l@ks.uiuc.edu" References: <4752fff5-e485-2d33-4f54-7ecf4a878ba4@mpi-muenster.mpg.de> <2AC71BC2-518A-4B1E-BE87-FBACE7CA8855@msu.edu> From: Vlad Cojocaru Organization: MPI Muenster In-Reply-To: <2AC71BC2-518A-4B1E-BE87-FBACE7CA8855@msu.edu> X-Originating-IP: [10.250.9.200] X-ClientProxiedBy: EXCMBX-05.um.gwdg.de (134.76.9.209) To excmbx-24.um.gwdg.de (134.76.9.234) X-Virus-Scanned: (clean) by clamav X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: BS4uPn3g6JNC3ZoGfbO5YGC8Z9uwpNYd X-Proofpoint-GUID: BS4uPn3g6JNC3ZoGfbO5YGC8Z9uwpNYd X-CLX-Response: 1TFkXGxIfEQpMehceEhEKWUQXaGxmBUdZGXIFSUMRClhYF2JNYHJ5TUkTT1l lEQp4ThdgX0RdeEV5W3BmaxEKeUwXZ3B5RnBaZWVFXU8RCkNIFwceGBIRCkNZFwcSHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscH3EeHhAadwYYGgYaEQpZXhdoY3kRCklGF19DX0l1Q kVZXk9OEQpDThdoeR5fekQZTRxgZGkZcEVtTEhlH3NtaRJwE19dWmRzThEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdzT0BOaREKTVwXHxwYEQpMWhdpe2lNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdjBR1GExtzHH9CfxEKQ1oXGxkeBB0cBBsbBBsdEQ pCXhcbEQpEXhcZEQpCRRdnR2JAYGNnTVBwaREKQk4XYF9EXXhFeVtwZmsRCkJMF2JNYHJ5TUkTT 1llEQpCbBdpS3obZB5fZ01BfhEKQkAXbnhdXFlaaBJOfWYRCkJYF2dzZXNAbmFhTF1iEQpaWBcc EQp5QxdiQUhBfH17WmATfhEKcGcXbUdha01jGUxTaW4QHhIRCnBoF2N9H1tyTUJYGAUTEBoRCnB oF2FIcltOcGMcHRlfEB4SEQpwaBdjYnBhQ1oYWEMabBAaEQpwaBdkR2hLUExiRB9EeRAeEhEKcG gXYlITWU9+bhhjcxgQGhEKcGcXZ1N+UkNjTkgZHVgQHhIRCnB9F2Nyb21HQnljHlBoEB4SEQpwf RdgGlJ7Y2BPXU9PZBAaEQpwZxdiWW5Oeh8Se3JDaRAaEQpwZxdtaVN+bU8eHx0YeRAaEQpwfRdv YmZiX1NucGxMRRAaEQpwfxdtRF9GRW19SHkZbhAbHhwRCnBfF2tGSxN5aGlufBN4EBsbGREKcH8 XZFAFWEltfklNTGwQGxsbEQpwXxd6QB5FXU9+SFpteBAaEQpwfxdhZm9bGmdkQkgdWxAbGR8RCn BfF2NiElBIY3gffEJ9EBMfEQpwbBdkWXx6HxJ4fkhBbRAaEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 clxscore=185 mlxlogscore=999 impostorscore=0 suspectscore=0 lowpriorityscore=0 malwarescore=0 mlxscore=0 phishscore=0 adultscore=0 priorityscore=48 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109170084 X-Spam-Score: 0 X-Spam-OrigSender: vlad.cojocaru@mpi-muenster.mpg.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vlad Cojocaru --------------Io8QGHVV2YSPbwsxxWL9rfmx Content-Type: text/plain; charset="UTF-8"; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Josh Thanks a lot for sharing this. I don't have experience with running the=20 GPU NAMD, this is the first time I actually decided to test it thoroughly. I think the NAMD build was not a pure SMP built. Maybe this is where the=20 problems come from in the first place .... I share below the build=20 procedure recommended by the HPC site. If there is anything that you=20 immediately spot to be problematic, I could give it a try to build NAMD=20 again. I will also share your email with the support team at the HPC site. Best wishes Vlad #### NAMD build procedure #### module load Intel ParaStationMPI FFTW Tcl tar -xf NAMD_2.14_Source.tar.gz cd NAMD_2.14_Source tar -xf charm-6.10.2.tar cd charm-6.10.2 ./build charm++ ucx-linux-x86_64 icc smp --with-production cd .. ./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc=C2=A0 --wit= h-tcl --tcl-prefix $EBROOTTCL=C2=A0 --cc "mpicc" --cc-opts "-O3 -march=3Dco= re-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++11"=C2= =A0 --cxx "mpicxx" --cxx-opts "-O3 -march=3Dcore-avx2 -ftz -fp-speculation= =3Dsafe -fp-model source -fPIC -std=3Dc++11 --std=3Dc++11"=C2=A0 --with-tcl= --tcl-prefix $EBROOTTCL=C2=A0 --with-fftw3=C2=A0 --fftw-prefix $EBROOTFFTW= --with-cuda cd Linux-x86_64-icc echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >> Make.config echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config make On 9/17/21 14:31, Vermaas, Josh wrote: > Hi Vlad, > > I've run NAMD on 4000 nodes, and it'll scale just fine (although the syst= em was much larger than 500k atoms!). There are a few gotchas involved with= multinode GPU NAMD. In no particular order: > > 1. This is an SMP build, yeah? Straight MPI builds with CUDA support are = *possible* to build, but perform terribly relative to their SMP bretheren > 2. I've found that each node performs best when a GPU gets its own rank/t= ask that command dedicated CPUs. On the local resources here at MSU, that l= ooks something like this: > > #!/bin/bash > #SBATCH --gres=3Dgpu:4 #4 GPUs per node > #SBATCH --nodes=3D2 > #SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the = number of GPUs > #SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12 > #SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a = CPU from trying to distribute work over multiple GPUs, and lowers PCIE cont= ention > > cd $SLURM_SUBMIT_DIR > module use /mnt/home/vermaasj/modules > module load NAMD/2.14-gpu > #other modules are loaded automatically by the NAMD module. > srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log > #With this setup, NAMD sees 8 logical nodes, 4 from each physical node. > > 3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs.= If the only thing you were doing is simulating 500k atoms (no replicas or = anything), each GPU is responsible for ~10k atoms. There are two layers of = communication for NAMD 2.14 on GPUs, transfers across the PCIe bus between = GPU and CPU every timestep, and communication between logical nodes wheneve= r pairlists get recomputed. If there isn't enough work for each GPU to do, = those extra communication steps are going to murder performance. TLDR, at s= ome point the scaling will break down, and for a system that small, it migh= t happen before you think it will. > > 4. If the simulations you are planning are going to be regular equilibriu= m simulations, NAMD3 will likely be faster on modern hardware, as it elimin= ates CPU-GPU communication at most timesteps. > > -Josh > > =EF=BB=BFOn 9/17/21, 6:44 AM,"owner-namd-l@ks.uiuc.edu on behalf of Vlad = Cojocaru" wrote: > > Dear all, > > We have been doing some tests with the CUDA (11 I believe) accelerat= ed > version of NAMD 2.14 on a remote supercomputer. On 1 node (96 thread= s, 4 > GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.1= 4. > There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs > almost no scaling. The simulation (classical MD) time per day for 50= 0K > atoms is similar to what expected (comparable to what is published on > the NAMD website). > > However, for a large scale project, the supercomputer site requires > scaling up to at least 10 nodes. And we are not able to get any scal= ing > to more than 1 node. In fact, as soon as running on 2 nodes (with 4 = GPUs > each), the performance is getting worse than on a single node. > > I know that lots of details are needed to actually pinpoint the > issue(s), many of these are architecture dependent and we do not have > all these details. > > However, I would still like to ask in general if any of you has > routinely managed to scale up the performance of the CUDA accelerated > NAMD 2.14 with the number of nodes. And if yes, are there any general > tips and tricks that could be tried ? > > Thank you for any insights ! > Vlad > > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/coj= ocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM2F0_C= 7PXf-jew$=20=20 > > > --=20 Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__= ;!!DZ3fjg!r1ccVWYnFhS8SM_XTIXz4Bvted68phFds9smvuTnBJXhCZq4CXh01dvJQFPjIgeDS= Q$=20 --------------Io8QGHVV2YSPbwsxxWL9rfmx Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Josh

Thanks a lot for sharing this. I don't have experience with running the GPU NAMD, this is the first time I actually decided to test it thoroughly.

I think the NAMD build was not a pure SMP built. Maybe this is where the problems come from in the first place .... I share below the build procedure recommended by the HPC site. If there is anything that you immediately spot to be problematic, I could give it a try to build NAMD again.

I will also share your email with the support team at the HPC site.

Best wishes
Vlad

#### NAMD build procedure ####
module load Intel ParaStationMPI FFTW Tcl
tar -xf NAMD_2.14_Source.tar.gz
cd NAMD_2.14_Source
tar -xf charm-6.10.2.tar
cd charm-6.10.2
./build charm++ ucx-linux-x86_64 icc smp --with-production
cd ..
./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc=C2=A0 --wit=
h-tcl --tcl-prefix $EBROOTTCL=C2=A0 --cc "mpicc" --cc-opts "-O3 -march=3Dco=
re-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++11"=C2=
=A0 --cxx "mpicxx" --cxx-opts "-O3 -march=3Dcore-avx2 -ftz -fp-speculation=
=3Dsafe -fp-model source -fPIC -std=3Dc++11 --std=3Dc++11"=C2=A0 --with-tcl=
 --tcl-prefix $EBROOTTCL=C2=A0 --with-fftw3=C2=A0 --fftw-prefix $EBROOTFFTW=
 --with-cuda
cd Linux-x86_64-icc
echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >> Make.c=
onfig
echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
make




On 9/17/21 14:31, Vermaas, Josh wrote:
Hi Vlad,

I've run NAMD on 4000 nodes, and it'll scale just fine (although the system=
 was much larger than 500k atoms!). There are a few gotchas involved with m=
ultinode GPU NAMD. In no particular order:

1. This is an SMP build, yeah? Straight MPI builds with CUDA support are *p=
ossible* to build, but perform terribly relative to their SMP bretheren
2. I've found that each node performs best when a GPU gets its own rank/tas=
k that command dedicated CPUs. On the local resources here at MSU, that loo=
ks something like this:

#!/bin/bash
#SBATCH --gres=3Dgpu:4 #4 GPUs per node
#SBATCH --nodes=3D2
#SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the nu=
mber of GPUs
#SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12
#SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a CP=
U from trying to distribute work over multiple GPUs, and lowers PCIE conten=
tion

cd $SLURM_SUBMIT_DIR
module use /mnt/home/vermaasj/modules
module load NAMD/2.14-gpu
#other modules are loaded automatically by the NAMD module.
srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log
#With this setup, NAMD sees 8 logical nodes, 4 from each physical node.

3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs. I=
f the only thing you were doing is simulating 500k atoms (no replicas or an=
ything), each GPU is responsible for ~10k atoms. There are two layers of co=
mmunication for NAMD 2.14 on GPUs, transfers across the PCIe bus between GP=
U and CPU every timestep, and communication between logical nodes whenever =
pairlists get recomputed. If there isn't enough work for each GPU to do, th=
ose extra communication steps are going to murder performance. TLDR, at som=
e point the scaling will break down, and for a system that small, it might =
happen before you think it will.

4. If the simulations you are planning are going to be regular equilibrium =
simulations, NAMD3 will likely be faster on modern hardware, as it eliminat=
es CPU-GPU communication at most timesteps.

-Josh

=EF=BB=BFOn 9/17/21, 6:44 AM, "owner-namd-l@ks.uiuc.=
edu on behalf of Vlad Cojocaru" <owner-namd-l@ks.uiuc.edu on behalf of vlad.cojocaru@mpi-muenster.m=
pg.de> wrote:

    Dear all,

    We have been doing some tests with the CUDA (11 I believe) accelerated=
=20
    version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads, =
4=20
    GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14.=
=20
    There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs=20
    almost no scaling. The simulation (classical MD) time per day for 500K=
=20
    atoms is similar to what expected (comparable to what is published on=20
    the NAMD website).

    However, for a large scale project, the supercomputer site requires=20
    scaling up to at least 10 nodes. And we are not able to get any scaling=
=20
    to more than 1 node. In fact, as soon as running on 2 nodes (with 4 GPU=
s=20
    each), the performance is getting worse than on a single node.

    I know that lots of details are needed to actually pinpoint the=20
    issue(s), many of these are architecture dependent and we do not have=20
    all these details.

    However, I would still like to ask in general if any of you has=20
    routinely managed to scale up the performance of the CUDA accelerated=20
    NAMD 2.14 with the number of nodes. And if yes, are there any general=20
    tips and tricks that could be tried ?

    Thank you for any insights !
    Vlad

    --=20
    Vlad Cojocaru, PD (Habil.), Ph.D.
    -----------------------------------------------
    Project Group Leader
    Department of Cell and Developmental Biology
    Max Planck Institute for Molecular Biomedicine
    R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
    -----------------------------------------------
    Tel: +49-251-70365-324; Fax: +49-251-70365-399
    Email: vlad.cojocaru[at]mpi-muenster.mpg.de
    https://urldefense.com/v=
3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2=
l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM2F0_C7PXf-jew$=20




--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.=
de/43241/cojocaru
= --------------Io8QGHVV2YSPbwsxxWL9rfmx-- From owner-namd-l@halifax.ks.uiuc.edu Fri Sep 17 08:42:16 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HDgDVq019375; Fri, 17 Sep 2021 08:42:15 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18HDgDL9019364; Fri, 17 Sep 2021 08:42:13 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HDg8TG019245; Fri, 17 Sep 2021 08:42:09 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18HDg83A019214; Fri, 17 Sep 2021 08:42:08 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18HDfsAf018915 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="00000000000000657b05cc31188f" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIZEQpMehcZHxgRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHxgbEQpDWRcHEh8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBlxHhgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XfWZFTWBJWHxeT2xTZW9gXWB4fVhAf2dTW3VcZ30bXVwRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdzT0ABEhEKTVwXGRgcEQpMWhd4aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBB scExEKQl4XGxEKRF4XGBEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY 2t7E1h+Gl9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3IdbmxPWHhg EQpCbBdhX3pTGUNEGnobfhEKQkAXbnhdXFlaaBJOfWYRCkJYF2dzZXNAbmFhTF1iEQpaWBcSEQp 5QxdiQUhBfH17WmATfhEKcGcXZ1N+UkNjTkgZHVgQHBoRCnBoF2gbfnNccgFGTRhiEBkaEQpwaB ducm5MTUFme2NyZxAZGhEKcGgXZhtvT3xJXUlOQ2QQGRoRCnBoF29mQV1mRnh4TWgeEBkaEQpwa BdrUx0acwUdexwYHRAZGhEKcH0XZWdOR2gafUJGUGAQGRoRCnBnF21HYWtNYxlMU2luEBwaEQpw ZxdtaVN+bU8eHx0YeRAeEhEKcH0XY3JvbUdCeWMeUGgQHBoRCnB9F2AaUntjYE9dT09kEBkaEQp wfRduZmRAYWRvYn1bfRAeEhEKcH0XY199XHhIf3lkRV8QGRoRCnB9F29iZmJfU25wbExFEB4SEQ pwfRdtQkkbBRJ4X1ocSBAeEhEKcH8XbmJkAUVaRUR+ZW8QHhsRCnBfF2d8E29JZkJObkRlEBkaE QpwfxdtRF9GRW19SHkZbhAbHh4RCnBfF2tGSxN5aGlufBN4EBsaEhEKcH8XZFAFWEltfklNTGwQ HRoRCnBfF3pAHkVdT35IWm14EBkaEQpwXxdjX31ceEh/eWRFXxAZGhEKcH8XYWZvWxpnZEJIHVs QGxkdEQpwXxdjYhJQSGN4H3xCfRAbGhgRCnBsF2Yfe1hcYgVLWGQfEB4SEQpwTBdtaGUZQVJ9ex hFUhAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: WLogJcrVteFyOEJwJRWrjUMyq_vMW1wv X-Proofpoint-ORIG-GUID: WLogJcrVteFyOEJwJRWrjUMyq_vMW1wv MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=183 lowpriorityscore=0 priorityscore=352 mlxscore=0 suspectscore=0 mlxlogscore=999 malwarescore=0 impostorscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109170088 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000000657b05cc31188f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Vlad, it seems that they recommended you to use the UCX backend for Charm++. This is a good idea, because the UCX middleware can help significantly toward optimizing the communication paths in a complex or congested network. *However,* Charm++ is still in its early stages of adoption of UCX, and there are several things to look at when building: https://urldefense.com/v3/__https://charm.readthedocs.io/en/latest/charm**A= /manual.html*ucx__;Kysj!!DZ3fjg!pOWdlhDBvbr6VHTZh5ExvS-1CcU6gDjRaPb7rpLe3t3= oC9Vq90c2MsIu2bp6SCHm7A$=20 One possibility in your case is that the wrong PMI (*distinct *from MPI) for the purpose is being picked up and the processes or threads aren't allocated correctly. If you're confident that you really do need multi-node (see Josh's good suggestion about NAMD 3) I suggest the following: 1. Build and test NAMD with Charm++/UCX without SMP and without CUDA. Between 1 and 2 nodes you ought to get linear scaling for 500k atoms. 2. Build and test NAMD with Charm++/UCX with SMP but still without CUDA. You should see a slight decrease of the whole scaling curve because the SMP backend separates communication and compute in separate threads, and wants dedicated ones for each. But SMP is also what works best when throwing in the GPUs. 3. Build and test NAMD with both SMP and CUDA. As a minor suggestion, try also to verify that the AVX instructions being recommended are actually paying off. Not all CPUs have a high enough clock rate for their AVX units to make it worth using them compared to standard floating-point ops. I don't know what is the level of support from the HPC staff of that facility. But in general it is a good rule to treat building a code as an experiment that needs verification at every step of the way (something we scientists are accustomed to, or ought to be). Giacomo On Fri, Sep 17, 2021 at 9:13 AM Vlad Cojocaru < vlad.cojocaru@mpi-muenster.mpg.de> wrote: > Hi Josh > > Thanks a lot for sharing this. I don't have experience with running the > GPU NAMD, this is the first time I actually decided to test it thoroughly. > > I think the NAMD build was not a pure SMP built. Maybe this is where the > problems come from in the first place .... I share below the build > procedure recommended by the HPC site. If there is anything that you > immediately spot to be problematic, I could give it a try to build NAMD > again. > > I will also share your email with the support team at the HPC site. > > Best wishes > Vlad > > #### NAMD build procedure #### > > module load Intel ParaStationMPI FFTW Tcl > tar -xf NAMD_2.14_Source.tar.gz > cd NAMD_2.14_Source > tar -xf charm-6.10.2.tar > cd charm-6.10.2 > ./build charm++ ucx-linux-x86_64 icc smp --with-production > cd .. > ./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc --with-t= cl --tcl-prefix $EBROOTTCL --cc "mpicc" --cc-opts "-O3 -march=3Dcore-avx2 = -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++11" --cxx "mp= icxx" --cxx-opts "-O3 -march=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-mo= del source -fPIC -std=3Dc++11 --std=3Dc++11" --with-tcl --tcl-prefix $EBRO= OTTCL --with-fftw3 --fftw-prefix $EBROOTFFTW --with-cuda > cd Linux-x86_64-icc > echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >> Make.config > echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config > echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config > make > > > > > On 9/17/21 14:31, Vermaas, Josh wrote: > > Hi Vlad, > > I've run NAMD on 4000 nodes, and it'll scale just fine (although the syst= em was much larger than 500k atoms!). There are a few gotchas involved with= multinode GPU NAMD. In no particular order: > > 1. This is an SMP build, yeah? Straight MPI builds with CUDA support are = *possible* to build, but perform terribly relative to their SMP bretheren > 2. I've found that each node performs best when a GPU gets its own rank/t= ask that command dedicated CPUs. On the local resources here at MSU, that l= ooks something like this: > > #!/bin/bash > #SBATCH --gres=3Dgpu:4 #4 GPUs per node > #SBATCH --nodes=3D2 > #SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the = number of GPUs > #SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12 > #SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a = CPU from trying to distribute work over multiple GPUs, and lowers PCIE cont= ention > > cd $SLURM_SUBMIT_DIR > module use /mnt/home/vermaasj/modules > module load NAMD/2.14-gpu > #other modules are loaded automatically by the NAMD module. > srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log > #With this setup, NAMD sees 8 logical nodes, 4 from each physical node. > > 3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs.= If the only thing you were doing is simulating 500k atoms (no replicas or = anything), each GPU is responsible for ~10k atoms. There are two layers of = communication for NAMD 2.14 on GPUs, transfers across the PCIe bus between = GPU and CPU every timestep, and communication between logical nodes wheneve= r pairlists get recomputed. If there isn't enough work for each GPU to do, = those extra communication steps are going to murder performance. TLDR, at s= ome point the scaling will break down, and for a system that small, it migh= t happen before you think it will. > > 4. If the simulations you are planning are going to be regular equilibriu= m simulations, NAMD3 will likely be faster on modern hardware, as it elimin= ates CPU-GPU communication at most timesteps. > > -Josh > > =EF=BB=BFOn 9/17/21, 6:44 AM, "owner-namd-l@ks.uiuc.edu on behalf of Vlad= Cojocaru" wrote: > > Dear all, > > We have been doing some tests with the CUDA (11 I believe) accelerated > version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads= , 4 > GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14. > There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs > almost no scaling. The simulation (classical MD) time per day for 500K > atoms is similar to what expected (comparable to what is published on > the NAMD website). > > However, for a large scale project, the supercomputer site requires > scaling up to at least 10 nodes. And we are not able to get any scali= ng > to more than 1 node. In fact, as soon as running on 2 nodes (with 4 G= PUs > each), the performance is getting worse than on a single node. > > I know that lots of details are needed to actually pinpoint the > issue(s), many of these are architecture dependent and we do not have > all these details. > > However, I would still like to ask in general if any of you has > routinely managed to scale up the performance of the CUDA accelerated > NAMD 2.14 with the number of nodes. And if yes, are there any general > tips and tricks that could be tried ? > > Thank you for any insights ! > Vlad > > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojo= caru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM2F0_C7= PXf-jew$ > > > > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de= /43241/cojocaru > > --00000000000000657b05cc31188f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Vlad, it seems that they recommended you to use the UCX= backend for Charm++.=C2=A0 This is a good idea, because the UCX middleware= can help=C2=A0significantly toward optimizing the communication paths in a= complex or congested network.=C2=A0 However, Charm++ is still in it= s early stages of adoption of UCX, and there are several things to look at = when building:

One possibility in your case is that the wrong PMI (distinct from= =C2=A0MPI) for the purpose is being picked up and the processes or threads = aren't allocated correctly.

If you're conf= ident that you really do need multi-node (see Josh's good suggestion ab= out NAMD 3) I suggest the following:
1. Build and test NAMD with = Charm++/UCX without SMP and without CUDA.=C2=A0 Between 1 and 2 nodes you o= ught to get linear scaling for 500k atoms.
2. Build and test NAMD= with Charm++/UCX with SMP=C2=A0but still without CUDA.=C2=A0 You should se= e a slight decrease of the whole scaling curve because the SMP backend sepa= rates communication and compute in separate=C2=A0threads, and wants dedicat= ed ones for each.=C2=A0 But SMP is also what works best when throwing in th= e GPUs.
3. Build and test NAMD with both SMP and CUDA.
=
As a minor suggestion, try also to verify that the AVX instr= uctions being recommended are actually paying off.=C2=A0 Not all CPUs have = a high enough clock rate for their AVX units to make it worth using them co= mpared to standard floating-point ops.

I don't= know what is the level of support from the HPC staff of that facility.=C2= =A0 But in general it is a good rule to treat building a code as an experim= ent that needs verification at=C2=A0every step of the way (something we sci= entists are accustomed to, or ought to be).

Giacom= o


On Fri, Sep 17, 2021 at 9:13 AM Vlad Cojocaru <vlad.cojocaru@mpi-muenste= r.mpg.de> wrote:
=20=20 =20=20=20=20 =20=20
Hi Josh

Thanks a lot for sharing this. I don't have experience with running the GPU NAMD, this is the first time I actually decided to test it thoroughly.

I think the NAMD build was not a pure SMP built. Maybe this is where the problems come from in the first place .... I share below the build procedure recommended by the HPC site. If there is anything that you immediately spot to be problematic, I could give it a try to build NAMD again.

I will also share your email with the support team at the HPC site.

Best wishes
Vlad

#### NAMD build procedure ####
module load Intel ParaStationMPI FFTW Tcl
tar -xf NAMD_2.14_Source.tar.gz
cd NAMD_2.14_Source
tar -xf charm-6.10.2.tar
cd charm-6.10.2
./build charm++ ucx-linux-x86_64 icc smp --with-production
cd ..
./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc=C2=A0 --wit=
h-tcl --tcl-prefix $EBROOTTCL=C2=A0 --cc "mpicc" --cc-opts "=
-O3 -march=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -=
std=3Dc++11"=C2=A0 --cxx "mpicxx" --cxx-opts "-O3 -marc=
h=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++=
11 --std=3Dc++11"=C2=A0 --with-tcl --tcl-prefix $EBROOTTCL=C2=A0 --wit=
h-fftw3=C2=A0 --fftw-prefix $EBROOTFFTW --with-cuda
cd Linux-x86_64-icc
echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >&=
gt; Make.config
echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
make




On 9/17/21 14:31, Vermaas, Josh wrote:
Hi Vlad,

I've run NAMD on 4000 nodes, and it'll scale just fine (although th=
e system was much larger than 500k atoms!). There are a few gotchas involve=
d with multinode GPU NAMD. In no particular order:

1. This is an SMP build, yeah? Straight MPI builds with CUDA support are *p=
ossible* to build, but perform terribly relative to their SMP bretheren
2. I've found that each node performs best when a GPU gets its own rank=
/task that command dedicated CPUs. On the local resources here at MSU, that=
 looks something like this:

#!/bin/bash
#SBATCH --gres=3Dgpu:4 #4 GPUs per node
#SBATCH --nodes=3D2
#SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the nu=
mber of GPUs
#SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12
#SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a CP=
U from trying to distribute work over multiple GPUs, and lowers PCIE conten=
tion

cd $SLURM_SUBMIT_DIR
module use /mnt/home/vermaasj/modules
module load NAMD/2.14-gpu
#other modules are loaded automatically by the NAMD module.
srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log
#With this setup, NAMD sees 8 logical nodes, 4 from each physical node.

3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs. I=
f the only thing you were doing is simulating 500k atoms (no replicas or an=
ything), each GPU is responsible for ~10k atoms. There are two layers of co=
mmunication for NAMD 2.14 on GPUs, transfers across the PCIe bus between GP=
U and CPU every timestep, and communication between logical nodes whenever =
pairlists get recomputed. If there isn't enough work for each GPU to do=
, those extra communication steps are going to murder performance. TLDR, at=
 some point the scaling will break down, and for a system that small, it mi=
ght happen before you think it will.

4. If the simulations you are planning are going to be regular equilibrium =
simulations, NAMD3 will likely be faster on modern hardware, as it eliminat=
es CPU-GPU communication at most timesteps.

-Josh

=EF=BB=BFOn 9/17/21, 6:44 AM, "owner-namd-l@ks.uiuc.edu on be=
half of Vlad Cojocaru" <owner-nam=
d-l@ks.uiuc.edu on behalf of vlad.cojocaru@mpi-muenster.mpg.de> wrot=
e:

    Dear all,

    We have been doing some tests with the CUDA (11 I believe) accelerated=
=20
    version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads, =
4=20
    GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14.=
=20
    There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs=20
    almost no scaling. The simulation (classical MD) time per day for 500K=
=20
    atoms is similar to what expected (comparable to what is published on=20
    the NAMD website).

    However, for a large scale project, the supercomputer site requires=20
    scaling up to at least 10 nodes. And we are not able to get any scaling=
=20
    to more than 1 node. In fact, as soon as running on 2 nodes (with 4 GPU=
s=20
    each), the performance is getting worse than on a single node.

    I know that lots of details are needed to actually pinpoint the=20
    issue(s), many of these are architecture dependent and we do not have=20
    all these details.

    However, I would still like to ask in general if any of you has=20
    routinely managed to scale up the performance of the CUDA accelerated=20
    NAMD 2.14 with the number of nodes. And if yes, are there any general=20
    tips and tricks that could be tried ?

    Thank you for any insights !
    Vlad

    --=20
    Vlad Cojocaru, PD (Habil.), Ph.D.
    -----------------------------------------------
    Project Group Leader
    Department of Cell and Developmental Biology
    Max Planck Institute for Molecular Biomedicine
    R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
    -----------------------------------------------
    Tel: +49-251-70365-324; Fax: +49-251-70365-399
    Email: vlad.cojocaru[at]mpi-muenster.mpg.de
    https://urldefense.com/v3/__http://www=
.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjz=
DgBZatmHwqU4VwajBWBxMQ4BM2F0_C7PXf-jew$=20




--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojoc=
aru
--00000000000000657b05cc31188f-- From owner-namd-l@halifax.ks.uiuc.edu Sat Sep 18 07:01:10 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18IC194C004323; Sat, 18 Sep 2021 07:01:09 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18IC17ns004274; Sat, 18 Sep 2021 07:01:08 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18IC12TS004167; Sat, 18 Sep 2021 07:01:02 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18IC11Hi004145; Sat, 18 Sep 2021 07:01:01 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18IC0m8t003898 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 18 Sep 2021 07:00:50 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18I8PRPC016524 for ; Sat, 18 Sep 2021 12:00:48 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=vlad.cojocaru@mpi-muenster.mpg.de Received: from gmailer.gwdg.de (gmailer.gwdg.de [134.76.11.17]) by mx0a-00007101.pphosted.com with ESMTP id 3b56kxa4w7-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 18 Sep 2021 12:00:47 +0000 Received: from excmbx-24.um.gwdg.de ([134.76.9.234] helo=email.gwdg.de) by mailer.gwdg.de with esmtp (GWDG Mailer) (envelope-from ) id 1mRZ1Q-00005r-Jd; Sat, 18 Sep 2021 14:00:45 +0200 Received: from [192.168.178.22] (10.250.9.200) by excmbx-24.um.gwdg.de (134.76.9.234) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P521) id 15.1.2308.14; Sat, 18 Sep 2021 14:00:44 +0200 Content-Type: multipart/alternative; boundary="------------zn9ZX4p0zRrQpeoclkKtc4sA" Message-ID: <445e8bca-6a89-2925-3c3b-adfaa17d40a7@mpi-muenster.mpg.de> Date: Sat, 18 Sep 2021 14:00:44 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.0.3 Subject: Re: namd-l: performance scaling of CUDA accelerated NAMD over multiple nodes Content-Language: en-US To: Giacomo Fiorin , NAMD list CC: "Vermaas, Josh" References: <4752fff5-e485-2d33-4f54-7ecf4a878ba4@mpi-muenster.mpg.de> <2AC71BC2-518A-4B1E-BE87-FBACE7CA8855@msu.edu> <78c910b7-8b21-73dd-198f-4f10d84bc35c@mpi-muenster.mpg.de> From: Vlad Cojocaru Organization: MPI Muenster In-Reply-To: X-Originating-IP: [10.250.9.200] X-ClientProxiedBy: excmbx-22.um.gwdg.de (134.76.9.232) To excmbx-24.um.gwdg.de (134.76.9.234) X-Virus-Scanned: (clean) by clamav X-Proofpoint-ORIG-GUID: P4iPH6FYfpNAXjv_eLvT7dqKRu1SGYgC X-CLX-Shades: MLX X-Proofpoint-GUID: P4iPH6FYfpNAXjv_eLvT7dqKRu1SGYgC X-CLX-Response: 1TFkXGx0TEQpMehceEhEKWUQXaGxmBUdZGXIFSUMRClhYF2JNYHJ5TUkTT1l lEQp4ThdgX0RdeEV5W3BmaxEKeUwXZ3B5RnBaZWVFXU8RCkNIFwceHxIRCkNZFwcTHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfE3EZEhAadwYYGgYaEQpZXhdoY3kRCklGF19DX0l1Q kVZXk9OEQpDThd6HkN6Yhxsc0xaZGtyQFx1T2Zcfh1OW2F4Xxt5bXNNaREKWFwXHwQaBBgZGQUb GgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3NPGUdmEQpNXBcbGBoRCkxaF3hpa01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XYwUdRhMbcxx/Qn8RCkNaFxsZHgQdHAQbGwQbHREKQl 4XGxEKRF4XGBEKREkXGxEKQkUXZ0diQGBjZ01QcGkRCkJOF2BfRF14RXlbcGZrEQpCTBdiTWBye U1JE09ZZREKQmwXaUt6G2QeX2dNQX4RCkJAF254XVxZWmgSTn1mEQpCWBdnc2VzQG5hYUxdYhEK TV4XGxEKWlgXHBEKeUMXYkFIQXx9e1pgE34RCnBnF2dTflJDY05IGR1YEBkaEQpwaBduS2ZzG3k eWV1/RxAZGhEKcGgXbhJuHl9TS2VQfF0QGRoRCnBoF2ZjTn0ZSXsTeBJMEBkaEQpwaBdvSWVaT1 kff0VieBAZGhEKcGgXYBNyeGFvfExnX28QGRoRCnB9F2VnTkdoGn1CRlBgEBkaEQpwZxdtR2FrT WMZTFNpbhAZGhEKcGcXbWlTfm1PHh8dGHkQGRoRCnB9F2NffVx4SH95ZEVfEBkaEQpwfRdjcm9t R0J5Yx5QaBAcGhEKcH0XYBpSe2NgT11PT2QQGRoRCnB9F25mZEBhZG9ifVt9EBkaEQpwZxdgXmd tHkwbcEZkYhAZGhEKcH8XbmJkAUVaRUR+ZW8QGR8RCnBfF2d8E29JZkJObkRlEBkaEQpwfxdkUA VYSW1+SU1MbBAbGRsRCnBfF2NffVx4SH95ZEVfEBkaEQpwfxdtRF9GRW19SHkZbhAbGxIRCnBfF 2tGSxN5aGlufBN4EBMaEQpwXxd6QB5FXU9+SFpteBAZGhEKcGwXZFl8eh8SeH5IQW0QGRoRCnBM F21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=179 bulkscore=0 mlxlogscore=999 suspectscore=0 priorityscore=48 spamscore=0 impostorscore=0 adultscore=0 phishscore=0 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109180083 X-Spam-Score: 0 X-Spam-OrigSender: vlad.cojocaru@mpi-muenster.mpg.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vlad Cojocaru --------------zn9ZX4p0zRrQpeoclkKtc4sA Content-Type: text/plain; charset="UTF-8"; format=flowed Content-Transfer-Encoding: Quoted-printable Thanks Giacomo, O forwarded your email to the HPC site. They are very helpful and will=20 try to see if we get the bottleneck of this by rebuilding NAMD. But coming back to Josh's point about the low workload on the GPU. This=20 may be a valid point. Of course, we will do replicate of those=20 simulations, so one way to circumvent the issue is to run at least 10=20 simulations in parallel, each of them using one node. ... But I am wondering ... Whithin one simulation, what would be the minimum=20 number of atoms allocated to 1 GPU to have a decent workload on the GPU ? Best Vlad On 9/17/21 15:41, Giacomo Fiorin wrote: > Hi Vlad, it seems that they recommended you to use the UCX backend for=20 > Charm++.=C2=A0 This is a good idea, because the UCX middleware can=20 > help=C2=A0significantly toward optimizing the communication paths in a=20 > complex or congested network. /However,/ Charm++ is still in its early=20 > stages of adoption of UCX, and there are several things to look at=20 > when building: > https://urldefense.com/v3/__https://charm.readthedocs.io/en/latest/charm*= *A/manual.html*ucx__;Kysj!!DZ3fjg!qAPIcV2wBNS8GLvobCT-sT20ffvzeu9rjB3HSAF1i= hXNYtQso266QAJ69ufqVo0JpA$=20 > > One possibility in your case is that the wrong PMI (/distinct=20 > /from=C2=A0MPI) for the purpose is being picked up and the processes or=20 > threads aren't allocated correctly. > > If you're confident that you really do need multi-node (see Josh's=20 > good suggestion about NAMD 3) I suggest the following: > 1. Build and test NAMD with Charm++/UCX without SMP and without CUDA.=C2= =A0=20 > Between 1 and 2 nodes you ought to get linear scaling for 500k atoms. > 2. Build and test NAMD with Charm++/UCX with SMP=C2=A0but still without=20 > CUDA.=C2=A0 You should see a slight decrease of the whole scaling curve=20 > because the SMP backend separates communication and compute in=20 > separate=C2=A0threads, and wants dedicated ones for each.=C2=A0 But SMP i= s also=20 > what works best when throwing in the GPUs. > 3. Build and test NAMD with both SMP and CUDA. > > As a minor suggestion, try also to verify that the AVX instructions=20 > being recommended are actually paying off.=C2=A0 Not all CPUs have a high= =20 > enough clock rate for their AVX units to make it worth using them=20 > compared to standard floating-point ops. > > I don't know what is the level of support from the HPC staff of that=20 > facility.=C2=A0 But in general it is a good rule to treat building a code= =20 > as an experiment that needs verification at=C2=A0every step of the way=20 > (something we scientists are accustomed to, or ought to be). > > Giacomo > > > On Fri, Sep 17, 2021 at 9:13 AM Vlad Cojocaru=20 > wrote: > > Hi Josh > > Thanks a lot for sharing this. I don't have experience with > running the GPU NAMD, this is the first time I actually decided to > test it thoroughly. > > I think the NAMD build was not a pure SMP built. Maybe this is > where the problems come from in the first place .... I share below > the build procedure recommended by the HPC site. If there is > anything that you immediately spot to be problematic, I could give > it a try to build NAMD again. > > I will also share your email with the support team at the HPC site. > > Best wishes > Vlad > > #### NAMD build procedure #### > > module load Intel ParaStationMPI FFTW Tcl > tar -xf NAMD_2.14_Source.tar.gz > cd NAMD_2.14_Source > tar -xf charm-6.10.2.tar > cd charm-6.10.2 > ./build charm++ ucx-linux-x86_64 icc smp --with-production > cd .. > ./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc=C2=A0= --with-tcl --tcl-prefix $EBROOTTCL=C2=A0 --cc "mpicc" --cc-opts "-O3 -marc= h=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++= 11"=C2=A0 --cxx "mpicxx" --cxx-opts "-O3 -march=3Dcore-avx2 -ftz -fp-specul= ation=3Dsafe -fp-model source -fPIC -std=3Dc++11 --std=3Dc++11"=C2=A0 --wit= h-tcl --tcl-prefix $EBROOTTCL=C2=A0 --with-fftw3=C2=A0 --fftw-prefix $EBROO= TFFTW --with-cuda > cd Linux-x86_64-icc > echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >> Make.c= onfig > echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config > echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config > make > > > > > On 9/17/21 14:31, Vermaas, Josh wrote: >> Hi Vlad, >> >> I've run NAMD on 4000 nodes, and it'll scale just fine (although the= system was much larger than 500k atoms!). There are a few gotchas involved= with multinode GPU NAMD. In no particular order: >> >> 1. This is an SMP build, yeah? Straight MPI builds with CUDA support= are *possible* to build, but perform terribly relative to their SMP brethe= ren >> 2. I've found that each node performs best when a GPU gets its own r= ank/task that command dedicated CPUs. On the local resources here at MSU, t= hat looks something like this: >> >> #!/bin/bash >> #SBATCH --gres=3Dgpu:4 #4 GPUs per node >> #SBATCH --nodes=3D2 >> #SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match= the number of GPUs >> #SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12 >> #SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Preven= ts a CPU from trying to distribute work over multiple GPUs, and lowers PCIE= contention >> >> cd $SLURM_SUBMIT_DIR >> module use /mnt/home/vermaasj/modules >> module load NAMD/2.14-gpu >> #other modules are loaded automatically by the NAMD module. >> srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log >> #With this setup, NAMD sees 8 logical nodes, 4 from each physical no= de. >> >> 3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 = GPUs. If the only thing you were doing is simulating 500k atoms (no replica= s or anything), each GPU is responsible for ~10k atoms. There are two layer= s of communication for NAMD 2.14 on GPUs, transfers across the PCIe bus bet= ween GPU and CPU every timestep, and communication between logical nodes wh= enever pairlists get recomputed. If there isn't enough work for each GPU to= do, those extra communication steps are going to murder performance. TLDR,= at some point the scaling will break down, and for a system that small, it= might happen before you think it will. >> >> 4. If the simulations you are planning are going to be regular equil= ibrium simulations, NAMD3 will likely be faster on modern hardware, as it e= liminates CPU-GPU communication at most timesteps. >> >> -Josh >> >> =EF=BB=BFOn 9/17/21, 6:44 AM,"owner-namd-l@ks.uiuc.edu on behalf of = Vlad Cojocaru" > vlad.cojocaru@mpi-muenster.mpg.de> wrote: >> >> Dear all, >> >> We have been doing some tests with the CUDA (11 I believe) acce= lerated >> version of NAMD 2.14 on a remote supercomputer. On 1 node (96 t= hreads, 4 >> GPUs), we see a 10 fold acceleration compared to a non-CUDA NAM= D 2.14. >> There is a decent scaling between 1 and 2 GPUs but from 2 to 4 = GPUs >> almost no scaling. The simulation (classical MD) time per day f= or 500K >> atoms is similar to what expected (comparable to what is publis= hed on >> the NAMD website). >> >> However, for a large scale project, the supercomputer site requ= ires >> scaling up to at least 10 nodes. And we are not able to get any= scaling >> to more than 1 node. In fact, as soon as running on 2 nodes (wi= th 4 GPUs >> each), the performance is getting worse than on a single node. >> >> I know that lots of details are needed to actually pinpoint the >> issue(s), many of these are architecture dependent and we do no= t have >> all these details. >> >> However, I would still like to ask in general if any of you has >> routinely managed to scale up the performance of the CUDA accel= erated >> NAMD 2.14 with the number of nodes. And if yes, are there any g= eneral >> tips and tricks that could be tried ? >> >> Thank you for any insights ! >> Vlad >> >> -- >> Vlad Cojocaru, PD (Habil.), Ph.D. >> ----------------------------------------------- >> Project Group Leader >> Department of Cell and Developmental Biology >> Max Planck Institute for Molecular Biomedicine >> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >> ----------------------------------------------- >> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/4324= 1/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM= 2F0_C7PXf-jew$=20=20 >> >> >> > > --=20 > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojo= caru__;!!DZ3fjg!qAPIcV2wBNS8GLvobCT-sT20ffvzeu9rjB3HSAF1ihXNYtQso266QAJ69ue= cuDqXRA$ > --=20 Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__= ;!!DZ3fjg!qAPIcV2wBNS8GLvobCT-sT20ffvzeu9rjB3HSAF1ihXNYtQso266QAJ69uecuDqXR= A$=20 --------------zn9ZX4p0zRrQpeoclkKtc4sA Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks Giacomo,

O forwarded your email to the HPC site. They are very helpful and will try to see if we get the bottleneck of this by rebuilding NAMD.

But coming back to Josh's point about the low workload on the GPU. This may be a valid point. Of course, we will do replicate of those simulations, so one way to circumvent the issue is to run at least 10 simulations in parallel, each of them using one node. ...

But I am wondering ... Whithin one simulation, what would be the minimum number of atoms allocated to 1 GPU to have a decent workload on the GPU ?

Best
Vlad


On 9/17/21 15:41, Giacomo Fiorin wrote:<= br>
Hi Vlad, it seems that they recommended you to use the UCX backend for Charm++.=C2=A0 This is a good idea, because the UCX middleware can help=C2=A0significantly toward optimizing the communication paths in a complex or congested network.=C2=A0 How= ever, Charm++ is still in its early stages of adoption of UCX, and there are several things to look at when building:

One possibility in your case is that the wrong PMI (distinct from=C2=A0MPI) for the purpose is being picked up and the processes or threads aren't allocated correctly.

If you're confident that you really do need multi-node (see Josh's good suggestion about NAMD 3) I suggest the following:
1. Build and test NAMD with Charm++/UCX without SMP and without CUDA.=C2=A0 Between 1 and 2 nodes you ought to get linear scaling for 500k atoms.
2. Build and test NAMD with Charm++/UCX with SMP=C2=A0but still without CUDA.=C2=A0 You should see a slight decrease of the whole scaling curve because the SMP backend separates communication and compute in separate=C2=A0threads, and wants dedicated ones for each.=C2=A0 But SMP is also what works best when throwing in the GPUs.
3. Build and test NAMD with both SMP and CUDA.

As a minor suggestion, try also to verify that the AVX instructions being recommended are actually paying off.=C2=A0 Not all CPUs have a high enough clock rate for their AVX units to make it worth using them compared to standard floating-point ops.

I don't know what is the level of support from the HPC staff of that facility.=C2=A0 But in general it is a good rule to treat building a code as an experiment that needs verification at=C2=A0every step of the way (something we scientists are accustomed to, or ought to be).

Giacomo


On Fri, Sep 17, 2021 at 9:13 AM Vlad Cojocaru <vlad.c= ojocaru@mpi-muenster.mpg.de> wrote:
Hi Josh

Thanks a lot for sharing this. I don't have experience with running the GPU NAMD, this is the first time I actually decided to test it thoroughly.

I think the NAMD build was not a pure SMP built. Maybe this is where the problems come from in the first place .... I share below the build procedure recommended by the HPC site. If there is anything that you immediately spot to be problematic, I could give it a try to build NAMD again.

I will also share your email with the support team at the HPC site.

Best wishes
Vlad

#### NAMD build procedure ####
module load Intel ParaStationMPI FFTW Tcl
tar -xf NAMD_2.14_Source.tar.gz
cd NAMD_2.14_Source
tar -xf charm-6.10.2.tar
cd charm-6.10.2
./build charm++ ucx-linux-x86_64 icc smp --with-production
cd ..
./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc=C2=A0 --wit=
h-tcl --tcl-prefix $EBROOTTCL=C2=A0 --cc "mpicc" --cc-opts "-O3 -march=3Dco=
re-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++11"=C2=
=A0 --cxx "mpicxx" --cxx-opts "-O3 -march=3Dcore-avx2 -ftz -fp-speculation=
=3Dsafe -fp-model source -fPIC -std=3Dc++11 --std=3Dc++11"=C2=A0 --with-tcl=
 --tcl-prefix $EBROOTTCL=C2=A0 --with-fftw3=C2=A0 --fftw-prefix $EBROOTFFTW=
 --with-cuda
cd Linux-x86_64-icc
echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >> Make.c=
onfig
echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
make




On 9/17/21 14:31, Vermaas, Josh wrote:
Hi Vlad,

I've run NAMD on 4000 nodes, and it'll scale just fine (although the system=
 was much larger than 500k atoms!). There are a few gotchas involved with m=
ultinode GPU NAMD. In no particular order:

1. This is an SMP build, yeah? Straight MPI builds with CUDA support are *p=
ossible* to build, but perform terribly relative to their SMP bretheren
2. I've found that each node performs best when a GPU gets its own rank/tas=
k that command dedicated CPUs. On the local resources here at MSU, that loo=
ks something like this:

#!/bin/bash
#SBATCH --gres=3Dgpu:4 #4 GPUs per node
#SBATCH --nodes=3D2
#SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the nu=
mber of GPUs
#SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12
#SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a CP=
U from trying to distribute work over multiple GPUs, and lowers PCIE conten=
tion

cd $SLURM_SUBMIT_DIR
module use /mnt/home/vermaasj/modules
module load NAMD/2.14-gpu
#other modules are loaded automatically by the NAMD module.
srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log
#With this setup, NAMD sees 8 logical nodes, 4 from each physical node.

3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs. I=
f the only thing you were doing is simulating 500k atoms (no replicas or an=
ything), each GPU is responsible for ~10k atoms. There are two layers of co=
mmunication for NAMD 2.14 on GPUs, transfers across the PCIe bus between GP=
U and CPU every timestep, and communication between logical nodes whenever =
pairlists get recomputed. If there isn't enough work for each GPU to do, th=
ose extra communication steps are going to murder performance. TLDR, at som=
e point the scaling will break down, and for a system that small, it might =
happen before you think it will.

4. If the simulations you are planning are going to be regular equilibrium =
simulations, NAMD3 will likely be faster on modern hardware, as it eliminat=
es CPU-GPU communication at most timesteps.

-Josh

=EF=BB=BFOn 9/17/21, 6:44 AM, "owner-namd=
-l@ks.uiuc.edu on behalf of Vlad Cojocaru" <owner-namd-l@ks.uiuc.edu on behalf of vlad.c=
ojocaru@mpi-muenster.mpg.de> wrote:

    Dear all,

    We have been doing some tests with the CUDA (11 I believe) accelerated=
=20
    version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads, =
4=20
    GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14.=
=20
    There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs=20
    almost no scaling. The simulation (classical MD) time per day for 500K=
=20
    atoms is similar to what expected (comparable to what is published on=20
    the NAMD website).

    However, for a large scale project, the supercomputer site requires=20
    scaling up to at least 10 nodes. And we are not able to get any scaling=
=20
    to more than 1 node. In fact, as soon as running on 2 nodes (with 4 GPU=
s=20
    each), the performance is getting worse than on a single node.

    I know that lots of details are needed to actually pinpoint the=20
    issue(s), many of these are architecture dependent and we do not have=20
    all these details.

    However, I would still like to ask in general if any of you has=20
    routinely managed to scale up the performance of the CUDA accelerated=20
    NAMD 2.14 with the number of nodes. And if yes, are there any general=20
    tips and tricks that could be tried ?

    Thank you for any insights !
    Vlad

    --=20
    Vlad Cojocaru, PD (Habil.), Ph.D.
    -----------------------------------------------
    Project Group Leader
    Department of Cell and Developmental Biology
    Max Planck Institute for Molecular Biomedicine
    R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
    -----------------------------------------------
    Tel: +49-251-70365-324; Fax: +49-251-70365-399
    Email: vlad.cojocaru[at]mpi-muen=
ster.mpg.de
    https://urldefense.com/v3/__http://www.mpi-muenster.mpg.=
de/43241/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBW=
BxMQ4BM2F0_C7PXf-jew$=20




--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster=
.mpg.de
http://www.mpi-mu=
enster.mpg.de/43241/cojocaru

--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.=
de/43241/cojocaru
= --------------zn9ZX4p0zRrQpeoclkKtc4sA-- From owner-namd-l@halifax.ks.uiuc.edu Sat Sep 18 10:53:55 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18IFrrMb011229; Sat, 18 Sep 2021 10:53:54 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18IFrqFd011194; Sat, 18 Sep 2021 10:53:53 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18IFrnpw011114; Sat, 18 Sep 2021 10:53:49 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18IFrmKJ011102; Sat, 18 Sep 2021 10:53:48 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18IFrUsE010704 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000007ff38b05cc470c54" X-Proofpoint-ORIG-GUID: I-K2CC47GyNE7oBc0wNCRtJzyev6w8My X-CLX-Shades: MLX X-Proofpoint-GUID: I-K2CC47GyNE7oBc0wNCRtJzyev6w8My X-CLX-Response: 1TFkXGxIeEQpMehcZHh4RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHx0cEQpDWRcHEx0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB5xHhkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XYwdhGGlpHh1tU2RvHUVoSRpdZGl4XmBQU09cHF0SZ1MRClhcFx8EGgQYGRkF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdzTx1rfxEKTVwXGRsZEQpMWhd7aWtNaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBB sdGBEKQl4XGxEKREkXGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3IdbmxPWHhgEQpCbBdh X3pTGUNEGnobfhEKQkAXbnhdXFlaaBJOfWYRCkJYF2dzZXNAbmFhTF1iEQpaWBccEQp5QxdiQUh BfH17WmATfhEKcGcXZ1N+UkNjTkgZHVgQHRoRCnBoF2ByRmRvRRtGQGNBEBkaEQpwaBdgTmJNE2 BSe2waRxAZGhEKcGgXaBt+c1xyAUZNGGIQGRoRCnBoF2cceV1ue01LHlxpEBkaEQpwaBdsfHxGb 19GQW8BRhAZGhEKcH0XZWdOR2gafUJGUGAQGRoRCnBnF21HYWtNYxlMU2luEB0aEQpwZxdtaVN+ bU8eHx0YeRAdGhEKcH0XY3JvbUdCeWMeUGgQHRoRCnB9F2AaUntjYE9dT09kEB4SEQpwfRduZmR AYWRvYn1bfRAdGhEKcH8XbmJkAUVaRUR+ZW8QHh4RCnBfF2d8E29JZkJObkRlEBkaEQpwfxdtRF 9GRW19SHkZbhAbGBsRCnBfF2tGSxN5aGlufBN4EBMcEQpwfxdkUAVYSW1+SU1MbBAcGhEKcF8Xe kAeRV1PfkhabXgQHhIRCnBsF2Yfe1hcYgVLWGQfEBwaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4X GhEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=184 bulkscore=0 mlxlogscore=999 suspectscore=0 priorityscore=344 spamscore=0 impostorscore=0 adultscore=0 phishscore=0 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109180113 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --0000000000007ff38b05cc470c54 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I believe that is highly dependent on which GPU models you are using, and how they're connected to the CPU. With modern GPUs compute capacity is not the limiting factor, but the speed of the connection with the CPUs matters whenever the app needs to do something that it doesn't have GPU code for. PCIe will be a lot slower than NVLink, regardless of CPU and GPU model. I'd search the mailing list of NAMD and other codes (e.g. GROMACS or LAMMPS using the GPU package), because this issue has been discussed many times. One way to circumvent the above limitation is to have everything run on the GPU itself (short- and long-range forces, thermostats, MD integration, etc), which is what NAMD 3 does (as well as AMBER, OpenMM, or LAMMPS using the Kokkos package). Needless to say, this scheme takes more implementation work because now you need to have GPU code for nearly every feature you're using (so the folks at UIUC have begun by re-coding again in CUDA the most common ones). But it does pay off greatly in speed. This particular point is also discussed fairly well in the new NAMD paper. TL;DR, because GPUs are more specialized and less flexible than CPUs, the application can't easily rebalance the workload and predicting the performance from little information is a lot harder. Giacomo On Sat, Sep 18, 2021 at 8:00 AM Vlad Cojocaru < vlad.cojocaru@mpi-muenster.mpg.de> wrote: > Thanks Giacomo, > > O forwarded your email to the HPC site. They are very helpful and will try > to see if we get the bottleneck of this by rebuilding NAMD. > > But coming back to Josh's point about the low workload on the GPU. This > may be a valid point. Of course, we will do replicate of those simulation= s, > so one way to circumvent the issue is to run at least 10 simulations in > parallel, each of them using one node. ... > > But I am wondering ... Whithin one simulation, what would be the minimum > number of atoms allocated to 1 GPU to have a decent workload on the GPU ? > > Best > Vlad > > > On 9/17/21 15:41, Giacomo Fiorin wrote: > > Hi Vlad, it seems that they recommended you to use the UCX backend for > Charm++. This is a good idea, because the UCX middleware can > help significantly toward optimizing the communication paths in a complex > or congested network. *However,* Charm++ is still in its early stages of > adoption of UCX, and there are several things to look at when building: > https://urldefense.com/v3/__https://charm.readthedocs.io/en/latest/charm*= *A/manual.html*ucx__;Kysj!!DZ3fjg!q46PU6xcaGK8jqycGVPshHR2_FMvyptIcQlhJscqG= r0oSm6aHTWKRCyU_MGscT1ktg$=20 > > One possibility in your case is that the wrong PMI (*distinct *from MPI) > for the purpose is being picked up and the processes or threads aren't > allocated correctly. > > If you're confident that you really do need multi-node (see Josh's good > suggestion about NAMD 3) I suggest the following: > 1. Build and test NAMD with Charm++/UCX without SMP and without CUDA. > Between 1 and 2 nodes you ought to get linear scaling for 500k atoms. > 2. Build and test NAMD with Charm++/UCX with SMP but still without CUDA. > You should see a slight decrease of the whole scaling curve because the S= MP > backend separates communication and compute in separate threads, and wants > dedicated ones for each. But SMP is also what works best when throwing in > the GPUs. > 3. Build and test NAMD with both SMP and CUDA. > > As a minor suggestion, try also to verify that the AVX instructions being > recommended are actually paying off. Not all CPUs have a high enough clo= ck > rate for their AVX units to make it worth using them compared to standard > floating-point ops. > > I don't know what is the level of support from the HPC staff of that > facility. But in general it is a good rule to treat building a code as an > experiment that needs verification at every step of the way (something we > scientists are accustomed to, or ought to be). > > Giacomo > > > On Fri, Sep 17, 2021 at 9:13 AM Vlad Cojocaru < > vlad.cojocaru@mpi-muenster.mpg.de> wrote: > >> Hi Josh >> >> Thanks a lot for sharing this. I don't have experience with running the >> GPU NAMD, this is the first time I actually decided to test it thoroughl= y. >> >> I think the NAMD build was not a pure SMP built. Maybe this is where the >> problems come from in the first place .... I share below the build >> procedure recommended by the HPC site. If there is anything that you >> immediately spot to be problematic, I could give it a try to build NAMD >> again. >> >> I will also share your email with the support team at the HPC site. >> >> Best wishes >> Vlad >> >> #### NAMD build procedure #### >> >> module load Intel ParaStationMPI FFTW Tcl >> tar -xf NAMD_2.14_Source.tar.gz >> cd NAMD_2.14_Source >> tar -xf charm-6.10.2.tar >> cd charm-6.10.2 >> ./build charm++ ucx-linux-x86_64 icc smp --with-production >> cd .. >> ./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc --with-= tcl --tcl-prefix $EBROOTTCL --cc "mpicc" --cc-opts "-O3 -march=3Dcore-avx2= -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++11" --cxx "m= picxx" --cxx-opts "-O3 -march=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-m= odel source -fPIC -std=3Dc++11 --std=3Dc++11" --with-tcl --tcl-prefix $EBR= OOTTCL --with-fftw3 --fftw-prefix $EBROOTFFTW --with-cuda >> cd Linux-x86_64-icc >> echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >> Make.conf= ig >> echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config >> echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config >> make >> >> >> >> >> On 9/17/21 14:31, Vermaas, Josh wrote: >> >> Hi Vlad, >> >> I've run NAMD on 4000 nodes, and it'll scale just fine (although the sys= tem was much larger than 500k atoms!). There are a few gotchas involved wit= h multinode GPU NAMD. In no particular order: >> >> 1. This is an SMP build, yeah? Straight MPI builds with CUDA support are= *possible* to build, but perform terribly relative to their SMP bretheren >> 2. I've found that each node performs best when a GPU gets its own rank/= task that command dedicated CPUs. On the local resources here at MSU, that = looks something like this: >> >> #!/bin/bash >> #SBATCH --gres=3Dgpu:4 #4 GPUs per node >> #SBATCH --nodes=3D2 >> #SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the= number of GPUs >> #SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12 >> #SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a= CPU from trying to distribute work over multiple GPUs, and lowers PCIE con= tention >> >> cd $SLURM_SUBMIT_DIR >> module use /mnt/home/vermaasj/modules >> module load NAMD/2.14-gpu >> #other modules are loaded automatically by the NAMD module. >> srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log >> #With this setup, NAMD sees 8 logical nodes, 4 from each physical node. >> >> 3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs= . If the only thing you were doing is simulating 500k atoms (no replicas or= anything), each GPU is responsible for ~10k atoms. There are two layers of= communication for NAMD 2.14 on GPUs, transfers across the PCIe bus between= GPU and CPU every timestep, and communication between logical nodes whenev= er pairlists get recomputed. If there isn't enough work for each GPU to do,= those extra communication steps are going to murder performance. TLDR, at = some point the scaling will break down, and for a system that small, it mig= ht happen before you think it will. >> >> 4. If the simulations you are planning are going to be regular equilibri= um simulations, NAMD3 will likely be faster on modern hardware, as it elimi= nates CPU-GPU communication at most timesteps. >> >> -Josh >> >> =EF=BB=BFOn 9/17/21, 6:44 AM, "owner-namd-l@ks.uiuc.edu on behalf of Vla= d Cojocaru" wrote: >> >> Dear all, >> >> We have been doing some tests with the CUDA (11 I believe) accelerat= ed >> version of NAMD 2.14 on a remote supercomputer. On 1 node (96 thread= s, 4 >> GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.1= 4. >> There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs >> almost no scaling. The simulation (classical MD) time per day for 50= 0K >> atoms is similar to what expected (comparable to what is published on >> the NAMD website). >> >> However, for a large scale project, the supercomputer site requires >> scaling up to at least 10 nodes. And we are not able to get any scal= ing >> to more than 1 node. In fact, as soon as running on 2 nodes (with 4 = GPUs >> each), the performance is getting worse than on a single node. >> >> I know that lots of details are needed to actually pinpoint the >> issue(s), many of these are architecture dependent and we do not have >> all these details. >> >> However, I would still like to ask in general if any of you has >> routinely managed to scale up the performance of the CUDA accelerated >> NAMD 2.14 with the number of nodes. And if yes, are there any general >> tips and tricks that could be tried ? >> >> Thank you for any insights ! >> Vlad >> >> -- >> Vlad Cojocaru, PD (Habil.), Ph.D. >> ----------------------------------------------- >> Project Group Leader >> Department of Cell and Developmental Biology >> Max Planck Institute for Molecular Biomedicine >> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >> ----------------------------------------------- >> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/coj= ocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjzDgBZatmHwqU4VwajBWBxMQ4BM2F0_C= 7PXf-jew$ >> >> >> >> -- >> Vlad Cojocaru, PD (Habil.), Ph.D. >> ----------------------------------------------- >> Project Group Leader >> Department of Cell and Developmental Biology >> Max Planck Institute for Molecular Biomedicine >> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >> ----------------------------------------------- >> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >> Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.d= e/43241/cojocaru >> >> > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de= /43241/cojocaru > > --0000000000007ff38b05cc470c54 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
I believe that is highly dependent on which GPU models you= are using, and how they're connected to the CPU.=C2=A0 With modern=C2= =A0GPUs compute=C2=A0capacity is not the limiting factor, but the speed of = the connection with the CPUs matters whenever the app needs to do something= that it doesn't have GPU code for.=C2=A0 PCIe will be a lot slower tha= n NVLink, regardless of CPU and GPU model.=C2=A0 I'd search the mailing= list of NAMD and other codes (e.g. GROMACS or LAMMPS using the GPU package= ), because this issue has been discussed many times.

One= way to circumvent the above limitation is to have everything run on the GP= U itself (short- and long-range forces, thermostats, MD integration, etc), = which is what NAMD 3 does (as well as AMBER,=C2=A0OpenMM, or LAMMPS using t= he Kokkos package).=C2=A0 Needless to say, this scheme takes more implement= ation work because now you need to have GPU code for nearly every feature y= ou're using (so the folks at UIUC have begun by re-coding again in CUDA= the most common ones).=C2=A0 But it does pay off greatly in speed.=C2=A0 T= his particular point is also discussed fairly well in the new NAMD paper.

TL;DR, because GPUs are more specialized and less f= lexible than CPUs, the application can't easily rebalance the workload = and predicting the performance from little information is a lot harder.

Giacomo


<= /div>

On Sat, Sep 18, 2021 at 8:00 AM Vlad Cojocaru <vlad.c= ojocaru@mpi-muenster.mpg.de> wrote:
=20=20 =20=20=20=20 =20=20
Thanks Giacomo,

O forwarded your email to the HPC site. They are very helpful and will try to see if we get the bottleneck of this by rebuilding NAMD.

But coming back to Josh's point about the low workload on the GPU. This may be a valid point. Of course, we will do replicate of those simulations, so one way to circumvent the issue is to run at least 10 simulations in parallel, each of them using one node. ...

But I am wondering ... Whithin one simulation, what would be the minimum number of atoms allocated to 1 GPU to have a decent workload on the GPU ?

Best
Vlad


On 9/17/21 15:41, Giacomo Fiorin wrote:
=20=20=20=20=20=20
Hi Vlad, it seems that they recommended you to use the UCX backend for Charm++.=C2=A0 This is a good idea, because the UCX middleware can help=C2=A0significantly toward optimizing the communication paths in a complex or congested network.=C2=A0 How= ever, Charm++ is still in its early stages of adoption of UCX, and there are several things to look at when building:

One possibility in your case is that the wrong PMI (distinct from=C2=A0MPI) for the purpose is being picked up and the processes or threads aren't allocated correctly.

If you're confident that you really do need multi-node (see Josh's good suggestion about NAMD 3) I suggest the following:=
1. Build and test NAMD with Charm++/UCX without SMP and without CUDA.=C2=A0 Between 1 and 2 nodes you ought to get linear scaling for 500k atoms.
2. Build and test NAMD with Charm++/UCX with SMP=C2=A0but still without CUDA.=C2=A0 You should see a slight decrease of the whole scaling curve because the SMP backend separates communication and compute in separate=C2=A0threads, and wants dedicated ones for each.=C2=A0 But SMP is also what works best when throwing in the GPUs.
3. Build and test NAMD with both SMP and CUDA.

As a minor suggestion, try also to verify that the AVX instructions being recommended are actually paying off.=C2=A0 Not all CPUs have a high enough clock rate for their AVX units to make it worth using them compared to standard floating-point ops.

I don't know what is the level of support from the HPC staff of that facility.=C2=A0 But in general it is a good rule to treat building a code as an experiment that needs verification at=C2=A0every step of the way (something we scientists are accustomed to, or ought to be).

Giacomo


On Fri, Sep 17, 2021 at 9:13 AM Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de> wrote:
Hi Josh

Thanks a lot for sharing this. I don't have experience with running the GPU NAMD, this is the first time I actually decided to test it thoroughly.

I think the NAMD build was not a pure SMP built. Maybe this is where the problems come from in the first place .... I share below the build procedure recommended by the HPC site. If there is anything that you immediately spot to be problematic, I could give it a try to build NAMD again.

I will also share your email with the support team at the HPC site.

Best wishes
Vlad

#### NAMD build procedure ####
module load Intel ParaStationMPI FFTW Tcl
tar -xf NAMD_2.14_Source.tar.gz
cd NAMD_2.14_Source
tar -xf charm-6.10.2.tar
cd charm-6.10.2
./build charm++ ucx-linux-x86_64 icc smp --with-production
cd ..
./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-smp-icc=C2=A0 --wit=
h-tcl --tcl-prefix $EBROOTTCL=C2=A0 --cc "mpicc" --cc-opts "=
-O3 -march=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -=
std=3Dc++11"=C2=A0 --cxx "mpicxx" --cxx-opts "-O3 -marc=
h=3Dcore-avx2 -ftz -fp-speculation=3Dsafe -fp-model source -fPIC -std=3Dc++=
11 --std=3Dc++11"=C2=A0 --with-tcl --tcl-prefix $EBROOTTCL=C2=A0 --wit=
h-fftw3=C2=A0 --fftw-prefix $EBROOTFFTW --with-cuda
cd Linux-x86_64-icc
echo "TCLLIB=3D-L\$(EBROOTTCL)/lib -ltcl8.6 -ldl -lpthread" >&=
gt; Make.config
echo "COPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
echo "CXXOPTS+=3D-DNAMD_DISABLE_SSE" >> Make.config
make




On 9/17/21 14:31, Vermaas, Josh wrote:
Hi Vlad,

I've run NAMD on 4000 nodes, and it'll scale just fine (although th=
e system was much larger than 500k atoms!). There are a few gotchas involve=
d with multinode GPU NAMD. In no particular order:

1. This is an SMP build, yeah? Straight MPI builds with CUDA support are *p=
ossible* to build, but perform terribly relative to their SMP bretheren
2. I've found that each node performs best when a GPU gets its own rank=
/task that command dedicated CPUs. On the local resources here at MSU, that=
 looks something like this:

#!/bin/bash
#SBATCH --gres=3Dgpu:4 #4 GPUs per node
#SBATCH --nodes=3D2
#SBATCH --ntasks-per-node=3D4 #Number of tasks per node should match the nu=
mber of GPUs
#SBATCH --cpus-per-task=3D12 #48 CPUs total, means each task gets 12
#SBATCH --gpu-bind=3Dsingle:1 #Bind the GPU to a single task. Prevents a CP=
U from trying to distribute work over multiple GPUs, and lowers PCIE conten=
tion

cd $SLURM_SUBMIT_DIR
module use /mnt/home/vermaasj/modules
module load NAMD/2.14-gpu
#other modules are loaded automatically by the NAMD module.
srun namd2 +ppn 11 +ignoresharing configfile.namd > logfile.log
#With this setup, NAMD sees 8 logical nodes, 4 from each physical node.

3. Set expectations appropriately. 10 nodes with 4 GPUs each =3D 40 GPUs. I=
f the only thing you were doing is simulating 500k atoms (no replicas or an=
ything), each GPU is responsible for ~10k atoms. There are two layers of co=
mmunication for NAMD 2.14 on GPUs, transfers across the PCIe bus between GP=
U and CPU every timestep, and communication between logical nodes whenever =
pairlists get recomputed. If there isn't enough work for each GPU to do=
, those extra communication steps are going to murder performance. TLDR, at=
 some point the scaling will break down, and for a system that small, it mi=
ght happen before you think it will.

4. If the simulations you are planning are going to be regular equilibrium =
simulations, NAMD3 will likely be faster on modern hardware, as it eliminat=
es CPU-GPU communication at most timesteps.

-Josh

=EF=BB=BFOn 9/17/21, 6:44 AM, "owner-namd-l@ks.uiuc.edu on be=
half of Vlad Cojocaru" <owner-nam=
d-l@ks.uiuc.edu on behalf of vlad.cojocaru@mpi-muenster.mpg.de> wrot=
e:

    Dear all,

    We have been doing some tests with the CUDA (11 I believe) accelerated=
=20
    version of NAMD 2.14 on a remote supercomputer. On 1 node (96 threads, =
4=20
    GPUs), we see a 10 fold acceleration compared to a non-CUDA NAMD 2.14.=
=20
    There is a decent scaling between 1 and 2 GPUs but from 2 to 4 GPUs=20
    almost no scaling. The simulation (classical MD) time per day for 500K=
=20
    atoms is similar to what expected (comparable to what is published on=20
    the NAMD website).

    However, for a large scale project, the supercomputer site requires=20
    scaling up to at least 10 nodes. And we are not able to get any scaling=
=20
    to more than 1 node. In fact, as soon as running on 2 nodes (with 4 GPU=
s=20
    each), the performance is getting worse than on a single node.

    I know that lots of details are needed to actually pinpoint the=20
    issue(s), many of these are architecture dependent and we do not have=20
    all these details.

    However, I would still like to ask in general if any of you has=20
    routinely managed to scale up the performance of the CUDA accelerated=20
    NAMD 2.14 with the number of nodes. And if yes, are there any general=20
    tips and tricks that could be tried ?

    Thank you for any insights !
    Vlad

    --=20
    Vlad Cojocaru, PD (Habil.), Ph.D.
    -----------------------------------------------
    Project Group Leader
    Department of Cell and Developmental Biology
    Max Planck Institute for Molecular Biomedicine
    R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
    -----------------------------------------------
    Tel: +49-251-70365-324; Fax: +49-251-70365-399
    Email: vlad.cojocaru[at]mpi-muenster.mpg.de
    https://urldefense.com/v3/__http://www=
.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!rk6Iphoo5rM4f2l2YT1vs5SwsRjz=
DgBZatmHwqU4VwajBWBxMQ4BM2F0_C7PXf-jew$=20




--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojoc=
aru

--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojoc=
aru
--0000000000007ff38b05cc470c54-- From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 21 07:56:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18LCuJGr008681; Tue, 21 Sep 2021 07:56:20 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18LCuIWw008647; Tue, 21 Sep 2021 07:56:19 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18LCu5JX008367; Tue, 21 Sep 2021 07:56:05 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18LCu5h3008366; Tue, 21 Sep 2021 07:56:05 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18LCtiVa007914 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 21 Sep 2021 07:55:46 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18LC5W7G024504 for ; Tue, 21 Sep 2021 12:55:44 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0a-00007101.pphosted.com with ESMTP id 3b6h6680um-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 21 Sep 2021 12:55:43 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 7D1641E406D6; Tue, 21 Sep 2021 14:55:41 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id NlF_atVMISHv; Tue, 21 Sep 2021 14:55:40 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id EEBEB1E406F1; Tue, 21 Sep 2021 14:55:38 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id qifyXUC44FQn; Tue, 21 Sep 2021 14:55:38 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id 8771F1E406D6; Tue, 21 Sep 2021 14:55:38 +0200 (CEST) Date: Tue, 21 Sep 2021 14:55:34 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , =?utf-8?Q?S=C3=A9bastien?= Hoyas Message-ID: <1203043814.2938328.1632228934718.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: Re: namd-l: Merge ABF windows MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_58f34f96-694a-4f90-b4ef-f2748ca261b1" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Merge ABF windows Thread-Index: BxwgdOzdw56jbi/OnO7YAsXGanj7nQ== X-Proofpoint-GUID: jjofOEopIz8AIkrDL0NV4nlvTAgYXVUR X-Proofpoint-ORIG-GUID: jjofOEopIz8AIkrDL0NV4nlvTAgYXVUR X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwTEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxgfGxEKQ1kXBx0SEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4TcRwaEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0BARUxlb0VaY1ASa2NBWG5mGmR8HkRGXH5rTXNyfH94EQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQbExAbHhofGhEKXlkXc0wZWFgRCk1cFxIaEQpMWhd8bWtNTREKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2hARUgYGHxrW3oZEQpDWhcbExkEHhMEGBkeBBgYGxEKQl 4XGxEKRF4XGBEKQkUXZFhcXE1+UkkbZUkRCkJOF2VPfhJDaWZZHAFpEQpCTBd6EmdpYFl5RkFPZ REKQmwXYRIST09MTX9PHgURCkJAF2MYRUJlQHJvGXJlEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEK WlgXGREKeUMXZBprWlBgc15AelMRCnBoF2wBZFtQXn9HZh5PEBkaEQpwaBdgGmtyenB/UnBlXhA cEhEKcGgXY2VNXUYfY399YUEQGRoRCnBoF2FjXh1uG11FW1hNEBkaEQpwaBdgARh7ekBsRGRJHB AZGhEKcH0XaXpiHW8TaW9Nbn8QGRoRCnB9F2BzZmlhGW1GaWMSEBkaEQpwfxdlWHIYHUkYXkZpf BAbGRwRCnBfF25rGGdDbmtQfU14EBkaEQpwfxdlGXlmXkdpG2RPcxAdGhEKcF8Xa1pYclhiY0Jp RUIQGRoRCnBsF2ZgE2RcTRpnT3pQEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxE g X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=169 impostorscore=0 bulkscore=0 phishscore=0 suspectscore=0 mlxlogscore=999 spamscore=0 lowpriorityscore=0 malwarescore=0 mlxscore=0 adultscore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109210081 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_58f34f96-694a-4f90-b4ef-f2748ca261b1 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear S=C3=A9bastien,=20 I just ran a test with NAMD 2.14, and I cannot reproduce the issue you desc= ribe. Can you send me your input files off-list?=20 Best,=20 J=C3=A9r=C3=B4me=20 ----- On 8 Sep 21, at 8:53, S=C3=A9bastien Hoyas wrote:=20 > Dear NAMD users, > I am running ABF calculations. My reaction coordinate is split into multi= ple > windows that I need to merge. > I followed the instructions in the tutorials and in the colvar manual ( [ > http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf= | > http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf= ] , [ > https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION00012620= 0000000000000 > | > https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION00012620= 0000000000000 > ] ) > I added all the *.grad, *.count files in the same directory, adapted the = colvar > file with the full range of boundaries and added the "inputPrefix" (follo= wed by > the windows names) in the abf section and run 0 steps). I do not get any > errors, but it does not produce the merged .pmf, .count and .grad (I am r= unning > calculations with NAMD 2.14). > However, it works perfectly with NAMD 2.13. > Is this a bug, or is there some additional keywords that must be added wh= en > using NAMD 2.14? > Thank you in advance. > Regards, > S=C3=A9bastien --=_58f34f96-694a-4f90-b4ef-f2748ca261b1 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear S=C3=A9bastien,

I just ran a test with NAMD 2.14, and I cannot repr= oduce the issue you describe. Can you send me your input files off-list?

Best,
J=C3=A9r=C3=B4m= e


----- On 8 Sep 21, at 8:53, S=C3=A9basti= en Hoyas <sebastien.hoyas.pro@gmail.com> wrote:
Dear NAMD users,
I am running ABF = calculations. My reaction coordinate is split into multiple windows that I = need to merge.

I added all the *.grad, = *.count files in the same directory, adapted the colvar file with the full = range of boundaries and added the "inputPrefix" (followed by the windows na= mes) in the abf section and run 0 steps). I do not get any errors, but it d= oes not produce the merged .pmf, .count and .grad (I am running calculation= s with NAMD 2.14).

However, it works perfectly with NAMD 2.13.
Is this a bug, or is there some additional keywords that must be added wh= en using NAMD 2.14?

Thank you in advance.

Regar= ds,

S=C3=A9bastien 

--=_58f34f96-694a-4f90-b4ef-f2748ca261b1-- From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 21 09:19:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18LEJFMg027912; Tue, 21 Sep 2021 09:19:16 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18LEJEjA027879; Tue, 21 Sep 2021 09:19:15 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18LEJBuq027824; Tue, 21 Sep 2021 09:19:12 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18LEJBk5027818; Tue, 21 Sep 2021 09:19:11 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18LEIhHT027203 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 21 Sep 2021 09:18:45 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18L8iu6d004660 for ; Tue, 21 Sep 2021 14:18:43 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0a-00007101.pphosted.com with ESMTP id 3b6h668w54-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 21 Sep 2021 14:18:42 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id AB7C21E406D6; Tue, 21 Sep 2021 16:18:39 +0200 (CEST) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id j0xnMwLUjkYn; Tue, 21 Sep 2021 16:18:37 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 6D5541E406F8; Tue, 21 Sep 2021 16:18:37 +0200 (CEST) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id yXnKUjsxSCQe; Tue, 21 Sep 2021 16:18:37 +0200 (CEST) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id 12DA41E405F3; Tue, 21 Sep 2021 16:18:37 +0200 (CEST) Date: Tue, 21 Sep 2021 16:18:36 +0200 (CEST) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= Cc: =?utf-8?Q?S=C3=A9bastien?= Hoyas Message-ID: <1229871153.2957419.1632233916044.JavaMail.zimbra@ibpc.fr> In-Reply-To: <1203043814.2938328.1632228934718.JavaMail.zimbra@ibpc.fr> References: <1203043814.2938328.1632228934718.JavaMail.zimbra@ibpc.fr> Subject: Re: namd-l: Merge ABF windows Content-Type: multipart/alternative; boundary="=_44d78d3e-8c63-4061-90cb-e474f1bd99be" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Merge ABF windows Thread-Index: BxwgdOzdw56jbi/OnO7YAsXGanj7nRyxCvw4 X-Proofpoint-GUID: bp5xX4uqrKdi0Ewcmw7BeHI6TTXSiHi8 X-Proofpoint-ORIG-GUID: bp5xX4uqrKdi0Ewcmw7BeHI6TTXSiHi8 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMcEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxkZHxEKQ1kXBx0TEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0ccR8dEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0haH1JyHl9bWGFOQxpvXUlHXR1oT2JjHH5+cnlDYkMSEQpYXBcfBBoEGBkZBRsa BBsaGgQeEgQYGRAbHhofGhEKXlkXc0weH08RCk1cFxkbGxEKTFoXaXhta01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XaEBFSBgYfGtbehkRCkNaFxsTGQQeEwQYGR4EGBgbEQ pCXhcbEQpEXhcYEQpESRcbEQpCRRdkWFxcTX5SSRtlSREKQk4XZU9+EkNpZlkcAWkRCkJMF3oSZ 2lgWXlGQU9lEQpCbBdhEhJPT0xNf08eBREKQkAXYxhFQmVAcm8ZcmURCkJYF2dzZXNAbmFhTF1i EQpaWBcfEQp5QxdkGmtaUGBzXkB6UxEKcGgXa3AZG1J7THteZB8QGhEKcGgXYkQef2V4TnlmRFI QGhEKcGgXYBprcnpwf1JwZV4QGxoaEQpwaBdnY159aQUcBWF/UxAZGhEKcGgXbktZRm1dEkMdfG MQGhEKcH0XbRMcYntNTEdZZkwQGhEKcH0XYFxfUnJuT15hWkIQGhEKcH0XaXpiHW8TaW9Nbn8QG RoRCnB9F2BzZmlhGW1GaWMSEBkaEQpwfxdrHWseU3tnY0ttehAbGh4RCnBfF29jWU0BHG5nbQEZ EBoRCnB/F2VYchgdSRheRml8EBsYHREKcF8XbmsYZ0Nua1B9TXgQGRoRCnB/F2UZeWZeR2kbZE9 zEBsaHhEKcF8Xa1pYclhiY0JpRUIQGRoRCnBsF2ZgE2RcTRpnT3pQEBkaEQpwTBdtaGUZQVJ9ex hFUhAaEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=196 impostorscore=0 bulkscore=0 phishscore=0 suspectscore=0 mlxlogscore=999 spamscore=0 lowpriorityscore=0 malwarescore=0 mlxscore=0 adultscore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109030001 definitions=main-2109210088 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_44d78d3e-8c63-4061-90cb-e474f1bd99be Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Dear S=C3=A9bastien,=20 based on the files you sent me, I could track the issue down to this change= :=20 [ https://urldefense.com/v3/__https://github.com/Colvars/colvars/commit/1e9= 64a542bf481b29cfd33ee4097dc6ca3371bda__;!!DZ3fjg!oiEXuVjuXpI4SXUUEFJc483paQ= XwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcpEPUntJaw$ | https://urldefense.com/v3/__ht= tps://github.com/Colvars/colvars/commit/1e964a542bf481b29cfd33ee4097dc6ca33= 71bda__;!!DZ3fjg!oiEXuVjuXpI4SXUUEFJc483paQXwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcp= EPUntJaw$ ]=20 which fixes cases where the output files were written twice at the end of a= run, but introduces the issue you are having.=20 A workaround to get the right result using the official NAMD 2.14 is to add= " outputFreq 0 " to the ABF block in your Colvars configuration.=20 I am also committing a fix here:=20 [ https://urldefense.com/v3/__https://github.com/Colvars/colvars/commit/ff2= f0d39ee5a06dd54f367d5b8d8a7dd23008efe__;!!DZ3fjg!oiEXuVjuXpI4SXUUEFJc483paQ= XwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcpGoxvlT8w$ | https://urldefense.com/v3/__ht= tps://github.com/Colvars/colvars/commit/ff2f0d39ee5a06dd54f367d5b8d8a7dd230= 08efe__;!!DZ3fjg!oiEXuVjuXpI4SXUUEFJc483paQXwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcp= GoxvlT8w$ ]=20 Please check that everything works for you now. Thank you for your report.= =20 Best regards,=20 J=C3=A9r=C3=B4me=20 ----- On 21 Sep 21, at 14:55, J=C3=A9r=C3=B4me H=C3=A9nin wrote:=20 > Dear S=C3=A9bastien, > I just ran a test with NAMD 2.14, and I cannot reproduce the issue you de= scribe. > Can you send me your input files off-list? > Best, > J=C3=A9r=C3=B4me > ----- On 8 Sep 21, at 8:53, S=C3=A9bastien Hoyas > wrote: >> Dear NAMD users, >> I am running ABF calculations. My reaction coordinate is split into mult= iple >> windows that I need to merge. >> I followed the instructions in the tutorials and in the colvar manual ( [ >> http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pd= f | >> http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pd= f ] , [ >> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION0001262= 00000000000000 >> | >> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION0001262= 00000000000000 >> ] ) >> I added all the *.grad, *.count files in the same directory, adapted the= colvar >> file with the full range of boundaries and added the "inputPrefix" (foll= owed by >> the windows names) in the abf section and run 0 steps). I do not get any >> errors, but it does not produce the merged .pmf, .count and .grad (I am = running >> calculations with NAMD 2.14). >> However, it works perfectly with NAMD 2.13. >> Is this a bug, or is there some additional keywords that must be added w= hen >> using NAMD 2.14? >> Thank you in advance. >> Regards, >> S=C3=A9bastien --=_44d78d3e-8c63-4061-90cb-e474f1bd99be Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Dear S=C3=A9bastien,

based on the files you sent me, I could track the i= ssue down to this change:

which fixes cases where the output files were wri= tten twice at the end of a run, but introduces the issue you are having.

A workaround to get the right r= esult using the official NAMD 2.14 is to add "outputFreq 0" to the ABF block in yo= ur Colvars configuration.

I am also committing a fix here:

Please check that everything works for you no= w. Thank you for your report.

Best regards,
J=C3=A9r=C3=B4me


----- On 21 Sep 21, = at 14:55, J=C3=A9r=C3=B4me H=C3=A9nin <jerome.henin@ibpc.fr> wrote:
Dear S=C3=A9bastie= n,

I just ran a test with NAMD 2.14, and I cannot reproduce t= he issue you describe. Can you send me your input files off-list?

=
Best,
J=C3=A9r=C3=B4me


= ----- On 8 Sep 21, at 8:53, S=C3=A9bastien Hoyas <sebastien.hoyas.pro@gm= ail.com> wrote:
Dear Sébastien,

I just ran a test with NAMD 2.14, and I cannot reproduce the issue you describe. Can you send me your input files off-list?

Best,
Jérôme


----- On 8 Sep 21, at 8:53, Sébastien Hoyas <sebastien.hoyas.pro@gmail.com> wrote:
Dear NAMD users,
I am running ABF calculations. My reaction coordinate is split into multiple windows that I need to merge.

I added all the *.grad, *.count files in the same directory, adapted the colvar file with the full range of boundaries and added the "inputPrefix" (followed by the windows names) in the abf section and run 0 steps). I do not get any errors, but it does not produce the merged .pmf, .count and .grad (I am running calculations with NAMD 2.14).

However, it works perfectly with NAMD 2.13.

Is this a bug, or is there some additional keywords that must be added when using NAMD 2.14?

Thank you in advance.

Regards,

Sébastien 


-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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boundary="000000000000c5996705ccae8abb" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRseEQpMehcbGhoRCllEF24FSEdSGEt/eU9aEQpYWBdhQnBObnN9WF1 DaxEKeE4XZB15H19kX2JHG3sRCnlMF2F4Gn0fT39YQW9JEQpDSBcHGxIfEQpDWRcHExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXHB5xGAYcGXcGGBoaBhoGGgYdGgYZGnEbEBp3BhoGBx8aBhoGGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThcSZkVwUmNiUn17ZGtbb2FucGdS Uh5+f2tpcn1tH3h9TBEKWFwXHwQaBBgZHAUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3NNREJaEQp NXBcbHhoRCkxaF2lsaU1raxEKTEYXb2tra2trEQpCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBB scHQQeEhEKQl4XGxEKQlwXGxEKXk4XGxEKQksXZB15H19kX2JHG3sRCkJJF2QdeR9fZF9iRxt7E QpCRRdlenhwUxJeGk9DWhEKQk4XZB15H19kX2JHG3sRCkJMF2FCcE5uc31YXUNrEQpCbBdgY21a WhJ/eGFyQREKQkAXYE95Ul5rekdYbGERCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdgT3lSXmt 6R1hsYREKWUsXHRwfExEKcGgXZWVZXWFcR0dpU0sQGhEKcGgXZF1dQlxjfn9Ja24QGhEKcGgXZ0 5Oe0ZCbVtpU0YQGhEKcGwXaEdsGmweaXwYWV4QBxkaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 8LoZxIHxWQNAqEKDZMxx4TUACXWG5RWf X-Proofpoint-GUID: 8LoZxIHxWQNAqEKDZMxx4TUACXWG5RWf X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=314 malwarescore=0 bulkscore=0 impostorscore=0 mlxscore=0 mlxlogscore=358 phishscore=0 spamscore=0 adultscore=0 suspectscore=0 lowpriorityscore=0 priorityscore=100 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109200000 definitions=main-2109230114 domainage_hfrom=7659 X-Spam-Score: 0 X-Spam-OrigSender: mosa@ualberta.ca X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Farag Mosa --000000000000c5996705ccae8abb Content-Type: text/plain; charset="UTF-8" Hi dear, I have been learning metadynamics simulations and well-tempered metadynamics recently. I finished the metadynamics tutorial using namd. However, I had a hard time finding the best conformation from metadynamics output. My question is how we can extract the local minimas conformations from the whole metadynamic's trajectory? Thank you, --000000000000c5996705ccae8abb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi dear,


I have been lea= rning metadynamics simulations and well-tempered metadynamics recently. I f= inished the metadynamics tutorial using namd. However, I had a hard=C2=A0ti= me finding the=C2=A0best conformation from metadynamics output. My=C2=A0que= stion is how we can =C2=A0extract the local minimas conformations from the = whole metadynamic's trajectory?=C2=A0



Thank you,
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boundary="_000_SN6PR11MB28787E12ACF875539668B8C3B0A49SN6PR11MB2878namp_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: SN6PR11MB2878.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 16afc8ad-d4d4-4a47-a2bf-08d97f7ceeb6 X-MS-Exchange-CrossTenant-originalarrivaltime: 24 Sep 2021 17:01:20.5815 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: XQd6JfMy/R0tWtnKxo9kD7uDt9dIIFNEJLuqw9rS/WllvHCh80li8zSH4r8HVO53p3xhG6h+cJjpxVr1O5CEjA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: SA0PR11MB4767 X-Proofpoint-ORIG-GUID: WiV-dgE5p77NRqiktoe5ClDWNYDhYlAt X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwTEQpMehcaEQpZRBdubXxreXl8TEJgeREKWFgXZ0IfGkhSaEAYRkI RCnhOF2hjAUx/RX9CQWVAEQp5TBd6b2tFcBgTG1JsWREKQ0gXBxsfGxEKQ1kXBxkdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4TcRwbEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF31DfAdOTW8fWh0dZHhbQ0FeRU8faUZufWRzbkJzRmteEQpYXBcfBBoEGBkcBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NNHEFiEQpNXBccGxEKTFoXaGlNTWsRCkxGF29ra2tra2s RCkJPF3pec0ESTxtpHEZzEQpDWhceGgQbGh0EExgEEx8RCkJeFxsRCkReFxgRCkJFF25uUB5sYR hhcx8fEQpCThdoYwFMf0V/QkFlQBEKQkwXZ0IfGkhSaEAYRkIRCkJsF2RiZgFncxNTRU9SEQpCQ BdpaXJITxsfZk9nYxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2lpZh9jSUleWHpS EQpwaBd6RWxvHnAeUB9cUBAZGhEKcGgXZ0VwR1pJbWIdRWAQHxgRCnBoF24caUgfWm8aH2RHEBk aEQpwaBdkAV94a35pWxtnfBAZGhEKcGgXbFxyTG8SW2AfHlsQGRoRCnBsF2ZNfWdrW2NJfkdJEB kaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: WiV-dgE5p77NRqiktoe5ClDWNYDhYlAt X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 adultscore=0 mlxscore=0 suspectscore=0 mlxlogscore=430 lowpriorityscore=0 malwarescore=0 impostorscore=0 phishscore=0 bulkscore=0 clxscore=169 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109240108 X-Spam-Score: 0 X-Spam-OrigSender: royi@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ishaan Roy --_000_SN6PR11MB28787E12ACF875539668B8C3B0A49SN6PR11MB2878namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello, I am trying to run SMD on a dimerized protein in a lipid membrane. However,= with my current settings, the lipid stretches in the direction the protein= is pulled (flexibleCell is on) and thins out in the middle. How can I prev= ent this from occurring? Thanks, Ishaan --_000_SN6PR11MB28787E12ACF875539668B8C3B0A49SN6PR11MB2878namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello,

 

I am trying to run SMD on a dimerized protein in a l= ipid membrane. However, with my current settings, the lipid stretches in th= e direction the protein is pulled (flexibleCell is on) and thins out in the= middle. How can I prevent this from occurring?

 

Thanks,

Ishaan

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boundary="=_b7622e71-824d-473e-8817-24ad1687c4f2" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC91 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: SMD in lipid Thread-Index: AQHXsWG43VOAVm95xEiYHtzIziF/sLcHLw9k X-Proofpoint-ORIG-GUID: w-AmnGZfPhjdQyZgcuD09zAeNt84-yoG X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxsSHxEKQ1kXBxIeEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwTcR4SEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF10Ha0dEbXBMekJATntTcE1JX24aE1BrT2ReEh4HU0VtEQpYXBcfBBoEGBkcBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NNExNCEQpNXBcZGh4RCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYgVoQ0BMWkBFck4RCkNaFxMeBBsSHgQbHRwEGx sbEQpCXhcbEQpEXhcYEQpCXBcbEQpCSxd6Hm1bS3xHX2IFehEKQkkXaF96YUYBYkBBT3kRCkJFF 2EdHmZrckFSGRl4EQpCThdoX3phRgFiQEFPeREKQkwXbRNBQVpBREMTfXgRCkJsF2FkGWddQhlF fGt4EQpCQBdkBU0ZBV9+fhsfGREKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF25/eUFrfnIZTn9 MEQpZSxcHGREKcGcXYxpjR0F/YUZ4GXwQGRoRCnBoF2toXxJCTktzGEljEBkaEQpwaBdlQ2FucF hrQFpNbBAZGhEKcGgXaFlBQlttf2xsb2QQGRoRCnBoF2JnSGdLbm9MHVpQEBkaEQpwaBdlQUhaa XJTeWx5QhAZGhEKcH0XY3N7TQVdHQF4QXAQGRoRCnBnF2lDblABWXNHAR5TEBkaEQpwfRdpGmVO XEgTYEd5RhAZGhEKcH8Xb0RhUBITfxscEn4QHR8RCnBfF2IYGhgfeEdMe3t7EBsbHREKcGwXb2B /bXlMQURrTk4QGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: w-AmnGZfPhjdQyZgcuD09zAeNt84-yoG MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 adultscore=0 mlxscore=0 suspectscore=0 mlxlogscore=843 lowpriorityscore=0 malwarescore=0 impostorscore=0 phishscore=0 bulkscore=0 clxscore=189 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109240125 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_b7622e71-824d-473e-8817-24ad1687c4f2 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable constant force or constant velocity?=20 If constant velocity protocol is adopted, then increase pulling velocity.=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!t47dQSVQ7MXPuxhbjW-aUvgB7uxQWxFC0gb7e1XnTZP47O1E-o_9RVjJ= ljMn5dQRcQ$ ]=20 From: "Ishaan Roy" =20 To: "namd-l" =20 Sent: Friday, September 24, 2021 8:31:20 PM=20 Subject: namd-l: SMD in lipid=20 Hello,=20 I am trying to run SMD on a dimerized protein in a lipid membrane. However,= with my current settings, the lipid stretches in the direction the protein= is pulled (flexibleCell is on) and thins out in the middle. How can I prev= ent this from occurring?=20 Thanks,=20 Ishaan=20 --=_b7622e71-824d-473e-8817-24ad1687c4f2 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
constant force or constant velocity?
If= constant velocity protocol is adopted, then increase pulling velocity.&nbs= p;

<= div dir=3D"ltr">
---
,Best
=
=
=
<= div dir=3D"ltr">
Ashkan Shekaari
PhD Candidate in Solid State Physics=
Depart= ment of Physics
K. N. Toosi Univer= sity of Technology, Tehran, 15875-4416, Iran
=


From: "Ishaan Roy" <royi@uchicago.edu>
To: "na= md-l" <namd-l@ks.uiuc.edu>
Sent: Friday, September 24, 2021= 8:31:20 PM
Subject: namd-l: SMD in lipid

Hello,

 

I am trying to run SMD on a dimerized protein in a l= ipid membrane. However, with my current settings, the lipid stretches in th= e direction the protein is pulled (flexibleCell is on) and thins out in the= middle. How can I prevent this from occurring?

 

Thanks,

Ishaan


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Tue, 28 Sep 2021 07:16:09 +0000 Date: Tue, 28 Sep 2021 07:16:04 +0000 (UTC) From: Vidhya Sankar To: NAMD List Message-ID: <708241072.1665136.1632813364664@mail.yahoo.com> Subject: namd-l: about compilation MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1665135_1886466739.1632813364663" References: <708241072.1665136.1632813364664.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19043 YMailNorrin X-Proofpoint-ORIG-GUID: 4xe9qmLbhsZ4wQ_3OQAbvt74qfXdHapW X-CLX-Response: 1TFkXGxIbEQpMehcZGRsRCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHGx8TEQpDWRcHGBofEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcbGnEbBhgadwYYGhoGGgYaBh4bBhkacRsQGncGGgYHGxoaBhoGG gYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThceUk8TW0dmSEJZcB5de3UZ ZXtrSFxeHR5bTHJOYktafREKWFwXHwQaBBgZGQUbGgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzQ21 ycxEKTVwXEhkRCkxaF2xpa2trEQpMRhdva2tva2sRCkJPF2JJH3pcWB9beRseEQpDWhcbGhwEGx oEGB4eBBIeEQpCXhcbEQpCXBcbEQpeThcbEQpCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ 2YRCkJFF3oZbUNbRV9oaX1lEQpCThd6RBwdb0VsbURDZhEKQkwXZmFiE2FtYmtJXEIRCkJsF2sd H3AZbGlFb3hcEQpCQBdkcxpLTRtMHnpiQBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnl DF258AUlgb25BBVxaEQpZSxcTHR8aEQpwaBdtRhkZS0xaWWluXBAZGhEKcGgXYmlSWx94f3NGTH MQGRoRCnBoF2drE3kFYAFCaRpQEBkaEQpwbBdkb05cRn5TaHxZWhAZGhEKcEwXZgVhHEcdRmF5Q 38QGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Proofpoint-GUID: 4xe9qmLbhsZ4wQ_3OQAbvt74qfXdHapW X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 spamscore=0 impostorscore=0 mlxlogscore=484 bulkscore=0 clxscore=181 priorityscore=331 adultscore=0 mlxscore=0 malwarescore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109280042 domainage_hfrom=9750 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_1665135_1886466739.1632813364663 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear namd user=C2=A0 ,=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0i would like to use path CV in namd meta dynamics .. To compile the namd= =C2=A0 with path CV variable (gs path )=C2=A0 What=C2=A0 version c++ compil= er=C2=A0 should i=C2=A0 include during compilation of namd=C2=A0 if any any one tell me command to include C++ latest compiler to enable gs = path option in meta dynamics if namd Thanks in advance=C2=A0S.Vidhya sanakr ------=_Part_1665135_1886466739.1632813364663 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Dear namd user  ,
               i would like to use path CV in namd meta dynamics .. To compile the namd  with path CV variable (gs path )  What  version c++ compiler  should i  include during compilation of namd 

if any any one tell me command to include C++ latest compiler to enable gs path option in meta dynamics if namd


Thanks in advance 
S.Vidhya sanakr
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charset="UTF-8" Hello Vidhya, that depends on how the computer system where you'll run is set up. The C++11 requirement was stated quite clearly, so if you don't know which compilers these are, you need to ask the admins. Tip: if there is a relatively recent version of GROMACS, the same compiler used there should work. Giacomo On Tue, Sep 28, 2021 at 3:24 AM Vidhya Sankar < vidhyasankar7928@remove_yahoo.com> wrote: > Dear namd user , > i would like to use path CV in namd meta dynamics .. To > compile the namd with path CV variable (gs path ) What version c++ > compiler should i include during compilation of namd > > if any any one tell me command to include C++ latest compiler to enable gs > path option in meta dynamics if namd > > > Thanks in advance > S.Vidhya sanakr > --00000000000071b45305cd0ddf56 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Vidhya, that depends on how the computer system wher= e you'll run is set up.=C2=A0 The C++11 requirement was stated quite cl= early, so if you don't know which compilers these are, you need to ask = the admins.

Tip: if there is a relatively recent version= of GROMACS, the same compiler used there should work.

=
Giacomo

On Tue, Sep 28, 2021 at 3:24 AM Vidhya Sankar <vidhyasanka= r7928@remove_yahoo.com> wrote:
Dea= r namd user=C2=A0 ,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0i would like to use path CV in namd meta dynamics .= . To compile the namd=C2=A0 with path CV variable (gs path )=C2=A0 What=C2= =A0 version c++ compiler=C2=A0 should i=C2=A0 include during compilation of= namd=C2=A0

if any any one= tell me command to include C++ latest compiler to enable gs path option in= meta dynamics if namd

Thanks in advance=C2=A0
S.Vid= hya sanakr
--00000000000071b45305cd0ddf56-- From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 28 09:59:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SExdT0019317; Tue, 28 Sep 2021 09:59:39 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18SExd24019308; Tue, 28 Sep 2021 09:59:39 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SExYLQ019253; Tue, 28 Sep 2021 09:59:35 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18SExYnL019249; Tue, 28 Sep 2021 09:59:34 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SEwkVZ018114 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000002f22bb05cd0f73e7" X-Proofpoint-GUID: NYirXSkKnABK7ungIFRFEryRwpG2ZOeT X-Proofpoint-ORIG-GUID: NYirXSkKnABK7ungIFRFEryRwpG2ZOeT X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIfEQpMehcZGx4RCllEF2ZbAUJEbk8cW09oEQpYWBdmHxN7GV8bWkV vWBEKeE4XY1Nja3sTWH4aX14RCnlMF2hGWEhJcEZLQAFBEQpDSBcHGx4cEQpDWRcHGx0TEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2RzQ1hyeUFhRGtoYR1fRE1jbHhsb1hTeF1abRhwZU9+EQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NDZGBrEQpNXBcdExEKTFoXbGlNTU0RCkxGF29ra2t raxEKQk8XaFheUEkFElx7ZHsRCkNaFxgaEwQSHwQYGBsEHhkRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXbH9BUkNuYxNkUB4RCkJOF2NTY2t7E 1h+Gl9eEQpCTBdmHxN7GV8bWkVvWBEKQmwXYxJOWkFfTGxaHBoRCkJAF29TZUROc0F5QxJhEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXaxsFYUN7ZE0eYh8RCnBoF29NenNNel8FYnt +EBkaEQpwaBdnbWZcEkdaQ1pkXRAZGhEKcGgXZ0xNGVJYbRISaH8QGRoRCnBoF25eYxtkXHtgZF p+EBkaEQpwaBdtHBhHYGVkYGZhQRAZGhEKcGwXbXoZe0ZsUm1NZGYQGRoRCm1+FxsRClhNF0sRI A== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=31 spamscore=31 mlxscore=31 phishscore=0 mlxlogscore=35 bulkscore=0 lowpriorityscore=0 clxscore=185 priorityscore=314 adultscore=0 malwarescore=0 impostorscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109280086 X-Spam-Score: 31 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: **** Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --0000000000002f22bb05cd0f73e7 Content-Type: text/plain; charset="UTF-8" Hi, I have some doubt regarding the replica run of constant pH MD. While running the replica run does an exchange between two systems with pH closer to each other occur similar to replica exchange method? If yes, when does this exchange occur and how can one track the systems to make sure that the proper pH sampling is done? Thanks in advance -- Diship Srivastava JRF Department of Chemistry IIT(ISM) - Dhanbad India --0000000000002f22bb05cd0f73e7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
I have some doubt regarding the replica run of con= stant pH MD. While running the replica run does an exchange between two sys= tems with pH closer to each other occur similar to replica exchange=C2=A0 m= ethod? If yes, when does this exchange occur and how can one track the syst= ems to make sure that the proper pH sampling is done?

<= div>Thanks in advance=C2=A0


--
<= div dir=3D"ltr">Diship Srivastava=C2=A0
JRF=C2=A0
Department = of Chemistry
IIT(ISM) - Dhanbad
India
=
--0000000000002f22bb05cd0f73e7-- From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 28 10:39:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SFdjK5012403; Tue, 28 Sep 2021 10:39:45 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18SFdjpb012395; Tue, 28 Sep 2021 10:39:45 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SFdgOS012360; Tue, 28 Sep 2021 10:39:43 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18SFdgGI012359; Tue, 28 Sep 2021 10:39:42 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SFdLPE011888 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 28 Sep 2021 10:39:22 -0500 (CDT) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18SFIkLl025703 for ; Tue, 28 Sep 2021 15:39:21 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=zdorevskyi@bitp.kiev.ua Received: from mail.bitp.kiev.ua (mail.bitp.kiev.ua [194.44.37.244]) by mx0b-00007101.pphosted.com with ESMTP id 3bb5v5e10n-1 (version=TLSv1 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 28 Sep 2021 15:39:20 +0000 Received: from localhost ([127.0.0.1] helo=mail.bitp.kiev.ua) by mail.bitp.kiev.ua with esmtp (Exim 4.76) (envelope-from ) id 1mVFCQ-000213-9f for namd-l@ks.uiuc.edu; Tue, 28 Sep 2021 18:39:18 +0300 Received: from 128.214.138.138 (SquirrelMail authenticated user zdorevskyi) by mail.bitp.kiev.ua with HTTP; Tue, 28 Sep 2021 18:39:18 +0300 Message-ID: <2db49fcf741294be0f29a25e84b6f7ca.squirrel@mail.bitp.kiev.ua> Date: Tue, 28 Sep 2021 18:39:18 +0300 Subject: namd-l: QM/MM live solvent selection - segmentation fault (with ORCA) From: "Oleksii Zdorevskyi" To: namd-l@ks.uiuc.edu User-Agent: SquirrelMail/1.4.22 Content-Type: text/plain;charset=utf-8 X-Priority: 3 (Normal) Importance: Normal X-Proofpoint-GUID: wIdL13fQRCjGmZoy_rCEed4CNHO12HV5 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0dEQpMehcaEQpZRBduYG19U1MTSXBFQxEKWFgXaERsXR9EQlxPYBI RCnhOF2QbZhlSYAFreBxYEQp5TBdkRkRYYHofa2ZbcxEKQ0gXBxkYHhEKQ1kXBxgYGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfHXEZHBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThddY05mGxlMe3hpQG1HcEVTdVhpb09OHmlkYmUbGGJ8HxEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdzQ2RcbhEKTVwXGRkbEQpMWhdoaU1NTREKQk8XbWBBaU1 DflBebh8RCkNaFxsTHgQeHgQZHQQYHh4RCkJeFxsRCkJFF2FYQVx9GVAcbmZ7EQpCThdkG2YZUm ABa3gcWBEKQkwXaERsXR9EQlxPYBIRCkJsF2cFGRlzcH9GHkxmEQpCQBdrbWVtfU4FGx8BWREKQ lgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF2N+AR1ZHB5bRn97EQpwaBdmT0doUnhuZnpjXxAaEQpw aBdkYhoaGHpoR0QSehAaEQpwaBdpUmQbQkd8SVpiGBAaEQpwaBdtE3hvQxh6RRlcSxAaEQpwaBd nGEBaT1NtU3NZWRAaEQpwfRdrGHkZEhthaVBnExAaEQpwfxdvRGFQEhN/GxwSfhAbGhwRCnBfF3 p7Wh17bmZkYkFLEBoRCnBsF29fc3lbXGtfGGB9EBoRCnBDF2NbYRtFa0FQWB1tEBoRCm1+FxoRC lhNF0sRIA== X-Proofpoint-ORIG-GUID: wIdL13fQRCjGmZoy_rCEed4CNHO12HV5 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=177 spamscore=0 mlxlogscore=999 priorityscore=0 bulkscore=0 adultscore=0 mlxscore=0 lowpriorityscore=0 phishscore=0 malwarescore=0 suspectscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109280090 X-Spam-Score: 0 X-Spam-OrigSender: zdorevskyi@bitp.kiev.ua X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 18SFdUPD011905 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Oleksii Zdorevskyi" Dear NAMD developers, I am facing an issue regarding the QM/MM setup of NAMD together with ORCA using Live solvent selection. Whenever I include a substantial number of water molecules to the QM region, my system firstly runs ok, but when it reaches the step for LSS exchange (listed in LSSfreq), the run immediately crashes with a Segmentation fault. I have tested this issue on different workstations and clusters with different amounts of memory allocation. On all the workstations, OpenMPI is configured correctly, so that NAMD+ORCA runs smoothly without LSS. To illustrate this problem with an example, please take a look at a very simple system of an H2O2 molecule in a water solution (71 water molecules in the QM region): https://urldefense.com/v3/__https://drive.google.com/drive/folders/1O1vSpSUC5VKC3y45BfeLJMxw4DWDy4vV?usp=sharing__;!!DZ3fjg!t-Iw6EdhA4PMwE_R3OWUQ2q9R32FPD7w52RwWQhjHc6Wk2VRDT6Koc3HdWe1jS5irQ$ Neither NAMD nor ORCA does not show any error, just a segmentation fault in the Slurm output file (qm_40c/slurm-719879.out): /var/spool/slurmd/job719879/slurm_script: line 19: 196326 Segmentation fault (core dumped) $NAMDDIR/namd2 +CmiSleepOnIdle qm1.conf > qm1.log Does NAMD implement some sophisticated calculations during the LSS exchange that clog up the memory immediately? Are there any limitations to the number of water molecules that can be chosen for LSS? Thanks in advance. Best regards, Oleksii From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 28 14:11:49 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SJBlCK024096; Tue, 28 Sep 2021 14:11:48 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18SJBlpI024081; Tue, 28 Sep 2021 14:11:47 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SJBaXM023874; Tue, 28 Sep 2021 14:11:37 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18SJBaEP023864; Tue, 28 Sep 2021 14:11:36 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18SJB9tK023250 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 28 Sep 2021 14:11:11 -0500 (CDT) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18SICXBB022619 for ; Tue, 28 Sep 2021 19:11:09 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=zdorevskyi@bitp.kiev.ua Received: from mail.bitp.kiev.ua (mail.bitp.kiev.ua [194.44.37.244]) by mx0b-00007101.pphosted.com with ESMTP id 3bc7v7rjwd-1 (version=TLSv1 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 28 Sep 2021 19:11:09 +0000 Received: from localhost ([127.0.0.1] helo=mail.bitp.kiev.ua) by mail.bitp.kiev.ua with esmtp (Exim 4.76) (envelope-from ) id 1mVIVO-00039u-Tj; Tue, 28 Sep 2021 22:11:07 +0300 Received: from 188.127.193.156 (SquirrelMail authenticated user zdorevskyi) by mail.bitp.kiev.ua with HTTP; Tue, 28 Sep 2021 22:11:06 +0300 Message-ID: <36174b60db2d00efc63b16a3a1b386ac.squirrel@mail.bitp.kiev.ua> In-Reply-To: <2db49fcf741294be0f29a25e84b6f7ca.squirrel@mail.bitp.kiev.ua> References: <2db49fcf741294be0f29a25e84b6f7ca.squirrel@mail.bitp.kiev.ua> Date: Tue, 28 Sep 2021 22:11:06 +0300 Subject: Re: namd-l: QM/MM live solvent selection - segmentation fault (with ORCA) From: "Oleksii Zdorevskyi" To: namd-l@ks.uiuc.edu, "Oleksii Zdorevskyi" User-Agent: SquirrelMail/1.4.22 MIME-Version: 1.0 Content-Type: text/plain;charset=utf-8 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-CLX-Response: 1TFkXGx4eEQpMehcaEQpZRBduYG19U1MTSXBFQxEKWFgXaERsXR9EQlxPYBI RCnhOF2QbZhlSYAFreBxYEQp5TBdkRkRYYHofa2ZbcxEKQ0gXBx4SHhEKQ1kXBxsfHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsYHnEZHhAbdwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdHbEZzW0ZwWh0fHXN4G0Jcb2t+fGFcQn9bZnV/eRMZHREKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4bEBseGh8aEQpeWRdzQ3sbRREKTVwXGBIYEQpMWhdpeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdtYEFpTUN+UF5uHxEKQ1oXGxMeBB4eBBkdBBgeHh EKQl4XGxEKRF4XGBEKQkUXYVhBXH0ZUBxuZnsRCkJOF2QbZhlSYAFreBxYEQpCTBdoRGxdH0RCX E9gEhEKQmwXZwUZGXNwf0YeTGYRCkJAF2BucxobbWh7T0BAEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXHhEKeUMXYHIZX1wFQWdLeFoRCnBoF3p9XWhwb2hOcl5DEB4SEQpwaBdtE3hvQxh6RRl cSxAeEhEKcGgXaUR+ehJcTUhsY2sQGhEKcGgXZkZDWVhFY0t/XEwQHhIRCnBoF2sYXhJsf1JmZx N8EBoRCnB9F29IYEJ5GXNsb2N5EB4SEQpwfxdhZm9bGmdkQkgdWxAbGBMRCnBfF2NiElBIY3gff EJ9EBMfEQpwbBdvX3N5W1xrXxhgfRAeEhEKcEMXYFBoTB1TemlTZlsQGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: mFlYqlZp757YR1hvEATVKvhUqL_US937 X-Proofpoint-ORIG-GUID: mFlYqlZp757YR1hvEATVKvhUqL_US937 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 spamscore=0 lowpriorityscore=0 priorityscore=0 bulkscore=0 clxscore=144 impostorscore=0 malwarescore=0 mlxscore=0 adultscore=0 suspectscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109280112 X-Spam-Score: 0 X-Spam-OrigSender: zdorevskyi@bitp.kiev.ua X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Oleksii Zdorevskyi" Dear all, My apologies, during the setup I have by chance deleted the selection of the H2O2 molecule from the QM atoms. This resulted in the absence of non-solvent atoms in the QM region, and, consequently, NAMD was not able to determine its center of mass, and dumped. The absence or NAMD and ORCA errors deceived me into that the problem was in the large number of solvent molecules for LSS. I apologize for such an obvious mistake. Best regards, Oleksii > Dear NAMD developers, > > I am facing an issue regarding the QM/MM setup of NAMD together with ORCA > using Live solvent selection. Whenever I include a substantial number of > water molecules to the QM region, my system firstly runs ok, but when it > reaches the step for LSS exchange (listed in LSSfreq), the run immediately > crashes with a Segmentation fault. I have tested this issue on different > workstations and clusters with different amounts of memory allocation. On > all the workstations, OpenMPI is configured correctly, so that NAMD+ORCA > runs smoothly without LSS. > > To illustrate this problem with an example, please take a look at a very > simple system of an H2O2 molecule in a water solution (71 water molecules > in the QM region): > > https://urldefense.com/v3/__https://drive.google.com/drive/folders/1O1vSpSUC5VKC3y45BfeLJMxw4DWDy4vV?usp=sharing__;!!DZ3fjg!t-Iw6EdhA4PMwE_R3OWUQ2q9R32FPD7w52RwWQhjHc6Wk2VRDT6Koc3HdWe1jS5irQ$ > > Neither NAMD nor ORCA does not show any error, just a segmentation fault > in the Slurm output file (qm_40c/slurm-719879.out): > > /var/spool/slurmd/job719879/slurm_script: line 19: 196326 Segmentation > fault (core dumped) $NAMDDIR/namd2 +CmiSleepOnIdle qm1.conf > qm1.log > > Does NAMD implement some sophisticated calculations during the LSS > exchange that clog up the memory immediately? > Are there any limitations to the number of water molecules that can be > chosen for LSS? > > Thanks in advance. > > Best regards, > Oleksii > > > From owner-namd-l@halifax.ks.uiuc.edu Tue Sep 28 20:12:30 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18T1CTaS012212; 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boundary="0000000000007be77a05cd1805f0" X-Proofpoint-GUID: _gUwJ7RrXiF9cFYWjMYVUXKmEx4qPB0h X-Proofpoint-ORIG-GUID: _gUwJ7RrXiF9cFYWjMYVUXKmEx4qPB0h X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehcZHx8RCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGxMeEQpDWRcHGx8bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwTcR4SEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3VNf11gHXhYckNsE0lsc31AZ3N8f3JhR29SHlt6aBpCEQpYXBcfBBoEGBkZ BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NDfWNlEQpNXBcbHBwRCkxaF3xpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHwQbHB wEHxsRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXaxMaYU5fXlgYHWURCkJOF2NTY2t7E1h+Gl9eEQpCTBdpSUgaS35pRht4cxEKQmwX YR4ZeFpubGdjX2IRCkJAF3ofBUVfHB9EGlB7EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXaFBYARJ4Rh9kc2sRCnBoF25QH2RAc3kee1N7EBkaEQpwaBdnWx1kbm8BZQVdWhAZGhEKcG gXa25aGRseTkdvYmYQGRoRCnBoF2VFRmhoX01pBXtNEBkaEQpwaBdkYhhTZ1oBG05zcxAZGhEKc GwXbh1mexJLGngSXG0QGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 phishscore=0 mlxlogscore=253 bulkscore=0 lowpriorityscore=0 clxscore=189 priorityscore=355 adultscore=0 malwarescore=0 impostorscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109290004 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --0000000000007be77a05cd1805f0 Content-Type: text/plain; charset="UTF-8" I've never seen this implemented in NAMD yet, so you'd have to share more details. Do you have a script? You might also need to modify the underlying code to get the extra information you want. BKR On Tue, Sep 28, 2021, 11:16 AM Diship Srivastava wrote: > Hi, > I have some doubt regarding the replica run of constant pH MD. While > running the replica run does an exchange between two systems with pH closer > to each other occur similar to replica exchange method? If yes, when does > this exchange occur and how can one track the systems to make sure that the > proper pH sampling is done? > > Thanks in advance > > > -- > Diship Srivastava > JRF > Department of Chemistry > IIT(ISM) - Dhanbad > India > --0000000000007be77a05cd1805f0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I've never seen this implemented in NAMD yet, so= you'd have to share more details. Do you have a script? You might also= need to modify the underlying code to get the extra information you want.= =C2=A0

BKR

On = Tue, Sep 28, 2021, 11:16 AM Diship Srivastava <dishipsrivastava@gmail.com> wrote:
Hi,
I have some doubt rega= rding the replica run of constant pH MD. While running the replica run does= an exchange between two systems with pH closer to each other occur similar= to replica exchange=C2=A0 method? If yes, when does this exchange occur an= d how can one track the systems to make sure that the proper pH sampling is= done?

Thanks in advance=C2=A0


--
Diship Srivastava=C2=A0
JRF=C2=A0
Departmen= t of Chemistry
IIT(ISM) - Dhanbad
India
--0000000000007be77a05cd1805f0-- From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 29 13:24:19 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TIOJ2r011571; Wed, 29 Sep 2021 13:24:19 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TIOJiO011570; Wed, 29 Sep 2021 13:24:19 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TIOIjk011566; Wed, 29 Sep 2021 13:24:18 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TIOISs011565; Wed, 29 Sep 2021 13:24:18 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TIOAnb011535 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 29 Sep 2021 13:24:11 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18TFQg31006097 for ; Wed, 29 Sep 2021 18:24:10 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=hasith.sathsindu@gmail.com; dkim=pass header.d=gmail.com header.s=20210112 Received: from mail-vs1-f47.google.com (mail-vs1-f47.google.com [209.85.217.47]) by mx0a-00007101.pphosted.com with ESMTP id 3bc38uc843-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 29 Sep 2021 18:24:10 +0000 Received: by mail-vs1-f47.google.com with SMTP id y141so4146723vsy.5 for ; Wed, 29 Sep 2021 11:24:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:from:date:message-id:subject:to; bh=cHtjhOAZOH+WeR7zrpO8vB4bA/VkXe7V7DP3pzBKXeY=; b=jzZ9PpxHFi/Gl+B6bdniQoAn1Chd5OmUb7IEi5kG0Pvdydzzd4ct4nStQIJ2YPQRoY vZmyKiLu9zwjK60lkFXH8cZoe6f7xwxNSSntDnqJYArwa2UrH01p5zwqXSgWVUX8FJvY jLwgCG5RMw67WhAHVilOOuVBf7ZtgSDEqsx6R/sz43dyc85CzWbW+WaLefVfIEwhLIXC VRBXz2k/yuU1vnKQ+ZOkvb0T5e4kbiH+MwIGW41kskLi9KdVTghyFWjv01qhUgzaZFRg jJYcVw11A2JYeDOHaw+M7vzxPnxi+ad86tFwK22UIMdjgDioJ41EA4mgpq3dx3Cf8ltZ dvQw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=cHtjhOAZOH+WeR7zrpO8vB4bA/VkXe7V7DP3pzBKXeY=; b=zNR+qkRqECKv8XeoyJE3EYP8+WXPzSbC1irStIYobgihtt1S3ckyhhkLbSDN9duKjz 28daO6W758TOdVVZm55Gy1SNioxlG5v4R9U3gz4vbu8zEgZ+39P/hcTOdW9ys7rB+85d ZJvWCISM0WM4grMIc/NDBHC2di9GUgd+5StZn3TqSpFyj2dDbg1YxlCGx2uA0n/jVtlt wz+EoMb7QPQWfYrwDzAlBR2tzaCr1ceRhfEBEDsPPBgDqHTd+6b70/Tu0s1S1dWD7yvf u74Y/AhCtAuFcjNgnp21/nLSqS99gqyBBQkmnNiBAN4zSXCOKU4eY+HNUAQBZOs4/2IF TLLw== X-Gm-Message-State: AOAM5304AalRc16e4yiQNdR5elbM+WEo73uGHdqAYxoo/3CEGsfB964r dYROvuWcYL2ARnYw/7+TzySOizmSgQnVfbFowrd1vWt2gfQ= X-Google-Smtp-Source: ABdhPJyK8z3/iqqvNSJsXY5Ub4/SA5PSCwao/4QoeqyitWrOFtR0KwT1gZuTBHTJu3L4cAqh8Y9naVGMlWU3yPvvpzs= X-Received: by 2002:a05:6102:1147:: with SMTP id j7mr1811498vsg.45.1632939848817; Wed, 29 Sep 2021 11:24:08 -0700 (PDT) MIME-Version: 1.0 From: Hasith Sathsindu Date: Wed, 29 Sep 2021 23:53:57 +0530 Message-ID: Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000a0dde305cd266f2c" X-Proofpoint-ORIG-GUID: nEEI0gGjTaCpN6n6kQ941Vjb0fDBHygW X-CLX-Response: 1TFkXGxIeEQpMehcZGRwRCllEF2hkGnNYH0lAfGFfEQpYWBdtW3NneFAaRnJ fEhEKeE4XY1Nja3sTWH4aX14RCnlMF21DUBh5Y31HSx1iEQpDSBcHHB4RCkNZFwcTGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGBxxGwYfGHcGGxgZBhoGGgYSHwYacRoQGncGGgYHHxoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF0Rvb2MaTW1AfktpWmQcRBxBexMe G3xASBpMbmhiU019EQpYXBcfBBoEGBkZBRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc0NGekYRCk1 cFxsdGhEKTFoXbGlNa2sRCkxGF29ra2traxEKQk8XYhlCZxxFc2NbQWARCkNaFxgaEwQSHwQYGx 0EHh0RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQ kUXYU5kE15kG2lJXWERCkJOF2NTY2t7E1h+Gl9eEQpCTBdtW3NneFAaRnJfEhEKQmwXYk1yHWsc e05Ma1kRCkJAF2xPQWdsHn95HnJiEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxgRCnlDF2t pHUYdU2EBRhtEEQpwaBdrQGZOY0JuHEV7SBAHGRoRCnBoF2BcZEAffHlPX1BFEAcZGhEKcGgXel IaRWVmYGtwHxMQBxkaEQpwaBdnH3teHEV/GnlGHxAHGRoRCnBoF21YQlJ+RltJEk9JEAcZGhEKc GwXbl1yYUseS2NcQXIQBxkaEQptfhcHGxEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-GUID: nEEI0gGjTaCpN6n6kQ941Vjb0fDBHygW X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 malwarescore=0 mlxlogscore=339 adultscore=0 suspectscore=0 bulkscore=0 clxscore=184 phishscore=0 impostorscore=0 mlxscore=0 priorityscore=336 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109290105 X-Spam-Score: 0 X-Spam-OrigSender: hasith.sathsindu@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hasith Sathsindu --000000000000a0dde305cd266f2c Content-Type: text/plain; charset="UTF-8" Hello, I am dealing with the type III collagen (single) molecule in a water box. I need to apply a constant force to all the carbon atoms except carbon atoms of last residue which are fixed. But that causes an error. * ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)* *ERROR: Atoms moving too fast; simulation has become unstable.* I used tip4 water molecules to the water box. Is that possible to do a Non equilibrium simulation to this structure? --000000000000a0dde305cd266f2c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,
I am dealing with the type III collagen (single= ) molecule in a water box. I need to apply a constant force to all the carb= on atoms except carbon atoms of last residue which are fixed.
But= that causes an error.

=C2=A0ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9= (limit is 6000)
ERROR: Atoms moving too fast; simula= tion has become unstable.


I used t= ip4 water molecules to the water box. Is that possible to do a Non equilibr= ium simulation to this structure?
--000000000000a0dde305cd266f2c-- From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 29 15:36:47 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKaltq025632; Wed, 29 Sep 2021 15:36:47 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKalDs025631; Wed, 29 Sep 2021 15:36:47 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKakFO025627; Wed, 29 Sep 2021 15:36:46 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKakYj025626; Wed, 29 Sep 2021 15:36:46 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKadYq025601 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 29 Sep 2021 15:36:40 -0500 (CDT) Received: from pps.filterd (m0272704.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18TJ1mtT020801 for ; Wed, 29 Sep 2021 20:36:38 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=shekaari@email.kntu.ac.ir; dkim=pass header.s=zimbraemail.kntu.ac.ir header.d=email.kntu.ac.ir Received: from mail.kntu.ac.ir (mail.kntu.ac.ir [94.184.176.111]) by mx0b-00007101.pphosted.com with ESMTP id 3bc5hhbnet-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 29 Sep 2021 20:36:37 +0000 Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 6720F1C3717; Thu, 30 Sep 2021 00:06:33 +0330 (+0330) Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id V_lLzMa9ge6r; Thu, 30 Sep 2021 00:06:32 +0330 (+0330) Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id B574B1C371B; Thu, 30 Sep 2021 00:06:32 +0330 (+0330) DKIM-Filter: OpenDKIM Filter v2.10.3 mail.kntu.ac.ir B574B1C371B DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=email.kntu.ac.ir; s=zimbraemail.kntu.ac.ir; t=1632947792; bh=b3ELYDU9lXUHXffoW9S70qgSmuFExsCtbmdCHInifGU=; h=Date:From:To:Message-ID:MIME-Version; b=Fqq6zdoCPBu1+WsGKdcrZjg6HyJuEX8k29rdZus7cn9sFneRMRphReSN2tH2BYSRt I+exvD7jfjH22t4bC+NtdwxCdjJZR9iUpMc85YeBPqrQtCxYBI4569aF617CLFbtxM Ki5Ucg0QX4vj8w6PIH1pBL1exmREj8YV9WXjhojJAnIq1NHuCFrmJ3Kwkqge58UCrW WhqeuphWZYusyBzDOXS1PNMTT71+q1Ri7FxwfRJqjQ+6U6s730wZFKDd4JsApxMGyA qsZOUOGyvqiXlfC76kmiyyWS0hp5Ajy7B5SPV5+uOKF7b6tUnTD4d9tIaJO19Y0GNe aUZp2ji8gNiZg== X-Virus-Scanned: amavisd-new at Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id CSdjxe0L-1Uq; Thu, 30 Sep 2021 00:06:32 +0330 (+0330) Received: from strga.kntu.ac.ir (strga.kntu.ac.ir [172.27.1.221]) by mail.kntu.ac.ir (Postfix) with ESMTP id 80E9A1C3717; Thu, 30 Sep 2021 00:06:32 +0330 (+0330) Date: Thu, 30 Sep 2021 00:06:27 +0330 (IRST) From: Ashkan Shekaari To: namd-l , Hasith Sathsindu Message-ID: <2129108276.307200.1632947787602.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: References: Subject: Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Content-Type: multipart/alternative; boundary="=_84521f74-9d74-49eb-928b-e9ced24c1fda" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC91 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Thread-Index: okdiJFnTwY/d0wPUvjBbcIEAv2DwTA== X-Proofpoint-GUID: igA9nPrSgHrm83ep8mtoT_WbRJA1FOG8 X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: igA9nPrSgHrm83ep8mtoT_WbRJA1FOG8 X-CLX-Response: 1TFkXGxIfEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBx0eEQpDWRcHExkRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHB9xHh4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XQ01rE0R6WHlNYlhHEhlPWhJHXkV+dX1IeGBrG2xlbRIRClhcFx8EGgQYGRkFGxoE GxoaBB4SBBgYEBseGh8aEQpeWRdzQ0RmUhEKTVwXGBoeEQpMWhd4aU1NaxEKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2IFaENATFpARXJOEQpDWhcTHgQbEh4EGx0cBBsbGx EKQl4XGxEKRF4XGBEKQlwXGxEKQksXeh5tW0t8R19iBXoRCkJJF2hfemFGAWJAQU95EQpCRRdhH R5ma3JBUhkZeBEKQk4XaF96YUYBYkBBT3kRCkJMF20TQUFaQURDE314EQpCbBdhZBlnXUIZRXxr eBEKQkAXYUZZWVkZEk9vYxsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdtckFlWn1 eWR1JEhEKWUsXBxkRCnBnF2MaY0dBf2FGeBl8EBkaEQpwaBdhS35yb39mb0FsTxAZGhEKcGgXaW IZGBxFbGEbHh8QGRoRCnBoF2hZQUJbbX9sbG9kEBkaEQpwaBdiZ0hnS25vTB1aUBAZGhEKcGgXZ UFIWmlyU3lseUIQGRoRCnB9F2Nze00FXR0BeEFwEBkaEQpwZxdpQ25QAVlzRwEeUxAZGhEKcH0X aRplTlxIE2BHeUYQGRoRCnB/F29EYVASE38bHBJ+EB0eEQpwXxdiGBoYH3hHTHt7exAbGh4RCnB sF29gf215TEFEa05OEBkaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 clxscore=185 adultscore=0 lowpriorityscore=0 phishscore=0 impostorscore=0 priorityscore=0 spamscore=0 malwarescore=0 mlxlogscore=828 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109290120 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_84521f74-9d74-49eb-928b-e9ced24c1fda Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Do you use margin?=20 Say "margin 3" in your input file?=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!vrLeITbBWwmIzRJivX7pxWVf9-AWwnBUHAMx56eZ1SMBwFfJNtbWE5An= LnLEj-0D2w$ ]=20 From: "Hasith Sathsindu" =20 To: "namd-l" =20 Sent: Wednesday, September 29, 2021 9:53:57 PM=20 Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstab= le.=20 Hello,=20 I am dealing with the type III collagen (single) molecule in a water box. I= need to apply a constant force to all the carbon atoms except carbon atoms= of last residue which are fixed.=20 But that causes an error.=20 ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)=20 ERROR: Atoms moving too fast; simulation has become unstable.=20 I used tip4 water molecules to the water box. Is that possible to do a Non = equilibrium simulation to this structure?=20 --=_84521f74-9d74-49eb-928b-e9ced24c1fda Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Do you use margin?
Say "margin&nb= sp;     3" in your input file?

-= --
,Best
<= /div>
=
<= div dir=3D"rtl" style=3D"text-align:left">
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran,&n= bsp;15875-4416, Iran
<= /div>
<= /div>


From: "Hasith Sathsin= du" <hasith.sathsindu@gmail.com>
To: "namd-l" <namd-l@ks= .uiuc.edu>
Sent: Wednesday, September 29, 2021 9:53:57 PM
<= b>Subject: namd-l: ERROR: Atoms moving too fast; simulation has become = unstable.

Hello,
I am dealing with the type III collagen (single) mo= lecule in a water box. I need to apply a constant force to all the carbon a= toms except carbon atoms of last residue which are fixed.
But tha= t causes an error.

 = ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)
ERROR:= Atoms moving too fast; simulation has become unstable.


I used tip4 water molecules to the water box. Is that possible t= o do a Non equilibrium simulation to this structure?

<= /div>= --=_84521f74-9d74-49eb-928b-e9ced24c1fda-- From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 29 15:40:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKeqeL028014; Wed, 29 Sep 2021 15:40:52 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKeq5k028009; Wed, 29 Sep 2021 15:40:52 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKepQC027999; Wed, 29 Sep 2021 15:40:51 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKepg4027998; Wed, 29 Sep 2021 15:40:51 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKehBn027889 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 29 Sep 2021 15:40:44 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18TJt2JD002984 for ; Wed, 29 Sep 2021 20:40:43 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=shekaari@email.kntu.ac.ir; dkim=pass header.d=email.kntu.ac.ir header.s=zimbraemail.kntu.ac.ir Received: from mail.kntu.ac.ir (mail.kntu.ac.ir [94.184.176.111]) by mx0a-00007101.pphosted.com with ESMTP id 3bc5gb3t0p-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 29 Sep 2021 20:40:43 +0000 Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 8F75E1C372F; Thu, 30 Sep 2021 00:10:44 +0330 (+0330) Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id rHuhOSddOj9K; Thu, 30 Sep 2021 00:10:44 +0330 (+0330) Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 1AE511C373D; Thu, 30 Sep 2021 00:10:44 +0330 (+0330) DKIM-Filter: OpenDKIM Filter v2.10.3 mail.kntu.ac.ir 1AE511C373D DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=email.kntu.ac.ir; s=zimbraemail.kntu.ac.ir; t=1632948044; bh=l1DN0GSlLiNZ7HAOgnCf8lDDniqkS84Rv8udHHGuaLk=; h=Date:From:To:Message-ID:MIME-Version; b=w4iT6VlooG0evim5bVajNQwOi0w6swYWfXYBEztPYSm8SBosV3XR/RZ+UiKrZZyCv jryU1NEFLX50oncPU7a7r/sDDW3WtIQ4swdDf0lN6rcg6AoONkn1sQdudrDvxrJIyQ f2xHfuPY605QmDlcNV6D38leXLxB/1Br8MW1BdVf1O8MOKCOot6D7FX84JNpac8DrS 6pkNLMT6S+/zMj6hBNfyMYVsCy4H9/nD9HO5pZV0DDdSn6GwjVTw/bYYQUav1KWSZx xmHHQAKDPkv7OJu3m4uNQJdyjNlKneJmFzAzjwpDvr1dfTtAd/Ci9cve8W/Lt80IJe fah2JRp9Sweeg== X-Virus-Scanned: amavisd-new at Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id VLTrdZ4BhNeQ; Thu, 30 Sep 2021 00:10:43 +0330 (+0330) Received: from strga.kntu.ac.ir (strga.kntu.ac.ir [172.27.1.221]) by mail.kntu.ac.ir (Postfix) with ESMTP id D88F11C372F; Thu, 30 Sep 2021 00:10:43 +0330 (+0330) Date: Thu, 30 Sep 2021 00:10:38 +0330 (IRST) From: Ashkan Shekaari To: namd-l , Hasith Sathsindu Message-ID: <229789014.307252.1632948038950.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: References: Subject: Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Content-Type: multipart/alternative; boundary="=_e153531b-a485-4aa2-b516-03716b0a8282" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC91 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Thread-Index: Svt3AWXbV4RgGlml2QH0p6x0XYejxw== X-Proofpoint-ORIG-GUID: ikSFszOnN2cUwWNCFA674zRW17g-ijYF X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIbEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxITEQpDWRcHExkRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHBtxHhoQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XQ0F5bFlQZURkGEl/XX1kaWxrHB0eUHh9Gx1NB0NAc2wRClhcFx8EGgQYGRkFGxoE GxsaBB8aBBseGxAbHhofGhEKXlkXc0NEekcRCk1cFxsdExEKTFoXeGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGx sRCkJeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXY R0eZmtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8 a3gRCkJAF2FGWVlZGRJPb2MbEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXbXJBZVp 9XlkdSRIRCllLFwcZEQpwZxdjGmNHQX9hRngZfBAZGhEKcGgXb1NDbWtDUklaG1IQGRoRCnBoF2 liGRgcRWxhGx4fEBkaEQpwaBdoWUFCW21/bGxvZBAZGhEKcGgXYmdIZ0tub0wdWlAQGRoRCnBoF 2VBSFppclN5bHlCEBkaEQpwfRdjc3tNBV0dAXhBcBAZGhEKcGcXaUNuUAFZc0cBHlMQGRoRCnB9 F2kaZU5cSBNgR3lGEBkaEQpwfxdvRGFQEhN/GxwSfhAdHBEKcF8XYhgaGB94R0x7e3sQGxsTEQp wbBdvYH9teUxBRGtOThAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: ikSFszOnN2cUwWNCFA674zRW17g-ijYF MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 suspectscore=0 impostorscore=0 mlxlogscore=813 spamscore=0 phishscore=0 clxscore=181 adultscore=0 bulkscore=0 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109290120 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_e153531b-a485-4aa2-b516-03716b0a8282 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Yes. No problem in performing non-equilibrium simulations...=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!vrpJJM_v7eo2i1D_wbJTsDnN-uTU3Lizm5RY0UBmFx2s5W6KhoSnEc1D= Yuh1PafhXA$ ]=20 From: "Hasith Sathsindu" =20 To: "namd-l" =20 Sent: Wednesday, September 29, 2021 9:53:57 PM=20 Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstab= le.=20 Hello,=20 I am dealing with the type III collagen (single) molecule in a water box. I= need to apply a constant force to all the carbon atoms except carbon atoms= of last residue which are fixed.=20 But that causes an error.=20 ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)=20 ERROR: Atoms moving too fast; simulation has become unstable.=20 I used tip4 water molecules to the water box. Is that possible to do a Non = equilibrium simulation to this structure?=20 --=_e153531b-a485-4aa2-b516-03716b0a8282 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Yes. No problem in performing non-equilibri= um simulations...

---
,Best
<= /div>
<= /div>
=
<= div dir=3D"ltr">
A= shkan Shekaari
PhD Candidate in So= lid State Physics
Department of Physics
K= . N. Toosi University of Technology, Tehran, 15875-4416, Iran
<= /div>
<= /div>


From: "Hasith Sathsindu" <hasith.sathsindu= @gmail.com>
To: "namd-l" <namd-l@ks.uiuc.edu>
Sent= : Wednesday, September 29, 2021 9:53:57 PM
Subject: namd-l: E= RROR: Atoms moving too fast; simulation has become unstable.
=
Hello,
= I am dealing with the type III collagen (single) molecule in a water box. I= need to apply a constant force to all the carbon atoms except carbon atoms= of last residue which are fixed.
But that causes an error.
=
 ERROR: Atom 343 velocity= is 8090.26 -7576.1 3976.9 (limit is 6000)
ERROR: Atoms moving too fast; = simulation has become unstable.


I used tip4 w= ater molecules to the water box. Is that possible to do a Non equilibrium s= imulation to this structure?

= --=_e153531b-a485-4aa2-b516-03716b0a8282-- From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 29 15:50:54 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKosV3003761; Wed, 29 Sep 2021 15:50:54 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKosj6003759; Wed, 29 Sep 2021 15:50:54 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKorIG003744; Wed, 29 Sep 2021 15:50:53 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKorA2003743; Wed, 29 Sep 2021 15:50:53 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKofre003670 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 29 Sep 2021 15:50:41 -0500 (CDT) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18TJvGfs008643 for ; Wed, 29 Sep 2021 20:50:40 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=shekaari@email.kntu.ac.ir; dkim=pass header.s=zimbraemail.kntu.ac.ir header.d=email.kntu.ac.ir Received: from mail.kntu.ac.ir (mail.kntu.ac.ir [94.184.176.111]) by mx0b-00007101.pphosted.com with ESMTP id 3bc3nsn2ng-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 29 Sep 2021 20:50:40 +0000 Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id A79241C3727; Thu, 30 Sep 2021 00:20:39 +0330 (+0330) Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id vq4kho4LrqSJ; Thu, 30 Sep 2021 00:20:39 +0330 (+0330) Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 2C7AD1C372F; Thu, 30 Sep 2021 00:20:39 +0330 (+0330) DKIM-Filter: OpenDKIM Filter v2.10.3 mail.kntu.ac.ir 2C7AD1C372F DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=email.kntu.ac.ir; s=zimbraemail.kntu.ac.ir; t=1632948639; bh=iO6hjhWRFwy35M1mZ+ppBiQzG0qoNe2v+WZqw9p7GUA=; h=Date:From:To:Message-ID:MIME-Version; b=h/jeMuqaXy5XxyjV/UBBP4d58SqPRIb7F6XimwfRmDNO7AV+LVu1pFk4eefyiPWhd JekIPLsgM4b1e+UX3Q1q67NWK1avjLGRk56GS0wjSTJ0vfvvrTymwn5NR1AljfUHy7 gbI9C1KQajYuPGSLaLxi1OO134GAkWW0IY95KcR7u8RroPbu/h2R3k5DJoIiz3RD3d eBw84e/ae21HAxUgQ911zcaU+AmezTsvpa56nnonSkPPUcfbyM/fMxXWd0NqjstDZW 6JlvVgg7VygfnIyS7ztZlAKjZOHw/dLCR/v9lMndfpAOfqI8/qnoctAXepIeJcRu7/ NM0U0i57HsjLw== X-Virus-Scanned: amavisd-new at Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id pEJefQkNvHJ5; Thu, 30 Sep 2021 00:20:39 +0330 (+0330) Received: from strga.kntu.ac.ir (strga.kntu.ac.ir [172.27.1.221]) by mail.kntu.ac.ir (Postfix) with ESMTP id ED4F31C3727; Thu, 30 Sep 2021 00:20:38 +0330 (+0330) Date: Thu, 30 Sep 2021 00:20:34 +0330 (IRST) From: Ashkan Shekaari To: namd-l , Hasith Sathsindu Message-ID: <121455294.307618.1632948634057.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: References: Subject: Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Content-Type: multipart/alternative; boundary="=_c81362f4-6b9a-4b00-9d2b-b0a5ac6470f2" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC91 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. 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N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!uiLwHRy5B5zo1Ekaz4fybmx6OP6u74-XX57g6Xc-2QArAyfG0b6NEHJV= n1h-wD3p5g$ ]=20 From: "Hasith Sathsindu" =20 To: "namd-l" =20 Sent: Wednesday, September 29, 2021 9:53:57 PM=20 Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstab= le.=20 Hello,=20 I am dealing with the type III collagen (single) molecule in a water box. I= need to apply a constant force to all the carbon atoms except carbon atoms= of last residue which are fixed.=20 But that causes an error.=20 ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)=20 ERROR: Atoms moving too fast; simulation has become unstable.=20 I used tip4 water molecules to the water box. Is that possible to do a Non = equilibrium simulation to this structure?=20 --=_c81362f4-6b9a-4b00-9d2b-b0a5ac6470f2 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
More importantly: what is the time-step???<= /div>

=
<= div dir=3D"ltr">
<= span style=3D"font-size:10pt">---
,Best
=
=
Ashkan Shekaari
PhD Candidate in Solid State Physics<= /span>
Departm= ent of Physics
K. N. Toosi Univers= ity of Technology, Tehran, 15875-4416, Iran
<= /div>


From: "Hasith Sathsindu" <hasith.sathsindu@gmail.com>
= To: "namd-l" <namd-l@ks.uiuc.edu>
Sent: Wednesday, S= eptember 29, 2021 9:53:57 PM
Subject: namd-l: ERROR: Atoms moving= too fast; simulation has become unstable.

Hello,
I am dealing with = the type III collagen (single) molecule in a water box. I need to apply a c= onstant force to all the carbon atoms except carbon atoms of last residue w= hich are fixed.
But that causes an error.

 ERROR: Atom 343 velocity is 8090.26 -7576.= 1 3976.9 (limit is 6000)
ERROR: Atoms moving too fast; simulation has bec= ome unstable.


I used tip4 water molecules to = the water box. Is that possible to do a Non equilibrium simulation to this = structure?

= --=_c81362f4-6b9a-4b00-9d2b-b0a5ac6470f2-- From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 29 15:54:19 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKsIDR006407; Wed, 29 Sep 2021 15:54:18 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKsI4v006404; Wed, 29 Sep 2021 15:54:18 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKsHba006381; Wed, 29 Sep 2021 15:54:17 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKsGPP006379; Wed, 29 Sep 2021 15:54:16 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKs88p006227 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 29 Sep 2021 15:54:09 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18TKs7K7022516 for ; Wed, 29 Sep 2021 20:54:08 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=shekaari@email.kntu.ac.ir; dkim=pass header.s=zimbraemail.kntu.ac.ir header.d=email.kntu.ac.ir Received: from mail.kntu.ac.ir (mail.kntu.ac.ir [94.184.176.111]) by mx0a-00007101.pphosted.com with ESMTP id 3bc8tuhs3y-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 29 Sep 2021 20:54:07 +0000 Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id EB7701C3727; Thu, 30 Sep 2021 00:23:20 +0330 (+0330) Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id eguOYPbLbCAo; Thu, 30 Sep 2021 00:23:20 +0330 (+0330) Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 5F1D51C372F; Thu, 30 Sep 2021 00:23:20 +0330 (+0330) DKIM-Filter: OpenDKIM Filter v2.10.3 mail.kntu.ac.ir 5F1D51C372F DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=email.kntu.ac.ir; s=zimbraemail.kntu.ac.ir; t=1632948800; bh=X0PMuK6KWlxxhrPR18E1gXKtn+UGQiKf3lpP7fZOBlM=; h=Date:From:To:Message-ID:MIME-Version; b=k2ctk+aEm5Yz9pCFJlf2TWjAoZe52226c0a4/xM87pBo7Kx4tliVNc7l7by0EjtR4 mrmWqUk/CQ0nq9QeCM+IPJUAvHzApHjhYCjwuub5NYTnoJIElnWORMGE1g8SazrEhR JDdtVn6A3E5SgYcFeo40M5CZ3kvSS4RGBxxu1Gs+py04Vvl+B+DrM7o0ZvybQsZv4N unGPEBDXf9lUb7H90Ar/xLr2ko+oA7dnDKeVove0vD2O6AiokMsaABFkH9naPdxDRq PxlEsB2LsAFLXbF2J3Xfa/Lt0iWE/5eY9/oM9qXNucnC6sXXIh1QfYYwZTUkJHIfdG DtQo6lFO/Q8Tg== X-Virus-Scanned: amavisd-new at Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id HavVvAgbVuRR; Thu, 30 Sep 2021 00:23:20 +0330 (+0330) Received: from strga.kntu.ac.ir (strga.kntu.ac.ir [172.27.1.221]) by mail.kntu.ac.ir (Postfix) with ESMTP id 27DC81C3727; Thu, 30 Sep 2021 00:23:20 +0330 (+0330) Date: Thu, 30 Sep 2021 00:23:15 +0330 (IRST) From: Ashkan Shekaari To: namd-l , Hasith Sathsindu Message-ID: <735922522.307651.1632948795248.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: References: Subject: Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Content-Type: multipart/alternative; boundary="=_17221737-d5e9-4de5-82aa-d6ccd01ab9f9" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC91 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Thread-Index: Bezxvqqdjd6gyWuxr2BGk27qsluMiw== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: MExHOJXhCQsfDoEHd5HX-GDdsVVNc5lT X-Proofpoint-GUID: MExHOJXhCQsfDoEHd5HX-GDdsVVNc5lT X-CLX-Response: 1TFkXGxIeEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxIfEQpDWRcHExkRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHB5xHhkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XZ29SYmVgckJpe1lMbkVvYk4fYnIHbW5OWXx8ZEkfRn4RClhcFx8EGgQYGRkFGxoE GxoaBB4SBBsTEBseGh8aEQpeWRdzQ0RJZhEKTVwXGx0eEQpMWhd4aU1NaxEKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2IFaENATFpARXJOEQpDWhcTHgQbEh4EGx0cBBsbGx EKQl4XGxEKRF4XGBEKQlwXGxEKQksXeh5tW0t8R19iBXoRCkJJF2hfemFGAWJAQU95EQpCRRdhH R5ma3JBUhkZeBEKQk4XaF96YUYBYkBBT3kRCkJMF20TQUFaQURDE314EQpCbBdhZBlnXUIZRXxr eBEKQkAXYUZZWVkZEk9vYxsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdtckFlWn1 eWR1JEhEKWUsXBxkRCnBnF2MaY0dBf2FGeBl8EBwaEQpwaBdjREF8eWFaSUBkSBAZGhEKcGgXaW IZGBxFbGEbHh8QGRoRCnBoF2hZQUJbbX9sbG9kEBwaEQpwaBdiZ0hnS25vTB1aUBAZGhEKcGgXZ UFIWmlyU3lseUIQHBoRCnB9F2Nze00FXR0BeEFwEBkaEQpwZxdpQ25QAVlzRwEeUxAcGhEKcH0X aRplTlxIE2BHeUYQGRoRCnB/F29EYVASE38bHBJ+EBwSEQpwXxdiGBoYH3hHTHt7exAbGxkRCnB sF29gf215TEFEa05OEBwaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 mlxscore=0 mlxlogscore=894 priorityscore=0 phishscore=0 impostorscore=0 lowpriorityscore=0 clxscore=184 suspectscore=0 adultscore=0 malwarescore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109290122 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_17221737-d5e9-4de5-82aa-d6ccd01ab9f9 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable For example, for a force with value about 11.5 kcal/mol.A =3D 800 pN,=20 dt =3D 0.1 is large and you have use dt =3D 0.05 in NAMD input file.=20 Find your optimized time-step...=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!qftRdbsnKie38qy3bcG-M8zMS7EnyWpnlSv_6w9sz-BjU8-RQGYWJxGA= N8cXb2I2ZA$ ]=20 From: "Hasith Sathsindu" =20 To: "namd-l" =20 Sent: Wednesday, September 29, 2021 9:53:57 PM=20 Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstab= le.=20 Hello,=20 I am dealing with the type III collagen (single) molecule in a water box. I= need to apply a constant force to all the carbon atoms except carbon atoms= of last residue which are fixed.=20 But that causes an error.=20 ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)=20 ERROR: Atoms moving too fast; simulation has become unstable.=20 I used tip4 water molecules to the water box. Is that possible to do a Non = equilibrium simulation to this structure?=20 --=_17221737-d5e9-4de5-82aa-d6ccd01ab9f9 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
For example, for a force with value about 1= 1.5 kcal/mol.A =3D 800 pN,
dt =3D 0.1 is large and you have use d= t =3D 0.05 in NAMD input file.
Find your optimized time-step...

<= div dir=3D"ltr">
---
,Best
<= /div>
<= div dir=3D"ltr">
Ashkan Shekaari=
PhD Candidate in Solid State Physics
Department= of Physics
K. N. Toosi University= of Technology, Tehran, 15875-4416, Iran<= /font>
=

=
From: "Hasith Sathsindu" <hasith.sathsindu@gmail.com>
To:
"namd-l" <namd-l@ks.uiuc.edu>
Sent: Wednesday, Sep= tember 29, 2021 9:53:57 PM
Subject: namd-l: ERROR: Atoms moving t= oo fast; simulation has become unstable.

Hello,
I am dealing with th= e type III collagen (single) molecule in a water box. I need to apply a con= stant force to all the carbon atoms except carbon atoms of last residue whi= ch are fixed.
But that causes an error.

 ERROR: Atom 343 velocity is 8090.26 -7576.1 = 3976.9 (limit is 6000)
ERROR: Atoms moving too fast; simulation has becom= e unstable.


I used tip4 water molecules to th= e water box. Is that possible to do a Non equilibrium simulation to this st= ructure?

= --=_17221737-d5e9-4de5-82aa-d6ccd01ab9f9-- From owner-namd-l@halifax.ks.uiuc.edu Wed Sep 29 15:54:29 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKsTZv006625; Wed, 29 Sep 2021 15:54:29 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKsTVo006618; Wed, 29 Sep 2021 15:54:29 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKsSPk006602; Wed, 29 Sep 2021 15:54:28 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 18TKsShv006599; Wed, 29 Sep 2021 15:54:28 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 18TKsKUo006439 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 29 Sep 2021 15:54:21 -0500 (CDT) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 18TKs0YX023552 for ; Wed, 29 Sep 2021 20:54:20 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=shekaari@email.kntu.ac.ir; dkim=pass header.d=email.kntu.ac.ir header.s=zimbraemail.kntu.ac.ir Received: from mail.kntu.ac.ir (mail.kntu.ac.ir [94.184.176.111]) by mx0a-00007101.pphosted.com with ESMTP id 3bc5gb3vu3-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Wed, 29 Sep 2021 20:54:19 +0000 Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 7BFF91C373D; Thu, 30 Sep 2021 00:24:20 +0330 (+0330) Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id dTeGNiBGdLLX; Thu, 30 Sep 2021 00:24:20 +0330 (+0330) Received: from localhost (localhost [127.0.0.1]) by mail.kntu.ac.ir (Postfix) with ESMTP id 065F51C3753; Thu, 30 Sep 2021 00:24:20 +0330 (+0330) DKIM-Filter: OpenDKIM Filter v2.10.3 mail.kntu.ac.ir 065F51C3753 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=email.kntu.ac.ir; s=zimbraemail.kntu.ac.ir; t=1632948860; bh=+Zsu/DSV+Ue2gPwi++a0bmO6SVd5AimCPYRKmUW95ME=; h=Date:From:To:Message-ID:MIME-Version; b=MZonI908x7proDrP4XKRVzyQxrlAjvsdT8sljdjqa4zz34M+tcCFreHVgW+W/vaqy PPJj+ZaGXW82bnZNRH2i/3Z7BdAQFcCDnmn2NTJ1G5ItaYSsUqDI7HmisVJKpnkAIQ lYgKPaDWWF/BlOF59owUnrvWs8iLeE+EUFy+GG43kxTlh9WkhzXzwk2/EbIL5dyoEC Y+0QuwumNjNxCnnaiTaYp4UrFBUvO+CFlMtcAXDGv/3DNDJqHZp99lTe5DWM5b5m8e VXwPBczjXoI0e1EeBfLyZvHPIG39I7kXDD1aEiSqkJy/qZlxLboTRiCyeCvkXTuEM9 pssoIdVGoPZFQ== X-Virus-Scanned: amavisd-new at Received: from mail.kntu.ac.ir ([127.0.0.1]) by localhost (mail.kntu.ac.ir [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id DFtLWVYAsxFH; Thu, 30 Sep 2021 00:24:19 +0330 (+0330) Received: from strga.kntu.ac.ir (strga.kntu.ac.ir [172.27.1.221]) by mail.kntu.ac.ir (Postfix) with ESMTP id CA0171C373D; Thu, 30 Sep 2021 00:24:19 +0330 (+0330) Date: Thu, 30 Sep 2021 00:24:14 +0330 (IRST) From: Ashkan Shekaari To: namd-l , Hasith Sathsindu Message-ID: <1435969929.307668.1632948854917.JavaMail.zimbra@email.kntu.ac.ir> In-Reply-To: References: Subject: Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Content-Type: multipart/alternative; boundary="=_5011acf5-3f9d-451c-ada2-66b642807eb5" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC91 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: ERROR: Atoms moving too fast; simulation has become unstable. Thread-Index: VK4+cyvPCEqHrVTE3GzoN5CQTJIXuA== X-Proofpoint-ORIG-GUID: BcZk7ZIwTlz6vgpF15ACsIz5ben4MENG X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxISEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXBxkcEQpDWRcHExkRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHBJxHh0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XaElwQR1wY11+RlAcXE1abBsfa2lZY1AfSE9EHmdvZG0RClhcFx8EGgQYGRkFGxoE GxsaBB8aBBseHxAbHhofGhEKXlkXc0NESX0RCk1cFxkbHhEKTFoXfGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGx sRCkJeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXY R0eZmtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8 a3gRCkJAF2FGWVlZGRJPb2MbEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxEKeUMXbXJBZVp9XlkdSRI RCllLFwcZEQpwZxdjGmNHQX9hRngZfBAeEhEKcGgXegVwWVpIH0wdH34QHRoRCnBoF2NEemdEQR t4Y094EBMbEQpwaBdkZ0UeWX5+QRNdbxAZGhEKcGgXZ3hiZHBNUGsFGGMQGRoRCnBoF25yfWxdb 0xba0JAEB0aEQpwfRdjc3tNBV0dAXhBcBAZGhEKcGcXaUNuUAFZc0cBHlMQHhIRCnB9F2kaZU5c SBNgR3lGEBkaEQpwfxdvRGFQEhN/GxwSfhAdGREKcF8XYhgaGB94R0x7e3sQGxgfEQpwbBdvYH9 teUxBRGtOThAeEhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: BcZk7ZIwTlz6vgpF15ACsIz5ben4MENG MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 suspectscore=0 impostorscore=0 mlxlogscore=900 spamscore=0 phishscore=0 clxscore=188 adultscore=0 bulkscore=0 lowpriorityscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109290122 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_5011acf5-3f9d-451c-ada2-66b642807eb5 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable For example, for a force with value about 11.5 kcal/mol.A =3D 800 pN,=20 dt =3D 0.1 is large and you have to use dt =3D 0.05 in NAMD input file.=20 Find your optimized time-step...=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!r0oVDxvdAs1LRL3fOcGEmpcPdJ8JmRF2ZPhvrU2w667l6hbw-G8Amkzw= 6TIbPpEZaQ$ ]=20 From: "Hasith Sathsindu" =20 To: "namd-l" =20 Sent: Wednesday, September 29, 2021 9:53:57 PM=20 Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstab= le.=20 Hello,=20 I am dealing with the type III collagen (single) molecule in a water box. I= need to apply a constant force to all the carbon atoms except carbon atoms= of last residue which are fixed.=20 But that causes an error.=20 ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)=20 ERROR: Atoms moving too fast; simulation has become unstable.=20 I used tip4 water molecules to the water box. Is that possible to do a Non = equilibrium simulation to this structure?=20 --=_5011acf5-3f9d-451c-ada2-66b642807eb5 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
For example, for a force wit= h value about 11.5 kcal/mol.A =3D 800 pN,
dt =3D 0.1 is= large and you have to use dt =3D 0.05 in NAMD input file.
Find your optimized time-step...


---
,Best
=
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics<= br>K. N. Toosi University of Technology,&nbs= p;Tehran, 15875-4416, Iran=


From: "Has= ith Sathsindu" <hasith.sathsindu@gmail.com>
To: "namd-l" &l= t;namd-l@ks.uiuc.edu>
Sent: Wednesday, September 29, 2021 9:53= :57 PM
Subject: namd-l: ERROR: Atoms moving too fast; simulation = has become unstable.

Hello,
I am dealing with the type III collagen = (single) molecule in a water box. I need to apply a constant force to all t= he carbon atoms except carbon atoms of last residue which are fixed.
<= div>But that causes an error.

 ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 600= 0)
ERROR: Atoms moving too fast; simulation has become unstable.

I used tip4 water molecules to the water box. Is that= possible to do a Non equilibrium simulation to this structure?
=
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Thu, 30 Sep 2021 16:15:52 +0000 Date: Thu, 30 Sep 2021 16:15:00 +0000 (UTC) From: Fateme Ghadirian To: NAMD List Message-ID: <2014701220.647391.1633018500410@mail.yahoo.com> Subject: namd-l: Simulation Box Size & Simulation speed MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_647390_930544065.1633018500405" References: <2014701220.647391.1633018500410.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19076 YMailNorrin X-Proofpoint-ORIG-GUID: kQMrexLafsFtvmZR7gfgL2fLvBTKpoTi X-Proofpoint-GUID: kQMrexLafsFtvmZR7gfgL2fLvBTKpoTi X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRgYEQpMehcZHxwRCllEF2tfQX1nbkdQaUxnEQpYWBd6X1lGGWZTY2M ZbxEKeE4XekQcHW9FbG1EQ2YRCnlMF2wTWF4YfUZtck4cEQpDSBcHExIRCkNZFwcbHB4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxgYcRsGHh53BhgaGgYaBhoGGxoaBhpxGhAadwYaBhoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF0F7Z1hPUmZLTFlsXlxHcHgdTUxN ZhhMZlxofmFaRX5DEQpYXBcfBBoEGBkZBRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NDHk5/EQp NXBceGBMRCkxaF2hpa2trEQpMRhdva2tva2sRCkJPF2tMbkRTXmlYeUJoEQpDWhccHAQbHBkEGx MaBBseHBEKQl4XGxEKQlwXGxEKXk4XGxEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmE QpCRRdlf08SUxxBBWMFbREKQk4XekQcHW9FbG1EQ2YRCkJMF3pfWUYZZlNjYxlvEQpCbBdrQUZA aGR8Ux1uQhEKQkAXZ05oR1tHbUlJWEMRCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGBEKeUM XY2lyc3p8aQFfGEgRCllLFxMdHxgRCnBoF2t/bU1SE20afGR+EAcZGhEKcGgXZ09PHx1Ne2ZLEh wQBxkaEQpwaBd6eGZiZBJObEtcRBAHGRoRCnBoF2RjfhtjX19sckIZEAcZGhEKcGgXb35hTntGS wVaHWAQBxkaEQpwbBdpWXgFU3x/E2liSxAHGRoRCnBMF2YFYRxHHUZheUN/EAcZGhEKbX4XBxsR ClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=322 lowpriorityscore=0 malwarescore=0 suspectscore=0 spamscore=0 impostorscore=0 adultscore=0 phishscore=0 priorityscore=356 mlxscore=0 bulkscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109300101 domainage_hfrom=9752 X-Spam-Score: 0 X-Spam-OrigSender: fateme.ghadirian@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fateme Ghadirian ------=_Part_647390_930544065.1633018500405 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable DearNAMD users, Ihave a system which contains one particle (HO) in vacuum. I am trying to s= imulatea gaseous system, it is a part of Heat of vaporization=E2=80=99s cal= culation. Langevinis set to off, due to lack of one particle=E2=80=99s ability to mai= ntain system=E2=80=99stemperature. Run is in NVT. As thesystem is trying to represent a gaseous system, simulation box size i= s large;500 Ang in each Direction (Simulation speed is 0.072 days/ns, so ~ = 17 hoursneeded to complete the simulation).=20 WhenI decrease the size of the simulation box to 50 Ang in each direction, = thesimulation speed increases (0.0016 days/ns~ 0.4 hour to complete the sim= ulation). As Iunderstood simulation speed can just be affected with number of particl= es, dueto the number of equations of motion which would be calculated. So h= ow simulationbox size can affect simulation speed in this case? Hereis my Configuration file: =C2=A0 structurex.psf coordinatesx.pdb setnew_run=C2=A0 run-0 outputName./$new_run/$new_run settemperature=C2=A0=C2=A0=C2=A0 123. firsttimestep=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 paraTypeCharmm=C2=A0 =C2=A0=C2=A0=C2=A0 on parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ./param/pa= r_all36_lipid.prm =C2=A0 temperature=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperature if{1} {=20 cellBasisVector1=C2=A0=C2=A0 500.0=C2=A0=C2=A00.0=C2=A0=C2=A0 0.0 cellBasisVector2=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0 500.0=C2=A0=C2=A0 0.0 cellBasisVector3=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0=C2=A0=C2=A00.0 500.0 cellOrigin=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 0.0=C2=A0=C2=A0 0.0=C2=A0=C2=A00.0 } wrapAll=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 on =C2=A0 #Force-Field Parameters exclude=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 scaled1-4 1-4scaling=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1.0 cutoff=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A012.=20 switching=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on switchdist=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 10.=20 pairlistdist=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 13.5=20 =C2=A0 =C2=A0 #Integrator Parameters timestep=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 2.0=C2=A0;# 2fs/step rigidBonds=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 all=C2=A0;= # needed for 2fs steps nonbondedFreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1 fullElectFrequency=C2=A0 2=C2=A0=20 stepspercycle=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 10 =C2=A0 =C2=A0 #PME(for full-system periodic electrostatics) if{1} { PME=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 yes PMEGridSpacing=C2=A0 =C2=A0=C2=A0=C2=A0 1.0 } =C2=A0 #Constant Temperature Control #langevin=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= on=C2=A0=C2=A0=C2=A0 ;# do langevin dynamics #langevinDamping=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0;# dampin= g coefficient (gamma) of 5/ps #langevinTemp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperature =C2=A0 #Constant Pressure Control (variable volume) if{0} { useGroupPressure=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 no ;# needed for 2fs steps useFlexibleCell=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 yes=C2=A0;# no for wate= r box, yes for membrane useConstantArea=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 yes=C2=A0;# no for wate= r box, yes for membrane =C2=A0 langevinPiston=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on langevinPistonTarget=C2=A0 1.01325 ;#=C2=A0in bar -> 1 atm langevinPistonPeriod=C2=A0 100. langevinPistonDecay=C2=A0=C2=A0 50. langevinPistonTemp=C2=A0=C2=A0=C2=A0 $temperature } =C2=A0 =C2=A0 restartfreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 100=C2=A0=C2=A0=C2=A0= =C2=A0 dcdfreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 5= 000 =C2=A0 xstFreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1= 00 outputEnergies=C2=A0=C2=A0=C2=A0=C2=A0 100 outputPressure=C2=A0=C2=A0=C2=A0=C2=A0 100 =C2=A0 #Minimization 5ps if{1} { minimize=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 10=20 reinitvels=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperatu= re } =C2=A0 run5000000 ;#10 ns =C2=A0 =C2=A0 Thanksin advance=20 ------=_Part_647390_930544065.1633018500405 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear NAMD users,

I have a system which contains one particle (HO) in vacuum. I am trying to si= mulate a gaseous system, it is a part of Heat of vaporization=E2=80=99s calculatio= n.

Langevin is set to off, due to lack of one particle=E2=80=99s ability to maintain sy= stem=E2=80=99s temperature. Run is in NVT.

As the system is trying to represent a gaseous system, simulation box size is larg= e; 500 Ang in each Direction (Simulation speed is 0.072 days/ns, so ~ 17 hours needed to complete the simulation).

When I decrease the size of the simulation box to 50 Ang in each direction, the simulation speed increases (0.0016 days/ns~ 0.4 hour to complete the simula= tion).

As I understood simulation speed can just be affected with number of particles, = due to the number of equations of motion which would be calculated. So how simu= lation box size can affect simulation speed in this case?

Here is my Configuration file:

 

structure x.psf

coordinates x.pdb

set new_run  run-0

outputName ./$new_run/$new_run

set temperature    123.

firsttimestep&nbs= p;     0

paraTypeCharmm&nb= sp;     on

parameters &= nbsp;        ./param/par_all36_li= pid.prm

 

temperature =         $temperature

if {1} {

cellBasisVector1&= nbsp;  500.0   0.0   0.0

cellBasisVector2&= nbsp;     0.0 500.0   0.0=

cellBasisVector3&= nbsp;     0.0   0.0 500.0

cellOrigin &= nbsp;          0.0   0.0   0.0

}

wrapAll &nbs= p;           on

 

# Force-Field Parameters

exclude &nbs= p;           scale= d1-4

1-4scaling &= nbsp;        1.0

cutoff  = ;           =  12.

switching &n= bsp;         on

switchdist &= nbsp;        10.

pairlistdist = ;       13.5

 

 

# Integrator Parameters

timestep &nb= sp;          2.0&= nbsp; ;# 2fs/step

rigidBonds &= nbsp;        all  ;# needed for 2fs steps

nonbondedFreq&nbs= p;      1

fullElectFrequency  2 

stepspercycle&nbs= p;      10

 

 

#PME (for full-system periodic electrostatics)

if {1} {

PME  &n= bsp;            = ;  yes

PMEGridSpacing&nb= sp;     1.0

}

 

# Constant Temperature Control

#langevin &n= bsp;          on&= nbsp;   ;# do langevin dynamics

#langevinDamping&= nbsp;    1     ;# damping coefficient (gamma) of 5/ps

#langevinTemp&nbs= p;       $temperature

 

# Constant Pressure Control (variable volume)

if {0} {

useGroupPressure&= nbsp;     no ;# needed for 2fs steps

useFlexibleCell&n= bsp;      yes  ;# no for water box, yes for membrane

useConstantArea&n= bsp;      yes  ;# no for water box, yes for membrane

 

langevinPiston&nb= sp;       on

langevinPistonTarget  1.01325 ;#  in bar -> 1 atm

langevinPistonPeriod  100.

langevinPistonDecay   50.

langevinPistonTemp    $temperature

}

 

 

restartfreq =        100   &nbs= p;

dcdfreq &nbs= p;          5000=

 

xstFreq &nbs= p;          100<= /span>

outputEnergies&nb= sp;    100

outputPressure&nb= sp;    100

 

# Minimization 5ps

if {1} {

minimize &nb= sp;          10 =

reinitvels &= nbsp;        $temperature<= /span>

}

 

run 5000000 ;#10 ns

 

 

Thanks in advance


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Thu, 30 Sep 2021 21:40:49 +0000 Date: Thu, 30 Sep 2021 21:40:12 +0000 (UTC) From: Fateme Ghadirian To: "namd-l@ks.uiuc.edu" , "Vermaas, Josh" Message-ID: <1034858543.778217.1633038012754@mail.yahoo.com> In-Reply-To: References: <2014701220.647391.1633018500410.ref@mail.yahoo.com> <2014701220.647391.1633018500410@mail.yahoo.com> Subject: Re: namd-l: Simulation Box Size & Simulation speed MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_778216_1940827279.1633038012749" X-Mailer: WebService/1.1.19076 YMailNorrin X-Proofpoint-ORIG-GUID: CxjpaJexd9cKxi_iGxnvXcMEHw4WSnzw X-Proofpoint-GUID: CxjpaJexd9cKxi_iGxnvXcMEHw4WSnzw X-CLX-Shades: MLX X-CLX-Response: 1TFkXGB8dEQpMehcZHxIRCllEF2tfQX1nbkdQaUxnEQpYWBd6X1lGGWZTY2M ZbxEKeE4XekQcHW9FbG1EQ2YRCnlMF2wTWF4YfUZtck4cEQpDSBcHGx0SEQpDWRcHGxwcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcbHXEbBhkedwYYGhoGGgYaBhsaGgYacRoQGncGGgYaBhoGBxwaB hoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF2lSQFpLYE9SThNJYVJDdUNt UkRccklnb2JdHn15RFBdEQpYXBcfBBoEGBkZBRsaBBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NDE2Q TEQpNXBcYHB8RCkxaF3hpTWtrEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk 8Xa0xuRFNeaVh5QmgRCkNaFxwcBBscGQQbEh8EGx4SEQpCXhcbEQpEXhcZEQpCXBcbEQpeThcbE QpCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRCkJFF2V/TxJTHEEFYwVtEQpCThd6RBwd b0VsbURDZhEKQkwXel9ZRhlmU2NjGW8RCkJsF2tBRkBoZHxTHW5CEQpCQBdhAXtBYmxGSFlzUhE KQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcYEQp5QxdgQV1oUEAZGGJMSBEKWUsXEx0fGBEKcG cXbUdha01jGUxTaW4QBxkaEQpwaBdvQ3hoS2BjaGBbSxAHGRoRCnBoF2BOBUQde0RdbUUfEAcZG hEKcGgXYWV4ZVgZZmtTfHsQBxkaEQpwaBdtUEQTYV9SHnN9fRAHGRoRCnBoF3oZUGllG0taZEBA EAcZGhEKcGcXY2JAaBlteFJZRUMQBxkaEQpwbBdpWXgFU3x/E2liSxAHHBoRCm1+FwcbEQpYTRd LESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=257 lowpriorityscore=0 malwarescore=0 suspectscore=0 spamscore=0 impostorscore=0 adultscore=0 phishscore=0 priorityscore=358 mlxscore=0 bulkscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2109300133 domainage_hfrom=9752 X-Spam-Score: 0 X-Spam-OrigSender: fateme.ghadirian@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fateme Ghadirian ------=_Part_778216_1940827279.1633038012749 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable =20 As you said, with PME set to off, Ihave got the same simulation speed for b= oth box sizes. That helped a lot. Thankyou so much. On Thursday, September 30, 2021, 10:27:05 PM GMT+3:30, Vermaas, Josh wrote: =20 =20 Hi Fateme, =20 =C2=A0 =20 The performance variation is almost assuredly PME=E2=80=99s fault, since PM= E decomposes the system into grids to calculate long-range electrostatics. = There are 1000x more grid elements in a cube of side length 500 Angstroms r= elative to one with 50 Angstroms. I=E2=80=99m betting if you turned PME off= , the simulation performance for your NVE systems would be identical regard= less of the box dimension. =20 =C2=A0 =20 -Josh =20 =C2=A0 =20 From: on behalf of Fateme Ghadirian Reply-To: "namd-l@ks.uiuc.edu" , Fateme Ghadirian Date: Thursday, September 30, 2021 at 12:40 PM To: NAMD List Subject: namd-l: Simulation Box Size & Simulation speed =20 =C2=A0 =20 Dear NAMD users, =20 I have a system which contains one particle (HO) in vacuum. I am trying to = simulate a gaseous system, it is a part of Heat of vaporization=E2=80=99s c= alculation. =20 Langevin is set to off, due to lack of one particle=E2=80=99s ability to ma= intain system=E2=80=99s temperature. Run is in NVT. =20 As the system is trying to represent a gaseous system, simulation box size = is large; 500 Ang in each Direction (Simulation speed is 0.072 days/ns, so = ~ 17 hours needed to complete the simulation).=20 =20 When I decrease the size of the simulation box to 50 Ang in each direction,= the simulation speed increases (0.0016 days/ns~ 0.4 hour to complete the s= imulation).=20 =20 As I understood simulation speed can just be affected with number of partic= les, due to the number of equations of motion which would be calculated. So= how simulation box size can affect simulation speed in this case? =20 Here is my Configuration file: =20 =C2=A0 =20 structure x.psf =20 coordinates x.pdb =20 set new_run=C2=A0 run-0 =20 outputName ./$new_run/$new_run =20 set temperature=C2=A0=C2=A0=C2=A0 123. =20 firsttimestep=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 =20 paraTypeCharmm=C2=A0 =C2=A0=C2=A0=C2=A0 on =20 parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ./param/pa= r_all36_lipid.prm =20 =C2=A0 =20 temperature=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperature =20 if {1} { =20 cellBasisVector1=C2=A0=C2=A0 500.0=C2=A0=C2=A0 0.0=C2=A0=C2=A0 0.0 =20 cellBasisVector2=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0 500.0=C2=A0=C2=A0 0.0 =20 cellBasisVector3=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0=C2=A0=C2=A0 0.0 500.0 =20 cellOrigin=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 0.0=C2=A0=C2=A0 0.0=C2=A0=C2=A0 0.0 =20 } =20 wrapAll=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 on =20 =C2=A0 =20 # Force-Field Parameters =20 exclude=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 scaled1-4 =20 1-4scaling=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1.0 =20 cutoff=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A012. =20 switching=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on =20 switchdist=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 10. =20 pairlistdist=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 13.5 =20 =C2=A0 =20 =C2=A0 =20 # Integrator Parameters =20 timestep=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 2.0=C2=A0 ;# 2fs/step =20 rigidBonds=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 all=C2=A0 = ;# needed for 2fs steps =20 nonbondedFreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1 =20 fullElectFrequency=C2=A0 2=C2=A0 =20 stepspercycle=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 10 =20 =C2=A0 =20 =C2=A0 =20 #PME (for full-system periodic electrostatics) =20 if {1} { =20 PME=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 yes =20 PMEGridSpacing=C2=A0 =C2=A0=C2=A0=C2=A0 1.0 =20 } =20 =C2=A0 =20 # Constant Temperature Control =20 #langevin=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= on=C2=A0=C2=A0=C2=A0 ;# do langevin dynamics =20 #langevinDamping=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0 ;# dampi= ng coefficient (gamma) of 5/ps =20 #langevinTemp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperature =20 =C2=A0 =20 # Constant Pressure Control (variable volume) =20 if {0} { =20 useGroupPressure=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 no ;# needed for 2fs steps =20 useFlexibleCell=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 yes=C2=A0 ;# no for wat= er box, yes for membrane =20 useConstantArea=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 yes=C2=A0 ;# no for wat= er box, yes for membrane =20 =C2=A0 =20 langevinPiston=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on =20 langevinPistonTarget=C2=A0 1.01325 ;#=C2=A0 in bar -> 1 atm =20 langevinPistonPeriod=C2=A0 100. =20 langevinPistonDecay=C2=A0=C2=A0 50. =20 langevinPistonTemp=C2=A0=C2=A0=C2=A0 $temperature =20 } =20 =C2=A0 =20 =C2=A0 =20 restartfreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 100=C2=A0=C2=A0=C2=A0= =C2=A0 =20 dcdfreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 5= 000 =20 =C2=A0 =20 xstFreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1= 00 =20 outputEnergies=C2=A0=C2=A0=C2=A0=C2=A0 100 =20 outputPressure=C2=A0=C2=A0=C2=A0=C2=A0 100 =20 =C2=A0 =20 # Minimization 5ps =20 if {1} { =20 minimize=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 10 =20 reinitvels=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperatu= re =20 } =20 =C2=A0 =20 run 5000000 ;#10 ns =20 =C2=A0 =20 =C2=A0 =20 Thanks in advance =20 =C2=A0 =20 ------=_Part_778216_1940827279.1633038012749 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

As you said, with PME set to off, I have got the same simulation speed for both box sizes. That helped a lot. T= hank you so much.


=20
=20
On Thursday, September 30, 2021, 10:27:05 PM GMT+3:30, = Vermaas, Josh <vermaasj@msu.edu> wrote:


Hi Fateme,

=20

 

=20

The performance variation is almost ass= uredly PME=E2=80=99s fault, since PME decomposes the system into grids to c= alculate long-range electrostatics. There are 1000x more grid elements in a= cube of side length 500 Angstroms relative to one with 50 Angstroms. I=E2=80=99m betting if you turned PME off, the simulation pe= rformance for your NVE systems would be identical regardless of the box dim= ension.

=20

 

=20

-Josh

=20

 

=20

From: &l= t;owner-namd-l@ks.uiuc.edu> on behalf of Fateme Ghadirian <fateme.gha= dirian@REMOVE_yahoo.com>
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, Fateme Gh= adirian <fateme.ghadirian@yahoo.com>
Date: Thursday, September 30, 2021 at 12:40 PM
To: NAMD List <namd-l@ks.uiuc.edu>
Subject: namd-l: Simulation Box Size & Simulation speed
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Dear NAMD users,

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I have a system wh= ich contains one particle (HO) in vacuum. I am trying to simulate a gaseous= system, it is a part of Heat of vaporization=E2=80=99s calculation.

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Langevin is set to= off, due to lack of one particle=E2=80=99s ability to maintain system=E2= =80=99s temperature. Run is in NVT.

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As the system is t= rying to represent a gaseous system, simulation box size is large; 500 Ang = in each Direction (Simulation speed is 0.072 days/ns, so ~ 17 hours needed to complete the simulation).

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When I decrease th= e size of the simulation box to 50 Ang in each direction, the simulation sp= eed increases (0.0016 days/ns~ 0.4 hour to complete the simulation).

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As I understood si= mulation speed can just be affected with number of particles, due to the nu= mber of equations of motion which would be calculated. So how simulation box size can affect simulation speed in t= his case?

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Here is my Configu= ration file:

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structure x.psf

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coordinates x.pdb<= /span>

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set new_run  = run-0

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outputName ./$new_= run/$new_run

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set temperature&nb= sp;   123.

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firsttimestep = ;     0

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paraTypeCharmm&nbs= p;     on

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parameters &n= bsp;        ./param/par_all36_lipid.prm<= /span>

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temperature &= nbsp;       $temperature

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if {1} {

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cellBasisVector1&n= bsp;  500.0   0.0   0.0

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cellBasisVector2&n= bsp;     0.0 500.0   0.0

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cellBasisVector3&n= bsp;     0.0   0.0 500.0

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cellOrigin &n= bsp;          0.0   = 0.0   0.0

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}

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wrapAll  = ;           on

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# Force-Field Para= meters

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exclude  = ;           scaled1-4

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1-4scaling &n= bsp;        1.0

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cutoff  =             12.

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switching &nb= sp;         on

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switchdist &n= bsp;        10.

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pairlistdist =        13.5

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# Integrator Param= eters

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timestep &nbs= p;          2.0  ;# 2fs/s= tep<= /p>=20

rigidBonds &n= bsp;        all  ;# needed for 2fs = steps

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nonbondedFreq = ;      1

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fullElectFrequency=   2 

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stepspercycle = ;      10

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#PME (for full-sys= tem periodic electrostatics)

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if {1} {

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PME  &nb= sp;            =   yes<= /span>

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PMEGridSpacing&nbs= p;     1.0

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}

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# Constant Tempera= ture Control

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#langevin &nb= sp;          on  &nb= sp; ;# do langevin dynamics

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#langevinDamping&n= bsp;    1     ;# damping coefficient (ga= mma) of 5/ps

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#langevinTemp = ;       $temperature

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# Constant Pressur= e Control (variable volume)

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if {0} {

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useGroupPressure&n= bsp;     no ;# needed for 2fs steps

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useFlexibleCell&nb= sp;      yes  ;# no for water box, yes for me= mbrane

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useConstantArea&nb= sp;      yes  ;# no for water box, yes for me= mbrane

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langevinPiston&nbs= p;       on

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langevinPistonTarg= et  1.01325 ;#  in bar -> 1 atm

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langevinPistonPeri= od  100.

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langevinPistonDeca= y   50.

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langevinPistonTemp=     $temperature

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}

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restartfreq &= nbsp;      100    

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dcdfreq  = ;          5000

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xstFreq  = ;          100

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outputEnergies&nbs= p;    100

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outputPressure&nbs= p;    100

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# Minimization 5ps=

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if {1} {

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minimize &nbs= p;          10

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reinitvels &n= bsp;        $temperature

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}

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run 5000000 ;#10 n= s=20

 

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Thanks in advance

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Sat, 2 Oct 2021 02:27:03 +0000 Date: Sat, 2 Oct 2021 02:25:01 +0000 (UTC) From: Vidhya Sankar To: NAMD List Message-ID: <1241875308.919161.1633141501335@mail.yahoo.com> Subject: namd-l: Salt bridge selection MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_919160_46058131.1633141501334" References: <1241875308.919161.1633141501335.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19076 YMailNorrin X-CLX-Shades: MLX X-Proofpoint-GUID: 8pvDC1IsjvxTZQnJWpVevDx3aFCNJxBt X-CLX-Response: 1TFkXGRsZEQpMehcZGxoRCllEF2BEU0QYc2dAW19tEQpYWBdmYWITYW1ia0l cQhEKeE4XekQcHW9FbG1EQ2YRCnlMF2lDHk9vYUJDBUQdEQpDSBcHGxgSEQpDWRcHGxofEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcbE3EbBhkddwYYGhoGGgYaBhMeBhpxGhAadwYaBhoGGgYaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOFxJaXG5pG2NZQFxSfnB7RGB9WnxP XG5SGUtsaWRgUmheEQpYXBcfBBoEGBkZBRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc0B9TXwRCk1 cFxsSExEKTFoXaGlra2sRCkxGF29ra29raxEKQk8XYkkfelxYH1t5Gx4RCkNaFxsaHAQbGgQYHh oEGxodEQpCXhcbEQpCXBcbEQpeThcbEQpCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRC kJFF3oZbUNbRV9oaX1lEQpCThd6RBwdb0VsbURDZhEKQkwXZmFiE2FtYmtJXEIRCkJsF2sdH3AZ bGlFb3hcEQpCQBdgTn9kRGxaBUJ5fxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcbEQp5Qxd ta0NvYXsFEnxpRREKWUsXEx0fHhEKcGgXaG59YUVzWAVjfH0QBxkaEQpwaBdme0Z5RGNsemMYaB AHGRoRCnBoF28ffmhuG1ocE34YEAcZGhEKcGgXbEtzY0BhWm9GE2sQBxkaEQpwbBdkb05cRn5Ta HxZWhAHGRoRCnBMF2YFYRxHHUZheUN/EAcZGhEKbX4XBxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: 8pvDC1IsjvxTZQnJWpVevDx3aFCNJxBt X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 clxscore=313 priorityscore=310 suspectscore=0 malwarescore=0 impostorscore=0 bulkscore=0 lowpriorityscore=0 mlxscore=0 phishscore=0 mlxlogscore=345 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110020014 domainage_hfrom=9754 X-Spam-Score: 0 X-Spam-OrigSender: vidhyasankar7928@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vidhya Sankar ------=_Part_919160_46058131.1633141501334 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Namd users=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0I would like to study salt= bridge interaction between DNA and Silicon nitride . Is it possible=C2=A0 = by salt bridge plugin available in=C2=A0 namd ?=C2=A0 =C2=A0.=C2=A0 i think= it is suitable for protein only otherwise can i select=C2=A0 nucleic acid = in selection tab. yet how=C2=A0 to select my Silicon nitride=C2=A0 ? It is = highly helpful if somebody tell me the way through which i need to select b= oth DNA and Silicon nitride With regardsS.Vidhya sankar ------=_Part_919160_46058131.1633141501334 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Dear Namd users
         I would like to study salt bridge interaction between DNA and Silicon nitride . Is it possible  by salt bridge plugin available in  namd ?   .  i think it is suitable for protein only otherwise can i select  nucleic acid in selection tab. yet how  to select my Silicon nitride  ? It is highly helpful if somebody tell me the way through which i need to select both DNA and Silicon nitride

With regards
S.Vidhya sankar
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Files which may include minimum 10 ns to maximum 50 ns trajectory. Plz guide Thanks in anticipataion. Regards Asma Tariq ------=_Part_1091207_2079409458.1633172531065 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Hello everyone,

Here is a question. if i need to send my dcd files to someone via email or another online source, how can i? Files which may include minimum 10 ns to maximum 50 ns trajectory. Plz guide

Thanks in anticipataion.

Regards

Asma Tariq
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Sat, 02 Oct 2021 04:17:14 -0700 (PDT) MIME-Version: 1.0 References: <1667679274.1091208.1633172531066.ref@mail.yahoo.com> <1667679274.1091208.1633172531066@mail.yahoo.com> In-Reply-To: <1667679274.1091208.1633172531066@mail.yahoo.com> From: Hemanth Haridas Date: Sat, 2 Oct 2021 16:43:20 +0530 Message-ID: Subject: Re: namd-l: how can email dcd files To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000705aee05cd5cd206" X-CLOUD-SEC-AV-Sent: true X-CLOUD-SEC-AV-Info: iitgn,google_mail,monitor X-Gm-Spam: 0 X-Gm-Phishy: 0 X-CLX-Response: 1TFkXGxMaEQpMehcaEQpZRBd6TGFZQlJpY2BGHxEKWFgXaUVcWHhmZhsYXxk RCnhOF2dpW2ZtYl9AGwFjEQp5TBdkbEseZX4TYmxkfhEKQ0gXBxkSEQpDWRcHGBwTEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF2x6HVpZYGlIc38eZHtDGH5GRnsdGR9JYBkbWx1ZRmtEEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhsQGx4aHxoRCl5ZF3NAT3hyEQpNXBcbHRoRCkxaF3hpTU1rEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XZkwfTWltQUAfE3MRCkNaFxgaEwQSHwQbHB0EGxIbEQ pCXhcbEQpCRRdiR2BvcgFcWlwdbREKQk4XZ2lbZm1iX0AbAWMRCkJMF2lFXFh4ZmYbGF8ZEQpCb BdmR2kFZXhSH2x6ThEKQkAXZnt4BRlHHG1gWloRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcY EQp5QxdkQxlPBVJ+U2ASHhEKWUsXHhwSEhEKcGgXbxJJTE0SSRhdZB8QGRoRCnBoF2sbSUdESWJ cZHpQEBkaEQpwaBdvHWJzZm5EUGtfRhAZGhEKcGgXaWEZQGZ9ZhNkYm0QGRoRCnBoF257RmUZZ3 hubB17EBkaEQpwbBdnZAVneBxIS29TcBAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: FP7psJCbYU4NQi2TllQ735cJ31q7slAn X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: FP7psJCbYU4NQi2TllQ735cJ31q7slAn X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 clxscore=190 lowpriorityscore=0 phishscore=0 bulkscore=0 mlxscore=0 spamscore=0 mlxlogscore=493 malwarescore=0 adultscore=0 suspectscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110020082 domainage_hfrom=4688 X-Spam-Score: 0 X-Spam-OrigSender: hemanth.h@iitgn.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hemanth Haridas --000000000000705aee05cd5cd206 Content-Type: text/plain; charset="UTF-8" Asma, The easiest way out for you is to upload the DCD file and the psf file into a file-sharing platform (like Google Drive), and share the link to the concerned user. Best, Hemanth On Sat, Oct 2, 2021 at 4:36 PM Asmi Mahmood wrote: > Hello everyone, > > Here is a question. if i need to send my dcd files to someone via email or > another online source, how can i? Files which may include minimum 10 ns to > maximum 50 ns trajectory. Plz guide > > Thanks in anticipataion. > > Regards > > Asma Tariq > -- *Hemanth H 18310019* Research Scholar IIT Gandhinagar --000000000000705aee05cd5cd206 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Asma,

The easiest way ou= t for you is to upload the DCD file and the psf file into a file-sharing pl= atform (like Google Drive), and share the link to the concerned user.
=

Best,
Hemanth

On Sat, Oct 2, 2021 = at 4:36 PM Asmi Mahmood <asmi_mahmood@remove_yahoo.com> wrote:
Hello = everyone,

Here is a questi= on. if i need to send my dcd files to someone via email or another online s= ource, how can i? Files which may include minimum 10 ns to maximum 50 ns tr= ajectory. Plz guide

Th= anks in anticipataion.

Reg= ards

Asma Tariq


--
Hemanth H 18310019
Research Scholar
IIT Gandhinagar
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boundary="=_1e39af26-127b-4954-a994-1d2410aa1955" X-Mailer: Zimbra 8.8.15_GA_3955 (ZimbraWebClient - GC76 (Linux)/8.8.15_GA_3953) Thread-Topic: namd-l: how can email dcd files Thread-Index: U35ivXGTjBHARkIei6MWAl7IF11vpA== X-Proofpoint-ORIG-GUID: oZiENQcoA8SnzmHFiyUyt5mNU-qwvx_N X-Proofpoint-GUID: oZiENQcoA8SnzmHFiyUyt5mNU-qwvx_N X-CLX-Response: 1TFkXGx0dEQpMehcaEQpZRBdpYmFJT24SeR9+bBEKWFgXbRNBQVpBREMTfXg RCnhOF2hfemFGAWJAQU95EQp5TBdrfGxrbEN6HkdlGxEKQ0gXHREKQ1kXBxgdGxEKQ0kXGgQaGh oRCllNF2dmchEKWUkXGnEaEBp3BhsfHXEZHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZX k9OEQpDThdFcENvZHtJRWsSeURQR2JsQ1N/U14fR2R/B1tdXFJ1ZBEKWFwXHwQaBBgZGQUbGgQb GhoEHhIEGBkQGx4aHxoRCl5ZF3NAT1JjEQpNXBceGxEKTFoXeGlNTU0RCkVZF29rEQpMXxd6BQU FBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiBWhDQExaQEVyThEKQ1oXEx4EGxIeBBsdHAQbGxsRCk JeFxsRCkReFxgRCkJcFxsRCkJLF3oebVtLfEdfYgV6EQpCSRdoX3phRgFiQEFPeREKQkUXYR0eZ mtyQVIZGXgRCkJOF2hfemFGAWJAQU95EQpCTBdtE0FBWkFEQxN9eBEKQmwXYWQZZ11CGUV8a3gR CkJAF2Z7eAUZRxxtYFpaEQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXZEMZTwVSflNgEh4RCll LFwcZEQpwZxdjGmNHQX9hRngZfBAaEQpwaBdhYUkBXX94b0VgXBAaEQpwaBdpYhkYHEVsYRseHx AaEQpwaBdoWUFCW21/bGxvZBAaEQpwaBdiZ0hnS25vTB1aUBAaEQpwaBdlQUhaaXJTeWx5QhAaE QpwfRdjc3tNBV0dAXhBcBAaEQpwZxduXHweAVwFQGBFUBAaEQpwfRdpGmVOXEgTYEd5RhAaEQpw fxdvRGFQEhN/GxwSfhAaBB8SEQpwXxdiGBoYH3hHTHt7exAbGxoRCnBsF29gf215TEFEa05OEBo RCm1+FxoRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 malwarescore=0 mlxlogscore=777 suspectscore=0 mlxscore=0 phishscore=0 bulkscore=0 lowpriorityscore=0 spamscore=0 impostorscore=0 adultscore=0 clxscore=177 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110020085 X-Spam-Score: 0 X-Spam-OrigSender: shekaari@email.kntu.ac.ir X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashkan Shekaari --=_1e39af26-127b-4954-a994-1d2410aa1955 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Use scp commands...=20 ---=20 ,Best=20 Ashkan Shekaari=20 PhD Candidate in Solid State Physics=20 Department of Physics=20 K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:she= kaari@email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.goog= le.com/citations?hl=3Den&user=3DLDzbXB4AAAAJ&view_op=3Dlist_works&sortby=3D= pubdate__;!!DZ3fjg!u8HJFAl-C35A6rCvMlcimqtccgdmoCiU5xs4vhx8sWJyre7wYhbSAvq2= igGUViY0VA$ ]=20 From: "Asmi Mahmood" =20 To: "namd-l" =20 Sent: Saturday, October 2, 2021 2:32:11 PM=20 Subject: namd-l: how can email dcd files=20 Hello everyone,=20 Here is a question. if i need to send my dcd files to someone via email or = another online source, how can i? Files which may include minimum 10 ns to = maximum 50 ns trajectory. Plz guide=20 Thanks in anticipataion.=20 Regards=20 Asma Tariq=20 --=_1e39af26-127b-4954-a994-1d2410aa1955 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Use scp commands...

---
,Best
=
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology,=  Tehran, 15875-4416, Iran<= /font>


From: "Asmi Mahmood" <asmi_mahmood@REMOVE_yahoo.com>
To: "namd-= l" <namd-l@ks.uiuc.edu>
Sent: Saturday, October 2, 2021 2:3= 2:11 PM
Subject: namd-l: how can email dcd files
Hello everyone,

Here is a question. if i need to s= end my dcd files to someone via email or another online source, how can i? = Files which may include minimum 10 ns to maximum 50 ns trajectory. Plz guid= e

Thanks in anticipata= ion.

Regards

=
Asma Tariq

=
= --=_1e39af26-127b-4954-a994-1d2410aa1955-- From owner-namd-l@halifax.ks.uiuc.edu Sun Oct 3 09:59:07 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 193Ex7V1020473; Sun, 3 Oct 2021 09:59:07 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 193Ex7EV020472; Sun, 3 Oct 2021 09:59:07 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 193Ex6D3020461; Sun, 3 Oct 2021 09:59:06 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 193Ex6kw020457; Sun, 3 Oct 2021 09:59:06 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 193Ewtt9020387 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000fbec7b05cd7408dd" X-CLX-Shades: MLX X-Proofpoint-GUID: N8uMEqqH7m1JVNXSeVBtr2itUTXB1sM4 X-Proofpoint-ORIG-GUID: N8uMEqqH7m1JVNXSeVBtr2itUTXB1sM4 X-CLX-Response: 1TFkXGxwSEQpMehcZGBwRCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHGxscEQpDWRcHGxkTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ScRgTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2QSX2dvW1tiHUcbYHxkcnlPfGheWBhDXn9+cmgbWWceEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc0AYRGERCk1cFxkdHhEKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8XbW1STWtsW29IbG0RCkNaFxgaEwQSHwQbHBwEGxIYEQpCXhcbEQpEXhcYEQpCXBcbEQ peThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2hacBhJH2Z4HkBeEQpCT hdjU2NrexNYfhpfXhEKQkwXbB9eWVpuTGFgW0ERCkJsF29CaX9uTltSGXgaEQpCQBdmclBHHRtl R0ZrHREKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF29GZBlEH2NibWR8EQpwaBdsWRNYHnpLSEt 5ExAZGhEKcGgXYm9AYQVbS2IfH00QGRoRCnBoF3p+eWtAax94TExvEBkaEQpwaBdvQG4TQmhgfE wTaRAZGhEKcGgXb1JCHUdIUBhefGkQGRoRCnBsF2d4c3NCR1xbfUZLEBkaEQptfhcaEQpYTRdLE SA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxscore=0 adultscore=0 clxscore=168 malwarescore=0 priorityscore=326 spamscore=0 bulkscore=0 suspectscore=0 lowpriorityscore=0 impostorscore=0 mlxlogscore=772 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110030108 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000fbec7b05cd7408dd Content-Type: text/plain; charset="UTF-8" Dear Colleagues, we want to calculate binding free energy of Ligand-Protein complex. After completing QM/MM run we got following energies for complex: ----------here Ligand@B3LYP/6-31G* and protein@UFF=qeq ------------- UFF calculation of energy. Energy= 0.453152500 NIter= 0. Dipole moment= -1.265215 2.913698 -3.244704 ONIOM: saving gridpoint 1 ONIOM: restoring gridpoint 3 ONIOM: calculating energy. ONIOM: gridpoint 1 method: low system: model energy: 0.453152500428 ONIOM: gridpoint 2 method: high system: model energy: -1573.304203057569 ONIOM: gridpoint 3 method: low system: real energy: 23.105333051841 ONIOM: extrapolated energy = -1550.652022506156 ONIOM: calculating electric field derivatives. ONIOM: Integrating ONIOM file 4 number 619 ONIOM: Dipole = 3.51466451D+00 7.85225957D+00 6.59929946D+00 ONIOM: Dipole moment (Debye): X= 8.9334 Y= 19.9585 Z= 16.7737 Tot= 27.5591 ------------------------ My question is how to get binding free energy from these values? or is there need to run ligand and protein separately on QM and MM levels also as in complex? Any information on working equations for QM?MM binding free energy calculation will be greatly appreciated!! Dr.Mi --000000000000fbec7b05cd7408dd Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
=C2=A0we want to calculate= binding free energy of Ligand-Protein complex. After completing QM/MM run = we got following energies for complex:
----------here Ligand@B3LY= P/6-31G* and protein@UFF=3Dqeq -------------
UFF calculation= of energy.
=C2=A0Energy=3D =C2=A0 =C2=A00.453152500 =C2=A0 =C2=A0 NIter= =3D =C2=A0 0.
=C2=A0Dipole moment=3D =C2=A0 =C2=A0 =C2=A0-1.265215 =C2= =A0 =C2=A0 =C2=A0 2.913698 =C2=A0 =C2=A0 =C2=A0-3.244704
=C2=A0ONIOM: sa= ving gridpoint =C2=A01
=C2=A0ONIOM: restoring gridpoint =C2=A03
=C2= =A0ONIOM: calculating energy.
=C2=A0ONIOM: gridpoint =C2=A01 method: =C2= =A0low =C2=A0 system: =C2=A0model energy: =C2=A0 =C2=A0 0.453152500428
= =C2=A0ONIOM: gridpoint =C2=A02 method: =C2=A0high =C2=A0system: =C2=A0model= energy: -1573.304203057569
=C2=A0ONIOM: gridpoint =C2=A03 method: =C2= =A0low =C2=A0 system: =C2=A0real =C2=A0energy: =C2=A0 =C2=A023.105333051841=
=C2=A0ONIOM: extrapolated energy =3D =C2=A0 -1550.652022506156
=C2= =A0ONIOM: calculating electric field derivatives.
=C2=A0ONIOM: Integrati= ng ONIOM file =C2=A04 number =C2=A0 619
=C2=A0ONIOM: Dipole =C2=A0 =C2= =A0 =C2=A0 =C2=A0=3D 3.51466451D+00 7.85225957D+00 6.59929946D+00
=C2=A0= ONIOM: Dipole moment (Debye):
=C2=A0 =C2=A0 X=3D =C2=A0 =C2=A0 8.9334 = =C2=A0 =C2=A0Y=3D =C2=A0 =C2=A019.9585 =C2=A0 =C2=A0Z=3D =C2=A0 =C2=A016.77= 37 =C2=A0Tot=3D =C2=A0 =C2=A027.5591
------------------------=
My question is how to get binding free energy from these val= ues? or is there need to run ligand and protein separately on QM and MM lev= els also as in complex?
Any information on working equations for = QM?MM binding free energy calculation will be greatly appreciated!!

Dr.Mi
--000000000000fbec7b05cd7408dd-- From owner-namd-l@halifax.ks.uiuc.edu Mon Oct 4 14:34:35 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 194JYZIi013196; Mon, 4 Oct 2021 14:34:35 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 194JYYux013158; Mon, 4 Oct 2021 14:34:34 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 194JYPMj012963; Mon, 4 Oct 2021 14:34:25 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 194JYPOJ012962; Mon, 4 Oct 2021 14:34:25 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 194JYCnJ012871 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000406ee905cd8bff22" X-Proofpoint-GUID: qXeXY3bp6ei4sPhicYm-_ZGMM_ijl-x0 X-CLX-Response: 1TFkXGxwbEQpMehcZHxkRCllEF3pfQXkSS0tBQh9QEQpYWBdgHV1gS2lyR14 ZeREKeE4XY1Nja3sTWH4aX14RCnlMF2xtQ0dwUmNGG19sEQpDSBcHGx0YEQpDWRcHGxIZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4bcR8bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1tyT3JzGUhaHE9DHll6QkNJc0cHdXBtZ2d1Q0BGB1IaEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc0F6XGURCk1cFxkcGxEKTFoXeGtNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trYmtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbEhoRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXa0BwG2d7TmEYeH4RCkJOF2NTY2t7E1h+Gl9eEQpCTBdgHV1gS2lyR14ZeREKQmwX YmNBHWFQRW0SEhMRCkJAF2hfbn9HfAFHa1x4EQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXem5 tH15CYgVaEhsRCnBnF2tNTXxOTF96Rx5NEB0aEQpwaBdtZk0YG1sSa1NoWBAcGhEKcGgXekNsbE ZDXmYfGEkQGRoRCnBoF2xBHnx9TGRmXUFyEBkaEQpwaBdiAU9GWEBJUBtHRxAbGx8RCnBoF2lZZ 2VcSWhTc3xmEBkaEQpwfRdubklHWmtJaU5PWxAeEhEKcGcXZWRtBX5IR38SXR8QGRoRCnB/F2VY chgdSRheRml8EBseHxEKcF8XZnBIXEB5AUEeTxIQHhIRCnBsF2xtWB1nXkJ/YWJaEBkaEQptfhc aEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: qXeXY3bp6ei4sPhicYm-_ZGMM_ijl-x0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 mlxlogscore=999 bulkscore=0 priorityscore=353 clxscore=161 impostorscore=0 adultscore=0 phishscore=0 spamscore=0 mlxscore=0 suspectscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110040132 X-Spam-Score: 0 X-Spam-OrigSender: eackad@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Dr. Eddie" --000000000000406ee905cd8bff22 Content-Type: text/plain; charset="UTF-8" Has this been added in any subsequent versions (2.15 or the nightly-build)? Thanks! Eddie On Tue, Sep 15, 2020 at 12:07 PM David Hardy wrote: > Dear Hemanth, > > Sorry, we do not yet have the NB-Thole terms ported to CUDA. It is on our > "to do" list. > > Best regards, > Dave > > -- > David J. Hardy, Ph.D. > Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews Ave., Urbana, IL 61801 > dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > > On Sep 5, 2020, at 2:15 AM, HEMANTH H wrote: > > Dear Community members, > > I found that drudeNbthole is not supported on the CUDA version of NAMD, > but I am in a position that requires the use of drudeNbthole for my > simulations. I do not want to lose out on the performance gain provided by > the gpu versions of NAMD over the cpu versions, but the present scenario > calls for a migration to the cpu code. Is there a version of NAMD with CUDA > support that has drudeNbthole enabled? > > Thanks in advance > Hemanth > -- > *Hemanth H 18310019* > Research Scholar > IIT Gandhinagar > > > -- Eddie --000000000000406ee905cd8bff22 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Has this been added in any subsequent versions (2.15 or th= e nightly-build)?
Thanks!
Eddie

On Tue, Sep 15, 2020 at = 12:07 PM David Hardy <dhardy@ks.ui= uc.edu> wrote:
Dear Hemanth,

Sorry, we do not yet have the NB-Thole terms ported to CUDA. It is on= our "to do" list.

Best regards,
Dave

--
D= avid J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
40= 5 N. Mathews Ave., Urbana, IL 61801

On Sep 5, 2020, at 2:15 AM, HEMANTH= H <hemanth.h= @iitgn.ac.in> wrote:

Dear Community members,

I f= ound that drudeNbthole is not supported on the CUDA versio= n of NAMD, but I am in a position that requires the use of drudeNbthole for my simulations. I do not want to lose out on the performa= nce gain provided by the gpu versions of NAMD over the cpu versions, but th= e present scenario calls for a migration to the cpu code. Is there a versio= n of NAMD with CUDA support that has drudeNbthole enabled?

Thanks in advance
Hemanth
--
Hem= anth H 18310019
Research Scholar
IIT Gandhinaga= r



--
Eddie
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Wed, 6 Oct 2021 07:24:18 +0000 Date: Wed, 6 Oct 2021 07:24:16 +0000 (UTC) From: Alexei Rossokhin To: "namd-l@ks.uiuc.edu" Message-ID: <176977769.140844.1633505056471@mail.yahoo.com> Subject: namd-l: NAMD Cuda on more than one node MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_140843_410481918.1633505056470" References: <176977769.140844.1633505056471.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19116 YMailNorrin X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: WpsgB9qzhLalxZ7cB6zOc6m0PZR9ZNzh X-CLX-Response: 1TFkXHBIRCkx6FxkZGhEKWUQXYXBQX3NaQ1oef1sRClhYF2EbYnATT11sfFM ZEQp4Thd6RBwdb0VsbURDZhEKeUwXZWJIGHMcREBwbHoRCkNIFwcbGB0RCkNZFwcYGRIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYeEnEYEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF31aWU1oE1tQQmZLRlJwHUloHFBlSRxHGnpweBNwZFBCEQpYXBcfBBoEGBkZBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NBXGUBEQpNXBcYHx8RCkxaF2xpTWtrEQpMRhdva2tva2s RCkJPF2tMbkRTXmlYeUJoEQpDWhccHAQbHBkEGxIcBBgaHhEKQl4XGxEKRF4XGBEKQlwXGxEKXk 4XGxEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmEQpCRRdmHAFtc1xTHnpDHREKQk4Xe kQcHW9FbG1EQ2YRCkJMF2EbYnATT11sfFMZEQpCbBdrE2JoWGtCXX9fHhEKQkAXYR0bRR1ZQB9L SGYRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdsbBhzaFlMTmtzHxEKWUsXEx0fEhE KcGgXelhscE5uZ05cZwUQGRoRCnBoF2R/W0ZtRhJkbXpCEBkaEQpwaBdtbnhvG2wTUm9tbhAZGh EKcGwXbGNJSHlCekRjBWYQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: WpsgB9qzhLalxZ7cB6zOc6m0PZR9ZNzh X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=68 phishscore=0 priorityscore=330 lowpriorityscore=0 mlxscore=0 adultscore=0 spamscore=0 malwarescore=0 impostorscore=0 mlxlogscore=596 bulkscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110060045 domainage_hfrom=9758 X-Spam-Score: 0 X-Spam-OrigSender: alrossokhin@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alexei Rossokhin ------=_Part_140843_410481918.1633505056470 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello NAMD users, I have=C2=A0 NAMD build=C2=A0 NAMD=C2=A0 2.11=C2=A0 Linux-x86_64-verbs-smp-= CUDA. However, I can properly run MD simulations only on one cluster node. Can anyone comment on how to run namd tasks on more than one Linux node.= =20 Alexey ------=_Part_140843_410481918.1633505056470 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello NAMD users,
=

I have&nb= sp; NAMD build  NAMD  2.11  Linux-x86_64-verbs-smp-CUD= A. However, I can properly run MD simulations only on one cluster node.
=
Can any= one comment on how to run namd tasks on more than one Linux node.

Alexey

<= /span>

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boundary="000000000000016d8805cdc22701" X-Proofpoint-GUID: HOiCt1QbzP_QdtB_c55HH8SNiG9slyIh X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxsYEQpMehcZHxkRCllEF2huZEZLHxxjG3xuEQpYWBdlXm9TWn5EXUR CYREKeE4XY1Nja3sTWH4aX14RCnlMF2Z/TX5DWXp4GhloEQpDSBcHGxwdEQpDWRcHGB0fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcZGHEbBhwZdwYdEgYaBhoGEhgGGnEaEBp3BhoGBx8aBhoGBxkaB hoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF2JlQ2leG3tIUHp1e05eaHVJ Hx9iYhJ5ZENtE1lGU2NCEQpYXBcfBBoEGBkZBRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc0ZjQkI RCk1cFxscHhEKTFoXfGlNa2sRCkVZF28RCkxfF3oFBQUFBQUFBQVDEQpMRhdva2tra2sRCkJPF2 1tUk1rbFtvSGxtEQpDWhcYGhMEEh8EGxwcBBsdGBEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja 3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdhBWxaTWNOQVMYHxEKQk4XY1Nja3sTWH4aX14R CkJMF2Veb1NafkRdREJhEQpCbBdlEhtbRnJTAV5oTBEKQkAXZ19/HGZbb3xJQm4RCkJYF2dzZXN AbmFhTF1iEQpNXhcHGxEKWlgXGBEKeUMXbRMTW0BySRlBfWsRCnBoF2trelNIel1zT2NwEAcZGh EKcGgXaEVLaHB5GmBFTQEQBxkaEQpwaBdsQWViZB5eWkdsQxAHGRoRCnBoF2VaZXtmUGFcb0FtE AcZGhEKcGgXYBhrTUtuXEwBW08QBxkaEQpwbBdvZn1YQENoRVMdTxAHGRoRCm1+FwcbEQpYTRdL ESA= X-Proofpoint-ORIG-GUID: HOiCt1QbzP_QdtB_c55HH8SNiG9slyIh X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 lowpriorityscore=0 priorityscore=353 malwarescore=0 mlxscore=0 suspectscore=0 bulkscore=0 adultscore=0 clxscore=112 mlxlogscore=534 phishscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110070083 X-Spam-Score: 0 X-Spam-OrigSender: premabasaknanda@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, PREMANANDA BASAK --000000000000016d8805cdc22701 Content-Type: text/plain; charset="UTF-8" I have run MD simulation on a fibril structure consisting of ten monomers in a tetragonal box using PBC in NAMD. When I visualize the DCD using VMD, I see that one or fewer monomers are jumping on the opposite side of the box. I believe that this is an issue of the PBC and which automatically puts the images in the central box if any monomer is out of the central box from any side. I wish to know the command to post-process the DCDs to reset the entire fibril into its original assembly, i.e. reversing the process of re-centering. Please help. --000000000000016d8805cdc22701 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

I have run MD= simulation on a fibril structure consisting of ten monomers in a tetragona= l box using PBC in NAMD. When I visualize the DCD using VMD, I see that one= or fewer monomers are jumping on the opposite side of the box. I believe t= hat this is an issue of the PBC and which automatically puts the images in = the central box if any monomer is out of the central box from any side. I w= ish to know the command to post-process the DCDs to reset the entire fibril= into its original assembly, i.e. reversing the process of re-centering.

Please help.


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charset="UTF-8" Use - pbc unwrap -all pbc wrap -compound fragment -center com -centersel "not water and not ion" -all animate write dcd wrapped.dcd On Thu, 7 Oct 2021 at 17:43, PREMANANDA BASAK wrote: > I have run MD simulation on a fibril structure consisting of ten monomers > in a tetragonal box using PBC in NAMD. When I visualize the DCD using VMD, > I see that one or fewer monomers are jumping on the opposite side of the > box. I believe that this is an issue of the PBC and which automatically > puts the images in the central box if any monomer is out of the central box > from any side. I wish to know the command to post-process the DCDs to reset > the entire fibril into its original assembly, i.e. reversing the process of > re-centering. > > Please help. > > -- Diship Srivastava JRF Department of Chemistry IIT(ISM) - Dhanbad India --0000000000000d242805cdc2f440 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Use -=C2=A0
pbc unwrap -all
pbc wrap -compound frag= ment -center com -centersel "not water and not ion" =C2=A0-allanimate write dcd wrapped.dcd

On Thu, 7 Oct 2021 at 17:43, PREMAN= ANDA BASAK <premabasaknanda= @gmail.com> wrote:

I = have run MD simulation on a fibril structure consisting of ten monomers in = a tetragonal box using PBC in NAMD. When I visualize the DCD using VMD, I s= ee that one or fewer monomers are jumping on the opposite side of the box. = I believe that this is an issue of the PBC and which automatically puts the= images in the central box if any monomer is out of the central box from an= y side. I wish to know the command to post-process the DCDs to reset the en= tire fibril into its original assembly, i.e. reversing the process of re-ce= ntering.

Please help.



--
Diship Srivastava=C2=A0
JRF= =C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
=
India
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boundary="0000000000001de20305ce1261be" X-CLX-Response: 1TFkXGx0ZEQpMehcZGR0RCllEF2wBb2EbHU5zfmZYEQpYWBdnUE1sT1Macxp fTxEKeE4XY1Nja3sTWH4aX14RCnlMF2FwYm16W0hDekNtEQpDSBcHHBIRCkNZFwcSGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGXEZGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdDXR4dGx97bX0fRHNTWU1SeH18eXh8U05IenlAQGISTBEKWFwXHwQaBBgZGQUb GgQbGxoEHxoEGx4fEBseGh8aEQpeWRdzR0laTxEKTVwXGB0RCkxaF2hpTU1NEQpMRhdva2tra2s RCkJPF2R+WE9mbnNJcFtPEQpDWhcYGhMEEh8EGBscBB4TEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2IdS3pbZExiYGZlEQpCThdjU2NrexNYf hpfXhEKQkwXZ1BNbE9TGnMaX08RCkJsF2lNeEAFenkfHltrEQpCQBdoHX9lZmlcUnxuYhEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2R9YEAdZn9kXlMbEQpwaBdvYxxHUnljYB0bThA ZGhEKcGgXZHJjGG16WHtObl0QGRoRCnBoF2VGW39wRxlmWGFdEBkaEQpwaBdoQGgZQWdke2BBHx AZGhEKcGwXaXpOE0VjfmgZTm0QGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: iw4715QGW5nYysgxRWVSRVydbPSjjH8f X-Proofpoint-GUID: iw4715QGW5nYysgxRWVSRVydbPSjjH8f X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 lowpriorityscore=0 phishscore=0 mlxlogscore=341 impostorscore=0 suspectscore=0 spamscore=0 priorityscore=337 adultscore=0 clxscore=173 malwarescore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110110068 X-Spam-Score: 0 X-Spam-OrigSender: kapoornancy25@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nancy Singh --0000000000001de20305ce1261be Content-Type: text/plain; charset="UTF-8" Dear NAMD users, I have calculated my MMPBSA value for my protein-ligand complex using the CAFE plugin. For one of my protein-ligand complexes the standard deviation is very high. I want to know is there a way I can reduce it? How important is it to consider standard deviation for my analysis? Thank you Regards, Nancy --0000000000001de20305ce1261be Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear NAMD users,
I have=C2=A0calculated my MMPBSA valu= e for my protein-ligand complex using the CAFE plugin. For one of my protei= n-ligand complexes the standard deviation is very high. I want to know is t= here a way I can reduce it? How important is it to consider standard deviat= ion for my analysis?=C2=A0
Thank you


Regards,
Nancy
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Wed, 13 Oct 2021 02:28:37 -0700 (PDT) From: Maxim Abalenkov Content-Type: multipart/mixed; boundary="Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD" Subject: namd-l: [containerising NAMD with Singularity] Message-Id: Date: Wed, 13 Oct 2021 10:28:36 +0100 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3654.120.0.1.13) X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: e3gSbPCWfto1ra0ZE2xXABVyELgKpE5F X-CLX-Response: 1TFkXGB4ZEQpMehcZGRMRCllEF2JPfmUTWXNibmESEQpYWBdsQFhESx99GUl fGxEKeE4XY1Nja3sTWH4aX14RCnlMF25ge15fG0UeTn9OEQpDSBcHGxIcEQpDWRcHGBkeEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcTcRsGGxJ3BhweBh0aQhsfBhoGGxoaBhpxGhAadwYaBhoGGgYaB hoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF08ZTXlIeml9TF5FG1hLGnBv GFJya2h8U29mTWFabx9sEQpYXBcfBBoEGBkZBRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc0RvXkA RCk1cFx4fGBEKTFoXaGlNa2sRCkxGF29ra2traxEKQk8XaFheUEkFElx7ZHsRCkNaFxgaEwQSHw QYGBsEHh8RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfX hEKQkUXYGhTZkdsTh1aG18RCkJOF2NTY2t7E1h+Gl9eEQpCTBdsQFhESx99GUlfGxEKQmwXYBle eBlaYxkfUxgRCkJAF2YdUG1NYxsZGXJ7EQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxgRCnl DF21BGE1He3gdZkNEEQpwaBdpaEl8Q2BieB1SGxAHGRoRCnBoF2NGYmtGYlB/eGFIEAcZGhEKcG gXYh1fREF7RmhoRQEQBxkaEQpwaBdmSxJzX0hvZU94bhAHGRoRCnBoF20eeEITTk5sXF5NEAcZG hEKcH0XYRNlZ0IZaWR4enwQBxkaEQpwaxdlYW1iUlxdehkZHBAHGRoRCnBLF2RSRXthRG5NZ0VJ EAcZGhEKcGsXaVpYSB5iSGRCT2sQBxkaEQpwSxdkc1h5T2MZW2RBSxAHGRoRCnBrF2V8AUhMbG0 eSG1tEAcZGhEKcEsXYR9bZWtkfxprZRMQBxkaEQpwaxdhXh5+HUBdc016QxAHGRoRCnBLF21oHl 1PQ3JPGWRaEAcZGhEKcH0XZEljS2VGBXpNGGAQBxkaEQpwfxdlGXlmXkdpG2RPcxAfGBEKcF8Xe nxIbhlvch5ZbxwQBxkaEQpwfxduHRxcWVJFb1hmYhAaEQpwXxdkSWNLZUYFek0YYBAHGRoRCnBs F2R6BXpJH1xrY3NvEAcZGhEKcEMXbFoYellsQmN/b3AQBxkaEQptfhcHGxEKWE0XSxEg X-Proofpoint-GUID: e3gSbPCWfto1ra0ZE2xXABVyELgKpE5F MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 clxscore=243 priorityscore=339 adultscore=0 malwarescore=0 lowpriorityscore=0 suspectscore=0 impostorscore=0 mlxlogscore=999 phishscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110130064 X-Spam-Score: 0 X-Spam-OrigSender: maxim.abalenkov@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Maxim Abalenkov --Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear all, As part of my project I would like to containerise NAMD with Singularity = to make it available on various HPC systems. At first I tried to utilise = a pre-compiled NAMD binary: Linux-x86_64-ibverbs-smp (InfiniBand plus = shared memory, no MPI needed) inside a container. I build my container = from a definition file (md-centos.def). Please find it attached for a = reference. According to a NAMD mailing list = (https://www.ks.uiuc.edu/Research//namd/mailing_list/namd-l.2020-2021/0310= .html) I used the ibverbs-smp variant of the NAMD binary. To enable = Charmrun I installed SSH onto the CentOS Linux inside my container. = Currently I see the same error as the person on the mailing list (Please = see the conversation thread using the link above). Charmrun is unable to = connect to the individual nodes of the HPC system. To launch the containerised NAMD job on an HPC system I login to one of = the nodes interactively with srun --pty /bin/bash. Once on a node a = submit the Slurm job with sbatch < namd.slurm Please find the script = file attached. The output of the failed run attempt is stored in = multiple error log files: 01.log and namd-t.295873.log. While I=E2=80=99m waiting for a reply of our local system administrator, = I thought I will investigate the problem further by trying to install = NAMD inside a container from source. To compile Charm++ I use the = =E2=80=9Cbuild" script from the "charm-6.10.2=E2=80=9D archive with the = following options: ./build charm++ verbs-linux-x86_64 gcc gfortran smp During the compilation I observe the fatal errors (infiniband/verbs.h: = No such file or directory). These errors make me think, maybe the "verbs = smp=E2=80=9D variant of Charm++ is not the one to follow? It seems = installing InfiniBand inside a container is an overkill. Plus it will = require detailed knowledge of the underlying InfiniBand setup on a = cluster. These setups will differ from cluster to cluster and therefore = reduce the portability effect of a Singularity container. What would be = your advice and recommendation? Is there a general guidance on preparing = a container with NAMD? Now I=E2=80=99m inclined to trying MPI variants = of Cham++ compilation. I hope these will be more portable. Thank you for your help and have a wonderful day ahead! =E2=80=94 Best wishes, Maxim --Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD Content-Disposition: attachment; filename=01.log Content-Type: application/octet-stream; x-unix-mode=0644; name="01.log" Content-Transfer-Encoding: quoted-printable Charmrun>=20scalable=20start=20enabled.=20=0D=0ACharmrun>=20scalable=20= start=20enabled.=20=0D=0ACharmrun>=20IBVERBS=20version=20of=20charmrun=0D= =0ACharmrun>=20IBVERBS=20version=20of=20charmrun=0D=0A= -------------------------------------------------------=0D=0APrimary=20= job=20=20terminated=20normally,=20but=201=20process=20returned=0D=0Aa=20= non-zero=20exit=20code..=20Per=20user-direction,=20the=20job=20has=20= been=20aborted.=0D=0A= -------------------------------------------------------=0D=0A= --------------------------------------------------------------------------= =0D=0Ampiexec=20detected=20that=20one=20or=20more=20processes=20exited=20= with=20non-zero=20status,=20thus=20causing=0D=0Athe=20job=20to=20be=20= terminated.=20The=20first=20process=20to=20do=20so=20was:=0D=0A=0D=0A=20=20= Process=20name:=20[[20592,1],1]=0D=0A=20=20Exit=20code:=20=20=20=201=0D=0A= --------------------------------------------------------------------------= =0D=0A= --Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD Content-Disposition: attachment; filename=md-centos.def Content-Type: application/octet-stream; x-unix-mode=0644; name="md-centos.def" Content-Transfer-Encoding: quoted-printable BootStrap:=20library=0D=0AFrom:=20library://library/default/centos:7=0D=0A= =0D=0A%post=0D=0A=20=20=20=20#=20set=20hostname=0D=0A=20=20=20=20echo=20= "md"=20>>=20/etc/hostname=0D=0A=0D=0A=20=20=20=20#=20verify=20new=20= hostname=0D=0A=20=20=20=20#=20cat=20/etc/hostname=0D=0A=0D=0A=20=20=20=20= #=20enable=20DNS=0D=0A=20=20=20=20echo=20"nameserver=208.8.8.8"=20>=20= /etc/resolv.conf=0D=0A=0D=0A= 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Process=20name:=20[[20592,1],1]=0A=20=20Exit=20code:=20=20=20=201=0A= --------------------------------------------------------------------------= --Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD Content-Disposition: attachment; filename=namd.slurm Content-Type: application/octet-stream; x-unix-mode=0644; name="namd.slurm" Content-Transfer-Encoding: quoted-printable #!/bin/bash=0D=0A#SBATCH=20--comment=3DNAMD-T=0D=0A#SBATCH=20--ntasks=3D2=0D= =0A#SBATCH=20--mem-per-cpu=3D1024=0D=0A#SBATCH=20--job-name=3DNAMD-T=0D=0A= #SBATCH=20--output=3Dnamd-t.%j.log=0D=0A#SBATCH=20--time=3D01:00:00=0D=0A= =0D=0Afunction=20namd_make_nodelist()=20{=0D=0A=20=20=20=20>=20= nodelist.${SLURM_JOBID}=0D=0A=0D=0A=20=20=20=20for=20n=20in=20`echo=20= $SLURM_NODELIST=20|=20scontrol=20show=20hostnames`;=20do=0D=0A=20=20=20=20= =20=20=20=20LINE=3D"host=20${n}.=20++cpus=20= ${SLURM_CPUS_ON_NODE}"=0D=0A=20=20=20=20=20=20=20=20echo=20"${LINE}"=20= >>=20nodelist.${SLURM_JOBID}=0D=0A=20=20=20=20done=0D=0A=0D=0A=20=20=20=20= CHARMRUN_ARGS=3D"++p=20${SLURM_NTASKS}=20++ppn=20${SLURM_CPUS_ON_NODE}"=0D= =0A=20=20=20=20CHARMRUN_ARGS=3D"${CHARMRUN_ARGS}=20++nodelist=20= nodelist.${SLURM_JOBID}"=0D=0A}=0D=0A=0D=0Aecho=20"Loading=20Slurm=20= modules..."=0D=0Amodule=20load=20gcc=20mpi=0D=0A=0D=0Aecho=20"Changing=20= to=20simulation=20directory..."=0D=0Acd=20$HOME/repo/git/alcnr/sim/mini=0D= =0Apwd=0D=0A=0D=0Aecho=20"Namd=20node=20list:"=0D=0Anamd_make_nodelist=0D= =0Acat=20nodelist.${SLURM_JOBID}=0D=0A=0D=0Aecho=20"Charmrun=20= arguments:"=0D=0Aecho=20${CHARMRUN_ARGS}=0D=0A=0D=0Aecho=20"Namd=20= arguments:"=0D=0Aecho=20${NAMD_ARGS}=0D=0A=0D=0Aecho=20"Launching=20NAMD=20= simulation=20with=20${SLURM_NTASKS}=20processes:"=0D=0Ampiexec=20-n=20= ${SLURM_NTASKS}=20singularity=20exec=20../../singularity/md.sif=20\=0D=0A= =20=20=20=20charmrun=20namd2=20${CHARMRUN_ARGS}=20${NAMD_ARGS}=2001.conf=20= |=20tee=2001.log= --Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: Quoted-printable Maxim Abalenkov \\ maxim.abalenkov@gmail.com +44 7 486 486 505 \\ https://urldefense.com/v3/__http://mabalenk.gitlab.io_= _;!!DZ3fjg!oJ3b3zeJxN2Spsk0oV4OLDFo1s__mFd6Sgve8d-7T3ee7sLmdJTR8mRhOgl38lCT= Iw$=20= --Apple-Mail=_62BFE742-C470-4107-8FA7-2B04B39E84AD-- From owner-namd-l@halifax.ks.uiuc.edu Wed Oct 13 08:26:47 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19DDQl3E022797; Wed, 13 Oct 2021 08:26:47 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19DDQl3I022796; Wed, 13 Oct 2021 08:26:47 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu 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X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBsbEQpMehcZHxgRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGBkaEQpDWRcHExMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbExtxGxwaEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0ddYVtAQE5MQVhyZUdAH0xuW29DQkUTc3wZWwdraX9CEQpYXBcfBBoEGBkZ BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc0RjZ0QRCk1cFxseGBEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHR8RCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2VTHV5+eFBofXJ5EQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHBE KeUMXZBNBRRhpSX1ZfBMRCnBoF2IdX0RBe0ZoaEUBEAcZGhEKcGgXelobSEt6WWlhWRwQGRoRCn BoF2ZLEnNfSG9lT3huEAcZGhEKcGgXbWRnfhpTZWFHTkgQGRoRCnBoF29sZ0ASSFh4WkVNEBkaE QpwfRdhE2VnQhlpZHh6fBAHGRoRCnB9F24ebmEeQn1AQG5pEAcZGhEKcH0Xb0NIaG5bHF9/YhsQ 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quoted-printable Hi Maxim, if you're using Singularity I assume that the compute nodes also have a reasonably modern Linux installation. How about using the pre-compiled binary directly onto the nodes? NAMD builds don't really have much in terms of dependencies through dynamic linking. Giacomo On Wed, Oct 13, 2021 at 5:31 AM Maxim Abalenkov wrote: > Dear all, > > As part of my project I would like to containerise NAMD with Singularity > to make it available on various HPC systems. At first I tried to utilise = a > pre-compiled NAMD binary: Linux-x86_64-ibverbs-smp (InfiniBand plus share= d > memory, no MPI needed) inside a container. I build my container from a > definition file (md-centos.def). Please find it attached for a reference. > According to a NAMD mailing list ( > https://www.ks.uiuc.edu/Research//namd/mailing_list/namd-l.2020-2021/0310= .html) > I used the ibverbs-smp variant of the NAMD binary. To enable Charmrun I > installed SSH onto the CentOS Linux inside my container. Currently I see > the same error as the person on the mailing list (Please see the > conversation thread using the link above). Charmrun is unable to connect = to > the individual nodes of the HPC system. > > To launch the containerised NAMD job on an HPC system I login to one of > the nodes interactively with srun --pty /bin/bash. Once on a node a submi= t > the Slurm job with sbatch < namd.slurm Please find the script file > attached. The output of the failed run attempt is stored in multiple erro= r > log files: 01.log and namd-t.295873.log. > > While I=E2=80=99m waiting for a reply of our local system administrator, = I thought > I will investigate the problem further by trying to install NAMD inside a > container from source. To compile Charm++ I use the =E2=80=9Cbuild" scrip= t from the > "charm-6.10.2=E2=80=9D archive with the following options: > > ./build charm++ verbs-linux-x86_64 gcc gfortran smp > > During the compilation I observe the fatal errors (infiniband/verbs.h: No > such file or directory). These errors make me think, maybe the "verbs smp= =E2=80=9D > variant of Charm++ is not the one to follow? It seems installing InfiniBa= nd > inside a container is an overkill. Plus it will require detailed knowledg= e > of the underlying InfiniBand setup on a cluster. These setups will differ > from cluster to cluster and therefore reduce the portability effect of a > Singularity container. What would be your advice and recommendation? Is > there a general guidance on preparing a container with NAMD? Now I=E2=80= =99m > inclined to trying MPI variants of Cham++ compilation. I hope these will = be > more portable. > > Thank you for your help and have a wonderful day ahead! > > =E2=80=94 > Best wishes, > Maxim > > > > Maxim Abalenkov \\ maxim.abalenkov@gmail.com > +44 7 486 486 505 \\ > https://urldefense.com/v3/__http://mabalenk.gitlab.io__;!!DZ3fjg!oJ3b3zeJ= xN2Spsk0oV4OLDFo1s__mFd6Sgve8d-7T3ee7sLmdJTR8mRhOgl38lCTIw$ --00000000000031fae005ce3be9ac Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Maxim, if you're using Singularity I assume that th= e compute nodes also have a reasonably modern=C2=A0Linux installation.=C2= =A0 How about using the pre-compiled binary directly onto the nodes?=C2=A0 = NAMD builds don't really have much in terms of=C2=A0dependencies=C2=A0t= hrough dynamic linking.

Giacomo

On Wed, Oct 13, 202= 1 at 5:31 AM Maxim Abalenkov <maxim.abalenkov@gmail.com> wrote:
Dear all,

As part of my project I would like to containerise NAMD with Singularity to= make it available on various HPC systems. At first I tried to utilise a pr= e-compiled NAMD binary: Linux-x86_64-ibverbs-smp (InfiniBand plus shared me= mory, no MPI needed) inside a container. I build my container from a defini= tion file (md-centos.def). Please find it attached for a reference. Accordi= ng to a NAMD mailing list (https://www.ks.uiuc.edu/Research//namd/mailing_list/namd-l.2020-2021/0= 310.html) I used the ibverbs-smp variant of the NAMD binary. To enable = Charmrun I installed SSH onto the CentOS Linux inside my container. Current= ly I see the same error as the person on the mailing list (Please see the c= onversation thread using the link above). Charmrun is unable to connect to = the individual nodes of the HPC system.

To launch the containerised NAMD job on an HPC system I login to one of the= nodes interactively with srun --pty /bin/bash. Once on a node a submit the= Slurm job with sbatch < namd.slurm Please find the script file attached= . The output of the failed run attempt is stored in multiple error log file= s: 01.log and namd-t.295873.log.

While I=E2=80=99m waiting for a reply of our local system administrator, I = thought I will investigate the problem further by trying to install NAMD in= side a container from source. To compile Charm++ I use the =E2=80=9Cbuild&q= uot; script from the "charm-6.10.2=E2=80=9D archive with the following= options:

./build charm++ verbs-linux-x86_64 gcc gfortran smp

During the compilation I observe the fatal errors (infiniband/verbs.h: No s= uch file or directory). These errors make me think, maybe the "verbs s= mp=E2=80=9D variant of Charm++ is not the one to follow? It seems installin= g InfiniBand inside a container is an overkill. Plus it will require detail= ed knowledge of the underlying InfiniBand setup on a cluster. These setups = will differ from cluster to cluster and therefore reduce the portability ef= fect of a Singularity container. What would be your advice and recommendati= on? Is there a general guidance on preparing a container with NAMD? Now I= =E2=80=99m inclined to trying MPI variants of Cham++ compilation. I hope th= ese will be more portable.

Thank you for your help and have a wonderful day ahead!

=E2=80=94
Best wishes,
Maxim



Maxim Abalenkov \\ maxim.abalenkov@gmail.com
+44 7 486 486 505 \\ https://urldefense.com= /v3/__http://mabalenk.gitlab.io__;!!DZ3fjg!oJ3b3zeJxN2Spsk0oV4OLDFo1s__mFd6= Sgve8d-7T3ee7sLmdJTR8mRhOgl38lCTIw$
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charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Maxim, For single node jobs, wrapping up the precompiled multicore binaries=20 will likely be your best bet. However, for multinode jobs, it is likely=20 going to be easier for testing to use MPI backends, since that is the=20 far more common framework. There is even reasonable documentation for=20 how this is supposed to work with singularity:=20 https://urldefense.com/v3/__https://sylabs.io/guides/3.8/user-guide/mpi.htm= l__;!!DZ3fjg!qxymKdMN-43XC6BhN1S2Cl0I2Kifep9cyZE8tZw4MMH2ih3EZacE37EX8CA63o= eq5g$ The downside to this=20 approach is that MPI+CUDA is a no-no with NAMD, and containerizing with=20 GPU support is one of the reasons you might prefer singularity over=20 docker. However, as Giacomo says, its usually not so bad to compile NAMD=20 for the handful of computing clusters you have access to. In the handful of times I've needed to make a singularity container, my=20 usual workflow was to build the program interactively from within a=20 sandbox singularity container, adding dependencies as I went along.=20 https://urldefense.com/v3/__https://sylabs.io/guides/3.8/user-guide/quick_s= tart.html*build-images-from-scratch__;Iw!!DZ3fjg!qxymKdMN-43XC6BhN1S2Cl0I2K= ifep9cyZE8tZw4MMH2ih3EZacE37EX8CCa_38tlw$=20 -Josh On 10/13/21 5:28 AM, Maxim Abalenkov wrote: > Dear all, > > As part of my project I would like to containerise NAMD with=20 > Singularity to make it available on various HPC systems. At first I=20 > tried to utilise a pre-compiled NAMD binary: Linux-x86_64-ibverbs-smp=20 > (InfiniBand plus shared memory, no MPI needed) inside a container. I=20 > build my container from a definition file (md-centos.def). Please find=20 > it attached for a reference. According to a NAMD mailing list=20 > (https://urldefense.com/v3/__https://www.ks.uiuc.edu/Research/*namd/maili= ng_list/namd-l.2020-2021/0310.html__;Lw!!HXCxUKc!j3RJZXL5DlTqYrU8yfi7niyn67= 1McJnLm_tSTNIUt9ufYDZLw9JVZHoXAMxoaPs$=20 > ) I used the ibverbs-smp variant of the NAMD binary. To enable=20 > Charmrun I installed SSH onto the CentOS Linux inside my container.=20 > Currently I see the same error as the person on the mailing list=20 > (Please see the conversation thread using the link above). Charmrun is=20 > unable to connect to the individual nodes of the HPC system. > > To launch the containerised NAMD job on an HPC system I login to one=20 > of the nodes interactively with srun --pty /bin/bash. Once on a node a=20 > submit the Slurm job with sbatch < namd.slurm Please find the script=20 > file attached. The output of the failed run attempt is stored in=20 > multiple error log files: 01.log and namd-t.295873.log. > > While I=E2=80=99m waiting for a reply of our local system administrator, = I=20 > thought I will investigate the problem further by trying to install=20 > NAMD inside a container from source. To compile Charm++ I use the=20 > =E2=80=9Cbuild" script from the "charm-6.10.2=E2=80=9D archive with the f= ollowing options: > > ./build charm++ verbs-linux-x86_64 gcc gfortran smp > > During the compilation I observe the fatal errors (infiniband/verbs.h:=20 > No such file or directory). These errors make me think, maybe the=20 > "verbs smp=E2=80=9D variant of Charm++ is not the one to follow? It seems= =20 > installing InfiniBand inside a container is an overkill. Plus it will=20 > require detailed knowledge of the underlying InfiniBand setup on a=20 > cluster. These setups will differ from cluster to cluster and=20 > therefore reduce the portability effect of a Singularity container.=20 > What would be your advice and recommendation? Is there a general=20 > guidance on preparing a container with NAMD? Now I=E2=80=99m inclined to= =20 > trying MPI variants of Cham++ compilation. I hope these will be more=20 > portable. > > Thank you for your help and have a wonderful day ahead! > > =E2=80=94 > Best wishes, > Maxim > > > > Maxim Abalenkov \\ maxim.abalenkov@gmail.com > +44 7 486 486 505 \\=20 > https://urldefense.com/v3/__http://mabalenk.gitlab.io__;!!DZ3fjg!oJ3b3zeJ= xN2Spsk0oV4OLDFo1s__mFd6Sgve8d-7T3ee7sLmdJTR8mRhOgl38lCTIw$=20 > =20 > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!qxymKdMN-43XC6BhN1S2Cl0I2Kifep9cyZE8tZw4MMH2ih3EZacE37E= X8CCmfJzThg$=20 --------------390C156C87ED1FD5CF9A9DE3 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Maxim,

For single node jobs, wrapping up the precompiled multicore binaries will likely be your best bet. However, for multinode jobs, it is likely going to be easier for testing to use MPI backends, since that is the far more common framework. There is even reasonable documentation for how this is supposed to work with singularity: https://sylabs.io/gui= des/3.8/user-guide/mpi.html The downside to this approach is that MPI+CUDA is a no-no with NAMD, and containerizing with GPU support is one of the reasons you might prefer singularity over docker. However, as Giacomo says, its usually not so bad to compile NAMD for the handful of computing clusters you have access to.

In the handful of times I've needed to make a singularity container, my usual workflow was to build the program interactively from within a sandbox singularity container, adding dependencies as I went along. https://sylabs.io/guides/3.8/user-guide/quick_start.html#build-i= mages-from-scratch

-Josh

On 10/13/21 5:28 AM, Maxim Abalenkov wrote:
=20=20=20=20=20=20
Dear all,

As part of my project I would like to containerise NAMD with Singularity to make it available on various HPC systems. At first I tried to utilise a pre-compiled NAMD binary: Linux-x86_64-ibverbs-smp (InfiniBand plus shared memory, no MPI needed) inside a container. I build my container from a definition file (md-centos.def). Please find it attached for a reference. According to a NAMD mailing list (https://urldefense.com/v3/__https://www.ks= .uiuc.edu/Research/*namd/mailing_list/namd-l.2020-2021/0310.html__;Lw!!HXCx= UKc!j3RJZXL5DlTqYrU8yfi7niyn671McJnLm_tSTNIUt9ufYDZLw9JVZHoXAMxoaPs$ ) I used the ibverbs-smp variant of the NAMD binary. To enable Charmrun I installed SSH onto the CentOS Linux inside my container. Currently I see the same error as the person on the mailing list (Please see the conversation thread using the link above). Charmrun is unable to connect to the individual nodes of the HPC system.

To launch the containerised NAMD job on an HPC system I login to one of the nodes interactively with srun --pty /bin/bash. Once on a node a submit the Slurm job with sbatch < namd.slurm Please find the script file attached. The output of the failed run attempt is stored in multiple error log files: 01.log and namd-t.295873.log.

While I=E2=80=99m waiting for a reply of our local system administrator, I thought I will investigate the problem further by trying to install NAMD inside a container from source. To compile Charm++ I use the =E2=80=9Cbuild" scr= ipt from the "charm-6.10.2=E2=80=9D archive with the following op= tions:

./build charm++ verbs-linux-x86_64 gcc gfortran smp

During the compilation I observe the fatal errors (infiniband/verbs.h: No such file or directory). These errors make me think, maybe the "verbs smp=E2=80=9D vari= ant of Charm++ is not the one to follow? It seems installing InfiniBand inside a container is an overkill. Plus it will require detailed knowledge of the underlying InfiniBand setup on a cluster. These setups will differ from cluster to cluster and therefore reduce the portability effect of a Singularity container. What would be your advice and recommendation? Is there a general guidance on preparing a container with NAMD? Now I=E2=80=99m inclined to trying MPI variants of Cham++ compilation. I hope these will be more portable.

Thank you for your help and have a wonderful day ahead!

=E2=80=94
Best wishes,
Maxim


--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
--------------390C156C87ED1FD5CF9A9DE3-- From owner-namd-l@halifax.ks.uiuc.edu Fri Oct 15 00:14:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F5Eq2B011498; Fri, 15 Oct 2021 00:14:52 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F5EqIn011497; Fri, 15 Oct 2021 00:14:52 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F5EpAP011493; Fri, 15 Oct 2021 00:14:51 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F5EpUL011492; Fri, 15 Oct 2021 00:14:51 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F5EecB011410 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 15 Oct 2021 00:14:40 -0500 (CDT) Received: from pps.filterd (m0272704.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 19F2b3HW022119 for ; Fri, 15 Oct 2021 05:14:39 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=fhh2626@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-io1-f45.google.com (mail-io1-f45.google.com [209.85.166.45]) by mx0b-00007101.pphosted.com with ESMTP id 3bpqhr6g4c-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 15 Oct 2021 05:14:39 +0000 Received: by mail-io1-f45.google.com with SMTP id e144so6441537iof.3 for ; Thu, 14 Oct 2021 22:14:39 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:from:date:message-id:subject:to; bh=0eotyZOKLOJJa5rbn5jVfiBrU9N+s56Q430yT7eFY/c=; b=VUc2P1wfwEO68iH9AB9YEPgbxFS8ih5uAZbWmUXH69jR1VYlPDGRoUqMNnIRu1uJvU +mi7eiz8spKJ0QKI7S23uDhk3BKgmqI52HcFTsVH0N48i/qYXIBE8nzwBFvUugdUSyI5 Jm7ORehVh1jbbOphrn+SDp1Wk71wQ30MXGd/h3m4+APLgvYowkiX0PYLBUyxN3NTBb26 MuQLfDkE9Ii01YP+WsZkp2E6uDbNMnCqlZUcxM7AZQqQL6V1KHTZvU/njcHXjoJOzXLY EL58UuU7HJg6FCuNJeosRqO/y/s8ebYH6GIlyvAFtgd+GMwi97v5VZOXaECqpOFI5hPu jdbA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=0eotyZOKLOJJa5rbn5jVfiBrU9N+s56Q430yT7eFY/c=; b=H71Ng1MDVMJRUoWq/W/cYjghkFLXdRz4y5pPy/wYKQK3F9HojCk1Q9NGHvM++nn3Bf 0nT5BFl0WNu9CCxFAO74pC/ja9OKZ2TwKlpsLIs+UE1CDzKqjP9yF8y+OSZBtfg4fiV/ bfxL1X00okx2DMopgZYjbql+8e25tEB09vyxrymZwg15wFHYPUueNQ1THolpWFmVVAR9 UOO2ql2Rs1YLFRBEcjQDcz2ypw2aKhZZlD4MNd1TRu+/UAAziiC9afEbFiK/tsvUL6UK FJhzt3S/Jw86JGN7PFV0f2bg+k16qzzxSFCydXRYJwtDlHMHtItvHdM17M/S4TwVtCMK zjIw== X-Gm-Message-State: AOAM533/TvwdzR8jYDKnZKrJckMCDdyW10BMuDya5i3iFvDJbh6JVQdB ZlXHtnHujokeBwR55uBSa6QnG3+gxYeJ+35oAr51AruLhU4= X-Google-Smtp-Source: ABdhPJzlz7vIGFu+f/e+d9thdZIb3eKl6NfW0z5UzqLqBnr/07/82xKZZURrG6r1noKTouc6z7YakqJatf0yv7qVQs0= X-Received: by 2002:a05:6602:2599:: with SMTP id p25mr2367643ioo.90.1634274877922; Thu, 14 Oct 2021 22:14:37 -0700 (PDT) MIME-Version: 1.0 From: Haohao Fu Date: Fri, 15 Oct 2021 13:14:33 +0800 Message-ID: Subject: namd-l: Job stopped without any error message (probably a load balancing issue?) To: NAMD Mailing-list Content-Type: multipart/alternative; boundary="00000000000090641705ce5d45cb" X-CLX-Shades: MLX X-Proofpoint-GUID: JrLr_gLAkoojSgxRhJmVD0c_Gk7dnz7d X-CLX-Response: 1TFkXGxkZEQpMehcZGh8RCllEF2VLEnMFU155ZHl9EQpYWBdoaBJnSBhnTh1 DTREKeE4XY1Nja3sTWH4aX14RCnlMF2hbXkJBHURGRUIdEQpDSBcHGxMcEQpDWRcHGRgcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcZGHEbBhwZdwYfGAYaBhoGGxoaBhpxGhAadwYaBgcfGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XYFhmWHVNZmtBRUVAeU1SeEJg R3xuGkl1bUEdTkRQHU4RClhcFx8EGgQYGRIFGxoEGxoaBB4SBBgYEBseGh8aEQpeWRdzRFhmSxE KTVwXGR0fEQpMWhdsaWtraxEKTEYXb2tra2trEQpCTxd6UHhka1pSclpGRhEKQ1oXGBoTBBIfBB scHAQeHxEKQl4XGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eE QpCRRdiGHJuS3x/Enl+fxEKQk4XY1Nja3sTWH4aX14RCkJMF2hoEmdIGGdOHUNNEQpCbBdkTGhC WXBraAVdchEKQkAXa0xyXXJ5TWhlU0kRCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGBEKeUM Xb1l+BWlPRxtSc0IRCnBoF2hAfFoZZm9YfUwSEAcZGhEKcGgXaURLGVkaElt+e2EQBxkaEQpwaB dpQWhPZHMFUnh4EhAHGRoRCnBoF2B8axhnTAVBSGFDEAcZGhEKcGgXaF1lfHJAWXxve3sQBxkaE QpwbBd6aX1aUAFEYVJNWRAHGRoRCnBMF2RGaHxvXXJIUEFoEAcZGhEKbX4XBxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: JrLr_gLAkoojSgxRhJmVD0c_Gk7dnz7d X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=676 malwarescore=0 impostorscore=0 suspectscore=0 spamscore=0 priorityscore=305 adultscore=0 clxscore=133 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110150032 X-Spam-Score: 0 X-Spam-OrigSender: fhh2626@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Haohao Fu --00000000000090641705ce5d45cb Content-Type: text/plain; charset="UTF-8" Hi, My system is modeled by the SIRAH CG force field. If I run the job using multiple CPU cores + 1 GPU, the simulation will stop after some time (usually 50000-5000000 steps) without any error message. The only weird thing is that messages like LDB: ============= START OF LOAD BALANCING ============== 12285.4 LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: Reverting to original mapping LDB: ============== END OF LOAD BALANCING =============== 12285.4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 12285.4 are much more frequent compared with a normal simulation. The last line of the log files of terminated jobs are always LDB: =============== DONE WITH MIGRATION ================ *****.*. If I run the job using 1 CPU core + 1 GPU, the simulation will not stop, but messages like LDB: ============= START OF LOAD BALANCING ============== 36312 LDB: ============== END OF LOAD BALANCING =============== 36312 LDB: =============== DONE WITH MIGRATION ================ 36312 are still super frequent. I suspect that the issue is due to a problem in the load balancing process, but how can I address this issue? Thanks for your help! Haohao --00000000000090641705ce5d45cb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

My system is modeled by the SIRAH C= G force field. If I run the job using multiple CPU cores=C2=A0+ 1 GPU, the = simulation will stop after some time (usually 50000-5000000 steps) without = any error message. The only weird thing is that messages like
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALA= NCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4
LDB: TIME 12285= .4 LOAD: AVG 0.0416106 MAX 0.0480318 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXP= ATCH 2 None MEM: 0 MB
LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.048031= 8 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
L= DB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 =C2=A0PROXIES: TOTAL 113= MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: Reverting to original = mapping
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALA= NCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4
Info: useSyn= c: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.= 4

are much more frequent compared with a norma= l simulation. The last line of the log files of terminated jobs are always<= /div>
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGR= ATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D *****.*.

If I run the job using 1 CPU core + 1 GPU, the simulation= will not stop, but messages like
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D 36312
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF L= OAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
LDB: = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
are still super= frequent.

I suspect that the issue is due to a pr= oblem in the load balancing process, but how can I address this issue?

Thanks for your help!
Haohao
<= br>

--00000000000090641705ce5d45cb-- From owner-namd-l@halifax.ks.uiuc.edu Fri Oct 15 01:36:11 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F6aBqP022442; Fri, 15 Oct 2021 01:36:11 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F6aBac022441; Fri, 15 Oct 2021 01:36:11 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F6aAhn022437; Fri, 15 Oct 2021 01:36:10 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F6aAhg022436; Fri, 15 Oct 2021 01:36:10 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F6ZubI022428 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 15 Oct 2021 01:35:57 -0500 (CDT) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 19EN66fR029582 for ; Fri, 15 Oct 2021 06:35:56 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=n.ostrowska@cent.uw.edu.pl; dkim=pass header.d=cent-uw-edu-pl.20210112.gappssmtp.com header.s=20210112 Received: from mail-lf1-f50.google.com (mail-lf1-f50.google.com [209.85.167.50]) by mx0a-00007101.pphosted.com with ESMTP id 3bppy7qj8a-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 15 Oct 2021 06:35:55 +0000 Received: by mail-lf1-f50.google.com with SMTP id g36so20634977lfv.3 for ; Thu, 14 Oct 2021 23:35:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=cent-uw-edu-pl.20210112.gappssmtp.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=8atb4eHx8+k++0HwaRVl9LCS0ssb21kbtsrKQhXlzEc=; b=cpfpaSVvJ+FuQwPrlMXCZP6jw00Ve4BIfEf/PUVazSsFGGpH1++R9gDId31/3U92Sz HWK9U2mCx6aOSQawvbozmrB9oS2XagEMqJLwgnvUYWd8GMIcBfS7VRtpecqHpgIVqdyh 06TJKdp4bygiLA3zHznB1EFPFtplulXImWq6FjuEQ79BO2K3gQUYcwZnOBOtVc1/3jwZ iefbJ2zakEQ4deN/UroPiLgJH3/YDeTboHVJYqrdrFsB1W1C75VPdiAXwI3yU0248Ufs uWUppBNy/IU15MZmWBPVUOFirj7min7kO6fMErNjeCJxItD5H74C3mvMp6H8taEprbXo 65jg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=8atb4eHx8+k++0HwaRVl9LCS0ssb21kbtsrKQhXlzEc=; b=qt7b5Nao6S1zBKcL09/+/zG0mctZy2wfJqtPC0upBOK4Rf0jSS11hztLwarVYxssmv 6Lbn52uW8Y39s1O33UtHyUrMQGOA/w5wYah19pp80QtbmdOmL/ft5z7e9r0CkCH45M+r BU6tmR3dGtBdyZih9OiTGPf5Wqvp7Q45iQXLswwh6UxG1ytWYni735/SJfxcQrKfG/z9 8X6ssg3c3EMxjDzvR7LnPp7p0y2ZHGEjbm8Z3VZUtBa4zIRx/aZZ1DtahZcsiVLI6nm/ gtKXhhYBhskeTHKGr+ronD0VtDVGKdSn7N6tSwv09DUpGLOISkYZpgZUboTn0+Vvaj/A 8c/A== X-Gm-Message-State: AOAM5302wOivHPn51PGeKKtvqRWQTHGXMZyQvX8jsAsbssz6jEcVf68C 7QxyyTUiSAI4qJPMeQ1DmNs2DxuhShMwq3YRZ/TsY4Zp3vg= X-Google-Smtp-Source: ABdhPJwGkhoMfrrCNkiwiJ8MBdDNKwcv95hJ141Ku4q+XSTNnAXEH/5Q5ryjBcZzWXN+ar4i3zKNboPkMbUrIh8UXaA= X-Received: by 2002:a05:6512:16a2:: with SMTP id bu34mr9502999lfb.147.1634279752509; Thu, 14 Oct 2021 23:35:52 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Natalia Ostrowska Date: Fri, 15 Oct 2021 08:35:40 +0200 Message-ID: Subject: Re: namd-l: Job stopped without any error message (probably a load balancing issue?) To: namd-l@ks.uiuc.edu, Haohao Fu Content-Type: multipart/alternative; boundary="0000000000001cc4a005ce5e6885" X-Proofpoint-GUID: a8_X8WI2cjDc4pTyOlhy1MIXPtOch8MO X-Proofpoint-ORIG-GUID: a8_X8WI2cjDc4pTyOlhy1MIXPtOch8MO X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0ZEQpMehccGhEKWUQXbV8dSUgcZ0JHQmIRClhYF217cn5nZVlCaGd FEQp4ThdjE19HZHpje0RubBEKeUwXbFBJEwFPZGZGH2YRCkNIFwcZGRMRCkNZFwcYGh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxlxGRkQGncGGBoGGhEKWV4XaGN5EQpJRhdfQ19Jd UJFWV5PThEKQ04XSxJ1chJ9YxhJQG5JHlp+U2VGQlMbZ2Nyel5lSUISZ2URClhcFx8EGgQYGRIF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzRFlyRxEKTVwXGx8YEQpMWhd8aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB8aEQ pCXhcbEQpEXhcYEQpCRRdnZR8eGUhIGWh5YREKQk4XYxNfR2R6Y3tEbmwRCkJMF217cn5nZVlCa GdFEQpCbBdkG2hARn9NWxxIYREKQkAXYkgeUmBbSH5TXlkRCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcbEQp5QxdkGB0SZ0QeYExvaBEKcGcXaHxSHF0YXFwZHFgQHhIRCnBoF29tSFxJYW5sXlt MEBkaEQpwaBd6W15BHmtcWgFTHRAZGhEKcGgXZVwFYGl7U2kcQ00QGRoRCnBoF2IcTnlNZn1/Gh hCEBkaEQpwaBdgE29AEnlDbUFFRhAZGhEKcGwXaWR6f0weQxhpThIQGRoRCm1+FxsRClhNF0sRI A== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 suspectscore=0 mlxlogscore=947 lowpriorityscore=0 spamscore=0 impostorscore=0 mlxscore=0 clxscore=173 priorityscore=60 adultscore=0 phishscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110150041 X-Spam-Score: 0 X-Spam-OrigSender: n.ostrowska@cent.uw.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Natalia Ostrowska --0000000000001cc4a005ce5e6885 Content-Type: text/plain; charset="UTF-8" Hi, I think you need to attach / paste longer portion of your .out file, up to correct steps - otherwise no one will be able to help here, maybe also conf file and a couple of words on the model I have ran CG simulations with namd, and I can tell you there is 99% chance your errors are caused by how the system is parameterized, also errors that look like server problems - could be pseudo-atom size, distance between them, atom parameters, all sorts of things. Also have a closer look at how does the trajectory look like, in vmd maybe? Check if the system is behaving 'nirmally' or if there is anything strange happening, like aggregation, vacuum bubbles etc On Fri, 15 Oct 2021, 07:16 Haohao Fu, wrote: > Hi, > > My system is modeled by the SIRAH CG force field. If I run the job using > multiple CPU cores + 1 GPU, the simulation will stop after some time > (usually 50000-5000000 steps) without any error message. The only weird > thing is that messages like > > LDB: ============= START OF LOAD BALANCING ============== 12285.4 > LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: Reverting to original mapping > LDB: ============== END OF LOAD BALANCING =============== 12285.4 > Info: useSync: 0 useProxySync: 0 > LDB: =============== DONE WITH MIGRATION ================ 12285.4 > > are much more frequent compared with a normal simulation. The last line of > the log files of terminated jobs are always > LDB: =============== DONE WITH MIGRATION ================ *****.*. > > If I run the job using 1 CPU core + 1 GPU, the simulation will not stop, > but messages like > LDB: ============= START OF LOAD BALANCING ============== 36312 > LDB: ============== END OF LOAD BALANCING =============== 36312 > LDB: =============== DONE WITH MIGRATION ================ 36312 > are still super frequent. > > I suspect that the issue is due to a problem in the load balancing > process, but how can I address this issue? > > Thanks for your help! > Haohao > > > --0000000000001cc4a005ce5e6885 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi, I think you need to attach / paste longer portion of = your .out file, up to correct steps - otherwise no one will be able to help= here, maybe also conf file and a couple of words on the model

I have ran CG simulations with namd, and I= can tell you there is 99% chance your errors are caused by how the system = is parameterized, also errors that look like server problems - could be pse= udo-atom size, distance between them, atom parameters, all sorts of things.= Also have a closer look at how does the trajectory look like, in vmd maybe= ? Check if the system is behaving 'nirmally' or if there is anythin= g strange happening, like aggregation, vacuum bubbles etc=C2=A0



On Fri, 15 Oct 2021, 07:16 Haohao Fu, <= fhh2626@gmail.com> wrote:
Hi,

= My system is modeled by the SIRAH CG force field. If I run the job using mu= ltiple CPU cores=C2=A0+ 1 GPU, the simulation will stop after some time (us= ually 50000-5000000 steps) without any error message. The only weird thing = is that messages like

LDB: =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D 12285.4
LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318= =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 1= 2285.4 LOAD: AVG 0.0416106 MAX 0.0480318 =C2=A0PROXIES: TOTAL 113 MAXPE 31 = MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 12285.4 LOAD: AVG 0.0416106= MAX 0.0480318 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB M= EM: 0 MB
LDB: Reverting to original mapping
LDB: =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D 12285.4
Info: useSync: 0 useProxySync: 0
LDB: =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4

a= re much more frequent compared with a normal simulation. The last line of t= he log files of terminated jobs are always
LDB: =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D *****.*.

If I run the= job using 1 CPU core + 1 GPU, the simulation will not stop, but messages l= ike
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BA= LANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
LDB: =3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D 36312
are still super frequent.

I suspect that the issue is due to a problem in the load balancing proce= ss, but how can I address this issue?

Thanks for y= our help!
Haohao


--0000000000001cc4a005ce5e6885-- From owner-namd-l@halifax.ks.uiuc.edu Fri Oct 15 03:11:01 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F8B1RY004158; Fri, 15 Oct 2021 03:11:01 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F8B0Al004157; Fri, 15 Oct 2021 03:11:00 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F8AxNC004153; Fri, 15 Oct 2021 03:10:59 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F8AxRh004152; Fri, 15 Oct 2021 03:10:59 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F8AiF9004136 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 15 Oct 2021 03:10:44 -0500 (CDT) Received: from pps.filterd (m0272704.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 19F7DIsV000365 for ; Fri, 15 Oct 2021 08:10:43 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=fhh2626@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-il1-f172.google.com (mail-il1-f172.google.com [209.85.166.172]) by mx0b-00007101.pphosted.com with ESMTP id 3bpqhr7eub-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 15 Oct 2021 08:10:43 +0000 Received: by mail-il1-f172.google.com with SMTP id i11so6250998ila.12 for ; Fri, 15 Oct 2021 01:10:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=ahN7qSa3W/0PejZGVyu+ryruPKHpEe73Nbd24ZOGGKE=; b=lgWvTByPtzDPoRIecJLmV8lVEl4ud2iWPeaAm3C7KR9i6DhGNgYgCh9KzdZAUUDPn+ bkqG8/BffxiukDBHil7tQAljJ9c0FC4nHJizpC2fZHInieUIh0wCHelmw75Ab5NuJ4NC Xz7pLNr3wSPJBvnyijfS+N6NVOKPVKylqwPBU02+GQCBkE2LJ/NeCjo/FWDtfjNXaOIC Ka0Lp0cbzOSkofZSa0ZDFpErt1As2BfkbxeeapIXNg4umOgyrKc5enhFyUQ6LUPzrBaj cD6LDPuPz6/zWl2ix++nnlCFKbIhJMGGxM4I8iHzx0Z89RGtcMW7AT1YwGiu6is1OSBc Xp3w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=ahN7qSa3W/0PejZGVyu+ryruPKHpEe73Nbd24ZOGGKE=; b=mfJxpwYO2wnvtoXNKmEYGSAHZTtIhoBo0aX3q0eQltvwqG2fOxmO01PuBLRrEIcZov VHKKhQ9TXiF1082UONsYL/JDD6zmx34h/W6PTUqN/2w1z5jD+/633TsUDh5WRjSnkSGf tcLkdXXwoZcE9baOi/rIVXFJ57FqT9mR4cxaccUWBnKzhXp7UU/0rbWwE7v+3550dZXN DYIEeJWSKL/IMokShgg0AqBUxI/DeuAOjYVShDI4XyMMpiHp2X6dFgOcIXjGJE555h1b +OE4femAeRAUnYrs8WZsEoHqj0qNtSsQXOsTv3VvMWnEPFvoiovqCtP/lzvwxlQgt+sS nogg== X-Gm-Message-State: AOAM532IWQG42W/4lp6KG+Y+fn+MzKy+Da8ZgPGnHRwAIDgkfC1krcv4 f0tL/ZEc5+wGmyyDBR/U3MgIBa/WIe4KXqg50JhEHFjG1nM= X-Google-Smtp-Source: ABdhPJweGQc2UR7kWn6uKJw/e5Fp1UskSYEhEYTpa4GK8YwkmLu+sRuyGCQLdjR5Big2KE38fzAOz3RIRjap90b2yW8= X-Received: by 2002:a05:6e02:13cd:: with SMTP id v13mr2783591ilj.55.1634285442305; Fri, 15 Oct 2021 01:10:42 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Haohao Fu Date: Fri, 15 Oct 2021 16:10:38 +0800 Message-ID: Subject: Re: namd-l: Job stopped without any error message (probably a load balancing issue?) To: Natalia Ostrowska Cc: NAMD Mailing-list Content-Type: multipart/alternative; boundary="00000000000040144d05ce5fbb20" X-CLX-Shades: MLX X-Proofpoint-GUID: g63OQAQ5_DiowqCbLFPWBtVDRV4VUXDE X-CLX-Response: 1TFkXGx4eEQpMehcZGhwRCllEF2VLEnMFU155ZHl9EQpYWBdoaBJnSBhnTh1 DTREKeE4XY1Nja3sTWH4aX14RCnlMF2hbXkJBHURGRUIdEQpDSBcHHRgRCkNZFwcYGh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxkYcRsGHBl3Bh4fBhoGGgYTHQYZGnEbEBp3BhoGGgYaBgccGgYaB hpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdNHBlle2t7H3VuQ0VdW2lIZmx6 fWhefG54fB58f3JubxEKWFwXHwQaBBgZEgUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3NEXl1PEQp NXBcbEx4RCkxaF3hpa2trEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbW 1STWtsW29IbG0RCkNaFxgaEwQSHwQbHBwEGx0YEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCS xdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2IYcm5LfH8SeX5/EQpCThdjU2NrexNY fhpfXhEKQkwXaGgSZ0gYZ04dQ00RCkJsF2RMaEJZcGtoBV1yEQpCQBdiSB5SYFtIflNeWREKQlg XZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2QYHRJnRB5gTG9oEQpwZxdvbEBgQAFCTgV7eRAaEQpwaB doZnNZek9kXl5aHBAaEQpwaBdsU38dEnp9Z25+HxAaEQpwaBdiRxtpaxtEeUlCGxAaEQpwaBdrY XBfAXNlWU9EWhAaEQpwaBduGlxoeAVzHVlnehAaEQpwbBd6aX1aUAFEYVJNWRAHHhIRCnBMF2RG aHxvXXJIUEFoEAcZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: g63OQAQ5_DiowqCbLFPWBtVDRV4VUXDE X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=999 malwarescore=0 impostorscore=0 suspectscore=0 spamscore=0 priorityscore=306 adultscore=0 clxscore=144 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110150052 X-Spam-Score: 0 X-Spam-OrigSender: fhh2626@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Haohao Fu --00000000000040144d05ce5fbb20 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Thanks a lot for your help. There is nothing but repeats of "START OF LOAD BALANCING...", like, LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128 LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: Reverting to original mapping LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6 LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: Reverting to original mapping LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1 LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2 LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7 LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7 Info: useSync: 0 useProxySync: 0 LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7 The input files are Amber-formatted. The force field has the same function form as the Amber FF. I used the latest patch at NAMD Gitlab to guarantee the correctness of reading Amber-formatted files. I used fullelectfrequency, nonbondedfreq and stepspercycle of 1 and margin of 10 to avoid possible problems caused by the fluctuation of the box. I checked all the things that you mentioned and succeed to run the simulation using the same parm7/pdb files through OpenMM. Hence, I suspect there is something wrong during the load balancing and migration. Best, Haohao Natalia Ostrowska =E4=BA=8E2021=E5=B9=B410=E6= =9C=8815=E6=97=A5=E5=91=A8=E4=BA=94 =E4=B8=8B=E5=8D=882:35=E5=86=99=E9=81= =93=EF=BC=9A > Hi, I think you need to attach / paste longer portion of your .out file, > up to correct steps - otherwise no one will be able to help here, maybe > also conf file and a couple of words on the model > > I have ran CG simulations with namd, and I can tell you there is 99% > chance your errors are caused by how the system is parameterized, also > errors that look like server problems - could be pseudo-atom size, distan= ce > between them, atom parameters, all sorts of things. Also have a closer lo= ok > at how does the trajectory look like, in vmd maybe? Check if the system i= s > behaving 'nirmally' or if there is anything strange happening, like > aggregation, vacuum bubbles etc > > > > On Fri, 15 Oct 2021, 07:16 Haohao Fu, wrote: > >> Hi, >> >> My system is modeled by the SIRAH CG force field. If I run the job using >> multiple CPU cores + 1 GPU, the simulation will stop after some time >> (usually 50000-5000000 steps) without any error message. The only weird >> thing is that messages like >> >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4 >> LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 >> MAXPE 31 MAXPATCH 2 None MEM: 0 MB >> LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 >> MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB >> LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 >> MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB >> LDB: Reverting to original mapping >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4 >> Info: useSync: 0 useProxySync: 0 >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4 >> >> are much more frequent compared with a normal simulation. The last line >> of the log files of terminated jobs are always >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D *****.*. >> >> If I run the job using 1 CPU core + 1 GPU, the simulation will not stop, >> but messages like >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312 >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312 >> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312 >> are still super frequent. >> >> I suspect that the issue is due to a problem in the load balancing >> process, but how can I address this issue? >> >> Thanks for your help! >> Haohao >> >> >> --00000000000040144d05ce5fbb20 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thanks a lot for your help.=C2=A0
There is nothing but= repeats of "START OF LOAD BALANCING...", like,
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D 47128
LDB: TIME 47128 LOAD: AVG 0.045555 MAX= 0.0602885 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
L= DB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 =C2=A0PROXIES: TOTAL 113 MA= XPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47128 LOAD: AVG 0.04= 5555 MAX 0.0602885 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorus= LB MEM: 0 MB
LDB: Reverting to original mapping
LDB: =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D 47128
Info: useSync: 0 useProxySync: 0
LDB: =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D 47130.5
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF= LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5
In= fo: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D 47130.5
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD B= ALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6
LDB: TIME 47= 130.6 LOAD: AVG 0.0455513 MAX 0.0602717 =C2=A0PROXIES: TOTAL 113 MAXPE 31 M= AXPATCH 2 None MEM: 0 MB
LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.060= 2717 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MBLDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 =C2=A0PROXIES: TOTAL = 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: Reverting to origin= al mapping
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD B= ALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6
Info: use= Sync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47= 130.6
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCI= NG =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133
LDB: =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D 47133
Info: useSync: 0 useProxySync: 0
LDB: =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D 47133.1
LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 =C2= =A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 47133= .1 LOAD: AVG 0.04589 MAX 0.0604653 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPAT= CH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0= 604653 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB=
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1
Info: useSync: 0 u= seProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE W= ITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1
L= DB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
LDB: =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D 47135.6
Info: useSync: 0 useProxySync: 0
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D 47135.6
LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 =C2= =A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 47135= .6 LOAD: AVG 0.04596 MAX 0.0609632 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPAT= CH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0= 609632 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB=
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
Info: useSync: 0 u= seProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE W= ITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
L= DB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1
LDB: =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D 47138.1
Info: useSync: 0 useProxySync: 0
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D 47138.2
LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 = =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 47= 138.2 LOAD: AVG 0.0456313 MAX 0.0603476 =C2=A0PROXIES: TOTAL 113 MAXPE 31 M= AXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47138.2 LOAD: AVG 0.0456313 = MAX 0.0603476 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB ME= M: 0 MB
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALA= NCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2
Info: useSyn= c: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.= 2
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6
LDB: =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D 47140.6
Info: useSync: 0 useProxySync: 0
LDB: = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6
LDB: =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D 47140.7
LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602= 817 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIM= E 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 =C2=A0PROXIES: TOTAL 113 MAXPE = 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47140.7 LOAD: AVG 0.0455= 321 MAX 0.0602817 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusL= B MEM: 0 MB
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD = BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7
Info: us= eSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47= 140.7

The input files are Amber-formatted. The force= field has the same function form as the Amber FF. I used the latest patch = at NAMD Gitlab to guarantee the correctness of reading Amber-formatted file= s. I used=C2=A0fullelectfrequency, nonbondedfreq and stepspercycle of 1 and= margin of 10 to avoid possible problems caused by the fluctuation of the b= ox. I checked all the things that you mentioned and succeed to run the simu= lation using the same parm7/pdb files through OpenMM. Hence, I suspect ther= e is something wrong during the load balancing and migration.

Best,
Haohao

Natalia Ostrowska <<= a href=3D"mailto:n.ostrowska@cent.uw.edu.pl">n.ostrowska@cent.uw.edu.pl= > =E4=BA=8E2021=E5=B9=B410=E6=9C=8815=E6=97=A5=E5=91=A8=E4=BA=94 =E4=B8= =8B=E5=8D=882:35=E5=86=99=E9=81=93=EF=BC=9A
Hi, I think you need to attac= h / paste longer portion of your .out file, up to correct steps - otherwise= no one will be able to help here, maybe also conf file and a couple of wor= ds on the model

I have ran CG = simulations with namd, and I can tell you there is 99% chance your errors a= re caused by how the system is parameterized, also errors that look like se= rver problems - could be pseudo-atom size, distance between them, atom para= meters, all sorts of things. Also have a closer look at how does the trajec= tory look like, in vmd maybe? Check if the system is behaving 'nirmally= ' or if there is anything strange happening, like aggregation, vacuum b= ubbles etc=C2=A0



On Fri, 15 Oct= 2021, 07:16 Haohao Fu, <fhh2626@gmail.com> wrote:
Hi,

My system = is modeled by the SIRAH CG force field. If I run the job using multiple CPU= cores=C2=A0+ 1 GPU, the simulation will stop after some time (usually 5000= 0-5000000 steps) without any error message. The only weird thing is that me= ssages like

LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 1= 2285.4
LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 =C2=A0PROXIES= : TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 12285.4 LOAD: A= VG 0.0416106 MAX 0.0480318 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 Ref= ineTorusLB MEM: 0 MB
LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318= =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LD= B: Reverting to original mapping
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D 12285.4
Info: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D 12285.4

are much more fr= equent compared with a normal simulation. The last line of the log files of= terminated jobs are always
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D *****.*.

If I run the job using 1 CP= U core + 1 GPU, the simulation will not stop, but messages like
L= DB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D 36312
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DO= NE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
are still super frequent.

I suspect th= at the issue is due to a problem in the load balancing process, but how can= I address this issue?

Thanks for your help!
=
Haohao


--00000000000040144d05ce5fbb20-- From owner-namd-l@halifax.ks.uiuc.edu Fri Oct 15 04:19:32 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F9JW6q005851; Fri, 15 Oct 2021 04:19:32 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F9JWXq005850; Fri, 15 Oct 2021 04:19:32 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F9JVK9005845; Fri, 15 Oct 2021 04:19:31 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19F9JVrM005844; Fri, 15 Oct 2021 04:19:31 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19F9ItvP005338 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 15 Oct 2021 04:18:57 -0500 (CDT) Received: from pps.filterd (m0272704.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 19ENs3Lc020786 for ; Fri, 15 Oct 2021 09:18:55 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=n.ostrowska@cent.uw.edu.pl; dkim=pass header.s=20210112 header.d=cent-uw-edu-pl.20210112.gappssmtp.com Received: from mail-lf1-f46.google.com (mail-lf1-f46.google.com [209.85.167.46]) by mx0b-00007101.pphosted.com with ESMTP id 3bpqhr7tpx-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Fri, 15 Oct 2021 09:18:54 +0000 Received: by mail-lf1-f46.google.com with SMTP id t9so38251311lfd.1 for ; Fri, 15 Oct 2021 02:18:54 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=cent-uw-edu-pl.20210112.gappssmtp.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=Wf51vHICGFSgHOMMc1kCs/8MwGE8V2pNc99bTMWzR4w=; b=Cea5i4vwcY/xEZfvMqVQg1JaFepbsVosOMUa3zJhZ3ZKR108Y1D+fNe3I572o9sS9g qf/2NmYuuaLoWQvGY5ZqAkC9tfrdj3XZRStY3wmCuafn8seUwL7DvtQgTCsmK7m6TSjx ofxSnhOxk/xwcEhwod3n5QSQmDSVuf+9gypr5CrSjmN7MBPJ9SuLovISFz6z9ESeqVs5 3zpuG4KSI9/SuUXH02KrKzUpjJ/is8vWig9yHPHP2EJIlctNOqB8TShA+iAOCTOjg77U +NZHPsWWNQBCTOUBQdu/jHZWvyyaefUzNMqKcp+wAQgcFqx33E/WD+L3UD+L+BxL+zC4 q3Lw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=Wf51vHICGFSgHOMMc1kCs/8MwGE8V2pNc99bTMWzR4w=; b=ewyQg4Pr6xFV8UvcXZ1cEV2l6yoAhmDxpIWdSb6WXhSwa8MYmawlZ37jEGdbNAQsTR NJ/uQoUCB9KyMogk8/yZditEfMkcNgXr8sqKOgCa/FdEhdeViOIefA8UDbT7wb+W/GQM pu4wVHr5JJsURtfLJe75++obBvJ7sUE1ZPut7ik2o8FYzrPDM9T9C7YoNgbgrbQguxW/ eE1JICS7XbhoMxqOVEBWV+GdfKHMVSn2l9hQCofAMNpVYyKo3+zSFI685p+VRNxNgBsE RML4P7S7tqmISL+fXnkscW91bIvJL9qwuuSdabuvkUXkIWhO1MjShSoLhHGc4yKrET/9 cXZg== X-Gm-Message-State: AOAM533+eQkdfq58gRkjXtG/U532rR4mYkYOgy7V5gk2UGeDJKa2UR9E 9VEE927ssCWL0lHDy2ZDNX4ZoOx3CUtT0w2DtkqsOg== X-Google-Smtp-Source: ABdhPJzMRaAkvugJITM2GHyrGLWrsWSz+fXzGyH2qPaEQirdJQVpAE6WgPt4ECfU2AeeSRDPOsV80yXQjpyZZ6EgPvU= X-Received: by 2002:a05:6512:68b:: with SMTP id t11mr2527216lfe.586.1634289532563; Fri, 15 Oct 2021 02:18:52 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Natalia Ostrowska Date: Fri, 15 Oct 2021 11:18:40 +0200 Message-ID: Subject: Re: namd-l: Job stopped without any error message (probably a load balancing issue?) To: Haohao Fu Cc: NAMD Mailing-list Content-Type: multipart/alternative; boundary="0000000000000c8b6c05ce60aff7" X-CLX-Shades: MLX X-Proofpoint-GUID: jN9f8W__9OEl_TJSHhxqrxKm2kdP2XoP X-CLX-Response: 1TFkXGx8eEQpMehcbGh4RCllEF21fHUlIHGdCR0JiEQpYWBdte3J+Z2VZQmh nRREKeE4XYxNfR2R6Y3tEbmwRCnlMF2xQSRMBT2RmRh9mEQpDSBcHGBoSEQpDWRcHGBodEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxkecRgbEBp3BhgaBhoRClleF2hjeREKSUYXX0NfS XVCRVleT04RCkNOF0BkE0wSfXV1E2VvRnV+YHliQlJbWFJhRxhBTnoYckV6EQpYXBcfBBoEGBkS BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc0RfXUsRCk1cFxkaExEKTFoXaXxpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XYmRPXR5kfE1fUlwRCkNaFxgaEwQSHwQbHB0EHh wRCkJeFxsRCkRJFxsRCkJFF2dlHx4ZSEgZaHlhEQpCThdjE19HZHpje0RubBEKQkwXbXtyfmdlW UJoZ0URCkJsF2QbaEBGf01bHEhhEQpCQBdiSB5SYFtIflNeWREKQlgXZ3Nlc0BuYWFMXWIRClpY FxsRCnlDF2QYHRJnRB5gTG9oEQpwZxdofFIcXRhcXBkcWBAeEhEKcGgXel5rUElaTU1FaUYQGhE KcGgXZ3pJbB16SUxlbhoQGhEKcGgXYkZeR0luYV5kTlgQGhEKcGgXYUlGTHptW1NnWUIQGhEKcG gXYFlDQUFcTR5PXHkQGhEKcGcXb2xAYEABQk4Fe3kQGRoRCnBsF2lken9MHkMYaU4SEBkaEQpwT BdkRmh8b11ySFBBaBAaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: jN9f8W__9OEl_TJSHhxqrxKm2kdP2XoP X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 mlxlogscore=999 malwarescore=0 impostorscore=0 suspectscore=0 spamscore=0 priorityscore=104 adultscore=0 clxscore=154 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110150058 X-Spam-Score: 0 X-Spam-OrigSender: n.ostrowska@cent.uw.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Natalia Ostrowska --0000000000000c8b6c05ce60aff7 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I think that if you managed to run a few steps there has to be something other than load balancing lines. Type something like grep -v LDB file.out | grep -v MAX etc so you cut those lines out and maybe it will be easier to search then The combination of amber files, CG model and namd may be very hard to debug - and pretty much impossible for me (namd + charmm exclusively) so I'm gonna leave this job to others But again, a .conf file and description of the CG model will be extremely helpful for anyone. Just the size of pseudo atoms, and maximum lengths of the bonds In the meantime you can do a quick test of completely turning off the 1-4exclusion (in your conf file) I know it sounds irrelevant but this is the place where sizes and lengths in your model can matter And other important question, does the simulation crash during thermalization / equilibration steps, just after that or later in the production part? Regards, Natalia On Fri, 15 Oct 2021, 10:10 Haohao Fu, wrote: > Thanks a lot for your help. > There is nothing but repeats of "START OF LOAD BALANCING...", like, > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128 > LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 PROXIES: TOTAL 113 MAXP= E > 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 PROXIES: TOTAL 113 MAXP= E > 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 PROXIES: TOTAL 113 MAXP= E > 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: Reverting to original mapping > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.5 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6 > LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: Reverting to original mapping > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1 > LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 > LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2 > LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7 > LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 None MEM: 0 MB > LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 PROXIES: TOTAL 113 > MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7 > Info: useSync: 0 useProxySync: 0 > LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7 > > The input files are Amber-formatted. The force field has the same functio= n > form as the Amber FF. I used the latest patch at NAMD Gitlab to guarantee > the correctness of reading Amber-formatted files. I > used fullelectfrequency, nonbondedfreq and stepspercycle of 1 and margin = of > 10 to avoid possible problems caused by the fluctuation of the box. I > checked all the things that you mentioned and succeed to run the simulati= on > using the same parm7/pdb files through OpenMM. Hence, I suspect there is > something wrong during the load balancing and migration. > > Best, > Haohao > > Natalia Ostrowska =E4=BA=8E2021=E5=B9=B410= =E6=9C=8815=E6=97=A5=E5=91=A8=E4=BA=94 =E4=B8=8B=E5=8D=882:35=E5=86=99=E9= =81=93=EF=BC=9A > >> Hi, I think you need to attach / paste longer portion of your .out file, >> up to correct steps - otherwise no one will be able to help here, maybe >> also conf file and a couple of words on the model >> >> I have ran CG simulations with namd, and I can tell you there is 99% >> chance your errors are caused by how the system is parameterized, also >> errors that look like server problems - could be pseudo-atom size, dista= nce >> between them, atom parameters, all sorts of things. Also have a closer l= ook >> at how does the trajectory look like, in vmd maybe? Check if the system = is >> behaving 'nirmally' or if there is anything strange happening, like >> aggregation, vacuum bubbles etc >> >> >> >> On Fri, 15 Oct 2021, 07:16 Haohao Fu, wrote: >> >>> Hi, >>> >>> My system is modeled by the SIRAH CG force field. If I run the job usin= g >>> multiple CPU cores + 1 GPU, the simulation will stop after some time >>> (usually 50000-5000000 steps) without any error message. The only weird >>> thing is that messages like >>> >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4 >>> LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 >>> MAXPE 31 MAXPATCH 2 None MEM: 0 MB >>> LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 >>> MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB >>> LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 PROXIES: TOTAL 113 >>> MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB >>> LDB: Reverting to original mapping >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4 >>> Info: useSync: 0 useProxySync: 0 >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4 >>> >>> are much more frequent compared with a normal simulation. The last line >>> of the log files of terminated jobs are always >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D *****.*. >>> >>> If I run the job using 1 CPU core + 1 GPU, the simulation will not stop= , >>> but messages like >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312 >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312 >>> LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312 >>> are still super frequent. >>> >>> I suspect that the issue is due to a problem in the load balancing >>> process, but how can I address this issue? >>> >>> Thanks for your help! >>> Haohao >>> >>> >>> --0000000000000c8b6c05ce60aff7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I thin= k that if you managed to run a few steps there has to be something other th= an load balancing lines. Type something like grep -v LDB file.out | grep -v= MAX etc so you cut those lines out and maybe it will be easier to search t= hen=C2=A0

The combination of ambe= r files, CG model and namd may be very hard to debug - and pretty much impo= ssible for me (namd + charmm exclusively) so I'm gonna leave this job t= o others

=
But again, a .conf file = and description of the CG model will be extremely helpful for anyone. Just = the size of pseudo atoms, and maximum lengths of the bonds=C2=A0

In the meantime you can do a quick test of = completely turning off the 1-4exclusion (in your conf file) I know it sound= s irrelevant but this is the place where sizes and lengths in your model ca= n matter

=

And other important question, does the= simulation crash during thermalization / equilibration steps, just after t= hat or later in the production part?

Regards,
Natali= a


On Fri, 15 Oct 2021, 10:10 Haohao Fu, <fhh2626@gmail.com> wrote:
Thanks a lot for your help.=C2=A0
There = is nothing but repeats of "START OF LOAD BALANCING...", like,LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128
LDB: TIME 47128 LOAD: AVG = 0.045555 MAX 0.0602885 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None ME= M: 0 MB
LDB: TIME 47128 LOAD: AVG 0.045555 MAX 0.0602885 =C2=A0PROXIES: = TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47128 LO= AD: AVG 0.045555 MAX 0.0602885 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2= RefineTorusLB MEM: 0 MB
LDB: Reverting to original mapping
LDB: =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128
Info: useSync: 0 useProxySync: 0=
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47128
LDB: =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D 47130.5
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = 47130.5
Info: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D 47130.5
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47130.6<= br>LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 =C2=A0PROXIES: TOTAL= 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 47130.6 LOAD: AVG 0.04= 55513 MAX 0.0602717 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineToru= sLB MEM: 0 MB
LDB: TIME 47130.6 LOAD: AVG 0.0455513 MAX 0.0602717 =C2=A0= PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: Reve= rting to original mapping
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 471= 30.6
Info: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D 47130.6
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D STA= RT OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133
LD= B: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133
Info: useSync: 0 useProxyS= ync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGR= ATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1
LDB: TIME 47133.1 LOAD: AVG 0.04589 = MAX 0.0604653 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MBLDB: TIME 47133.1 LOAD: AVG 0.04589 MAX 0.0604653 =C2=A0PROXIES: TOTAL 11= 3 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47133.1 LOAD: AV= G 0.04589 MAX 0.0604653 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 Refine= TorusLB MEM: 0 MB
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF= LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47133.1
In= fo: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D 47133.1
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD B= ALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
Info: useSync: 0 useProxySync: 0<= br>LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
LDB: =3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D 47135.6
LDB: TIME 47135.6 LOAD: AVG 0.04596 MAX= 0.0609632 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
L= DB: TIME 47135.6 LOAD: AVG 0.04596 MAX 0.0609632 =C2=A0PROXIES: TOTAL 113 M= AXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47135.6 LOAD: AVG 0= .04596 MAX 0.0609632 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTor= usLB MEM: 0 MB
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LO= AD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47135.6
Info:= useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= 47135.6
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALA= NCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1
LDB: =3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1
Info: useSync: 0 useProxySync: 0
= LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.1
LDB: =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D 47138.2
LDB: TIME 47138.2 LOAD: AVG 0.0456313 MAX = 0.0603476 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LD= B: TIME 47138.2 LOAD: AVG 0.0456313 MAX 0.0603476 =C2=A0PROXIES: TOTAL 113 = MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47138.2 LOAD: AVG = 0.0456313 MAX 0.0603476 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 Refine= TorusLB MEM: 0 MB
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF= LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47138.2
In= fo: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D 47138.2
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD B= ALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6
Info: useSync: 0 useProxySync: 0<= br>LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH MIGRATION = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.6
LDB: =3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D 47140.7
LDB: TIME 47140.7 LOAD: AVG 0.0455321 M= AX 0.0602817 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 None MEM: 0 MBLDB: TIME 47140.7 LOAD: AVG 0.0455321 MAX 0.0602817 =C2=A0PROXIES: TOTAL 1= 13 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: TIME 47140.7 LOAD: A= VG 0.0455321 MAX 0.0602817 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 Ref= ineTorusLB MEM: 0 MB
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END= OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 47140.7Info: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D 47140.7

The input files are Amber-formatted. = The force field has the same function form as the Amber FF. I used the late= st patch at NAMD Gitlab to guarantee the correctness of reading Amber-forma= tted files. I used=C2=A0fullelectfrequency, nonbondedfreq and stepspercycle= of 1 and margin of 10 to avoid possible problems caused by the fluctuation= of the box. I checked all the things that you mentioned and succeed to run= the simulation using the same parm7/pdb files through OpenMM. Hence, I sus= pect there is something wrong during the load balancing and migration.

Best,
Haohao

Natalia Ostrow= ska <n.ostrowska@cent.uw.edu.pl> =E4=BA=8E2021=E5=B9=B410= =E6=9C=8815=E6=97=A5=E5=91=A8=E4=BA=94 =E4=B8=8B=E5=8D=882:35=E5=86=99=E9= =81=93=EF=BC=9A
=
Hi, I think you need to attach / paste longer portion of = your .out file, up to correct steps - otherwise no one will be able to help= here, maybe also conf file and a couple of words on the model

I have ran CG simulations with namd, and I= can tell you there is 99% chance your errors are caused by how the system = is parameterized, also errors that look like server problems - could be pse= udo-atom size, distance between them, atom parameters, all sorts of things.= Also have a closer look at how does the trajectory look like, in vmd maybe= ? Check if the system is behaving 'nirmally' or if there is anythin= g strange happening, like aggregation, vacuum bubbles etc=C2=A0



On Fri, 15 Oct 2021, 07:16 Haohao Fu, <= f= hh2626@gmail.com> wrote:
Hi,

My system is modele= d by the SIRAH CG force field. If I run the job using multiple CPU cores=C2= =A0+ 1 GPU, the simulation will stop after some time (usually 50000-5000000= steps) without any error message. The only weird thing is that messages li= ke

LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ST= ART OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 =C2=A0PROXIES: TOTAL 1= 13 MAXPE 31 MAXPATCH 2 None MEM: 0 MB
LDB: TIME 12285.4 LOAD: AVG 0.0416= 106 MAX 0.0480318 =C2=A0PROXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusL= B MEM: 0 MB
LDB: TIME 12285.4 LOAD: AVG 0.0416106 MAX 0.0480318 =C2=A0PR= OXIES: TOTAL 113 MAXPE 31 MAXPATCH 2 RefineTorusLB MEM: 0 MB
LDB: Revert= ing to original mapping
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 12285.4=
Info: useSync: 0 useProxySync: 0
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D 12285.4

are much more frequent compa= red with a normal simulation. The last line of the log files of terminated = jobs are always
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D DONE WITH MIGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D **= ***.*.

If I run the job using 1 CPU core + 1 G= PU, the simulation will not stop, but messages like
LDB: =3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D START OF LOAD BALANCING =3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D END OF LOAD BALANCING =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D 36312
LDB: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DONE WITH M= IGRATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 36312
are still super frequent.

I suspect that the is= sue is due to a problem in the load balancing process, but how can I addres= s this issue?

Thanks for your help!
Haoh= ao


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Fri, 15 Oct 2021 14:04:31 +0200 Received: from ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6]) by ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6%2]) with mapi id 15.01.2308.015; Fri, 15 Oct 2021 14:04:31 +0200 From: Alessandro Ruda To: "namd-l@ks.uiuc.edu" Subject: namd-l: Re: MD run terminated with singnal 11 Thread-Topic: MD run terminated with singnal 11 Thread-Index: AQHXsICejlnVUcPicEKrCLWPP+bjG6vUGBDA Date: Fri, 15 Oct 2021 12:04:30 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [130.237.154.251] Content-Type: multipart/alternative; boundary="_000_c1b3cf59f92b4afca4d4164a6d2d835fsuse_" MIME-Version: 1.0 X-Proofpoint-GUID: 67H32LPyFRi2DlpKj-zc-9wj-S4QDpw4 X-Proofpoint-ORIG-GUID: 67H32LPyFRi2DlpKj-zc-9wj-S4QDpw4 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx4cEQpMehcaEQpZRBdgenpdaUtdZR9fThEKWFgXelppARp9AU1icEA RCnhOF2ccf0h8X0tOXxwaEQp5TBdkQXISRl1wRwVwYxEKQ0gXBxkeGBEKQ1kXBxgaGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsYHHEbHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThccHWIZGGZ6U2x4QxhuRlphQAdQSQcTXUAHeR57blpdHhEKWFwXHwQaBBgZEgUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NEUmZfEQpNXBcfEhEKTFoXaGlNa2sRCkxGF29va2tsaWs RCkJPF21/AQVCY0FBWAUfEQpDWhcdHQQYGRIEGR0EGBoTEQpCXhcbEQpEXhcYEQpCXBcbEQpeTh cbEQpCSxdnHH9IfF9LTl8cGhEKQkkXZxx/SHxfS05fHBoRCkJFF2hdXEtuWxhAWAF9EQpCThdnH H9IfF9LTl8cGhEKQkwXelppARp9AU1icEARCkJsF2l+aBJDYV5JbWhBEQpCQBdueGJrbn8FXF5L ThEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxsRCnlDF2BZE0JFQEViHkABEQpwZxdpQ25QAVl zRwEeUxAZGhEKcGgXZll4RgVoQ00aSBkQGRoRCnBoF2RMRUVHZhkfeGlmEBkaEQpwaBdna3h8c2 tIfHgbaRAZGhEKcGgXZnBBcGgTAUNaTWkQGRoRCnBoF2RIGkl5cgVgGXppEBkaEQpwbBdmTV5jZ Gxfel95ARAZGhEKcEMXbUsbHXNgQGx7aV4QHRIRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 suspectscore=0 mlxlogscore=999 lowpriorityscore=0 spamscore=0 impostorscore=0 mlxscore=0 clxscore=146 priorityscore=0 adultscore=0 phishscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110150073 X-Spam-Score: 0 X-Spam-OrigSender: alessandro.ruda@su.se X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alessandro Ruda --_000_c1b3cf59f92b4afca4d4164a6d2d835fsuse_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable It seems related to the PME parameters anyway. I tried to change parameters= such as the size of the grid or the spacing from 0.5 to 1.5 but it didn't = work as well. Any hints on what could cause the instability? All the best, Alex ________________________________ From: Alessandro Ruda Sent: 23 September 2021 15:46:31 To: namd-l@ks.uiuc.edu Subject: MD run terminated with singnal 11 Dear NAMD comunity, I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl - = 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization fo= llowed by heating and short equilibration (few us) but when I start the pro= duction it stops after few seconds with this error in slurm (i am running o= n a cluster). * namd2:37211 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a= 0. Backtrace: * namd2:37213 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a12= 0. Backtrace: * namd2:110002 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3f= 20. Backtrace: * namd2:37217 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe224b27a= 0. Backtrace: ..etc...etc.... * software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_= chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14] ..etc...etc please find attached file if needed.The log file simply states: * mpprun info: Job terminated with error It happened to another simulation also with a very much similar tetrasaccha= ride and I managed to make it work by building the tetrasaccharide again, s= olvate it, minimize etc etc. It worked but I don't know why. It didn't work for this one and every time I restart the simulation I get t= he same error. This is the configuration file I am using: ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- structure /.pdf coordinates /.pdb bincoordinates /.coor binvelocities /.vel set temperature 300 firsttimestep 0 # Input paraTypeCharmm on parameters /Parameters/par_all36_carb.inp parameters /Parameters/par_water_ions.inp parameters /Parameters/par_all36_prot.inp parameters /Parameters/par_all36m_prot.inp parameters /Parameters/par_hbond.inp # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 16.0 margin 0 # Integrator Parameters timestep 4.0 ; rigidBonds all ; nonbondedFreq 1 fullElectFrequency 1 stepspercycle 20 pairlistsPerCycle 2 wrapWater on wrapAll on # Constant Temperature Control langevin on ; langevinDamping 1 ; langevinTemp $temperature langevinHydrogen off ; # PME PME yes PMEGridSpacing 1.0 #manual grid definition PMEGridSizeX 60 PMEGridSizeY 60 PMEGridSizeZ 60 # Constant Pressure Control (variable volume) useGroupPressure yes ; useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 50.0 langevinPistonDecay 25.0 langevinPistonTemp $temperature # Output outputName $outputname restartfreq 2500 ;# 2500steps =3D every 10ps dcdfreq 2500 ;# =3D every 10ps xstFreq 2500 outputEnergies 2500 outputtiming 2500 outputPressure 150 binaryoutput yes extendedSystem /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_Le= X4_HMR/3_equilibration/LeX4_heated.restart.xsc run 125000000 ;# 500 ns ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- I really don't know what the problem is related to. Does anybody have some = hints about it? Thank you in advance, Alessandro --_000_c1b3cf59f92b4afca4d4164a6d2d835fsuse_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

It seems related to the PME parameters anyway. I tried to change paramet= ers such as the size of the grid or the spacing from 0.5 to 1.5 but it didn= 't work as well.


Any hints on what could cause the instability?


All the best,

Alex


From: Alessandro Ruda
Sent: 23 September 2021 15:46:31
To: namd-l@ks.uiuc.edu
Subject: MD run terminated with singnal 11
 

Dear NAMD comunity,

I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl -= 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization f= ollowed by heating and short equilibration (few us) but when I start the production it stops after few seconds with t= his error in slurm (i am running on a cluster).

  • namd2:37211 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee= 6a0.  Backtrace:
  • namd2:37213 terminated with si= gnal 11 at PC=3Dfc9213 SP=3D7ffca5b2a120.  Backtrace:
  • <= li>namd2:110002 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3= f20.  Backtrace:
  • namd2:37217 terminated with si= gnal 11 at PC=3Dfc9213 SP=3D7ffe224b27a0.  Backtrace:
  • <= /ul> ...etc...etc....
    • software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
    • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace1= 2fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
    • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSp= ace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
    • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRe= alSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]<= /span>
    • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10C= omputePme6doWorkEv+0x1684)[0xb92d14]
    • /software/= sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_R= iS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
    • /softw= are/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684= )[0xb92d14]
    ...etc...etc

    please find attached file if needed.The log file simply states:

    • mpprun info:   Job terminated with error
    • <= /ul>
      It happened to another simulation also with a very much similar tetrasacch= aride and I managed to make it work by building the tetrasaccharide again, = solvate it, minimize etc etc. It worked but I don't know why.
      It didn't work for this one and every time I restart the simulation I get = the same error.

This is the configuration file I am using:

-----------------------------------------------------= -------------------------------------------------------------------= --------------------------------------------------------------------------------------------------------------

structure          /.pdf
coordinates        /.pdb
bincoordinates     /.coor
binvelocities      /.vel

set temperature    300

firsttimestep      0

# Input
paraTypeCharmm        on
parameters          /Parameter= s/par_all36_carb.inp
parameters          /Parameter= s/par_water_ions.inp
parameters          /Parameter= s/par_all36_prot.inp
parameters          /Parameter= s/par_all36m_prot.inp
parameters          /Parameter= s/par_hbond.inp


# Force-Field Parameters
exclude           &n= bsp; scaled1-4
1-4scaling          1.0
cutoff           &nb= sp;  12.0
switching           on switchdist          10.0
pairlistdist        16.0
margin           &nb= sp;  0

# Integrator Parameters
timestep            = 4.0    ;
rigidBonds          all  = ;
nonbondedFreq       1
fullElectFrequency  1
stepspercycle       20
pairlistsPerCycle   2
wrapWater           on wrapAll           &n= bsp; on


# Constant Temperature Control
langevin            = on    ;
langevinDamping     1     ;
langevinTemp        $temperature
langevinHydrogen    off    ;

# PME
PME            =      yes
PMEGridSpacing      1.0

#manual grid definition
PMEGridSizeX        60
PMEGridSizeY        60
PMEGridSizeZ        60


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  50.0
langevinPistonDecay   25.0
langevinPistonTemp    $temperature


# Output
outputName          $outputnam= e

restartfreq         2500  = ;   ;# 2500steps =3D every 10ps
dcdfreq           &n= bsp; 2500    ;# =3D every 10ps
xstFreq           &n= bsp; 2500
outputEnergies      2500
outputtiming        2500
outputPressure      150
binaryoutput        yes


extendedSystem      /proj/carbohydratedynamics/use= rs/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibration/LeX4_heated.restart.xsc

run 125000000 ;#  500 ns
---------------------------------------------------------------------= -------------------------------------------------------------------= ------------------------------------------------------------------= ----------------------------

I really don't know what the problem is related to. Does anybody have= some hints about it?

Thank you in advance,
Alessandro





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charset=windows-1252; format=flowed Content-Transfer-Encoding: Quoted-printable Hi Alex, Are you sure that you have the right structure, coordinates,=20 bincoordinates, and binvelocities files? Those do not look sane to me. -Josh On 10/15/21 8:04 AM, Alessandro Ruda wrote: > > It seems related to the PME parameters anyway. I tried to change=20 > parameters such as the size of the grid or the spacing from 0.5 to 1.5=20 > but it didn't work as well. > > > Any hints on what could cause the instability? > > > All the best, > > Alex > > ------------------------------------------------------------------------ > *From:* Alessandro Ruda > *Sent:* 23 September 2021 15:46:31 > *To:* namd-l@ks.uiuc.edu > *Subject:* MD run terminated with singnal 11 > Dear NAMD comunity, > > I am running a simulation of a tetrasaccharide in salty water (0.2M=20 > NaCl - 50x50x50 wb) using Hydrogen Mass Repartition. I run a first=20 > minimization followed by heating and short equilibration (few us) but=20 > when I start the production it stops after few seconds with this error=20 > in slurm (i am running on a cluster). > > * *namd2:37211 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffe9c9ee6a0. Backtrace:* > * *namd2:37213 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffca5b2a120. Backtrace:* > * *namd2:110002 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffe5edf3f20.=A0 Backtrace:* > * *namd2:37217 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffe224b27a0.=A0 Backtrace:* > > ...etc...etc.... > > * *software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > * */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > * */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > * */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > * */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWork= Ev+0x1684)[0xb92d14]* > * */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > * */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWork= Ev+0x1684)[0xb92d14]* > > ...etc...etc > > please find attached file if needed.The log file simply states: > > * *mpprun info:=A0=A0 Job terminated with error* > > > It happened to another simulation also with a very much similar=20 > tetrasaccharide and I managed to make it work by building the=20 > tetrasaccharide again, solvate it, minimize etc etc. It worked but I=20 > don't know why. > It didn't work for this one and every time I restart the simulation I=20 > get the same error. > > This is the configuration file I am using: > > -------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ------- > > structure=A0=A0=A0=A0=A0=A0=A0=A0=A0 /.pdf > coordinates=A0=A0=A0=A0=A0=A0=A0 /.pdb > bincoordinates=A0=A0=A0=A0 /.coor > binvelocities=A0=A0=A0=A0=A0 /.vel > > set temperature=A0=A0=A0 300 > > firsttimestep=A0=A0=A0=A0=A0 0 > > # Input > paraTypeCharmm=A0=A0 =A0=A0=A0=A0 on > parameters=A0=A0=A0=A0=A0=A0=A0=A0=A0 /Parameters/par_all36_carb.inp > parameters=A0=A0=A0=A0=A0=A0=A0=A0=A0 /Parameters/par_water_ions.inp > parameters=A0=A0=A0=A0=A0=A0=A0=A0=A0 /Parameters/par_all36_prot.inp > parameters=A0=A0=A0=A0=A0=A0=A0=A0=A0 /Parameters/par_all36m_prot.inp > parameters=A0=A0=A0=A0=A0=A0=A0=A0=A0 /Parameters/par_hbond.inp > > > # Force-Field Parameters > exclude=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 scaled1-4 > 1-4scaling=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.0 > cutoff=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 12.0 > switching=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 on > switchdist=A0=A0=A0=A0=A0=A0=A0=A0=A0 10.0 > pairlistdist=A0=A0=A0=A0=A0=A0=A0 16.0 > margin=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0 > > # Integrator Parameters > timestep=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.0=A0=A0=A0 ; > rigidBonds=A0=A0=A0=A0=A0=A0=A0=A0=A0 all=A0 ; > nonbondedFreq=A0=A0=A0=A0=A0=A0 1 > fullElectFrequency=A0 1 > stepspercycle=A0=A0=A0=A0=A0=A0 20 > pairlistsPerCycle=A0=A0 2 > wrapWater=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 on > wrapAll=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 on > > > # Constant Temperature Control > langevin=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 on=A0=A0=A0 ; > langevinDamping=A0=A0=A0=A0 1=A0=A0=A0=A0 ; > langevinTemp=A0=A0=A0=A0=A0=A0=A0 $temperature > langevinHydrogen=A0=A0=A0 off=A0=A0=A0 ; > > # PME > PME=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 yes > PMEGridSpacing=A0=A0=A0=A0=A0 1.0 > > #manual grid definition > PMEGridSizeX=A0=A0=A0=A0=A0=A0=A0 60 > PMEGridSizeY=A0=A0=A0=A0=A0=A0=A0 60 > PMEGridSizeZ=A0=A0=A0=A0=A0=A0=A0 60 > > > # Constant Pressure Control (variable volume) > useGroupPressure=A0=A0=A0=A0=A0 yes ; > useFlexibleCell=A0=A0=A0=A0=A0=A0 no > useConstantArea=A0=A0=A0=A0=A0=A0 no > > langevinPiston=A0=A0=A0=A0=A0=A0=A0 on > langevinPistonTarget=A0 1.01325 ;#=A0 in bar -> 1 atm > langevinPistonPeriod=A0 50.0 > langevinPistonDecay=A0=A0 25.0 > langevinPistonTemp=A0=A0=A0 $temperature > > > # Output > outputName=A0=A0=A0=A0=A0=A0=A0=A0=A0 $outputname > > restartfreq=A0=A0=A0=A0=A0=A0=A0=A0 2500=A0=A0=A0=A0 ;# 2500steps =3D eve= ry 10ps > dcdfreq=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2500=A0=A0=A0 ;# =3D every 10= ps > xstFreq=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2500 > outputEnergies=A0=A0=A0=A0=A0 2500 > outputtiming=A0=A0=A0=A0=A0=A0=A0 2500 > outputPressure=A0=A0=A0=A0=A0 150 > binaryoutput=A0=A0=A0=A0=A0=A0=A0 yes > > > extendedSystem=20 > /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibra= tion/LeX4_heated.restart.xsc > > run 125000000 ;#=A0 500 ns > -------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ------- > > I really don't know what the problem is related to. Does anybody have=20 > some hints about it? > > Thank you in advance, > Alessandro > > > > > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!spYkFKkj0fQUJXSEems8CaSy0q8jHdR2dc3CotzbZV18VP6XZuHlSV-= 9gSEtocG6gA$=20 --------------E4C1C635966B577FE0506E72 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: Quoted-printable Hi Alex,

Are you sure that you have the right structure, coordinates, bincoordinates, and binvelocities files? Those do not look sane to me.

-Josh

On 10/15/21 8:04 AM, Alessandro Ruda wrote:
=20=20=20=20=20=20

It seems related to the PME parameters anyway. I tried to change parameters such as the size of the grid or the spacing from 0.5 to 1.5 but it didn't work as well.


Any hints on what could cause the instability?


All the best,

Alex


From: Alessandro Ruda
Sent: 23 September 2021 15:46:31
To: namd-l@ks.uiuc.edu
Subject: MD run terminated with singnal 11
 
Dear NAMD comunity,

I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl - 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization followed by heating and short equilibration (few us) but when I start the production it stops after few seconds with this error in slurm (i am running on a cluster).

  • namd2:37211 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a0.  Backtrace:
  • namd2:37213 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a120.  Backtrace:
  • namd2:110002 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3f20.  Backtrace:
  • namd2:37217 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe224b27a0.  Backtrace:
...etc...etc....
  • software/sse/manual/namd/= 2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeP= article+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]<= /li>
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/nam= d/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]=
...etc...etc

please find attached file if needed.The log file simply states:

  • mpprun info:  = Job terminated with error

It happened to another simulation also with a very much similar tetrasaccharide and I managed to make it work by building the tetrasaccharide again, solvate it, minimize etc etc. It worked but I don't know why.
It didn't work for this one and every time I restart the simulation I get the same error.

This is the configuration file I am using:

--------------------= ---------------------------------------------------------------------= ----------------------------------------------= ----------------------------------------------= ----------------------------------------------= ---

structure        &n= bsp; /.pdf
coordinates        /.pdb=
bincoordinates     /.coor
binvelocities      /.vel

set temperature    300

firsttimestep      0

# Input
paraTypeCharmm        on
parameters        &= nbsp; /Parameters/par_all36_carb.inp
parameters        &= nbsp; /Parameters/par_water_ions.inp
parameters        &= nbsp; /Parameters/par_all36_prot.inp
parameters        &= nbsp; /Parameters/par_all36m_prot.inp
parameters        &= nbsp; /Parameters/par_hbond.inp


# Force-Field Parameters
exclude        &nbs= p;    scaled1-4
1-4scaling        &= nbsp; 1.0
cutoff         = ;     12.0
switching        &n= bsp;  on
switchdist        &= nbsp; 10.0
pairlistdist        16.0=
margin         = ;     0

# Integrator Parameters
timestep        &nb= sp;   4.0    ;
rigidBonds        &= nbsp; all  ;
nonbondedFreq       1
fullElectFrequency  1
stepspercycle       20
pairlistsPerCycle   2
wrapWater        &n= bsp;  on
wrapAll        &nbs= p;    on


# Constant Temperature Control
langevin        &nb= sp;   on    ;
langevinDamping     1   =   ;
langevinTemp        $tem= perature
langevinHydrogen    off    ;<= br>
# PME
PME         &n= bsp;       yes
PMEGridSpacing      1.0

#manual grid definition
PMEGridSizeX        60 PMEGridSizeY        60 PMEGridSizeZ        60

# Constant Pressure Control (variable volume)
useGroupPressure      yes ;
useFlexibleCell       no
useConstantArea       no

langevinPiston        on=
langevinPistonTarget  1.01325 ;#  in bar -> 1 = atm
langevinPistonPeriod  50.0
langevinPistonDecay   25.0
langevinPistonTemp    $temperature


# Output
outputName        &= nbsp; $outputname

restartfreq        = 2500     ;# 2500steps =3D every 10ps
dcdfreq        &nbs= p;    2500    ;# =3D every 10ps
xstFreq        &nbs= p;    2500
outputEnergies      2500
outputtiming        2500=
outputPressure      150
binaryoutput        yes<= br>

extendedSystem      /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibrati= on/LeX4_heated.restart.xsc

run 125000000 ;#  500 ns
-------------------------------------------------------------------------------------= ----------------------------------------------= ----------------------------------------------= --------------------------------------------= ---------

I really don't know what the problem is related to. Does anybody have some hints about it?

Thank you in advance,
Alessandro






--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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Fri, 15 Oct 2021 15:56:04 +0200 Received: from ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6]) by ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6%2]) with mapi id 15.01.2308.015; Fri, 15 Oct 2021 15:56:04 +0200 From: Alessandro Ruda To: Josh Vermaas , "namd-l@ks.uiuc.edu" Subject: Re: namd-l: Re: MD run terminated with singnal 11 Thread-Topic: namd-l: Re: MD run terminated with singnal 11 Thread-Index: AQHXsICejlnVUcPicEKrCLWPP+bjG6vUGBDA///27oCAACisUQ== Date: Fri, 15 Oct 2021 13:56:04 +0000 Message-ID: <38fa28cabdf5496d962628fc00a5a0c3@su.se> References: ,<7e513d7c-9f37-dc52-5386-c54461384fd0@msu.edu> In-Reply-To: <7e513d7c-9f37-dc52-5386-c54461384fd0@msu.edu> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [130.237.154.251] Content-Type: multipart/alternative; boundary="_000_38fa28cabdf5496d962628fc00a5a0c3suse_" X-Proofpoint-GUID: aBcA8tzpAgnLdXudA9huCckNjtwlqmvn X-CLX-Response: 1TFkXGxIfEQpMehcaEQpZRBdgenpdaUtdZR9fThEKWFgXelppARp9AU1icEA RCnhOF2ccf0h8X0tOXxwaEQp5TBdkQXISRl1wRwVwYxEKQ0gXBxgcGxEKQ1kXBxwcEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF0toSWsSXlBaa01EZk5yX05rE0JfaUlBZEBeXUZbR1xEEQpYXBcfBBoEGBkSBRsa BBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NEUxp+EQpNXBcZGh8RCkxaF2l8aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdvb2trbGtrEQpCTxdtfwEFQmNBQVgFHxEKQ1oXHR0EGBkSBBkdBB gaExEKQl4XGxEKRF4XGREKQlwXGxEKXk4XGxEKQksXZxx/SHxfS05fHBoRCkJJF2ccf0h8X0tOX xwaEQpCRRdoXVxLblsYQFgBfREKQk4XZxx/SHxfS05fHBoRCkJMF3paaQEafQFNYnBAEQpCbBdp fmgSQ2FeSW1oQREKQkAXYUxYHwVBHn94GUkRCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp5QxduGHx vUn9cHRwdSREKcGcXaUNuUAFZc0cBHlMQHBoRCnBoF25PfmtHS2VgaE5OEBIZEQpwaBdlWxtkWF hwfx5QchATHhEKcGgXaRNLTUxyZFIdbkEQGhEKcGgXYH5oHVhmRnh+R2QQHR4RCnBoF2BkXE5ZU 05YS0IFEBoRCnB9F2t6HGBTGRhvUEVgEBoRCnBnF2MeT2duSW9tZWJvEBkaEQpwfxduH2ddfV5A E3hkeRAbGxoRCnBfF2RjaG0efVBrTFBgEBkaEQpwbBdmTV5jZGxfel95ARAeEhEKcEMXZ0NYYGd pWBNmRnkQHhIRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: aBcA8tzpAgnLdXudA9huCckNjtwlqmvn X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 spamscore=0 priorityscore=0 clxscore=185 malwarescore=0 impostorscore=0 suspectscore=0 mlxscore=0 bulkscore=0 lowpriorityscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110150085 X-Spam-Score: 0 X-Spam-OrigSender: alessandro.ruda@su.se X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alessandro Ruda --_000_38fa28cabdf5496d962628fc00a5a0c3suse_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable Hi Josh, yes, I checked them and they are ok, I just removed the entire path for the= sake of clarity when I posted the question! Thank you! /alex ________________________________ From: Josh Vermaas Sent: 15 October 2021 15:30:05 To: namd-l@ks.uiuc.edu; Alessandro Ruda Subject: Re: namd-l: Re: MD run terminated with singnal 11 Hi Alex, Are you sure that you have the right structure, coordinates, bincoordinates= , and binvelocities files? Those do not look sane to me. -Josh On 10/15/21 8:04 AM, Alessandro Ruda wrote: It seems related to the PME parameters anyway. I tried to change parameters= such as the size of the grid or the spacing from 0.5 to 1.5 but it didn't = work as well. Any hints on what could cause the instability? All the best, Alex ________________________________ From: Alessandro Ruda Sent: 23 September 2021 15:46:31 To: namd-l@ks.uiuc.edu Subject: MD run terminated with singnal 11 Dear NAMD comunity, I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl - = 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization fo= llowed by heating and short equilibration (few us) but when I start the pro= duction it stops after few seconds with this error in slurm (i am running o= n a cluster). * namd2:37211 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a= 0. Backtrace: * namd2:37213 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a12= 0. Backtrace: * namd2:110002 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3f= 20. Backtrace: * namd2:37217 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe224b27a= 0. Backtrace: ..etc...etc.... * software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_= chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14] ..etc...etc please find attached file if needed.The log file simply states: * mpprun info: Job terminated with error It happened to another simulation also with a very much similar tetrasaccha= ride and I managed to make it work by building the tetrasaccharide again, s= olvate it, minimize etc etc. It worked but I don't know why. It didn't work for this one and every time I restart the simulation I get t= he same error. This is the configuration file I am using: ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- structure /.pdf coordinates /.pdb bincoordinates /.coor binvelocities /.vel set temperature 300 firsttimestep 0 # Input paraTypeCharmm on parameters /Parameters/par_all36_carb.inp parameters /Parameters/par_water_ions.inp parameters /Parameters/par_all36_prot.inp parameters /Parameters/par_all36m_prot.inp parameters /Parameters/par_hbond.inp # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 16.0 margin 0 # Integrator Parameters timestep 4.0 ; rigidBonds all ; nonbondedFreq 1 fullElectFrequency 1 stepspercycle 20 pairlistsPerCycle 2 wrapWater on wrapAll on # Constant Temperature Control langevin on ; langevinDamping 1 ; langevinTemp $temperature langevinHydrogen off ; # PME PME yes PMEGridSpacing 1.0 #manual grid definition PMEGridSizeX 60 PMEGridSizeY 60 PMEGridSizeZ 60 # Constant Pressure Control (variable volume) useGroupPressure yes ; useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 50.0 langevinPistonDecay 25.0 langevinPistonTemp $temperature # Output outputName $outputname restartfreq 2500 ;# 2500steps =3D every 10ps dcdfreq 2500 ;# =3D every 10ps xstFreq 2500 outputEnergies 2500 outputtiming 2500 outputPressure 150 binaryoutput yes extendedSystem /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_Le= X4_HMR/3_equilibration/LeX4_heated.restart.xsc run 125000000 ;# 500 ns ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- I really don't know what the problem is related to. Does anybody have some = hints about it? Thank you in advance, Alessandro -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!ovA5jPIGK0ftfdPkI0iJDcW_ouWGbNnNoOhzWZAEwzMlu9jI6XCEvgP= -0nJ0sERZpw$=20 --_000_38fa28cabdf5496d962628fc00a5a0c3suse_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable

Hi Josh,


yes, I checked them and they are ok, I just removed the entire pa= th for the sake of clarity when I posted the question!


Thank you!


/alex



From: Josh Vermaas <verm= aasj@msu.edu>
Sent: 15 October 2021 15:30:05
To: namd-l@ks.uiuc.edu; Alessandro Ruda
Subject: Re: namd-l: Re: MD run terminated with singnal 11
 
Hi Alex,

Are you sure that you have the right structure, coordinates, bincoordinates= , and binvelocities files? Those do not look sane to me.

-Josh

On 10/15/21 8:04 AM, Alessandro Ruda wrote:<= br>

It seems related to the PME parameters anyway. I tried to change paramet= ers such as the size of the grid or the spacing from 0.5 to 1.5 but it didn= 't work as well.


Any hints on what could cause the instability?


All the best,

Alex


From: Alessandro Ruda
Sent: 23 September 2021 15:46:31
To: namd-l@ks.uiuc.edu
Subject: MD run terminated with singnal 11
 
Dear NAMD comunity,

I am running a simulation of a tetrasacchar= ide in salty water (0.2M NaCl - 50x50x50 wb) using Hydrogen Mass Repartitio= n. I run a first minimization followed by heating and short equilibration (few us) but when I start the production it stops = after few seconds with this error in slurm (i am running on a cluster).

  • namd2:37211 terminated wi= th signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a0.  Backtrace:
  • namd2:37213 terminated wi= th signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a120.  Backtrace:
  • namd2:110002 terminated w= ith signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3f20.  Backtrace:
  • namd2:37217 terminated w= ith signal 11 at PC=3Dfc9213 SP=3D7ffe224b27a0.  Backtrace:
...etc...etc....
  • software/sse/manual/namd/= 2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeP= article+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]<= /b>
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/nam= d/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]
...etc...etc

please find attached file if needed.The log= file simply states:

  • mpprun info:  = Job terminated with error

It happened to another simulation also with= a very much similar tetrasaccharide and I managed to make it work by build= ing the tetrasaccharide again, solvate it, minimize etc etc. It worked but I don't know why.
It didn't work for this one and every time = I restart the simulation I get the same error.

This is the configuration file I am using:<= /span>

--------------------= ---------------------------------------------------------------------= ----------------------------------------------= ----------------------------------------------= ----------------------------------------------= ---

structure          /.pdf
coordinates        /.pdb
bincoordinates     /.coor
binvelocities      /.vel

set temperature    300

firsttimestep      0

# Input
paraTypeCharmm        on
parameters          /Parameter= s/par_all36_carb.inp
parameters          /Parameter= s/par_water_ions.inp
parameters          /Parameter= s/par_all36_prot.inp
parameters          /Parameter= s/par_all36m_prot.inp
parameters          /Parameter= s/par_hbond.inp


# Force-Field Parameters
exclude           &n= bsp; scaled1-4
1-4scaling          1.0
cutoff           &nb= sp;  12.0
switching           on
switchdist          10.0
pairlistdist        16.0
margin           &nb= sp;  0

# Integrator Parameters
timestep            = 4.0    ;
rigidBonds          all  = ;
nonbondedFreq       1
fullElectFrequency  1
stepspercycle       20
pairlistsPerCycle   2
wrapWater           on
wrapAll           &n= bsp; on


# Constant Temperature Control
langevin            = on    ;
langevinDamping     1     ;
langevinTemp        $temperature
langevinHydrogen    off    ;

# PME
PME            =      yes
PMEGridSpacing      1.0

#manual grid definition
PMEGridSizeX        60
PMEGridSizeY        60
PMEGridSizeZ        60


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  50.0
langevinPistonDecay   25.0
langevinPistonTemp    $temperature


# Output
outputName          $outputnam= e

restartfreq         2500  = ;   ;# 2500steps =3D every 10ps
dcdfreq           &n= bsp; 2500    ;# =3D every 10ps
xstFreq           &n= bsp; 2500
outputEnergies      2500
outputtiming        2500
outputPressure      150
binaryoutput        yes


extendedSystem      /proj/carbohydratedynamics/use= rs/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibration/LeX4_heated.restart.xsc

run 125000000 ;#  500 ns
-------------------------------------------------------------------------------------= ----------------------------------------------= ----------------------------------------------= --------------------------------------------= ---------

I really don't know what th= e problem is related to. Does anybody have some hints about it?

Thank you in advance,
Alessandro






--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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charset="UTF-8" Hello, I have a ligand that includes a dichloro-benzene as a substituent. The psf file has a lone pair on each chloro, which is correct, and equilibration with namd2 proceeded without a problem. Production with namd3 failed right away with the error: FATAL ERROR: FOUND LONE PAIR HOSTS IN PSF WITH "LONEPAIRS" DISABLED IN CONFIG FILE The config file does have lonepairs on. I ran namd2 and worked fine, so most likely it is a problem with namd3. Please let me know if there is a work-around, or if you have any other suggestions. Thank you in advance, Maria --000000000000f07a9f05ce674d5a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello,
I have a ligand that includes a dichloro-benzene = as a substituent. The psf file has a lone pair on each chloro, which i= s correct, and equilibration with namd2 proceeded without a problem. Produc= tion with namd3 failed right away with the error: 

FATAL ERROR: FOUND LONE PAIR HOSTS IN PSF WITH "LONEPAIRS" = DISABLED IN CONFIG FILE

The config file does h= ave lonepairs on. I ran namd2 and worked fine, so most likely it is a = problem with namd3. Please let me know if there is a work-around, or i= f you have any other suggestions.

Thank you in advance, Maria=  
--000000000000f07a9f05ce674d5a-- From owner-namd-l@halifax.ks.uiuc.edu Mon Oct 18 02:38:41 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19I7cfIS017442; Mon, 18 Oct 2021 02:38:41 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19I7cfXd017441; Mon, 18 Oct 2021 02:38:41 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19I7cfrQ017436; Mon, 18 Oct 2021 02:38:41 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19I7ceIC017435; Mon, 18 Oct 2021 02:38:40 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19I7cQ5L017371 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000005053ca05ce9ba140" X-Proofpoint-ORIG-GUID: lueE0rWx80MfPWyofiIKlE8vLmFEYAEq X-CLX-Response: 1TFkXGxwSEQpMehcZHhwRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHGRsRCkNZFwcYEx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhJxHxMQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XRl9PbxpYfVISGmdMen1TRUxDY2FGbxJcZkdsb3Nrb1sRClhcFx8EGgQYGRIF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc0VZQWQRCk1cFxgaHBEKTFoXaGlNTU0RCkxGF29ra2t raxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHBoEGx0dEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2ZpGF1seG1jYVAdEQpCThdjU2Nre xNYfhpfXhEKQkwXZHtPUn8TSVp6cxwRCkJsF2UYRUViR0thaEtsEQpCQBdrZxh7HkFzWHlIHBEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF28SUG1EbFhBTxlsEQpwaBdlTGxjRgEaYWR DRRAZGhEKcGgXb3JjRmUFaG56HUQQGRoRCnBoF2BFbWxucBlwbk1LEBkaEQpwaBdkemZGemxmYX NQYBAZGhEKcGgXbhJ6Q2FtZEBlGWMQGRoRCnBsF2R5fmRZZx5TU2lvEBkaEQptfhcbEQpYTRdLE SA= X-CLX-Shades: MLX X-Proofpoint-GUID: lueE0rWx80MfPWyofiIKlE8vLmFEYAEq X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 impostorscore=0 lowpriorityscore=0 clxscore=168 phishscore=0 mlxscore=0 mlxlogscore=366 malwarescore=0 priorityscore=346 spamscore=0 adultscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110180046 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000005053ca05ce9ba140 Content-Type: text/plain; charset="UTF-8" Hello all While attempting minimization of a protein-ribonucleotide containing modified nucleotides, error arose FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) These atom types relate, in the given order, to atomnames C6 C5 N1 N6 of protonated 1-methyladenosine *resname 1MA in the most recent CHARMM36 psarameterization, Jul21) Added parameters included par_all36_na.prm, ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place from where such impropers are available> Thanks for advice francesco pietra --0000000000005053ca05ce9ba140 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello all
While attempting minimization of = a protein-ribonucleotide containing modified nucleotides, error arose
=

FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2= R64 CG2RC0 NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)

These atom types relate, in the given order, to atomnames C6 C5 N1 N6 of p= rotonated 1-methyladenosine *resname 1MA in the most recent CHARMM36 psaram= eterization, Jul21)

Added parameters included=C2= =A0 par_all36_na.prm, ppar_all36_na_rna_modified.str, par_all36_carb.prm. I= s any other place from where such impropers are available>

Thanks for advice
francesco pietra
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bh=dzMcd7gorPqJ4xvic+NPI82z9abXENYhwOOju0YCy34=; b=LUboLbpQdOU/pbmh3OVC53VJIuiYnG46q4MmIXOUhnX9Fy2eypAy5j6rPOJTyVGWEif3r9Wpqp/s0goGMxFPx2wPZCifJdWDlykP5V8nv5kyFNHsbCJJ0wF4IUX0kDd+2K5tdWPCfez7WKTA2NU/fgDIg7eUV+sKW00O877Ezpw= Received: from BYAPR11MB2949.namprd11.prod.outlook.com (2603:10b6:a03:81::32) by BYAPR11MB3736.namprd11.prod.outlook.com (2603:10b6:a03:f6::10) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.4608.16; Mon, 18 Oct 2021 17:55:27 +0000 Received: from BYAPR11MB2949.namprd11.prod.outlook.com ([fe80::d122:1420:3787:85ad]) by BYAPR11MB2949.namprd11.prod.outlook.com ([fe80::d122:1420:3787:85ad%3]) with mapi id 15.20.4608.018; Mon, 18 Oct 2021 17:55:27 +0000 From: Dongyue Liang To: "namd-l@ks.uiuc.edu" Subject: namd-l: Ewald for charged systems Thread-Topic: Ewald for charged systems Thread-Index: AQHXxEC/umEl1CrLm02OJiygdcx+EA== Date: Mon, 18 Oct 2021 17:55:27 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: suggested_attachment_session_id: 3c9db11b-8989-0ecb-1e3a-3eac4bd071b3 authentication-results: ks.uiuc.edu; 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boundary="_000_BYAPR11MB2949763E8C9EE7DCF4753560B3BC9BYAPR11MB2949namp_" MIME-Version: 1.0 X-OriginatorOrg: uchicago.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BYAPR11MB2949.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 990a3006-a561-487d-1120-08d9926077c2 X-MS-Exchange-CrossTenant-originalarrivaltime: 18 Oct 2021 17:55:27.1319 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 83b02c92-5f26-48ed-9e5b-6c2fca46a8e6 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 0JenwWx6VdAuYPZYubad68DtBexVDIsoZ/XH5AW01pBRmY6EeWjXuwAxHtXJt5NsifXlreSX1LU6exF4xUC1Cw== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BYAPR11MB3736 X-Proofpoint-ORIG-GUID: DqGuCECB4J1J1y9sdKBjSnOJabD6-3nO X-CLX-Shades: MLX X-CLX-Response: 1TFkXHhgeEQpMehcZGhEKWUQXaW5+GkRuBWVafXARClhYF29uS19ocBpYeVt vEQp4ThdoYwFMf0V/QkFlQBEKeUwXZ2VYXllSeB5gfRwRCkNIFwcYGxkRCkNZFwcYGBsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxkccRsGHRt3BhgaGgYTGkIcBhoGExIGGnEaEBp3BhoGGgYaBhoGG gYacRoQGncGGhEKWV4XaG55EQpJRhdfQ19JdUJFWV5PThEKQ04XblttX2lvaWgeYBtgG1MTWU5h aEB5RGVgS0huHAcZRGURClhcFx8EGgQYGRIFGxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzRRtHXhE KTVwXGxMcEQpMWhdoaU1raxEKTEYXb2tra2traxEKQk8Xeh5/Zm9CH1Nya30RCkNaFx4aBBsaHQ QYHhkEGxgSEQpCXhcbEQpEXhcYEQpCRRdke114eH9Bf35NQhEKQk4XaGMBTH9Ff0JBZUARCkJMF 29uS19ocBpYeVtvEQpCbBdgZxJYRGlsHB1jWBEKQkAXeh8ebxsbU2VjfEcRCkJYF2dzZXNAbmFh TF1iEQpNXhcHGxEKWlgXGBEKeUMXaRhkXhNgAU5pRhgRCnBoF2laeUASZ3IeQ30SEAcZGhEKcGg XYk9HXE0BfmdHQ1IQBxkaEQpwaBdtQ25IY0ZMH08SfxAHGRoRCnBoF2BHRF9uSB5CYmxgEAcZGh EKcGgXZ0dofFtBR2tfZV0QBxkaEQpwfRdkRk5OaW1mHFhoZRAHGRoRCnB/F2UZeWZeR2kbZE9zE BwaEQpwXxdpHkdpbGBIAWZ4TBAHGRoRCnBsF2xIYx1pfGloEx4cEAcZGhEKbX4XBxsRClhNF0sR IA== X-Proofpoint-GUID: DqGuCECB4J1J1y9sdKBjSnOJabD6-3nO X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 clxscore=424 priorityscore=30 impostorscore=0 suspectscore=0 mlxlogscore=867 mlxscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110180101 X-Spam-Score: 0 X-Spam-OrigSender: dliang25@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Dongyue Liang --_000_BYAPR11MB2949763E8C9EE7DCF4753560B3BC9BYAPR11MB2949namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear NAMD users, I'm simulating a charged residue in solution with periodic boundary conditi= ons. For my purpose in later research, I would prefer if no additional ions= are added to the simulation box (for charge neutralization of the entire s= ystem), and I only care about the conformations. In other words, I won't mi= nd if the energies calculated in the MD are wrong or differ by a constant, = as far as the forces are correct. I'm still hoping to take advantage of Ewald/PME for electrostatics. I found= this old discussion in the mail list, and it appears that 1) the use of a = uniform neutralizing plasma avoids the divergence problem of Ewald and give= s correct dynamics; 2) with NAMD, people "implicitly" use the uniform neutr= alizing plasma method to treat Ewald for charged systems. https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2005-2006/2314.ht= ml I tried to do MD on a charged system with PME with conventional commands (j= ust like for a neutral system) with NAMD 2.14. The simulation runs "normall= y" but I'm not seeing additional output information regarding doing PME wit= h a charged system. I did not find relevant information in the NAMD manual = either. I'm wondering whether NAMD automatically "corrects" the Ewald with = a uniform neutralizing plasma (or does some tweaks on the diverging term, e= tc.) if the system is charged. If not, is there a way that one may manually= add it? Any discussions or insights on this topic will be appreciated. Best Regards, Dongyue --_000_BYAPR11MB2949763E8C9EE7DCF4753560B3BC9BYAPR11MB2949namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear NAMD users,

I'm simulating a charged residue in solution with periodic boundary conditi= ons. For my purpose in later research, I would prefer if no additional ions= are added to the simulation box (for charge neutralization of the entire s= ystem), and I only care about the conformations. In other words, I won't mind if the energies calculated in = the MD are wrong or differ by a constant, as far as the forces are correct.=   

I'm still hoping to take advantage of Ewald/PME for electrostatics. I found= this old discussion in the mail list, and it appears that 1) the use= of a uniform neutralizing plasma avoids the divergence problem of Ewald an= d gives correct dynamics; 2) with NAMD, people "implicitly" use the uniform neutralizing plasma = method to treat Ewald for charged systems. 


I tried to do MD on a charged system with PME with conventional commands (j= ust like for a neutral system) with NAMD 2.14. The simulation runs "no= rmally" but I'm not seeing additional output information regarding doi= ng PME with a charged system. I did not find relevant information in the NAMD manual either. I'm wondering whether NAMD= automatically "corrects" the Ewald with a uniform neutralizing plasma (or does some tweaks on the diverging term, = etc.) if the system is charged. If not, is there a way that one may = manually add it?

Any discussions or insights on this topic will be appreciated. 

Best Regards,
Dongyue

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charset="UTF-8" I also seems to me that the requested parameters are not needed: N6 is part of an aromatic system whose planarity is assured by the nature of the atom type involved. Could namd be forced to proceed without? fp --000000000000b3497b05cea60a60 Content-Type: text/html; charset="UTF-8"
I also seems to me that the requested parameters are not needed: N6 is part of an aromatic system whose planarity is assured by the nature of the atom type involved. Could namd be forced to proceed without?
fp
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In this case the parameter is in par_all36_cgenff.prm, which goes with the top_all36_cgenff.rtf where the B1MA residue is defined. -Josh On 10/18/21 3:38 AM, Francesco Pietra wrote: > Hello all > While attempting minimization of a protein-ribonucleotide containing > modified nucleotides, error arose > > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) > > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 > of protonated 1-methyladenosine *resname 1MA in the most recent > CHARMM36 psarameterization, Jul21) > > Added parameters included  par_all36_na.prm, > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place > from where such impropers are available> > > Thanks for advice > francesco pietra -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!rTtit1Fs-jv9-w5brWl3U2LIMMx0OSW90qwYl2LvlBh0FSGhnTWhewlN7H8-7ET2fw$ From owner-namd-l@halifax.ks.uiuc.edu Mon Oct 18 17:15:07 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19IMF72B028152; Mon, 18 Oct 2021 17:15:07 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19IMF71Q028151; Mon, 18 Oct 2021 17:15:07 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19IMF6wO028147; Mon, 18 Oct 2021 17:15:06 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19IMF6nh028146; Mon, 18 Oct 2021 17:15:06 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19IMEhNO027731 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 18 Oct 2021 17:14:44 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 19IKlahg003769 for ; Mon, 18 Oct 2021 22:14:43 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=biodano.geo@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-ua1-f52.google.com (mail-ua1-f52.google.com [209.85.222.52]) by mx0a-00007101.pphosted.com with ESMTP id 3bs4u2e94x-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Mon, 18 Oct 2021 22:14:43 +0000 Received: by mail-ua1-f52.google.com with SMTP id e2so6780143uax.7 for ; Mon, 18 Oct 2021 15:14:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:content-transfer-encoding:mime-version:subject:message-id:date :to; bh=KF5T719rUU9qtATRYb4TXFnQXQ1/G+OZDyV0ceFeIVI=; b=hYBDl3odn9vPDXC/gtl2gD4w5AbLzg+TWOubB35OVXwGwRXaDV8jDgyaWODlN6KRu5 lI3d1r0/0Hwqo3ozs8UK276o59h76GGP2/bHLlLVQL8pyyKhIwRj5orMkkguSQVVcqI3 s7bghX7XgZyCrf66N28u9XsFBVzbrJSVLQumheTOO3Scr0fk35xEWy3mq/jbXvEXEqrJ vUxvRU8DQM+apuHpxKrqQiPmlLUbsaATxI/Uxks1hGxiqi9WtJ9CNUJeHYv49IQyNQVQ Ur1AeO+kQvaZ8cmbn2PYznPo64i8ZrDswpwKuBQg79YEkOpvYtfyCuChq96+bnmvHZLl eZJQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:content-transfer-encoding:mime-version :subject:message-id:date:to; bh=KF5T719rUU9qtATRYb4TXFnQXQ1/G+OZDyV0ceFeIVI=; b=8Nq1lJOz7PPRvan0cASfZdhj2uiOrSsIhcNBtFox/d4j4digAI/SAAPxzD+Ztq5yTe +ovKrrASk5/FRKZRW4e5pcUTC8FARWRB+1wP70JMdR4NYhtl1YBVXZAaPrbwOGrqcijL HGPgOLyUqJJbmRmMbRMY/tbcp4ulmZtjiOi0m1Gs+s9/0R0CJwJ/cHRXgHMaUIRt8572 0vhVz/zfaM6O9cpxmaxxlzYUn2W3H8+s3lMIoNoeEKqK956cb29joezDJ67D3LA/nhbl Xo6yW5527Hqzt6J/LsVyr7NawMfBwf5ebZe4tyB+WZ0sW4hT3+BPy3M7hfbL6VZo/ZZm +dgw== X-Gm-Message-State: AOAM533K/ttZ4rXrkqqTGPmMJkiUMLmlaV8Kyenzrl49ET9s9vpHT8vB DHc6UOkZRjOcj+2iPwoaHp4atLL/mQA= X-Google-Smtp-Source: ABdhPJxRjWtmsOC5nghDMqgC08qZlu2NB7woJKtlmfuz6vkZa/SzZWndRlEAYk5V95mhZqR2kQRdqw== X-Received: by 2002:a67:8cca:: with SMTP id o193mr31059045vsd.56.1634595281910; Mon, 18 Oct 2021 15:14:41 -0700 (PDT) Received: from ?IPv6:2001:1388:3cc3:77f0:492:7f45:3e3c:f6db? ([2001:1388:3cc3:77f0:492:7f45:3e3c:f6db]) by smtp.gmail.com with ESMTPSA id 203sm9791026vkt.37.2021.10.18.15.14.40 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 18 Oct 2021 15:14:41 -0700 (PDT) From: =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.7\)) Subject: namd-l: NAMD3 information Message-Id: <48F4933D-5C3A-4CFE-B458-8AAB6C8F91AC@gmail.com> Date: Mon, 18 Oct 2021 17:14:47 -0500 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3608.120.23.2.7) X-Proofpoint-ORIG-GUID: pjyS7ZjvbXTRXSY0EJWifRg1pWxbE81i X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIcEQpMehcZGhIRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHHRgRCkNZFwcbGh8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBxxHh8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWkBTeR1wQFxIcn54cnlzGm9gfUNMeE0bWn1SSG8SG0MRClhcFx8EGgQYGRIF GxoEGxoaBB4SBBgZEBseGh8aEQpeWRdzRR9wXxEKTVwXGxkdEQpMWhdoYU1BaxEKTEYXb29ra2t raxEKQk8XYGRrH2dEGHBmGFoRCkNaFxgaEwQSHwQYGBgEHxgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXY2x5Y316fmFGT2YRCkJOF2NTY2t7E 1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXb09kQVpCUG1ma1kRCkJAF2huQU9QHmZsfgVuEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXbG5zX3wcQx4eYR8RCnBoF3obGEh4eFxERAV vEBkaEQpwaBdobxNGRmx/TmFPbBAZGhEKcGwXaWEBf0lme0IZeh4QGRoRCm1+FxsRClhNF0sRIA == X-Proofpoint-GUID: pjyS7ZjvbXTRXSY0EJWifRg1pWxbE81i X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 clxscore=186 priorityscore=308 impostorscore=0 suspectscore=0 mlxlogscore=522 mlxscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110180119 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 19IMEnNN027744 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= Dear users, I want to use NAMD3 to do SMD and umbrella sampling, is this version supported? Best, Geo. 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Colvars isn't supported with CUDASOAIntegrate turned on at present. -Josh On 10/18/21, 6:21 PM, "owner-namd-l@ks.uiuc.edu on behalf of "ROPÓN-PALACIOS G."" wrote: Dear users, I want to use NAMD3 to do SMD and umbrella sampling, is this version supported? Best, Geo. 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=7ia/ubfjLq6vzGuc3vOutUg/AF55wC/i0T5iZhjPFBU=; b=YTpwSMln//I/tRHh2mmvW7MsCmvTZ8n9RzdZtSTHSzpQ8CndwMypywCWm/qQDmW1/g 0R4H2N4maaAEd69kMSaCNly7rDsReT1AbDC47G5ii06h+uxh4GGn3SlS+JiQIrFmhiqs jekL5jbR8TpmcWc+rnKfdJV2P44pRjb4PJnoGs51ms7qAnu8s/fOoA8C59egj5x9nady Ena/kh11eQIHsymFYr/gzEU5RgwtfV0Q8TXI3nX3ZUvF32v7lFhi5AVsRRPpSCyebZk3 3dMJ2EeMqRkxKgsNOZJ67roQwjf59e19XA6cCkLLUr3i3D1kYTPWPzd2unraHqI+vkJY N1ow== X-Gm-Message-State: AOAM531LGF4x3g1zR4+llpBZZZwn6QX3kjKfrtb1Cc9X8GgnBDVTvBZq 4Owft/LyWTJyQKWKTdNo2AzOb0nh4Ip7xUCNXSU= X-Google-Smtp-Source: ABdhPJxEVCCxEAthc9Ahrhy4X+Zka6DbTf3OYiE3jvVePrwIT+e3111VW1d4V0wFFKZESWhRHol0SNmIqEXWGczFFVM= X-Received: by 2002:a37:6551:: with SMTP id z78mr25917751qkb.96.1634628752905; Tue, 19 Oct 2021 00:32:32 -0700 (PDT) References: <327c9dd5-1114-6e97-9825-7d9355b63525@msu.edu> In-Reply-To: <327c9dd5-1114-6e97-9825-7d9355b63525@msu.edu> From: Francesco Pietra Date: Tue, 19 Oct 2021 09:32:21 +0200 Message-ID: Subject: Re: namd-l: impropers for protonated 1-methyladenosine To: Josh Vermaas Cc: NAMD Content-Type: multipart/alternative; boundary="0000000000002819b705ceafaac5" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwSEQpMehcZHxkRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHGR8aEQpDWRcHGB0YEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ScR8SEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1lzGhpjY2IYHHUeEwd5Hx55GnlAUmsdRRhZeFtwGURtEQpYXBcfBBoEGBkS BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NaaEFZEQpNXBcZGRgRCkxaF3hpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGB gEGx0cEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2ZpGF1seG1jYVAdEQpCThdjU2NrexNYfhpfXhEKQkwXZHtPUn8TSVp6cxwRCkJs F2UYRUViR0thaEtsEQpCQBdhTgVwbAVFBVNtQREKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF2d AYHpgeHAbe2J6EQpwaBdpGFx/ZxJ7cx5pTxAeEhEKcGgXZHpmRnpsZmFzUGAQGRoRCnBoF2NdTh 5YEx9ZaUVmEBkaEQpwaBdjYkRLU155H0t9aRAZGhEKcGgXb2FEYhpufxppG0UQGRoRCnB9F2t6H GBTGRhvUEVgEBkaEQpwfxduH2ddfV5AE3hkeRAbGxoRCnBfF2RjaG0efVBrTFBgEBkaEQpwbBdk eX5kWWceU1NpbxAeEhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: sY00IIH26_49-S54S0SjxA7o2sRqZ3nG X-Proofpoint-GUID: sY00IIH26_49-S54S0SjxA7o2sRqZ3nG MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 spamscore=0 priorityscore=353 adultscore=0 clxscore=168 bulkscore=0 suspectscore=0 mlxscore=0 mlxlogscore=424 malwarescore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110190045 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000002819b705ceafaac5 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Josh Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you rightly suggested (the requested params are of genff type) par_all36_carb.prm par_all36_cgenff.prm par_all36_lipid.prm par_all36m_prot.prm par_all36_na.prm toppar_all36_na_modifications.str toppar_all36_na_rna_modified.str toppar_all36_prot_arg0.str toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand) this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains) thanks for you care francesco On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: > If impropers are defined in the psf, NAMD will expect parameters for > them. In this case the parameter is in par_all36_cgenff.prm, which goes > with the top_all36_cgenff.rtf where the B1MA residue is defined. > > -Josh > > On 10/18/21 3:38 AM, Francesco Pietra wrote: > > Hello all > > While attempting minimization of a protein-ribonucleotide containing > > modified nucleotides, error arose > > > > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 > > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) > > > > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 > > of protonated 1-methyladenosine *resname 1MA in the most recent > > CHARMM36 psarameterization, Jul21) > > > > Added parameters included par_all36_na.prm, > > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place > > from where such impropers are available> > > > > Thanks for advice > > francesco pietra > > -- > Josh Vermaas > > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and > Molecular Biology > Michigan State University > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/__;!!DZ3fjg!ucN_Frml1nkTrFlYilsQtNCnbHQ9fvsqU8FXnVb53oc3xFHZT-2ky= og2QfcnJop2hQ$=20 > > --0000000000002819b705ceafaac5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Josh
Most unfortunately I missed to indi= cate the full list of parameter files used, which includes the one that you= =C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.p= rm
toppar_all36_na_modifications.str
toppar_all36_na_rn= a_modified.str
toppar_all36_prot_arg0.str
toppar_water_= ions_namd_adapted.str (I just commented out what namd does not understand)<= br>

this is why I don't understand namd's = request (the requested params are available and unnecessary) and I asked wh= ether namd can be forced to override psfgen (I used autopsfgen because ther= e are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at = 10:23 PM Josh Vermaas <vermaasj@msu.= edu> wrote:
If impropers are defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing <= br> > modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6 =
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place=
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu<= br> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
https://prl.n= atsci.msu.edu/people/faculty/josh-vermaas/

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Tue, 19 Oct 2021 18:32:23 +0200 Received: from ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6]) by ebox-prod-srv13.win.su.se ([fe80::f071:3d85:b2d0:c2f6%2]) with mapi id 15.01.2308.015; Tue, 19 Oct 2021 18:32:23 +0200 From: Alessandro Ruda To: "namd-l@ks.uiuc.edu" Subject: Re: namd-l: Re: MD run terminated with singnal 11 Thread-Topic: namd-l: Re: MD run terminated with singnal 11 Thread-Index: AQHXsICejlnVUcPicEKrCLWPP+bjG6vUGBDA///27oCAACisUYAGdOod Date: Tue, 19 Oct 2021 16:32:23 +0000 Message-ID: <5b9e9882ea2943abba9629348afb0828@su.se> References: ,<7e513d7c-9f37-dc52-5386-c54461384fd0@msu.edu>,<38fa28cabdf5496d962628fc00a5a0c3@su.se> In-Reply-To: <38fa28cabdf5496d962628fc00a5a0c3@su.se> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [130.237.154.250] Content-Type: multipart/alternative; boundary="_000_5b9e9882ea2943abba9629348afb0828suse_" X-Proofpoint-ORIG-GUID: Qj3xCKg9U_3AG3Vfe9D9oqS-xdWXauY5 X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBdgenpdaUtdZR9fThEKWFgXelppARp9AU1icEA RCnhOF2ccf0h8X0tOXxwaEQp5TBdkQXISRl1wRwVwYxEKQ0gXBxgdGBEKQ1kXBxsaEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseGXEYHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd7QBlSaWFNE391GWttGXxMTxNuE0VbeQdSTn1yS19zHxEKWFwXHwQaBBgZEgUb GgQbGhoEHhIEGxMQGx4aHxoRCl5ZF3NaYE8YEQpNXBceGhwRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29va2tsa2sRCkJPF21/AQVCY0FBWAUfEQpDWhcdHQQYGRIEGRwEGx oSEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdnHH9IfF9LTl8cGhEKQkkXZxx/SHxfS05fH BoRCkJFF2hdXEtuWxhAWAF9EQpCThdnHH9IfF9LTl8cGhEKQkwXelppARp9AU1icEARCkJsF2l+ aBJDYV5JbWhBEQpCQBdhTFgfBUEef3gZSREKQlgXZ3Nlc0BuYWFMXWIRClpYFx4RCnlDF24YfG9 Sf1wdHB1JEQpwZxdpQ25QAVlzRwEeUxAZGhEKcGgXbk9+a0dLZWBoTk4QEhoRCnBoF2VbG2RYWH B/HlByEBsaEhEKcGgXaRNLTUxyZFIdbkEQGRoRCnBoF2B+aB1YZkZ4fkdkEBIfEQpwaBdiHEBTU 05dR0hcQhAZGhEKcGcXZX1dQRpcfkRrRWsQGRoRCnB9F2t6HGBTGRhvUEVgEBkaEQpwZxdjHk9n bklvbWVibxAZGhEKcH8Xbh9nXX1eQBN4ZHkQGxsbEQpwXxdkY2htHn1Qa0xQYBAZGhEKcGwXZk1 eY2RsX3pfeQEQGRoRCnBDF2dDWGBnaVgTZkZ5EBMfEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: Qj3xCKg9U_3AG3Vfe9D9oqS-xdWXauY5 X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 clxscore=163 impostorscore=0 malwarescore=0 bulkscore=0 phishscore=0 adultscore=0 spamscore=0 mlxscore=0 mlxlogscore=999 lowpriorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110190097 X-Spam-Score: 0 X-Spam-OrigSender: alessandro.ruda@su.se X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alessandro Ruda --_000_5b9e9882ea2943abba9629348afb0828suse_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable Anyway, I solved it by decreasing the time-step to 3 fs. /alex ________________________________ From: Alessandro Ruda Sent: 15 October 2021 15:56:04 To: Josh Vermaas; namd-l@ks.uiuc.edu Subject: Re: namd-l: Re: MD run terminated with singnal 11 Hi Josh, yes, I checked them and they are ok, I just removed the entire path for the= sake of clarity when I posted the question! Thank you! /alex ________________________________ From: Josh Vermaas Sent: 15 October 2021 15:30:05 To: namd-l@ks.uiuc.edu; Alessandro Ruda Subject: Re: namd-l: Re: MD run terminated with singnal 11 Hi Alex, Are you sure that you have the right structure, coordinates, bincoordinates= , and binvelocities files? Those do not look sane to me. -Josh On 10/15/21 8:04 AM, Alessandro Ruda wrote: It seems related to the PME parameters anyway. I tried to change parameters= such as the size of the grid or the spacing from 0.5 to 1.5 but it didn't = work as well. Any hints on what could cause the instability? All the best, Alex ________________________________ From: Alessandro Ruda Sent: 23 September 2021 15:46:31 To: namd-l@ks.uiuc.edu Subject: MD run terminated with singnal 11 Dear NAMD comunity, I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl - = 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization fo= llowed by heating and short equilibration (few us) but when I start the pro= duction it stops after few seconds with this error in slurm (i am running o= n a cluster). * namd2:37211 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a= 0. Backtrace: * namd2:37213 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a12= 0. Backtrace: * namd2:110002 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3f= 20. Backtrace: * namd2:37217 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe224b27a= 0. Backtrace: ..etc...etc.... * software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_= chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213] * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14] ..etc...etc please find attached file if needed.The log file simply states: * mpprun info: Job terminated with error It happened to another simulation also with a very much similar tetrasaccha= ride and I managed to make it work by building the tetrasaccharide again, s= olvate it, minimize etc etc. It worked but I don't know why. It didn't work for this one and every time I restart the simulation I get t= he same error. This is the configuration file I am using: ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- structure /.pdf coordinates /.pdb bincoordinates /.coor binvelocities /.vel set temperature 300 firsttimestep 0 # Input paraTypeCharmm on parameters /Parameters/par_all36_carb.inp parameters /Parameters/par_water_ions.inp parameters /Parameters/par_all36_prot.inp parameters /Parameters/par_all36m_prot.inp parameters /Parameters/par_hbond.inp # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 16.0 margin 0 # Integrator Parameters timestep 4.0 ; rigidBonds all ; nonbondedFreq 1 fullElectFrequency 1 stepspercycle 20 pairlistsPerCycle 2 wrapWater on wrapAll on # Constant Temperature Control langevin on ; langevinDamping 1 ; langevinTemp $temperature langevinHydrogen off ; # PME PME yes PMEGridSpacing 1.0 #manual grid definition PMEGridSizeX 60 PMEGridSizeY 60 PMEGridSizeZ 60 # Constant Pressure Control (variable volume) useGroupPressure yes ; useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 50.0 langevinPistonDecay 25.0 langevinPistonTemp $temperature # Output outputName $outputname restartfreq 2500 ;# 2500steps =3D every 10ps dcdfreq 2500 ;# =3D every 10ps xstFreq 2500 outputEnergies 2500 outputtiming 2500 outputPressure 150 binaryoutput yes extendedSystem /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_Le= X4_HMR/3_equilibration/LeX4_heated.restart.xsc run 125000000 ;# 500 ns ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- I really don't know what the problem is related to. Does anybody have some = hints about it? Thank you in advance, Alessandro -- Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!p7Vns7ycoXlsEBI8bEmbeNhwQYYkPJxgZkUQ9RUly9aKSjy4uemJ6iH= ynFHsH-646g$=20 --_000_5b9e9882ea2943abba9629348afb0828suse_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: Quoted-printable

Anyway, I solved it by decreasing the time-step to 3 fs.


/alex


From: Alessandro Ruda
Sent: 15 October 2021 15:56:04
To: Josh Vermaas; namd-l@ks.uiuc.edu
Subject: Re: namd-l: Re: MD run terminated with singnal 11
 

Hi Josh,


yes, I checked them and they are ok, I just removed the entire pa= th for the sake of clarity when I posted the question!


Thank you!


/alex



From: Josh Vermaas <verm= aasj@msu.edu>
Sent: 15 October 2021 15:30:05
To: namd-l@ks.uiuc.edu; Alessandro Ruda
Subject: Re: namd-l: Re: MD run terminated with singnal 11
 
Hi Alex,

Are you sure that you have the right structure, coordinates, bincoordinates= , and binvelocities files? Those do not look sane to me.

-Josh

On 10/15/21 8:04 AM, Alessandro Ruda wrote:<= br>

It seems related to the PME parameters anyway. I tried to change paramet= ers such as the size of the grid or the spacing from 0.5 to 1.5 but it didn= 't work as well.


Any hints on what could cause the instability?


All the best,

Alex


From: Alessandro Ruda
Sent: 23 September 2021 15:46:31
To: namd-l@ks.uiuc.edu
Subject: MD run terminated with singnal 11
 
Dear NAMD comunity,

I am running a simulation of a tetrasacchar= ide in salty water (0.2M NaCl - 50x50x50 wb) using Hydrogen Mass Repartitio= n. I run a first minimization followed by heating and short equilibration (few us) but when I start the production it stops = after few seconds with this error in slurm (i am running on a cluster).

  • namd2:37211 terminated wi= th signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a0.  Backtrace:
  • namd2:37213 terminated wi= th signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a120.  Backtrace:
  • namd2:110002 terminated w= ith signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3f20.  Backtrace:
  • namd2:37217 terminated w= ith signal 11 at PC=3Dfc9213 SP=3D7ffe224b27a0.  Backtrace:
...etc...etc....
  • software/sse/manual/namd/= 2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeP= article+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]<= /b>
  • /software/sse/manual/namd= /2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11Pme= Particle+0x2d43)[0xfc9213]
  • /software/sse/manual/nam= d/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]
...etc...etc

please find attached file if needed.The log= file simply states:

  • mpprun info:  = Job terminated with error

It happened to another simulation also with= a very much similar tetrasaccharide and I managed to make it work by build= ing the tetrasaccharide again, solvate it, minimize etc etc. It worked but I don't know why.
It didn't work for this one and every time = I restart the simulation I get the same error.

This is the configuration file I am using:<= /span>

--------------------= ---------------------------------------------------------------------= ----------------------------------------------= ----------------------------------------------= ----------------------------------------------= ---

structure          /.pdf
coordinates        /.pdb
bincoordinates     /.coor
binvelocities      /.vel

set temperature    300

firsttimestep      0

# Input
paraTypeCharmm        on
parameters          /Parameter= s/par_all36_carb.inp
parameters          /Parameter= s/par_water_ions.inp
parameters          /Parameter= s/par_all36_prot.inp
parameters          /Parameter= s/par_all36m_prot.inp
parameters          /Parameter= s/par_hbond.inp


# Force-Field Parameters
exclude           &n= bsp; scaled1-4
1-4scaling          1.0
cutoff           &nb= sp;  12.0
switching           on
switchdist          10.0
pairlistdist        16.0
margin           &nb= sp;  0

# Integrator Parameters
timestep            = 4.0    ;
rigidBonds          all  = ;
nonbondedFreq       1
fullElectFrequency  1
stepspercycle       20
pairlistsPerCycle   2
wrapWater           on
wrapAll           &n= bsp; on


# Constant Temperature Control
langevin            = on    ;
langevinDamping     1     ;
langevinTemp        $temperature
langevinHydrogen    off    ;

# PME
PME            =      yes
PMEGridSpacing      1.0

#manual grid definition
PMEGridSizeX        60
PMEGridSizeY        60
PMEGridSizeZ        60


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  50.0
langevinPistonDecay   25.0
langevinPistonTemp    $temperature


# Output
outputName          $outputnam= e

restartfreq         2500  = ;   ;# 2500steps =3D every 10ps
dcdfreq           &n= bsp; 2500    ;# =3D every 10ps
xstFreq           &n= bsp; 2500
outputEnergies      2500
outputtiming        2500
outputPressure      150
binaryoutput        yes


extendedSystem      /proj/carbohydratedynamics/use= rs/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibration/LeX4_heated.restart.xsc

run 125000000 ;#  500 ns
-------------------------------------------------------------------------------------= ----------------------------------------------= ----------------------------------------------= --------------------------------------------= ---------

I really don't know what th= e problem is related to. Does anybody have some hints about it?

Thank you in advance,
Alessandro






--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="0000000000000176ad05ceb8011e" X-Proofpoint-GUID: 1_y2fepQ5Z4ZMyy2fnAI4c1ZIlgzazCw X-Proofpoint-ORIG-GUID: 1_y2fepQ5Z4ZMyy2fnAI4c1ZIlgzazCw X-CLX-Response: 1TFkXGxwTEQpMehcZHxIRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHh0eEQpDWRcHGRMfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4TcRwaEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxt1UxhMT1p7H3AecGdTUxhMRGtjHkkbcGNGTVBLUGldEQpYXBcfBBoEGBkS BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc1phf30RCk1cFxseGREKTFoXfGFNQU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbHR0RCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQ kUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwXZRhFRWJH S2FoS2wRCkJAF2lQQXlQYQEfcH9iEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXZ0B gemB4cBt7YnoRCnBnF2V9XUEaXH5Ea0VrEBwaEQpwaBdpRUl5bm1PeR0aYhAZGhEKcGgXbm8SQ2 8aZWt4fBkQGRoRCnBoF2kYXH9nEntzHmlPEBwaEQpwaBdkemZGemxmYXNQYBAeEhEKcGgXb2FEY hpufxppG0UQHBoRCnBnF2lDblABWXNHAR5TEBwaEQpwfRdrehxgUxkYb1BFYBAZGhEKcH8Xbh9n XX1eQBN4ZHkQGxseEQpwXxdkY2htHn1Qa0xQYBAZGhEKcGwXZHl+ZFlnHlNTaW8QHBoRCm1+Fxs RClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 suspectscore=0 clxscore=169 mlxscore=0 adultscore=0 malwarescore=0 phishscore=0 priorityscore=358 bulkscore=0 impostorscore=0 mlxlogscore=624 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110190103 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000000176ad05ceb8011e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong francesco ---------- Forwarded message --------- From: Francesco Pietra Date: Tue, Oct 19, 2021, 9:32 AM Subject: Re: namd-l: impropers for protonated 1-methyladenosine To: Josh Vermaas Cc: NAMD Hi Josh Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you rightly suggested (the requested params are of genff type) par_all36_carb.prm par_all36_cgenff.prm par_all36_lipid.prm par_all36m_prot.prm par_all36_na.prm toppar_all36_na_modifications.str toppar_all36_na_rna_modified.str toppar_all36_prot_arg0.str toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand) this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains) thanks for you care francesco On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: > If impropers are defined in the psf, NAMD will expect parameters for > them. In this case the parameter is in par_all36_cgenff.prm, which goes > with the top_all36_cgenff.rtf where the B1MA residue is defined. > > -Josh > > On 10/18/21 3:38 AM, Francesco Pietra wrote: > > Hello all > > While attempting minimization of a protein-ribonucleotide containing > > modified nucleotides, error arose > > > > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 > > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) > > > > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 > > of protonated 1-methyladenosine *resname 1MA in the most recent > > CHARMM36 psarameterization, Jul21) > > > > Added parameters included par_all36_na.prm, > > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place > > from where such impropers are available> > > > > Thanks for advice > > francesco pietra > > -- > Josh Vermaas > > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and > Molecular Biology > Michigan State University > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/__;!!DZ3fjg!tQ1PXRTRF7UXNRkBTP2F0NqsuWXWHcGhbxm3-AcwsEqcQ-2cJnGvc= 5CIke4d8wqMCw$=20 > > --0000000000000176ad05ceb8011e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Perhaps there is a discrepancy from topology and params, = i.e. autopsf sets unnecessary impropers while params for them do not exist = just because they are not needed. I wasn't unable to find the requested= improper params in the list of prm and str above files. But I may be easil= y wrong
francesco

---------- Forwarded message ------= ---
From: Francesco Piet= ra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AMSubject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Jo= sh Vermaas <vermaasj@msu.edu>=
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfort= unately I missed to indicate the full list of parameter files used, which i= ncludes the one that you=C2=A0 rightly suggested (the requested params are = of genff type)

par_all36_carb.prm
par_al= l36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm<= /div>
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str=
toppar_water_ions_namd_adapted.str (I just commented out what na= md does not understand)

this is why I don'= t understand namd's request (the requested params are available and unn= ecessary) and I asked whether namd can be forced to override psfgen (I used= autopsfgen because there are so many chains)

than= ks for you care
francesco


=

If improper= s are defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing <= br> > modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6 =
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place=
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

ve= rmaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology
Michigan State University
ht= tps://prl.natsci.msu.edu/people/faculty/josh-vermaas/

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charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable You didn't happen to mix a topology file from toppar_c36_jul20 with a=20 parameter file from toppar_c36_jul21, did you? In the July 2020 release,=20 there is a line like this in par_all36_cgenff.prm: CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu,=20 TO BE OPTIMIZED, RNA This corresponds to the improper definition in that version of the force=20 field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6" In the 2021 r= elease, the order in the=20 improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6=C2=A0=C2=A0 C5= ", so the parameter that=20 would be looked up also changes: CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC,=20 yxu, TO BE OPTIMIZED, RNA To be honest, I hadn't realized that changes like this happened, but in=20 this case it is all laid out in toppar_all.history: "!following removed due to conflict CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE=20 OPTIMIZED, RNA CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0=20 NG2P1=C2=A0 NG2P1 CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE=20 OPTIMIZED, RNA !which will be treated with CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE=20 OPTIMIZED, RNA CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE=20 OPTIMIZED, RNA CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0=C2=A0= =C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu,=20 TO BE OPTIMIZED" -Josh On 10/19/21 1:29 PM, Francesco Pietra wrote: > Perhaps there is a discrepancy from topology and params, i.e. autopsf=20 > sets unnecessary impropers while params for them do not exist just=20 > because they are not needed. I wasn't unable to find the requested=20 > improper params in the list of prm and str above files. But I may be=20 > easily wrong > francesco > > ---------- Forwarded message --------- > From: *Francesco Pietra* > > Date: Tue, Oct 19, 2021, 9:32 AM > Subject: Re: namd-l: impropers for protonated 1-methyladenosine > To: Josh Vermaas > > Cc: NAMD > > > > Hi Josh > Most unfortunately I missed to indicate the full list of parameter=20 > files used, which includes the one that you rightly suggested (the=20 > requested params are of genff type) > > par_all36_carb.prm > par_all36_cgenff.prm > par_all36_lipid.prm > par_all36m_prot.prm > par_all36_na.prm > toppar_all36_na_modifications.str > toppar_all36_na_rna_modified.str > toppar_all36_prot_arg0.str > toppar_water_ions_namd_adapted.str (I just commented out what namd=20 > does not understand) > > this is why I don't understand namd's request (the requested params=20 > are available and unnecessary) and I asked whether namd can be forced=20 > to override psfgen (I used autopsfgen because there are so many chains) > > thanks for you care > francesco > > > > On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas > wrote: > > If impropers are defined in the psf, NAMD will expect parameters for > them. In this case the parameter is in par_all36_cgenff.prm, which > goes > with the top_all36_cgenff.rtf where the B1MA residue is defined. > > -Josh > > On 10/18/21 3:38 AM, Francesco Pietra wrote: > > Hello all > > While attempting minimization of a protein-ribonucleotide > containing > > modified nucleotides, error arose > > > > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 > > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) > > > > These atom types relate, in the given order, to atomnames C6 C5 > N1 N6 > > of protonated 1-methyladenosine *resname 1MA in the most recent > > CHARMM36 psarameterization, Jul21) > > > > Added parameters included=C2=A0 par_all36_na.prm, > > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other > place > > from where such impropers are available> > > > > Thanks for advice > > francesco pietra > > --=20 > Josh Vermaas > > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry > and Molecular Biology > Michigan State University > https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty= /josh-vermaas/__;!!DZ3fjg!qNT4ZozbCnn8bUfxdAuMtyVkLckSj-chLESEsk9oXna7Kt5KE= SWU32r_Ts7Pw0NFAg$=20 > > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!qNT4ZozbCnn8bUfxdAuMtyVkLckSj-chLESEsk9oXna7Kt5KESWU32r= _Ts7Pw0NFAg$=20 --------------529EE6E29E1E0DBEEB1F3D5B Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1  NG2P1     42.00  0&n= bsp;    0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6   C5   N1   N6= " In the 2021 release, the order in the improper is different "IMPR C6   N1   N= 6   C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1  NG2P1  CG2RC0    52.00  0&n= bsp;    0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, but in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1  NG2P1     42.00  0&n= bsp;    0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1  NG2P1     42.00  0&n= bsp;    0.00 ! from CG2R64 CG2RC0 NG2P1  NG2P1
CG2R64 CG2R62 NG2P1  NG2P1     42.00  0&n= bsp;    0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1  NG2P1  CG2R62    52.00  0&n= bsp;    0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1  NG2P1  CG2R61    52.00  0&n= bsp;    0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1  NG2P1  CG2RC0    52.00  0&n= bsp;    0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20=20=20=20=20=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you  rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.e= du> wrote:
If impropers are defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included  par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/facu= lty/josh-vermaas/


--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="0000000000005cd6fe05ceb8d4dd" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcZHxoRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHxgeEQpDWRcHGBwYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxNhQUMbU0RjR0NCS1xdcGxYQRNsRl5LcnVGQHVkZWMHEQpYXBcfBBoEGBkS BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc1pmZl0RCk1cFxkZGxEKTFoXfGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbHRIRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwX ZRhFRWJHS2FoS2wRCkJAF24acxMTbmF9Wm8fEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxEKeUMXZ0B gemB4cBt7YnoRCnBnF2lDblABWXNHAR5TEB0aEQpwaBdpRUl5bm1PeR0aYhAeEhEKcGgXYUh+fh xwGWd/GGMQGRoRCnBoF2RNAWNPXUIYXlJPEBkaEQpwaBdheHNaGH1jWEVHHxAZGhEKcGgXZAFCH HkbYmJ/GGUQGRoRCnB9F2t6HGBTGRhvUEVgEBkaEQpwfRdkHEl6HVBnHQFoGhAeEhEKcH8Xbh9n XX1eQBN4ZHkQGxoZEQpwXxdkY2htHn1Qa0xQYBAZGhEKcH8XYWZvWxpnZEJIHVsQGxkfEQpwXxd jYhJQSGN4H3xCfRATHREKcGwXZHl+ZFlnHlNTaW8QHhIRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: 9Kki1ynImihavwZFrk9FltaX_lj_NOI- X-Proofpoint-GUID: 9Kki1ynImihavwZFrk9FltaX_lj_NOI- MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 bulkscore=0 spamscore=0 adultscore=0 phishscore=0 malwarescore=0 clxscore=171 lowpriorityscore=0 mlxlogscore=822 suspectscore=0 mlxscore=0 priorityscore=350 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110190107 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000005cd6fe05ceb8d4dd Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable According to the README created for this work: AUTOPSFGEN > Using topology from toppar_c36_jul21 > Maintaining the few original water molecules > Replaced wrong names for modified nucleosides with those in file > toppar_all36_na_rna_modified.str > .......... > ............. > MD > Minimization using parameters from toppar_c36_jul21 > Not using toppar_water_ions.str because it has known problems with namd. > Using instead > par_water_ions.prm from namd-adapted 2016 charmm36: > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 > NG2P1 > (ATOMS 4433 C6, 4432 C5, 4437 N1, 4434 N6), resid 1MA > I will consider accurately your reply tomorrow, it is late in the night here and my lucidity is largely vanished Thanks indeed francesco On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas wrote: > You didn't happen to mix a topology file from toppar_c36_jul20 with a > parameter file from toppar_c36_jul21, did you? In the July 2020 release, > there is a line like this in par_all36_cgenff.prm: > > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, > TO BE OPTIMIZED, RNA > > This corresponds to the improper definition in that version of the force > field. "IMPR C6 C5 N1 N6" In the 2021 release, the order in the > improper is different "IMPR C6 N1 N6 C5", so the parameter that wou= ld > be looked up also changes: > > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, B1MA, from 3MC, > yxu, TO BE OPTIMIZED, RNA > > To be honest, I hadn't realized that changes like this happened, but in > this case it is all laid out in toppar_all.history: > > "!following removed due to conflict > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! B1MA, yxu, TO BE > OPTIMIZED, RNA > CG2R64 CG2R61 NG2P1 NG2P1 42.00 0 0.00 ! from CG2R64 CG2RC0 > NG2P1 NG2P1 > CG2R64 CG2R62 NG2P1 NG2P1 42.00 0 0.00 ! B3MC, yxu, TO BE > OPTIMIZED, RNA > !which will be treated with > CG2R64 NG2P1 NG2P1 CG2R62 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2R61 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, from 3MC, yxu, TO > BE OPTIMIZED" > > -Josh > > On 10/19/21 1:29 PM, Francesco Pietra wrote: > > Perhaps there is a discrepancy from topology and params, i.e. autopsf sets > unnecessary impropers while params for them do not exist just because they > are not needed. I wasn't unable to find the requested improper params in > the list of prm and str above files. But I may be easily wrong > francesco > > ---------- Forwarded message --------- > From: Francesco Pietra > Date: Tue, Oct 19, 2021, 9:32 AM > Subject: Re: namd-l: impropers for protonated 1-methyladenosine > To: Josh Vermaas > Cc: NAMD > > > Hi Josh > Most unfortunately I missed to indicate the full list of parameter files > used, which includes the one that you rightly suggested (the requested > params are of genff type) > > par_all36_carb.prm > par_all36_cgenff.prm > par_all36_lipid.prm > par_all36m_prot.prm > par_all36_na.prm > toppar_all36_na_modifications.str > toppar_all36_na_rna_modified.str > toppar_all36_prot_arg0.str > toppar_water_ions_namd_adapted.str (I just commented out what namd does > not understand) > > this is why I don't understand namd's request (the requested params are > available and unnecessary) and I asked whether namd can be forced to > override psfgen (I used autopsfgen because there are so many chains) > > thanks for you care > francesco > > > > On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: > >> If impropers are defined in the psf, NAMD will expect parameters for >> them. In this case the parameter is in par_all36_cgenff.prm, which goes >> with the top_all36_cgenff.rtf where the B1MA residue is defined. >> >> -Josh >> >> On 10/18/21 3:38 AM, Francesco Pietra wrote: >> > Hello all >> > While attempting minimization of a protein-ribonucleotide containing >> > modified nucleotides, error arose >> > >> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 >> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) >> > >> > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 >> > of protonated 1-methyladenosine *resname 1MA in the most recent >> > CHARMM36 psarameterization, Jul21) >> > >> > Added parameters included par_all36_na.prm, >> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place >> > from where such impropers are available> >> > >> > Thanks for advice >> > francesco pietra >> >> -- >> Josh Vermaas >> >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and >> Molecular Biology >> Michigan State University >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!sWf9yEyiGEPfRJxfNvpsfnM8cY3ouwihhgOewmRdZFM3WYMYbyy6= MlPRaDU5oDcOqw$=20 >> >> >> > -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > --0000000000005cd6fe05ceb8d4dd Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
According to the README created for this work:
<= div>
AUTOPS= FGEN
Using topology from toppar_c36_jul21
Maintaining the few origina= l water molecules
Replaced wrong names for modified nucleosides with tho= se in file toppar_all36_na_rna_modified.str
..........
= ............
MD
Minimization using parameters from toppar_c36= _jul21
Not using toppar_water_ions.str because it has known problems wit= h namd. Using instead
par_water_ions.prm from namd-adapted 2016 charmm3= 6:
FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2= P1 NG2P1
(ATOMS 4433 C6, 4432 C5, 4437 N1, 4434 N6), resid 1MA

I will consider accurately your reply tomorro= w, it is late in the night here and my lucidity is largely vanished

Thanks indeed
francesco

=

On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas <vermaasj@msu.edu> wrote:
=20=20
You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6= " In the 2021 release, the order in the improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N= 6=C2=A0=C2=A0 C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, but in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1
CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20=20=20=20=20=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you=C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.edu> wrote:
If impropers ar= e defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
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boundary="000000000000cc60e805ceb8e96e" X-Proofpoint-ORIG-GUID: XoWfQTkN58a1hWIGbALnY7y7T1tXeP8a X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0YEQpMehcZHxgRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHhITEQpDWRcHGB0cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8YcRkYEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3JFfUx7fkFkHxJLG0J9Y21Ia2ZEcx1THX4bXnJPehJLEQpYXBcfBBoEGBkS BRsaBBsaGgQeEgQYGBAbHhofGhEKXlkXc1pmeHIRCk1cFxsdHxEKTFoXeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbHRgRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwX ZRhFRWJHS2FoS2wRCkJAF2xrW0JnREYFWVpSEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHxE KeUMXZ0BgemB4cBt7YnoRCnBnF2lDblABWXNHAR5TEBMaEQpwaBd6SWISHxNmTmFYExAaEQpwaB dhSH5+HHAZZ38YYxAdGhEKcGgXZE0BY09dQhheUk8QHRoRCnBoF2F4c1oYfWNYRUcfEB0aEQpwa BdkAUIceRtiYn8YZRAdGhEKcH0Xa3ocYFMZGG9QRWAQHRoRCnB9F2QcSXodUGcdAWgaEB0SEQpw fxduH2ddfV5AE3hkeRAbGh4RCnBfF2RjaG0efVBrTFBgEB0aEQpwfxdhZm9bGmdkQkgdWxAbGRk RCnBfF2NiElBIY3gffEJ9EBMSEQpwbBdkeX5kWWceU1NpbxAdEhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: XoWfQTkN58a1hWIGbALnY7y7T1tXeP8a MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 clxscore=172 priorityscore=352 impostorscore=0 suspectscore=0 mlxlogscore=828 mlxscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110190108 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --000000000000cc60e805ceb8e96e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable "Using instead par_water_ions.prm from namd-adapted 2016 charmm36" Should be read "Using toppar_water_ions_namd_adapted.str from toppar_c36_jul21 modifies as I wrote before fp ---------- Forwarded message --------- From: Francesco Pietra Date: Tue, Oct 19, 2021 at 8:28 PM Subject: Re: Fwd: namd-l: impropers for protonated 1-methyladenosine To: Josh Vermaas Cc: NAMD According to the README created for this work: AUTOPSFGEN > Using topology from toppar_c36_jul21 > Maintaining the few original water molecules > Replaced wrong names for modified nucleosides with those in file > toppar_all36_na_rna_modified.str > .......... > ............. > MD > Minimization using parameters from toppar_c36_jul21 > Not using toppar_water_ions.str because it has known problems with namd. > Using instead > par_water_ions.prm from namd-adapted 2016 charmm36: > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 > NG2P1 > (ATOMS 4433 C6, 4432 C5, 4437 N1, 4434 N6), resid 1MA > I will consider accurately your reply tomorrow, it is late in the night here and my lucidity is largely vanished Thanks indeed francesco On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas wrote: > You didn't happen to mix a topology file from toppar_c36_jul20 with a > parameter file from toppar_c36_jul21, did you? In the July 2020 release, > there is a line like this in par_all36_cgenff.prm: > > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, > TO BE OPTIMIZED, RNA > > This corresponds to the improper definition in that version of the force > field. "IMPR C6 C5 N1 N6" In the 2021 release, the order in the > improper is different "IMPR C6 N1 N6 C5", so the parameter that wou= ld > be looked up also changes: > > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, B1MA, from 3MC, > yxu, TO BE OPTIMIZED, RNA > > To be honest, I hadn't realized that changes like this happened, but in > this case it is all laid out in toppar_all.history: > > "!following removed due to conflict > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! B1MA, yxu, TO BE > OPTIMIZED, RNA > CG2R64 CG2R61 NG2P1 NG2P1 42.00 0 0.00 ! from CG2R64 CG2RC0 > NG2P1 NG2P1 > CG2R64 CG2R62 NG2P1 NG2P1 42.00 0 0.00 ! B3MC, yxu, TO BE > OPTIMIZED, RNA > !which will be treated with > CG2R64 NG2P1 NG2P1 CG2R62 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2R61 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, from 3MC, yxu, TO > BE OPTIMIZED" > > -Josh > > On 10/19/21 1:29 PM, Francesco Pietra wrote: > > Perhaps there is a discrepancy from topology and params, i.e. autopsf sets > unnecessary impropers while params for them do not exist just because they > are not needed. I wasn't unable to find the requested improper params in > the list of prm and str above files. But I may be easily wrong > francesco > > ---------- Forwarded message --------- > From: Francesco Pietra > Date: Tue, Oct 19, 2021, 9:32 AM > Subject: Re: namd-l: impropers for protonated 1-methyladenosine > To: Josh Vermaas > Cc: NAMD > > > Hi Josh > Most unfortunately I missed to indicate the full list of parameter files > used, which includes the one that you rightly suggested (the requested > params are of genff type) > > par_all36_carb.prm > par_all36_cgenff.prm > par_all36_lipid.prm > par_all36m_prot.prm > par_all36_na.prm > toppar_all36_na_modifications.str > toppar_all36_na_rna_modified.str > toppar_all36_prot_arg0.str > toppar_water_ions_namd_adapted.str (I just commented out what namd does > not understand) > > this is why I don't understand namd's request (the requested params are > available and unnecessary) and I asked whether namd can be forced to > override psfgen (I used autopsfgen because there are so many chains) > > thanks for you care > francesco > > > > On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: > >> If impropers are defined in the psf, NAMD will expect parameters for >> them. In this case the parameter is in par_all36_cgenff.prm, which goes >> with the top_all36_cgenff.rtf where the B1MA residue is defined. >> >> -Josh >> >> On 10/18/21 3:38 AM, Francesco Pietra wrote: >> > Hello all >> > While attempting minimization of a protein-ribonucleotide containing >> > modified nucleotides, error arose >> > >> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 >> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) >> > >> > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 >> > of protonated 1-methyladenosine *resname 1MA in the most recent >> > CHARMM36 psarameterization, Jul21) >> > >> > Added parameters included par_all36_na.prm, >> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place >> > from where such impropers are available> >> > >> > Thanks for advice >> > francesco pietra >> >> -- >> Josh Vermaas >> >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and >> Molecular Biology >> Michigan State University >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!pCJqeo66t_4Co9DXTrPYIKonskVkf-hQ3oSNTeS6Xfoh4DaNO8Ic= 9EOm6LHqvZ10qw$=20 >> >> >> > -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > --000000000000cc60e805ceb8e96e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

"Using instead par_water_ions.prm from namd-= adapted 2016 charmm36"
Should be read "Using toppar_wat= er_ions_namd_adapted.str from toppar_c36_jul21 modifies as I wrote before
fp
---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com&g= t;
Date: Tue, Oct 19, 2021 at 8:28 PM
Subject: Re: Fwd: namd-l= : impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>

<= br>
According to the README created for this work:

AUT= OPSFGEN
Using topology from toppar_c36_jul21
Maintaining the few orig= inal water molecules
Replaced wrong names for modified nucleosides with = those in file toppar_all36_na_rna_modified.str
..........
.............
MD
Minimization using parameters from toppar_= c36_jul21
Not using toppar_water_ions.str because it has known problems = with namd. Using instead
par_water_ions.prm from namd-adapted 2016 char= mm36:
FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 = NG2P1 NG2P1
(ATOMS 4433 C6, 4432 C5, 4437 N1, 4434 N6), resid 1MA
=

I will consider accurately your reply tomo= rrow, it is late in the night here and my lucidity is largely vanished
=

Thanks indeed
francesco
<= br>

On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas <vermaasj@msu.edu> wrote:
=20=20
You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6= " In the 2021 release, the order in the improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N= 6=C2=A0=C2=A0 C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, but in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1
CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20=20=20=20=20=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you=C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.edu> wrote:
If impropers ar= e defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
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boundary="00000000000052e09b05ceb95453" X-Proofpoint-ORIG-GUID: WG7OwPewbrwCJQc8mSoVC4PpxpziFcMi X-CLX-Shades: MLX X-Proofpoint-GUID: WG7OwPewbrwCJQc8mSoVC4PpxpziFcMi X-CLX-Response: 1TFkXGx0bEQpMehcZHh8RCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHxsdEQpDWRcHGB0cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF31tHWVdek9dSFhdaWB7SRJHeUV8aR56WlJaUENsSWdDEQpYXBcfBBoEGBkS BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NaZl55EQpNXBcYHxsRCkxaF3xpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbVJzEkFbaUQTHkwRCkNaFxgaEwQSHwQYGx MEHxsRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwX ZRhFRWJHS2FoS2wRCkJAF2xrW0JnREYFWVpSEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXHxE KeUMXZ0BgemB4cBt7YnoRCnBnF2lDblABWXNHAR5TEB4SEQpwaBd6SWISHxNmTmFYExAaEQpwaB dhSH5+HHAZZ38YYxAZGhEKcGgXZE0BY09dQhheUk8QGRoRCnBoF2F4c1oYfWNYRUcfEBkaEQpwa BdkAUIceRtiYn8YZRAZGhEKcH0Xa3ocYFMZGG9QRWAQHhIRCnB9F2QcSXodUGcdAWgaEBkaEQpw fxduH2ddfV5AE3hkeRAbGxkRCnBfF2RjaG0efVBrTFBgEB4SEQpwfxdhZm9bGmdkQkgdWxAbGBs RCnBfF2NiElBIY3gffEJ9EBMeEQpwbBdkeX5kWWceU1NpbxAZGhEKbX4XGxEKWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 clxscore=171 mlxscore=0 phishscore=0 suspectscore=0 lowpriorityscore=0 malwarescore=0 priorityscore=345 spamscore=0 mlxlogscore=871 adultscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110190110 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --00000000000052e09b05ceb95453 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Perhaps my mistake was not erasing the default topologies from autopsf before adding those from jul21. fp ---------- Forwarded message --------- From: Francesco Pietra Date: Tue, Oct 19, 2021 at 8:34 PM Subject: Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine To: , NAMD "Using instead par_water_ions.prm from namd-adapted 2016 charmm36" Should be read "Using toppar_water_ions_namd_adapted.str from toppar_c36_jul21 modifies as I wrote before fp ---------- Forwarded message --------- From: Francesco Pietra Date: Tue, Oct 19, 2021 at 8:28 PM Subject: Re: Fwd: namd-l: impropers for protonated 1-methyladenosine To: Josh Vermaas Cc: NAMD According to the README created for this work: AUTOPSFGEN > Using topology from toppar_c36_jul21 > Maintaining the few original water molecules > Replaced wrong names for modified nucleosides with those in file > toppar_all36_na_rna_modified.str > .......... > ............. > MD > Minimization using parameters from toppar_c36_jul21 > Not using toppar_water_ions.str because it has known problems with namd. > Using instead > par_water_ions.prm from namd-adapted 2016 charmm36: > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 > NG2P1 > (ATOMS 4433 C6, 4432 C5, 4437 N1, 4434 N6), resid 1MA > I will consider accurately your reply tomorrow, it is late in the night here and my lucidity is largely vanished Thanks indeed francesco On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas wrote: > You didn't happen to mix a topology file from toppar_c36_jul20 with a > parameter file from toppar_c36_jul21, did you? In the July 2020 release, > there is a line like this in par_all36_cgenff.prm: > > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, > TO BE OPTIMIZED, RNA > > This corresponds to the improper definition in that version of the force > field. "IMPR C6 C5 N1 N6" In the 2021 release, the order in the > improper is different "IMPR C6 N1 N6 C5", so the parameter that wou= ld > be looked up also changes: > > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, B1MA, from 3MC, > yxu, TO BE OPTIMIZED, RNA > > To be honest, I hadn't realized that changes like this happened, but in > this case it is all laid out in toppar_all.history: > > "!following removed due to conflict > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! B1MA, yxu, TO BE > OPTIMIZED, RNA > CG2R64 CG2R61 NG2P1 NG2P1 42.00 0 0.00 ! from CG2R64 CG2RC0 > NG2P1 NG2P1 > CG2R64 CG2R62 NG2P1 NG2P1 42.00 0 0.00 ! B3MC, yxu, TO BE > OPTIMIZED, RNA > !which will be treated with > CG2R64 NG2P1 NG2P1 CG2R62 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2R61 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, from 3MC, yxu, TO > BE OPTIMIZED" > > -Josh > > On 10/19/21 1:29 PM, Francesco Pietra wrote: > > Perhaps there is a discrepancy from topology and params, i.e. autopsf sets > unnecessary impropers while params for them do not exist just because they > are not needed. I wasn't unable to find the requested improper params in > the list of prm and str above files. But I may be easily wrong > francesco > > ---------- Forwarded message --------- > From: Francesco Pietra > Date: Tue, Oct 19, 2021, 9:32 AM > Subject: Re: namd-l: impropers for protonated 1-methyladenosine > To: Josh Vermaas > Cc: NAMD > > > Hi Josh > Most unfortunately I missed to indicate the full list of parameter files > used, which includes the one that you rightly suggested (the requested > params are of genff type) > > par_all36_carb.prm > par_all36_cgenff.prm > par_all36_lipid.prm > par_all36m_prot.prm > par_all36_na.prm > toppar_all36_na_modifications.str > toppar_all36_na_rna_modified.str > toppar_all36_prot_arg0.str > toppar_water_ions_namd_adapted.str (I just commented out what namd does > not understand) > > this is why I don't understand namd's request (the requested params are > available and unnecessary) and I asked whether namd can be forced to > override psfgen (I used autopsfgen because there are so many chains) > > thanks for you care > francesco > > > > On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: > >> If impropers are defined in the psf, NAMD will expect parameters for >> them. In this case the parameter is in par_all36_cgenff.prm, which goes >> with the top_all36_cgenff.rtf where the B1MA residue is defined. >> >> -Josh >> >> On 10/18/21 3:38 AM, Francesco Pietra wrote: >> > Hello all >> > While attempting minimization of a protein-ribonucleotide containing >> > modified nucleotides, error arose >> > >> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 >> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) >> > >> > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 >> > of protonated 1-methyladenosine *resname 1MA in the most recent >> > CHARMM36 psarameterization, Jul21) >> > >> > Added parameters included par_all36_na.prm, >> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place >> > from where such impropers are available> >> > >> > Thanks for advice >> > francesco pietra >> >> -- >> Josh Vermaas >> >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and >> Molecular Biology >> Michigan State University >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!pP8ASrdtBtFUV9xwEBbGbXgYTo-qPJm-ejKJzNetT8g9EWupnEAb= okZj7uefkoNXDg$=20 >> >> >> > -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > --00000000000052e09b05ceb95453 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Perhaps my mistake was not erasing the default topolo= gies from autopsf before adding those from jul21.
fp

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tu= e, Oct 19, 2021 at 8:34 PM
Subject: Fwd: Fwd: namd-l: impropers for prot= onated 1-methyladenosine
To: <ve= rmaasj@msu.edu>, NAMD <namd= -l@ks.uiuc.edu>



"Usi= ng instead par_water_ions.prm from namd-adapted 2016 charmm36"
Should be read "Using toppar_water_ions_namd_adapted.str from toppa= r_c36_jul21 modifies as I wrote before
fp
---------- Forwarded message ---------
From: Francesco Pietra <chienda= rret@gmail.com>
Date: Tue, Oct 19, 2021 at 8:28 PM
Subj= ect: Re: Fwd: namd-l: impropers for protonated 1-methyladenosine
To: Jos= h Vermaas <vermaas= j@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


According to the README created for this work:

AUTOPSFGEN
Using to= pology from toppar_c36_jul21
Maintaining the few original water molecule= s
Replaced wrong names for modified nucleosides with those in file toppa= r_all36_na_rna_modified.str
..........
.............
MD
Minimization using parameters from toppar_c36_jul21
Not us= ing toppar_water_ions.str because it has known problems with namd. Using in= stead
par_water_ions.prm from namd-adapted 2016 charmm36:
FATAL ERRO= R: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 NG2P1
(AT= OMS 4433 C6, 4432 C5, 4437 N1, 4434 N6), resid 1MA
<= br>
I will consider accurately your reply tomorrow, it is late in= the night here and my lucidity is largely vanished

Thanks indeed
francesco


=
On Tue, Oc= t 19, 2021 at 8:03 PM Josh Vermaas <vermaasj@msu.edu> wrote:
=20=20
You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6= " In the 2021 release, the order in the improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N= 6=C2=A0=C2=A0 C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, but in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1
CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20=20=20=20=20=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you=C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.edu> wrote:
If impropers ar= e defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
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boundary="000000000000fb285205cebde949" X-Proofpoint-GUID: JKnea2TG7O8OMbV0tr2rdFC9V8xasqst X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBseEQpMehcZGB0RCllEF2BkGmkeckh4Xx5gEQpYWBdhW3Noc28ZSWF yXBEKeE4XY1Nja3sTWH4aX14RCnlMF2YSfXlJX2BjQWNFEQpDSBcHGBIaEQpDWRcHGxseEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxMecRsdGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdgYURPSxh+bR1lEmVnSHwaXlgYWE5saRN8ElJLWVtZXhEKWFwXHwQaBBgZ EgUbGgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3Nae00BEQpNXBceGRkRCkxaF3hpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYGRrH2dEGHBmGFoRCkNaFxgaEwQSHwQYGB gEHxoRCkJeFxsRCkReFxgRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXZH5zfHlzHWtLTEARCkJOF2NTY2t7E1h+Gl9eEQpCTBdhW3Noc28ZSWFy XBEKQmwXentiH1B6RWcFR2gRCkJAF2FMWB8FQR5/eBlJEQpCWBdnc2VzQG5hYUxdYhEKWlgXHxE KeUMXbhh8b1J/XB0cHUkRCnBnF2lDblABWXNHAR5TEB0aEQpwaBdtQ2Z/WxlneX4dTBAZGhEKcG gXYmRdexNaeVxrXloQGRoRCnBoF25yTR1MHl5bbX1DEBkaEQpwaBdlc298RGZoUExdRhAZGhEKc GgXZVlgf2FjcH5OTXwQGRoRCnB9F2t6HGBTGRhvUEVgEBwaEQpwfRdkE0FPTmN9UmtTThAZGhEK cH0XY0FjemtpBR5iGlkQGRoRCnB/F24fZ119XkATeGR5EBsaHREKcF8XZGNobR59UGtMUGAQHBo RCnB/F2Fmb1saZ2RCSB1bEBsZGREKcF8XY2ISUEhjeB98Qn0QGxodEQpwfxdjQWN6a2kFHmIaWR AZGhEKcGwXaEkbbx8TU0VOQlsQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: JKnea2TG7O8OMbV0tr2rdFC9V8xasqst MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 adultscore=0 malwarescore=0 lowpriorityscore=0 spamscore=0 bulkscore=0 suspectscore=0 priorityscore=327 mlxscore=0 mlxlogscore=999 phishscore=0 clxscore=214 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110200000 X-Spam-Score: 0 X-Spam-OrigSender: jeffcomer@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Jeff Comer --000000000000fb285205cebde949 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Are you sure =E2=80=9C/.pdf=E2=80=9D is your psf file? There are multiple r= easons, I=E2=80=99m 95% sure that is not the correct file name. Jeff On Fri, Oct 15, 2021 at 08:58 Alessandro Ruda wrote: > Hi Josh, > > > yes, I checked them and they are ok, I just removed the entire path for > the sake of clarity when I posted the question! > > > Thank you! > > > /alex > > ------------------------------ > *From:* Josh Vermaas > *Sent:* 15 October 2021 15:30:05 > *To:* namd-l@ks.uiuc.edu; Alessandro Ruda > *Subject:* Re: namd-l: Re: MD run terminated with singnal 11 > > Hi Alex, > > Are you sure that you have the right structure, coordinates, > bincoordinates, and binvelocities files? Those do not look sane to me. > > -Josh > > On 10/15/21 8:04 AM, Alessandro Ruda wrote: > > It seems related to the PME parameters anyway. I tried to change > parameters such as the size of the grid or the spacing from 0.5 to 1.5 but > it didn't work as well. > > > Any hints on what could cause the instability? > > > All the best, > > Alex > ------------------------------ > *From:* Alessandro Ruda > *Sent:* 23 September 2021 15:46:31 > *To:* namd-l@ks.uiuc.edu > *Subject:* MD run terminated with singnal 11 > > Dear NAMD comunity, > > I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl - > 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization > followed by heating and short equilibration (few us) but when I start the > production it stops after few seconds with this error in slurm (i am > running on a cluster). > > > - *namd2:37211 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffe9c9ee6a0. Backtrace:* > - *namd2:37213 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffca5b2a120. Backtrace:* > - *namd2:110002 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffe5edf3f20. Backtrace:* > - *namd2:37217 terminated with signal 11 at PC=3Dfc9213 > SP=3D7ffe224b27a0. Backtrace:* > > ...etc...etc.... > > - > *software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_= chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > - > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > - > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > - > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > - > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14]* > - > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill= _chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]* > - > */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkE= v+0x1684)[0xb92d14]* > > ...etc...etc > > please find attached file if needed.The log file simply states: > > > - *mpprun info: Job terminated with error* > > > It happened to another simulation also with a very much similar > tetrasaccharide and I managed to make it work by building the > tetrasaccharide again, solvate it, minimize etc etc. It worked but I don't > know why. > It didn't work for this one and every time I restart the simulation I get > the same error. > > This is the configuration file I am using: > > ---------------------------------------------- > ---------------------------------------------- > ---------------------------------------------- > ---------------------------------------------- > ---------------------------------------------- > > structure /.pdf > coordinates /.pdb > bincoordinates /.coor > binvelocities /.vel > > set temperature 300 > > firsttimestep 0 > > # Input > paraTypeCharmm on > parameters /Parameters/par_all36_carb.inp > parameters /Parameters/par_water_ions.inp > parameters /Parameters/par_all36_prot.inp > parameters /Parameters/par_all36m_prot.inp > parameters /Parameters/par_hbond.inp > > > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12.0 > switching on > switchdist 10.0 > pairlistdist 16.0 > margin 0 > > # Integrator Parameters > timestep 4.0 ; > rigidBonds all ; > nonbondedFreq 1 > fullElectFrequency 1 > stepspercycle 20 > pairlistsPerCycle 2 > wrapWater on > wrapAll on > > > # Constant Temperature Control > langevin on ; > langevinDamping 1 ; > langevinTemp $temperature > langevinHydrogen off ; > > # PME > PME yes > PMEGridSpacing 1.0 > > #manual grid definition > PMEGridSizeX 60 > PMEGridSizeY 60 > PMEGridSizeZ 60 > > > # Constant Pressure Control (variable volume) > useGroupPressure yes ; > useFlexibleCell no > useConstantArea no > > langevinPiston on > langevinPistonTarget 1.01325 ;# in bar -> 1 atm > langevinPistonPeriod 50.0 > langevinPistonDecay 25.0 > langevinPistonTemp $temperature > > > # Output > outputName $outputname > > restartfreq 2500 ;# 2500steps =3D every 10ps > dcdfreq 2500 ;# =3D every 10ps > xstFreq 2500 > outputEnergies 2500 > outputtiming 2500 > outputPressure 150 > binaryoutput yes > > > extendedSystem > /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibra= tion/LeX4_heated.restart.xsc > > run 125000000 ;# 500 ns > ---------------------------------------------- > ---------------------------------------------- > ---------------------------------------------- > ---------------------------------------------- > ---------------------------------------------- > > I really don't know what the problem is related to. Does anybody have some > hints about it? > > Thank you in advance, > Alessandro > > > > > > > -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > -- =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80= =94 Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: 334 Coles Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!q2fiX8U= D1ps11Uo5FeQxorcgPUXVFyXZhL6aMz0X3SBUBKS6eRnfQ0iuEBLaPazcbg$=20 --000000000000fb285205cebde949 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Are you sure =E2=80=9C/.pdf=E2=80=9D is your psf file? Th= ere are multiple reasons, I=E2=80=99m 95% sure that is not the correct file= name.

Jeff



On Fri, Oct 15, 2021 at 08:= 58 Alessandro Ruda <alessandro.= ruda@su.se> wrote:

Hi Josh,


yes, I checked them and they are ok,=C2=A0I=C2=A0just removed the entire pa= th for the sake of clarity when I posted the question!


Thank you!


/alex



From: = Josh Vermaas <verm= aasj@msu.edu>
Sent: 15 October 2021 15:30:05
To: namd-l@k= s.uiuc.edu; Alessandro Ruda
Subject: Re: namd-l: Re: MD run terminated with singnal 11
=C2=A0
Hi Alex,

Are you sure that you have the right structure, coordinates, bincoordinates= , and binvelocities files? Those do not look sane to me.

-Josh

On 10/15/21 8:04 AM, Alessandro Ruda wrote:

It seems related to the PME parameters anyway. I tried to change paramet= ers such as the size of the grid or the spacing from 0.5 to 1.5 but it didn= 't work as well.


Any hints on what could cause the instability?


All the best,

Alex


From: = Alessandro Ruda
Sent: 23 September 2021 15:46:31
To: namd-l@k= s.uiuc.edu
Subject: MD run terminated with singnal 11
=C2=A0
= Dear NAMD comunity,

I am = running a simulation of a tetrasaccharide in salty water (0.2M NaCl - 50x50= x50 wb) using Hydrogen Mass Repartition. I run a first minimization followe= d by heating and short equilibration (few us) but when I start the production it stops = after few seconds with this error in slurm (i am running on a cluster).

  • namd2:37211 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe9c9ee6a0.= =C2=A0 Backtrace:
  • namd2:37213 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffca5b2a1= 20.=C2=A0 Backtrace:
  • namd2:110002 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe5edf3= f20.=C2=A0 Backtrace:
  • namd2:37217 terminated with signal 11 at PC=3Dfc9213 SP=3D7ffe224b27= a0.=C2=A0 Backtrace:
...et= c...etc....
  • software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_char= gesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWork= Ev+0x1684)[0xb92d14]
  • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fil= l_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]
  • /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWork= Ev+0x1684)[0xb92d14]
...et= c...etc

pleas= e find attached file if needed.The log file simply states:

  • <= b>mpprun info:=C2=A0=C2=A0 Job terminated with error

It ha= ppened to another simulation also with a very much similar tetrasaccharide = and I managed to make it work by building the tetrasaccharide again, solvat= e it, minimize etc etc. It worked but I don't know why.
It di= dn't work for this one and every time I restart the simulation I get th= e same error.
=
= This is the configuration file I am using:
=
= -----------------------------------------------------------------------= -----------------------------------------------------------------------= -------------------------------------------------------------------------= ---------------

structure=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /.pdf
coordinates=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /.pdb
bincoordinates=C2=A0=C2=A0=C2=A0=C2=A0 /.coor
binvelocities=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /.vel

set temperature=C2=A0=C2=A0=C2=A0 300

firsttimestep=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0

# Input
paraTypeCharmm=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 on
parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /Parameter= s/par_all36_carb.inp
parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /Parameter= s/par_water_ions.inp
parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /Parameter= s/par_all36_prot.inp
parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /Parameter= s/par_all36m_prot.inp
parameters=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /Parameter= s/par_hbond.inp


# Force-Field Parameters
exclude=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 scaled1-4
1-4scaling=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1.0
cutoff=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 12.0
switching=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on
switchdist=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 10.0
pairlistdist=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 16.0
margin=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 0

# Integrator Parameters
timestep=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 4.0=C2=A0=C2=A0=C2=A0 ;
rigidBonds=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 all=C2=A0 = ;
nonbondedFreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
fullElectFrequency=C2=A0 1
stepspercycle=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 20
pairlistsPerCycle=C2=A0=C2=A0 2
wrapWater=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on
wrapAll=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 on


# Constant Temperature Control
langevin=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = on=C2=A0=C2=A0=C2=A0 ;
langevinDamping=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0 ;
langevinTemp=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $temperature
langevinHydrogen=C2=A0=C2=A0=C2=A0 off=C2=A0=C2=A0=C2=A0 ;

# PME
PME=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 yes
PMEGridSpacing=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1.0

#manual grid definition
PMEGridSizeX=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 60
PMEGridSizeY=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 60
PMEGridSizeZ=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 60


# Constant Pressure Control (variable volume)
useGroupPressure=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 yes ;
useFlexibleCell=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 no
useConstantArea=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 no

langevinPiston=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 on
langevinPistonTarget=C2=A0 1.01325 ;#=C2=A0 in bar -> 1 atm
langevinPistonPeriod=C2=A0 50.0
langevinPistonDecay=C2=A0=C2=A0 25.0
langevinPistonTemp=C2=A0=C2=A0=C2=A0 $temperature


# Output
outputName=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 $outputnam= e

restartfreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 2500=C2=A0=C2= =A0=C2=A0=C2=A0 ;# 2500steps =3D every 10ps
dcdfreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 2500=C2=A0=C2=A0=C2=A0 ;# =3D every 10ps
xstFreq=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 2500
outputEnergies=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 2500
outputtiming=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 2500
outputPressure=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 150
binaryoutput=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 yes


extendedSystem=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 /proj/carbohydratedynamics/use= rs/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibration/LeX4_heated.restart.xsc

run 125000000 ;#=C2=A0 500 ns
---------------------------------------------------------------------------= -----------------------------------------------------------------------= --------------------------------------------------------------------------------= ----
=
= I really don't know what the problem is related to. Does anybody have s= ome hints about it?
=
= Thank you in advance,
= Alessandro






--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
--

=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80= =93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93= =E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2=80=93=E2= =80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94=E2=80=94
Jeffrey Com= er, PhD
Associate Professor
Department of Anatomy and Physiology
K= ansas State University
Office: 334 Coles Hall
Phone: 785-532-6311
= Website: http://jeffcomer.us
--000000000000fb285205cebde949-- From owner-namd-l@halifax.ks.uiuc.edu Wed Oct 20 05:41:54 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19KAfsjg010795; Wed, 20 Oct 2021 05:41:54 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19KAfsis010794; Wed, 20 Oct 2021 05:41:54 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19KAfrDC010789; Wed, 20 Oct 2021 05:41:53 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19KAfrhj010788; Wed, 20 Oct 2021 05:41:53 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19KAfcot010669 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000d6305e05cec66b0d" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcZGRgRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHh4bEQpDWRcHGBweEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1xmQU5ubUISZ1B9fXBFXWRSeWtDdVoeHnATem57ZnBdEQpYXBcfBBoEGBkS BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc1pwSBIRCk1cFxkTGxEKTFoXeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEw QeEhEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmaRhdbHhtY2FQHREKQk4XY1Nja3sTWH4aX14RCkJMF2R7T1J/E0laenMcEQpCbBdl GEVFYkdLYWhLbBEKQkAXbhpzExNuYX1abx8RCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp5QxdnQGB 6YHhwG3tiehEKcGcXaUNuUAFZc0cBHlMQHRoRCnBoF29vHEtpeW5vYAFdEBkaEQpwaBdhSH5+HH AZZ38YYxAeEhEKcGgXaEdmUxJsSUZNRUUQGRoRCnBoF2QBQhx5G2JifxhlEB4SEQpwaBd6ZR1of 3phQUFOaxAZGhEKcH0Xa3ocYFMZGG9QRWAQHBoRCnB9F2QcSXodUGcdAWgaEB4SEQpwfxduH2dd fV5AE3hkeRAbGxoRCnBfF2RjaG0efVBrTFBgEBwaEQpwfxdhZm9bGmdkQkgdWxAbGxIRCnBfF2N iElBIY3gffEJ9EBISEQpwbBdkeX5kWWceU1NpbxAcGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: vLkdDGh8MzWWZowNxSAi_p44Z9PDQLZw X-Proofpoint-ORIG-GUID: vLkdDGh8MzWWZowNxSAi_p44Z9PDQLZw MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 phishscore=0 malwarescore=0 mlxlogscore=833 bulkscore=0 priorityscore=332 suspectscore=0 mlxscore=0 clxscore=171 adultscore=0 spamscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110200061 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --000000000000d6305e05cec66b0d Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I repeated autopsfgen scratch, this time erasing all default topology files in autopsfgen before adding topologies from toppar_c36_jul21 (newly taken from Mackerell web site), plus my own ligand.str top_all36_lipid.rtf/home/francesco/softw/CHARMM_FF/toppar_c36_jul21 > top_all36_na.rtf > toppar_all36_prot_arg0.str > toppar_all36_na_rna_modified.str > toppar_water_ions_namd_adapted.str > ligand.str > Then, I repeated minimization from scratch adding params from > toppar_c36_jul21 (newly taken from Mackerell web site) > par_all36_carb.prm par_all36_cgenff.prm par_all36_lipid.prm par_all36m_prot.prm par_all36_na.prm plus the above .str Same error as before. This time any mixing with top/par is absolutely ruled out Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SUMMARY OF PARAMETERS: > Info: 1227 BONDS > Info: 3939 ANGLES > Info: 10859 DIHEDRAL > Info: 280 IMPROPER > Info: 6 CROSSTERM > Info: 403 VDW > Info: 103 VDW_PAIRS > Info: 0 NBTHOLE_PAIRS > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 > NG2P1 (ATOMS 4433 4432 4437 4434) > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 > NG2P1 (ATOMS 4433 4432 4437 4434) > Whether my mistake or intrinsic problems, I am stuck thanks for advice francesco On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas wrote: > You didn't happen to mix a topology file from toppar_c36_jul20 with a > parameter file from toppar_c36_jul21, did you? In the July 2020 release, > there is a line like this in par_all36_cgenff.prm: > > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, > TO BE OPTIMIZED, RNA > > This corresponds to the improper definition in that version of the force > field. "IMPR C6 C5 N1 N6" In the 2021 release, the order in the > improper is different "IMPR C6 N1 N6 C5", so the parameter that wou= ld > be looked up also changes: > > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, B1MA, from 3MC, > yxu, TO BE OPTIMIZED, RNA > > To be honest, I hadn't realized that changes like this happened, but in > this case it is all laid out in toppar_all.history: > > "!following removed due to conflict > CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! B1MA, yxu, TO BE > OPTIMIZED, RNA > CG2R64 CG2R61 NG2P1 NG2P1 42.00 0 0.00 ! from CG2R64 CG2RC0 > NG2P1 NG2P1 > CG2R64 CG2R62 NG2P1 NG2P1 42.00 0 0.00 ! B3MC, yxu, TO BE > OPTIMIZED, RNA > !which will be treated with > CG2R64 NG2P1 NG2P1 CG2R62 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2R61 52.00 0 0.00 ! CYTp, yxu, TO BE > OPTIMIZED, RNA > CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, from 3MC, yxu, TO > BE OPTIMIZED" > > -Josh > > On 10/19/21 1:29 PM, Francesco Pietra wrote: > > Perhaps there is a discrepancy from topology and params, i.e. autopsf sets > unnecessary impropers while params for them do not exist just because they > are not needed. I wasn't unable to find the requested improper params in > the list of prm and str above files. But I may be easily wrong > francesco > > ---------- Forwarded message --------- > From: Francesco Pietra > Date: Tue, Oct 19, 2021, 9:32 AM > Subject: Re: namd-l: impropers for protonated 1-methyladenosine > To: Josh Vermaas > Cc: NAMD > > > Hi Josh > Most unfortunately I missed to indicate the full list of parameter files > used, which includes the one that you rightly suggested (the requested > params are of genff type) > > par_all36_carb.prm > par_all36_cgenff.prm > par_all36_lipid.prm > par_all36m_prot.prm > par_all36_na.prm > toppar_all36_na_modifications.str > toppar_all36_na_rna_modified.str > toppar_all36_prot_arg0.str > toppar_water_ions_namd_adapted.str (I just commented out what namd does > not understand) > > this is why I don't understand namd's request (the requested params are > available and unnecessary) and I asked whether namd can be forced to > override psfgen (I used autopsfgen because there are so many chains) > > thanks for you care > francesco > > > > On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: > >> If impropers are defined in the psf, NAMD will expect parameters for >> them. In this case the parameter is in par_all36_cgenff.prm, which goes >> with the top_all36_cgenff.rtf where the B1MA residue is defined. >> >> -Josh >> >> On 10/18/21 3:38 AM, Francesco Pietra wrote: >> > Hello all >> > While attempting minimization of a protein-ribonucleotide containing >> > modified nucleotides, error arose >> > >> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 >> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) >> > >> > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 >> > of protonated 1-methyladenosine *resname 1MA in the most recent >> > CHARMM36 psarameterization, Jul21) >> > >> > Added parameters included par_all36_na.prm, >> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place >> > from where such impropers are available> >> > >> > Thanks for advice >> > francesco pietra >> >> -- >> Josh Vermaas >> >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and >> Molecular Biology >> Michigan State University >> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/jo= sh-vermaas/__;!!DZ3fjg!uGX6MySUjWBm360WO5eAk2b6JJAYghHwzVvxBw-NXWR5XlaypVXK= 0Uvdmt9_tyd_sw$=20 >> >> >> > -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > --000000000000d6305e05cec66b0d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
I repeated autopsfgen scratch, this time erasing all = default topology files in autopsfgen before adding topologies from
toppar_c36_jul21 (newly taken from Mackerell web site), plus my own = ligand.str

top_all36_lipid.rtf/home/francesco/softw/CHARMM_FF/toppar_c= 36_jul21
top_all36_na.rtf
toppar_all36_prot_arg0.str
toppar_all36_na_rna_modified.str
toppar_water_ions_na= md_adapted.str
ligand.str

T= hen, I repeated minimization from scratch adding params from
toppar_c36_jul21 (newly taken = from Mackerell web site)
par_all36= _carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
plus the abo= ve .str
Same error as before. This time any mixing w= ith top/par is absolutely ruled out

Info: SKIPPING rtf SECTION IN STREAM = FILE
Info: SUMMARY OF PARAMETERS:
Info: 1227 BONDS
Info: 3939 ANGL= ES
Info: 10859 DIHEDRAL
Info: 280 IMPROPER
Info: 6 CROSSTERM
In= fo: 403 VDW
Info: 103 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR:= UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 NG2P1 (ATOMS 44= 33 4432 4437 4434)
FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR C= G2R64 CG2RC0 NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)

Whether my mistake or intrinsic problems, I am stuck
<= div>
thanks for advice
francesco
On Tue, O= ct 19, 2021 at 8:03 PM Josh Vermaas <vermaasj@msu.edu> wrote:
=20=20
You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6= " In the 2021 release, the order in the improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N= 6=C2=A0=C2=A0 C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, but in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1
CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20=20=20=20=20=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you=C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.edu> wrote:
If impropers ar= e defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
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Thu, 21 Oct 2021 02:16:08 -0700 (PDT) References: <327c9dd5-1114-6e97-9825-7d9355b63525@msu.edu> <506457cb-b17b-dd22-fd9e-30a246637063@msu.edu> In-Reply-To: From: Francesco Pietra Date: Thu, 21 Oct 2021 11:15:56 +0200 Message-ID: Subject: Re: vmd-l: Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine To: VMD Mailing List , NAMD Content-Type: multipart/alternative; boundary="00000000000051374d05ced95845" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: icBjleZ4FhxyUkxslMv2w3lWonp8Sdvg X-CLX-Response: 1TFkXGx0eEQpMehcYHhgRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHxgTEQpDWRcHGxgYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ecRkeEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0NJaEBGT3AebEJSU39BUllGZ1wYXRlGfUVEWhJ5TlxNEQpYXBcfBBoEGBkT BRsaBBsaGgQeEgQbExAbHhofGhEKXlkXc1peeBsRCk1cFxkaGxEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGA QbHRgRCkJeFxsRCkRYFxgRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpz HBEKQmwXZRhFRWJHS2FoS2wRCkJAF2NiQntcWXJQXGNmEQpaWBcfEQp5QxdlZhxLfkEZRWcYQRE KcGcXZX1dQRpcfkRrRWsQGRoRCnBoF2gZQltcUn98G3pNEBkaEQpwaBdlQXpfeF5OSB5SbhAZGh EKcGgXaEdmUxJsSUZNRUUQGRoRCnBoF2QBQhx5G2JifxhlEBkaEQpwaBd6ZR1of3phQUFOaxAZG hEKcGcXaUNuUAFZc0cBHlMQGRoRCnB9F2t6HGBTGRhvUEVgEBkaEQpwfRdkHEl6HVBnHQFoGhAZ GhEKcH0XYGxSfnpvfFBAQFkQGRoRCnB/F24fZ119XkATeGR5EBsaExEKcF8XZGNobR59UGtMUGA QGRoRCnB/F2Fmb1saZ2RCSB1bEBsbHREKcF8XY2ISUEhjeB98Qn0QExsRCnBsF2R5fmRZZx5TU2 lvEBkaEQpwTBdjaGd9YmESQ31uBRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: icBjleZ4FhxyUkxslMv2w3lWonp8Sdvg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 spamscore=0 malwarescore=0 mlxscore=0 adultscore=0 mlxlogscore=999 impostorscore=0 bulkscore=0 priorityscore=242 lowpriorityscore=0 suspectscore=0 clxscore=174 classifier=spam adjust=0 reason=mlx scancount=2 engine=8.12.0-2109230001 definitions=main-2110210046 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --00000000000051374d05ced95845 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Having no answer, I choose the shortest route to bypass the error, i.e., I added "CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA" to par_all36_cgen.prm, renamed par_all36_cgen_MOD.prm Minimization went on correctly, no conflict came out. May I ask whether there could anything unsafe on going on following this shortcut? thanks francesco pietra On Wed, Oct 20, 2021 at 4:14 PM Francesco Pietra wrote: > Forwarding to VMD, which is also concerned > > ---------- Forwarded message --------- > From: Francesco Pietra > Date: Wed, Oct 20, 2021 at 12:41 PM > Subject: Re: Fwd: namd-l: impropers for protonated 1-methyladenosine > To: Josh Vermaas > Cc: NAMD > > > I repeated autopsfgen scratch, this time erasing all default topology > files in autopsfgen before adding topologies from > toppar_c36_jul21 (newly taken from Mackerell web site), plus my own > ligand.str > > top_all36_lipid.rtf/home/francesco/softw/CHARMM_FF/toppar_c36_jul21 >> top_all36_na.rtf >> toppar_all36_prot_arg0.str >> toppar_all36_na_rna_modified.str >> toppar_water_ions_namd_adapted.str >> ligand.str >> > > Then, I repeated minimization from scratch adding params from > >> toppar_c36_jul21 (newly taken from Mackerell web site) >> > par_all36_carb.prm > par_all36_cgenff.prm > par_all36_lipid.prm > par_all36m_prot.prm > par_all36_na.prm > plus the above .str > > Same error as before. This time any mixing with top/par is absolutely > ruled out > > Info: SKIPPING rtf SECTION IN STREAM FILE >> Info: SUMMARY OF PARAMETERS: >> Info: 1227 BONDS >> Info: 3939 ANGLES >> Info: 10859 DIHEDRAL >> Info: 280 IMPROPER >> Info: 6 CROSSTERM >> Info: 403 VDW >> Info: 103 VDW_PAIRS >> Info: 0 NBTHOLE_PAIRS >> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 >> NG2P1 (ATOMS 4433 4432 4437 4434) >> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 >> NG2P1 (ATOMS 4433 4432 4437 4434) >> > > Whether my mistake or intrinsic problems, I am stuck > > thanks for advice > francesco > > On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas wrote: > >> You didn't happen to mix a topology file from toppar_c36_jul20 with a >> parameter file from toppar_c36_jul21, did you? In the July 2020 release, >> there is a line like this in par_all36_cgenff.prm: >> >> CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, >> TO BE OPTIMIZED, RNA >> >> This corresponds to the improper definition in that version of the force >> field. "IMPR C6 C5 N1 N6" In the 2021 release, the order in the >> improper is different "IMPR C6 N1 N6 C5", so the parameter that wo= uld >> be looked up also changes: >> >> CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, B1MA, from 3MC, >> yxu, TO BE OPTIMIZED, RNA >> >> To be honest, I hadn't realized that changes like this happened, but in >> this case it is all laid out in toppar_all.history: >> >> "!following removed due to conflict >> CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! B1MA, yxu, TO BE >> OPTIMIZED, RNA >> CG2R64 CG2R61 NG2P1 NG2P1 42.00 0 0.00 ! from CG2R64 CG2RC0 >> NG2P1 NG2P1 >> CG2R64 CG2R62 NG2P1 NG2P1 42.00 0 0.00 ! B3MC, yxu, TO BE >> OPTIMIZED, RNA >> !which will be treated with >> CG2R64 NG2P1 NG2P1 CG2R62 52.00 0 0.00 ! CYTp, yxu, TO BE >> OPTIMIZED, RNA >> CG2R64 NG2P1 NG2P1 CG2R61 52.00 0 0.00 ! CYTp, yxu, TO BE >> OPTIMIZED, RNA >> CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, from 3MC, yxu, >> TO BE OPTIMIZED" >> >> -Josh >> >> On 10/19/21 1:29 PM, Francesco Pietra wrote: >> >> Perhaps there is a discrepancy from topology and params, i.e. autopsf >> sets unnecessary impropers while params for them do not exist just becau= se >> they are not needed. I wasn't unable to find the requested improper para= ms >> in the list of prm and str above files. But I may be easily wrong >> francesco >> >> ---------- Forwarded message --------- >> From: Francesco Pietra >> Date: Tue, Oct 19, 2021, 9:32 AM >> Subject: Re: namd-l: impropers for protonated 1-methyladenosine >> To: Josh Vermaas >> Cc: NAMD >> >> >> Hi Josh >> Most unfortunately I missed to indicate the full list of parameter files >> used, which includes the one that you rightly suggested (the requested >> params are of genff type) >> >> par_all36_carb.prm >> par_all36_cgenff.prm >> par_all36_lipid.prm >> par_all36m_prot.prm >> par_all36_na.prm >> toppar_all36_na_modifications.str >> toppar_all36_na_rna_modified.str >> toppar_all36_prot_arg0.str >> toppar_water_ions_namd_adapted.str (I just commented out what namd does >> not understand) >> >> this is why I don't understand namd's request (the requested params are >> available and unnecessary) and I asked whether namd can be forced to >> override psfgen (I used autopsfgen because there are so many chains) >> >> thanks for you care >> francesco >> >> >> >> On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: >> >>> If impropers are defined in the psf, NAMD will expect parameters for >>> them. In this case the parameter is in par_all36_cgenff.prm, which goes >>> with the top_all36_cgenff.rtf where the B1MA residue is defined. >>> >>> -Josh >>> >>> On 10/18/21 3:38 AM, Francesco Pietra wrote: >>> > Hello all >>> > While attempting minimization of a protein-ribonucleotide containing >>> > modified nucleotides, error arose >>> > >>> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 >>> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) >>> > >>> > These atom types relate, in the given order, to atomnames C6 C5 N1 N6 >>> > of protonated 1-methyladenosine *resname 1MA in the most recent >>> > CHARMM36 psarameterization, Jul21) >>> > >>> > Added parameters included par_all36_na.prm, >>> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place >>> > from where such impropers are available> >>> > >>> > Thanks for advice >>> > francesco pietra >>> >>> -- >>> Josh Vermaas >>> >>> vermaasj@msu.edu >>> Assistant Professor, Plant Research Laboratory and Biochemistry and >>> Molecular Biology >>> Michigan State University >>> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/j= osh-vermaas/__;!!DZ3fjg!vzoNN17sb33pENUpfrDpaIvn3CkGjXihJA9J6Jel3-oTVYMfC8w= GDIQZjEBl9jj_4g$=20 >>> >>> >>> >> -- >> Josh Vermaas >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and Mole= cular Biology >> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-= vermaas/ >> >> --00000000000051374d05ced95845 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Having no answer, I choose the shortest route to bypa= ss the error, i.e., I added
"CG2R64 CG2RC0 NG2P1 =C2=A0NG2P1= =C2=A0 =C2=A0 42.00 =C2=A00 =C2=A0 =C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO = BE OPTIMIZED, RNA"
to par_all36_cgen.prm, renamed par_all36_= cgen_MOD.prm

Minimization went on correctly, no co= nflict came out.

May I ask whether there could= anything unsafe on going on following this shortcut?
thanks
francesco pietra

On Wed, Oct 20, 2021 at 4:14 PM Francesco P= ietra <chiendarret@gmail.com> wrote:
Forwarding to VMD, which is also concerned

---------- Forwa= rded message ---------
From: = Francesco Pietra <
chiendarret@gmail.com>
Date: W= ed, Oct 20, 2021 at 12:41 PM
Subject: Re: Fwd: namd-l: impropers for pro= tonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu&g= t;


I repeated autopsfgen scratch, th= is time erasing all default topology files in autopsfgen before adding topo= logies from
toppar_c36_jul21 (newly taken from Mackerell web= site), plus my own ligand.str

top_all36_lipid.rtf/home/francesco/softw= /CHARMM_FF/toppar_c36_jul21
top_all36_na.rtf
toppar_all= 36_prot_arg0.str
toppar_all36_na_rna_modified.str
t= oppar_water_ions_namd_adapted.str
ligand.str

Then, I repeated minimization from scratch adding params = from
toppar_c36_= jul21 (newly taken from Mackerell web site)
par_all36_carb.prm
par_all36_cgenff.prm
par_a= ll36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
plus the above .str
Same error as before. Thi= s time any mixing with top/par is absolutely ruled out

=
Info: SKIPPING rtf S= ECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 1227 BONDSInfo: 3939 ANGLES
Info: 10859 DIHEDRAL
Info: 280 IMPROPER
Info: = 6 CROSSTERM
Info: 403 VDW
Info: 103 VDW_PAIRS
Info: 0 NBTHOLE_PAIR= S
FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P= 1 NG2P1 (ATOMS 4433 4432 4437 4434)
FATAL ERROR: UNABLE TO FIND IMPROPER= PARAMETERS FOR CG2R64 CG2RC0 NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
=

Whether my mistake or intrinsic problems, = I am stuck

thanks for advice
francesco

On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas <vermaasj@msu.edu> wrote:
=20
You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6= " In the 2021 release, the order in the improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N= 6=C2=A0=C2=A0 C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, bu= t in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1
CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you=C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.edu> wrote:
If impropers ar= e defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/


--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/peopl=
e/faculty/josh-vermaas/
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boundary="0000000000009e48e605cedc6b53" X-CLX-Response: 1TFkXGx0bEQpMehcZGBsRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHh0SEQpDWRcHHBkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxtxGRsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XRkJHbllcEh9+ZUN4S0B1SHBEZhoaZn9SYRhkWVxJHmURClhcFx8EGgQYGRMF GxoEGxsaBB8aBBseGxAbHhofGhEKXlkXc1pdTWQRCk1cFx4dGhEKTFoXfGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGA QbHR4RCkJeFxsRCkRYFxgRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpz HBEKQmwXZRhFRWJHS2FoS2wRCkJAF29gGE1DaHgaYFhtEQpaWBcfEQp5Qxdrf3hEZnJgaV5QbRE KWUsXEx8cHBEKcGcXZX1dQRpcfkRrRWsQGxoaEQpwaBdheUNic2hLRl9+GRAZGhEKcGgXZUF6X3 heTkgeUm4QEh8RCnBoF2hHZlMSbElGTUVFEBIfEQpwaBdhcGNeT34FSXBZSRAcGhEKcGgXemUda H96YUFBTmsQEh8RCnBnF2lDblABWXNHAR5TEBMaEQpwfRdrehxgUxkYb1BFYBASHxEKcH0XZBxJ eh1QZx0BaBoQEh8RCnB9F2BsUn56b3xQQEBZEBIfEQpwfxduH2ddfV5AE3hkeRAbGxMRCnBfF2R jaG0efVBrTFBgEBMaEQpwfxdhZm9bGmdkQkgdWxAbGR0RCnBfF2NiElBIY3gffEJ9EBsaGREKcG wXZHl+ZFlnHlNTaW8QHRoRCnBMF2NoZ31iYRJDfW4FEBkaEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-GUID: lhmDsv85TOiRaj_bZnL00LUxK2Nsvc4O X-Proofpoint-ORIG-GUID: lhmDsv85TOiRaj_bZnL00LUxK2Nsvc4O MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 malwarescore=0 mlxscore=0 lowpriorityscore=0 impostorscore=0 phishscore=0 mlxlogscore=999 clxscore=171 spamscore=0 priorityscore=321 bulkscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110210069 domainage_hfrom=9566 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000009e48e605cedc6b53 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I do not understand 'pass through cgenff' On Thu, Oct 21, 2021, 12:04 PM Ashar Malik wrote: > Haven=E2=80=99t followed the full thread here. Sorry if my answer repeats > something or is completely off. > > > > If you have to add parameters (which is what the error is about) - perhaps > you could pass your =E2=80=9Cmolecule=E2=80=9D through cgenff? And get a = guess from there. > And then for the same dihedral parameters match yours (the one you use (42 > 0 0) and see if the values are similar? If yes, it=E2=80=99s still not > =E2=80=9Ccompletely=E2=80=9D safe but more safe then =E2=80=9Ccompletely= =E2=80=9D unsafe. If the values are > off, then perhaps there is reason to be worried :) > > > > > On Thu, 21 Oct 2021 at 5:50 PM, Francesco Pietra > wrote: > >> Having no answer, I choose the shortest route to bypass the error, i.e., >> I added >> "CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu, >> TO BE OPTIMIZED, RNA" >> to par_all36_cgen.prm, renamed par_all36_cgen_MOD.prm >> >> Minimization went on correctly, no conflict came out. >> >> May I ask whether there could anything unsafe on going on following this >> shortcut? >> thanks >> francesco pietra >> >> On Wed, Oct 20, 2021 at 4:14 PM Francesco Pietra >> wrote: >> >>> Forwarding to VMD, which is also concerned >>> >>> ---------- Forwarded message --------- >>> From: Francesco Pietra >>> Date: Wed, Oct 20, 2021 at 12:41 PM >>> Subject: Re: Fwd: namd-l: impropers for protonated 1-methyladenosine >>> To: Josh Vermaas >>> Cc: NAMD >>> >>> >>> I repeated autopsfgen scratch, this time erasing all default topology >>> files in autopsfgen before adding topologies from >>> toppar_c36_jul21 (newly taken from Mackerell web site), plus my own >>> ligand.str >>> >>> top_all36_lipid.rtf/home/francesco/softw/CHARMM_FF/toppar_c36_jul21 >>>> top_all36_na.rtf >>>> toppar_all36_prot_arg0.str >>>> toppar_all36_na_rna_modified.str >>>> toppar_water_ions_namd_adapted.str >>>> ligand.str >>>> >>> >>> Then, I repeated minimization from scratch adding params from >>> >>>> toppar_c36_jul21 (newly taken from Mackerell web site) >>>> >>> par_all36_carb.prm >>> par_all36_cgenff.prm >>> par_all36_lipid.prm >>> par_all36m_prot.prm >>> par_all36_na.prm >>> plus the above .str >>> >>> Same error as before. This time any mixing with top/par is absolutely >>> ruled out >>> >>> Info: SKIPPING rtf SECTION IN STREAM FILE >>>> Info: SUMMARY OF PARAMETERS: >>>> Info: 1227 BONDS >>>> Info: 3939 ANGLES >>>> Info: 10859 DIHEDRAL >>>> Info: 280 IMPROPER >>>> Info: 6 CROSSTERM >>>> Info: 403 VDW >>>> Info: 103 VDW_PAIRS >>>> Info: 0 NBTHOLE_PAIRS >>>> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 >>>> NG2P1 (ATOMS 4433 4432 4437 4434) >>>> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 >>>> NG2P1 (ATOMS 4433 4432 4437 4434) >>>> >>> >>> Whether my mistake or intrinsic problems, I am stuck >>> >>> thanks for advice >>> francesco >>> >>> On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas wrote: >>> >>>> You didn't happen to mix a topology file from toppar_c36_jul20 with a >>>> parameter file from toppar_c36_jul21, did you? In the July 2020 releas= e, >>>> there is a line like this in par_all36_cgenff.prm: >>>> >>>> CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, >>>> yxu, TO BE OPTIMIZED, RNA >>>> >>>> This corresponds to the improper definition in that version of the >>>> force field. "IMPR C6 C5 N1 N6" In the 2021 release, the order i= n the >>>> improper is different "IMPR C6 N1 N6 C5", so the parameter that = would >>>> be looked up also changes: >>>> >>>> CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, B1MA, from >>>> 3MC, yxu, TO BE OPTIMIZED, RNA >>>> >>>> To be honest, I hadn't realized that changes like this happened, but in >>>> this case it is all laid out in toppar_all.history: >>>> >>>> "!following removed due to conflict >>>> CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! B1MA, yxu, TO BE >>>> OPTIMIZED, RNA >>>> CG2R64 CG2R61 NG2P1 NG2P1 42.00 0 0.00 ! from CG2R64 CG2RC0 >>>> NG2P1 NG2P1 >>>> CG2R64 CG2R62 NG2P1 NG2P1 42.00 0 0.00 ! B3MC, yxu, TO BE >>>> OPTIMIZED, RNA >>>> !which will be treated with >>>> CG2R64 NG2P1 NG2P1 CG2R62 52.00 0 0.00 ! CYTp, yxu, TO BE >>>> OPTIMIZED, RNA >>>> CG2R64 NG2P1 NG2P1 CG2R61 52.00 0 0.00 ! CYTp, yxu, TO BE >>>> OPTIMIZED, RNA >>>> CG2R64 NG2P1 NG2P1 CG2RC0 52.00 0 0.00 ! ADEp, from 3MC, yxu, >>>> TO BE OPTIMIZED" >>>> >>>> -Josh >>>> >>>> On 10/19/21 1:29 PM, Francesco Pietra wrote: >>>> >>>> Perhaps there is a discrepancy from topology and params, i.e. autopsf >>>> sets unnecessary impropers while params for them do not exist just bec= ause >>>> they are not needed. I wasn't unable to find the requested improper pa= rams >>>> in the list of prm and str above files. But I may be easily wrong >>>> francesco >>>> >>>> ---------- Forwarded message --------- >>>> From: Francesco Pietra >>>> Date: Tue, Oct 19, 2021, 9:32 AM >>>> Subject: Re: namd-l: impropers for protonated 1-methyladenosine >>>> To: Josh Vermaas >>>> Cc: NAMD >>>> >>>> >>>> Hi Josh >>>> Most unfortunately I missed to indicate the full list of parameter >>>> files used, which includes the one that you rightly suggested (the >>>> requested params are of genff type) >>>> >>>> par_all36_carb.prm >>>> par_all36_cgenff.prm >>>> par_all36_lipid.prm >>>> par_all36m_prot.prm >>>> par_all36_na.prm >>>> toppar_all36_na_modifications.str >>>> toppar_all36_na_rna_modified.str >>>> toppar_all36_prot_arg0.str >>>> toppar_water_ions_namd_adapted.str (I just commented out what namd does >>>> not understand) >>>> >>>> this is why I don't understand namd's request (the requested params are >>>> available and unnecessary) and I asked whether namd can be forced to >>>> override psfgen (I used autopsfgen because there are so many chains) >>>> >>>> thanks for you care >>>> francesco >>>> >>>> >>>> >>>> On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas wrote: >>>> >>>>> If impropers are defined in the psf, NAMD will expect parameters for >>>>> them. In this case the parameter is in par_all36_cgenff.prm, which >>>>> goes >>>>> with the top_all36_cgenff.rtf where the B1MA residue is defined. >>>>> >>>>> -Josh >>>>> >>>>> On 10/18/21 3:38 AM, Francesco Pietra wrote: >>>>> > Hello all >>>>> > While attempting minimization of a protein-ribonucleotide containing >>>>> > modified nucleotides, error arose >>>>> > >>>>> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 >>>>> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434) >>>>> > >>>>> > These atom types relate, in the given order, to atomnames C6 C5 N1 >>>>> N6 >>>>> > of protonated 1-methyladenosine *resname 1MA in the most recent >>>>> > CHARMM36 psarameterization, Jul21) >>>>> > >>>>> > Added parameters included par_all36_na.prm, >>>>> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other >>>>> place >>>>> > from where such impropers are available> >>>>> > >>>>> > Thanks for advice >>>>> > francesco pietra >>>>> >>>>> -- >>>>> Josh Vermaas >>>>> >>>>> vermaasj@msu.edu >>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and >>>>> Molecular Biology >>>>> Michigan State University >>>>> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty= /josh-vermaas/__;!!DZ3fjg!vTHp5PZ8IpvGPjts7_3aVt3imu9UGWxZI3Q--orxyAuTy14nS= crfmUmtjSub5f_7AA$=20 >>>>> >>>>> >>>>> >>>> -- >>>> Josh Vermaas >>>> vermaasj@msu.edu >>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Mo= lecular Biology >>>> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/jos= h-vermaas/ >>>> >>>> --0000000000009e48e605cedc6b53 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I do not understand 'pass through cgenff'
On Thu, = Oct 21, 2021, 12:04 PM Ashar Malik <asharjm@gmail.com> wrote:
<= div dir=3D"auto">Haven=E2=80=99t followed the full thread here. Sorry if my= answer repeats something or is completely off.=C2=A0



If you have to add parameters (which is what the error is about)= - perhaps you could pass your =E2=80=9Cmolecule=E2=80=9D through cgenff? A= nd get a guess from there. And then for the same dihedral parameters match = yours (the one you use (42 0 0) =C2=A0and see if the values are similar? If= yes, it=E2=80=99s still not =E2=80=9Ccompletely=E2=80=9D safe but more saf= e then =E2=80=9Ccompletely=E2=80=9D unsafe. If the values are off, then per= haps there is reason to be worried :)=C2=A0




On Thu, 21 Oct 202= 1 at 5:50 PM, Francesco Pietra <chiendarret@gmail.com> wrote:<= br>
Having no answer, I choose = the shortest route to bypass the error, i.e., I added
"CG2R6= 4 CG2RC0 NG2P1 =C2=A0NG2P1 =C2=A0 =C2=A0 42.00 =C2=A00 =C2=A0 =C2=A0 0.00 != 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA"
to par_all36_cg= en.prm, renamed par_all36_cgen_MOD.prm

Minimizatio= n went on correctly, no conflict came out.

May= I ask whether there could anything unsafe on going on following this short= cut?
thanks
francesco pietra
=

On Wed, Oct 20, 2021 at 4:14 PM Francesco Pietra <chiendarret@g= mail.com> wrote:
Forwardi= ng to VMD, which is also concerned

<= div dir=3D"ltr" class=3D"gmail_attr">---------- Forwarded message ---------=
From: Francesco Pietra <= span dir=3D"auto"><chiendarret@gmail.com>
Date: Wed,= Oct 20, 2021 at 12:41 PM
Subject: Re: Fwd: namd-l: impropers for proton= ated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc= : NAMD <namd-l@ks.uiuc.edu>


I repeated autopsfgen scratch, this time erasing all default topology fil= es in autopsfgen before adding topologies from
toppar_c36_ju= l21 (newly taken from Mackerell web site), plus my own ligand.str
=

top_all36_lipid.rtf/home/francesco/sof= tw/CHARMM_FF/toppar_c36_jul21
top_all36_na.rtf
toppar_a= ll36_prot_arg0.str
toppar_all36_na_rna_modified.str
toppar_water_ions_namd_adapted.str
ligand.str
=

Then, I repeated minimization from scratch adding param= s from
toppar_c36_jul21 (newly taken from Mackere= ll web site)
par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_al= l36m_prot.prm
par_all36_na.prm
plus the above .str
Same error as before. This time any mixing with top/par = is absolutely ruled out

Info: SKI= PPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 1= 227 BONDS
Info: 3939 ANGLES
Info: 10859 DIHEDRAL
Info: 280 IMPROPE= R
Info: 6 CROSSTERM
Info: 403 VDW
Info: 103 VDW_PAIRS
Info: 0 N= BTHOLE_PAIRS
FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 = CG2RC0 NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
FATAL ERROR: UNABLE TO FI= ND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1 NG2P1 (ATOMS 4433 4432 4437 = 4434)

Whether my mistake or intrinsic= problems, I am stuck

thanks for advice
= francesco

On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas <vermaasj@= msu.edu> wrote:
=20
You didn't happen to mix a topology file from toppar_c36_jul20 with a parameter file from toppar_c36_jul21, did you? In the July 2020 release, there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! 34HC, from 3MCn, yxu, TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force field. "IMPR C6=C2=A0=C2=A0 C5=C2=A0=C2=A0 N1=C2=A0=C2=A0 N6= " In the 2021 release, the order in the improper is different "IMPR C6=C2=A0=C2=A0 N1=C2=A0=C2=A0 N= 6=C2=A0=C2=A0 C5", so the parameter that would be looked up also changes:

CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, B1MA, from 3MC, yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, bu= t in this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B1MA, yxu, TO BE OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! from CG2R64 CG2RC0 NG2P1=C2=A0 NG2P1
CG2R64 CG2R62 NG2P1=C2=A0 NG2P1=C2=A0=C2=A0=C2=A0=C2=A0 42.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! B3MC, yxu, TO BE OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R62=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2R61=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! CYTp, yxu, TO BE OPTIMIZED, RNA
CG2R64 NG2P1=C2=A0 NG2P1=C2=A0 CG2RC0=C2=A0=C2=A0=C2=A0 52.00=C2=A0 0= =C2=A0=C2=A0=C2=A0=C2=A0 0.00 ! ADEp, from 3MC, yxu, TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
=20
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets unnecessary impropers while params for them do not exist just because they are not needed. I wasn't unable to find the requested improper params in the list of prm and str above files. But I may be easily wrong
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com&= gt;
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj@msu.edu>
Cc: NAMD <namd-l@ks.uiuc.edu>


Hi Josh
Most unfortunately I missed to indicate the full list of parameter files used, which includes the one that you=C2=A0 rightly suggested (the requested params are of genff type)

par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not understand)

this is why I don't understand namd's request (the requested params are available and unnecessary) and I asked whether namd can be forced to override psfgen (I used autopsfgen because there are so many chains)

thanks for you care
francesco



On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj@msu.edu> wrote:
If impropers are defined in the psf, NAMD will expect parameters for
them. In this case the parameter is in par_all36_cgenff.prm, which goes
with the top_all36_cgenff.rtf where the B1MA residue is defined.

-Josh

On 10/18/21 3:38 AM, Francesco Pietra wrote:
> Hello all
> While attempting minimization of a protein-ribonucleotide containing
> modified nucleotides, error arose
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
>
> These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> of protonated 1-methyladenosine *resname 1MA in the most recent
> CHARMM36 psarameterization, Jul21)
>
> Added parameters included=C2=A0 par_all36_na.prm,
> ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> from where such impropers are available>
>
> Thanks for advice
> francesco pietra

--
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas= /


--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/<=
/a>
--0000000000009e48e605cedc6b53-- From owner-namd-l@halifax.ks.uiuc.edu Thu Oct 21 12:41:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19LHfptG021291; Thu, 21 Oct 2021 12:41:51 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19LHfpgP021273; Thu, 21 Oct 2021 12:41:51 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19LHfSWW020781; Thu, 21 Oct 2021 12:41:29 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19LHfSEn020775; Thu, 21 Oct 2021 12:41:28 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19LHfIaN020750 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT); 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boundary="000000000000dd18d905cee06659" X-CLX-Shades: MLX X-Proofpoint-GUID: fxRMEmvPodq2OuMiGRhGFx6W-2Yc_pjj X-Proofpoint-ORIG-GUID: fxRMEmvPodq2OuMiGRhGFx6W-2Yc_pjj X-CLX-Response: 1TFkXGx4aEQpMehcZGBIRCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHHB0RCkNZFwcYExsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGBpxGx8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XTFJ4Z29HXHpFTlsYZV9nQ214Qm1sUhx9BxhzSXVaQEARClhcFx8EGgQYGRMF GxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc1oaWHARCk1cFxsbGxEKTFoXaGlNa2sRCkxGF29ra2t raxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHwQbHBwEHx4RCkJeFxsRCkRYFxgRCkReFxkRCk JcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaFpwGEkfZngeQ F4RCkJOF2NTY2t7E1h+Gl9eEQpCTBdsH15ZWm5MYWBbQREKQmwXb0Jpf25OW1IZeBoRCkJAF21E bkBuTHxib0RrEQpNXhcbEQpaWBcYEQp5QxdnXUVrZ39cTEh4UBEKWUsXEx8cHBEKcGgXZWRicB9 vS0lCZXgQGRoRCnBoF2V6Xn1lTl5MR0RgEBkaEQpwaBduRkBAUlpSa2trUhAZGhEKcGgXZlNkGl 9gXnpvTnIQGRoRCnBoF2hfYWwFXQVff0RaEBkaEQpwbBdneHNzQkdcW31GSxAZGhEKbX4XGxEKW E0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 mlxlogscore=676 priorityscore=328 suspectscore=0 mlxscore=0 adultscore=0 clxscore=140 spamscore=0 phishscore=0 malwarescore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2109230001 definitions=main-2110210087 domainage_hfrom=9566 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000dd18d905cee06659 Content-Type: text/plain; charset="UTF-8" Dear Colleagues, Anyone who has a script for contact Vs Freq and would like to share with us. Highly appreciating as you know, nowaday, reviewers used to demand every possible parameter in paper... Dr.Shabbir --000000000000dd18d905cee06659 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
Anyone who has a script fo= r contact Vs Freq and would like to share with us. Highly appreciating as y= ou know, nowaday, reviewers used to demand every possible parameter in pape= r...

Dr.Shabbir
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boundary="00000000000058ea0105cf5addd5" --00000000000058ea0105cf5addd5 Content-Type: text/plain; charset="UTF-8" Hi All I want to run eABF with namd and I am getting following errors colvars: Collective variables initialized, 2 in total. colvars: Error: keyword "abf" found without configuration. FATAL ERROR: Error in the collective variables module (see above for details) FATAL ERROR: Error in the collective variables module (see above for details). I was able to run collective variables but when trying to run eABF it gives an error. Kindly have a look at the attached input file and suggest. Many thanks --00000000000058ea0105cf5addd5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi All
I want to run eABF with namd and I a= m getting following errors

colvars: Collectiv= e variables initialized, 2 in total.
colvars: Error: keyword "abf&q= uot; found without configuration.
FATAL ERROR: Error in the collective v= ariables module (see above for details)
FATAL ERROR: Error in the collec= tive variables module (see above for details).

I w= as able to run collective variables but when trying to run eABF it gives an= error. Kindly have a look at the attached input file and suggest.

Many thanks

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--00000000000058ea0305cf5addd7-- From owner-namd-l@halifax.ks.uiuc.edu Wed Oct 27 19:28:25 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19S0SO82000616; Wed, 27 Oct 2021 19:28:24 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19S0SOeM000615; Wed, 27 Oct 2021 19:28:24 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19S0SOCW000611; Wed, 27 Oct 2021 19:28:24 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19S0SNlW000610; Wed, 27 Oct 2021 19:28:23 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 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AOAM531G7+yqB6+x04bQPNblrPDOKssFbsf6VtaGHuON2xF+nuHBUr3G pm5xF8LJlghpsJRB4HD35d1+ORzS+hQXczTPMQ7xAESvQHMimg== X-Google-Smtp-Source: ABdhPJzobepdMABQvMW7iMpNdfxp8RZ8QVyHTQS6CTZcOWv1mLWZaAcaQbaUiGTjecF5G+n0Ja8lqAdkI8zH2Lz6Chg= X-Received: by 2002:a05:6808:f8f:: with SMTP id o15mr579049oiw.137.1635380888006; Wed, 27 Oct 2021 17:28:08 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Michael Robinson Date: Thu, 28 Oct 2021 11:27:57 +1100 Message-ID: Subject: Re: namd-l: Error: keyword "abf" found without configuration To: namd-l@ks.uiuc.edu, Ashutosh Shandilya Content-Type: multipart/alternative; boundary="000000000000e7409605cf5ec890" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: yqpnVOlXb0pkYeS62ScmLuwXUxyU5dj1 X-Proofpoint-GUID: yqpnVOlXb0pkYeS62ScmLuwXUxyU5dj1 X-CLX-Response: 1TFkXGxITEQpMehcdEhEKWUQXZGZbXRoBQkMbfV8RClhYF2ZFS3xkTVsecFh vEQp4ThdvGBIbTAVFQWdoehEKeUwXbx9uTEZHRB9wbxIRCkNIFwcYGRMRCkNZFwcbGBMRCkNJFx 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classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110280000 domainage_hfrom=7936 X-Spam-Score: 0 X-Spam-OrigSender: michael.robinson1@monash.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Robinson --000000000000e7409605cf5ec890 Content-Type: text/plain; charset="UTF-8" Hi Ashutosh, Your input file has a line break between 'abf' and the curly bracket '{' that opens the configuration block - this is causing the ABF configuration block to be skipped, and so your input file is failing. I can't test your given file without the associated system, but I double-checked that this would occur with one of my own ABF input files, and this caused the same error. Hopefully that helps, Regards, Michael Robinson On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya wrote: > Hi All > I want to run eABF with namd and I am getting following errors > > colvars: Collective variables initialized, 2 in total. > colvars: Error: keyword "abf" found without configuration. > FATAL ERROR: Error in the collective variables module (see above for > details) > FATAL ERROR: Error in the collective variables module (see above for > details). > > I was able to run collective variables but when trying to run eABF it > gives an error. Kindly have a look at the attached input file and suggest. > > Many thanks > > --000000000000e7409605cf5ec890 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Ashutosh,

Your input file= has a line break between 'abf' and the curly bracket '{' t= hat opens the configuration block - this is causing the ABF configuration b= lock to be skipped, and so your input file is failing. I can't test you= r given file without the associated system, but I double-checked that this = would occur with one of my own ABF input files, and this caused the same er= ror.

Hopefully that helps,
Regards,=
Michael Robinson

=
Hi All
I want to run eABF with namd and I a= m getting following errors

colvars: Collectiv= e variables initialized, 2 in total.
colvars: Error: keyword "abf&q= uot; found without configuration.
FATAL ERROR: Error in the collective v= ariables module (see above for details)
FATAL ERROR: Error in the collec= tive variables module (see above for details).

I w= as able to run collective variables but when trying to run eABF it gives an= error. Kindly have a look at the attached input file and suggest.

Many thanks

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boundary="000000000000fa34ef05cf669d95" X-Proofpoint-ORIG-GUID: 5IT-bcH4BH853gGf4WwBTzUv5qGhsASv X-CLX-Response: 1TFkXGx4cEQpMehcYEx0RCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHGx0aEQpDWRcHGxMYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxgccRsdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx9jfgdISWIeaGISHxlNbUwefV1oflB/XB9bbUJZa3lcEQpYXBcfBBoEGBkT BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NZaEtIEQpNXBcdHREKTFoXaGlNa2sRCkxGF29ra2t raxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHwQbHBwEHhgRCkJeFxsRCkRYFxgRCkReFxkRCk JcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXaFpwGEkfZngeQ F4RCkJOF2NTY2t7E1h+Gl9eEQpCTBdsH15ZWm5MYWBbQREKQmwXb0Jpf25OW1IZeBoRCkJAF2l8 GlMTRRJ8ZUh9EQpNXhcbEQpaWBcYEQp5QxdvYhxsXF8FUHAFExEKWUsXEx8dGREKcGgXZWtLS2J vSXJ+SWUQGRoRCnBoF2JYQl9jU29OSEFsEBkaEQpwaBdmch97GEdYHn1YeRAZGhEKcGgXaBxMW0 dYGR5bXwUQGRoRCnBsF2d4c3NCR1xbfUZLEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: 5IT-bcH4BH853gGf4WwBTzUv5qGhsASv X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=621 priorityscore=297 adultscore=0 suspectscore=0 bulkscore=0 lowpriorityscore=0 mlxscore=0 clxscore=146 phishscore=0 impostorscore=0 spamscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110280053 domainage_hfrom=9573 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --000000000000fa34ef05cf669d95 Content-Type: text/plain; charset="UTF-8" Dear Colleagues, We have performed MD for RMSD and RMSF calculation of Ligand-protein complex using NAMD/VMD. Now, one reviewer is insisting us to also calculate RMSD and RMSF of Ligand only. Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file or through a separate MD? I have tried RSMD calculator of VMD after opening the psf,pdb and dcd file but "atom selection" is giving error. I wrote UNK and/or LIG ETC. as per psf file but none worked... Many thanks in advance1 DR.SHABBIR --000000000000fa34ef05cf669d95 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
We have performed MD for R= MSD and RMSF calculation of Ligand-protein complex using NAMD/VMD. Now, one= reviewer is insisting us to also calculate RMSD and RMSF of Ligand only.
Is there a way to extract RMSD and RMSF of Ligand only from a .dcd= file or through a separate MD?
I have tried RSMD calculator of V= MD after opening the psf,pdb and dcd file but "atom selection" is= giving error. I wrote UNK and/or LIG ETC. as per psf file but none worked.= .

Many thanks in advance1
DR.SHABBIR
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charset="UTF-8" Hi, You don't have to run any additional simulations etc Let me introduce you to the glorious tk console :P :P let's say you have 1000 frames. type something like set n 0 set ref atomselect ["your ligand" frame 0] for {set i 0} {$i<1001} {incr i} { set conf [atomselect top "your ligand" frame $i] puts "$i [measure rmsd $ref $conf]" } "Your ligand" will be something like "resid X" or "chain Y and resid 23 to 39", have a look at your pdb file, and find how is the ligand called etc and look for the atomselect commands in the tutorial. I think pdb + dcd files will work, you don't need PSF for this particular case How-to: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html On Thu, 28 Oct 2021, 11:50 Mi Yang, wrote: > Dear Colleagues, > We have performed MD for RMSD and RMSF calculation of Ligand-protein > complex using NAMD/VMD. Now, one reviewer is insisting us to also calculate > RMSD and RMSF of Ligand only. > Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file or > through a separate MD? > I have tried RSMD calculator of VMD after opening the psf,pdb and dcd file > but "atom selection" is giving error. I wrote UNK and/or LIG ETC. as per > psf file but none worked.. > > Many thanks in advance1 > DR.SHABBIR > --000000000000c521d905cf681fcf Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
You don= 't have to run any additional simulations etc
Let me introduce you= to the glorious tk console :P :P=C2=A0
let's sa= y you have 1000 frames. type something like=C2=A0
set n 0<= br>
set ref atomselect ["your ligand" frame 0]
for {set i 0} {$i<1001} {incr i} {
=C2=A0 =C2=A0set conf [atomselect top "your ligand" fra= me $i]
=C2=A0 =C2=A0puts "$i [measure rmsd $ref= $conf]" }

"Yo= ur ligand" will be something like "resid X" or "chain Y= and resid 23 to 39", have a look at your pdb file, and find how is th= e ligand called etc and look for the atomselect commands in the tutorial. I= think pdb + dcd files will work, you don't need PSF for this particula= r case



On Thu, 28 Oct 2021, 11:50 Mi Yang, <<= a href=3D"mailto:drmiyang2019@gmail.com">drmiyang2019@gmail.com> wro= te:
Dear Coll= eagues,
We have performed MD for RMSD and RMSF calculation of Lig= and-protein complex using NAMD/VMD. Now, one reviewer is insisting us to al= so calculate RMSD and RMSF of Ligand only.
Is there a way to extr= act RMSD and RMSF of Ligand only from a .dcd file or through a separate MD?=
I have tried RSMD calculator of VMD after opening the psf,pdb an= d dcd file but "atom selection" is giving error. I wrote UNK and/= or LIG ETC. as per psf file but none worked..

Many= thanks in advance1
DR.SHABBIR
--000000000000c521d905cf681fcf-- From owner-namd-l@halifax.ks.uiuc.edu Thu Oct 28 06:42:59 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19SBgx3Q016822; Thu, 28 Oct 2021 06:42:59 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19SBgxpE016821; Thu, 28 Oct 2021 06:42:59 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19SBgwF5016807; Thu, 28 Oct 2021 06:42:58 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19SBgwtk016805; Thu, 28 Oct 2021 06:42:58 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19SBgjJL016673 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=bDXUe9LQU/llZ/NeKgQhOaAhsOvA+/xU2r2ex0JGj4Y=; b=DOwPU9o4iZJy9d9GR0DVngwoVDCaMfKhCckCCTcuEBnnl1VlwTcOKPCNCafNQulBBo 0fxu64fDYgqaUQqa57B8PyHMbQAtIKJWGWAj1BURL2PforayzLFkB8oZtleVnYXsH1aV AQpaRK8C3VXkY9Wa6D7jZjyKqXf5GAnSpL07PLPQtq+iewEde/DZrOmT9laQLUUD8h7j NpGC08lwRGJIqgMUxDUAA2Wc/6gN+Dai2X0lCcc1dC0pG6nIspoE4FCG+gD0IuOFVjY5 fG8SHtXPYbV/w7DxnChNL/GrihnUi5IlTCM8POU2IUnnSkUyGq9VikxKTgzvzUjEt+PW LEkQ== X-Gm-Message-State: AOAM532ROxj/NWFeZiawkkcHzV5Zd5jZZKcz/Mkyn4ETieNI4OlGmxvi rzZorRWnU3bIfN7ggp5iAIQxI8cxkVCpW3VRkzMVMdR00BI= X-Google-Smtp-Source: ABdhPJxeQl61wTRAStS6tYJZwPA6WpMRo9wL6gG9pAc1HFWt6fZuThtPRHATgrXidi/Rc+ITOtxgZTzj6btK95h3Keg= X-Received: by 2002:a2e:810c:: with SMTP id d12mr4210692ljg.177.1635421362833; Thu, 28 Oct 2021 04:42:42 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Natalia Ostrowska Date: Thu, 28 Oct 2021 13:42:29 +0200 Message-ID: Subject: Re: namd-l: RMSD and RMSF of ligand Only To: NAMD Mailing-list , Mi Yang Content-Type: multipart/alternative; boundary="00000000000063e0de05cf6835fc" X-Proofpoint-GUID: jKVxs7HfgMSHRDTJ9lboi5GFJ8bfm_vb X-Proofpoint-ORIG-GUID: jKVxs7HfgMSHRDTJ9lboi5GFJ8bfm_vb X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMbEQpMehcbGxsRCllEF21fHUlIHGdCR0JiEQpYWBdte3J+Z2VZQmh nRREKeE4XYxNfR2R6Y3tEbmwRCnlMF2xQSRMBT2RmRh9mEQpDSBcHGB0SEQpDWRcHGx4fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0bcR8aEBp3BhgaBhoRClleF2hjeREKSUYXX0NfS XVCRVleT04RCkNOF0BhfFJZHWJMTWd5YnhufmATRkhFQx9tbGASSExHdVxIEQpYXBcfBBoEGBkT BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc1lubHsRCk1cFxseEhEKTFoXaXtpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGhIEGx 0SEQpCXhcbEQpEXhcYEQpCRRdnZR8eGUhIGWh5YREKQk4XYxNfR2R6Y3tEbmwRCkJMF217cn5nZ VlCaGdFEQpCbBdkG2hARn9NWxxIYREKQkAXa2dzWn18HU9zaVIRCkJYF2dzZXNAbmFhTF1iEQpN XhcbEQpaWBcYEQp5QxdpGh54RhheU0cBTREKcGcXb2xAYEABQk4Fe3kQGhEKcGgXb05rWGhQbx1 rW2UQGhEKcGgXYGBeR18fGVJiG0cQGhEKcGgXZHNGWHxMU10Zf0AQGRoRCnBoF2UFWEZHXFITHB 9/EBkaEQpwaBdiaG1bEmwSf398TRAaEQpwfRdoX2dzAV55eVNjbBAZGhEKcH0XZhhaeHJCRERvR B0QGRoRCnBnF2NNSRtyXkdJaGdQEB4SEQpwfxdlWHIYHUkYXkZpfBAbHhoRCnBfF2RJfm4cTWBi YhhzEBkaEQpwfxdlGXlmXkdpG2RPcxATHxEKcF8XZF9NR0YfQXsbSVsQGRoRCnBsF2lken9MHkM YaU4SEBkaEQpwTBdkRmh8b11ySFBBaBAaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=999 spamscore=0 clxscore=191 mlxscore=0 lowpriorityscore=0 priorityscore=111 impostorscore=0 adultscore=0 suspectscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110280064 X-Spam-Score: 0 X-Spam-OrigSender: n.ostrowska@cent.uw.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Natalia Ostrowska --00000000000063e0de05cf6835fc Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I made like three mistakes in these commands =F0=9F=98=85 I was writing fro= m my phone. You can email me for the correct version later, but this is definitely the kind of script you need On Thu, 28 Oct 2021, 13:33 Natalia Ostrowska, wrote: > Hi, > You don't have to run any additional simulations etc > Let me introduce you to the glorious tk console :P :P > let's say you have 1000 frames. type something like > set n 0 > set ref atomselect ["your ligand" frame 0] > for {set i 0} {$i<1001} {incr i} { > set conf [atomselect top "your ligand" frame $i] > puts "$i [measure rmsd $ref $conf]" } > > "Your ligand" will be something like "resid X" or "chain Y and resid 23 t= o > 39", have a look at your pdb file, and find how is the ligand called etc > and look for the atomselect commands in the tutorial. I think pdb + dcd > files will work, you don't need PSF for this particular case > > How-to: > http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html > https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html > > > On Thu, 28 Oct 2021, 11:50 Mi Yang, wrote: > >> Dear Colleagues, >> We have performed MD for RMSD and RMSF calculation of Ligand-protein >> complex using NAMD/VMD. Now, one reviewer is insisting us to also calcul= ate >> RMSD and RMSF of Ligand only. >> Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file >> or through a separate MD? >> I have tried RSMD calculator of VMD after opening the psf,pdb and dcd >> file but "atom selection" is giving error. I wrote UNK and/or LIG ETC. a= s >> per psf file but none worked.. >> >> Many thanks in advance1 >> DR.SHABBIR >> > --00000000000063e0de05cf6835fc Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I made like three mistakes in these commands =F0=9F=98=85= I was writing from my phone. You can email me for the correct version late= r, but this is definitely the kind of script you need

On Thu, 28 Oct 2021,= 13:33 Natalia Ostrowska, <n.ostrowska@cent.uw.edu.pl> wrote:
Hi,
You don't have to run any additional simulations etc
Let me intro= duce you to the glorious tk console :P :P=C2=A0
let&= #39;s say you have 1000 frames. type something like=C2=A0
= set n 0
set ref atomselect ["your ligand" fr= ame 0]
for {set i 0} {$i<1001} {incr i} {
=C2=A0 =C2=A0set conf [atomselect top "your ligand&quo= t; frame $i]
=C2=A0 =C2=A0puts "$i [measure rms= d $ref $conf]" }

&q= uot;Your ligand" will be something like "resid X" or "c= hain Y and resid 23 to 39", have a look at your pdb file, and find how= is the ligand called etc and look for the atomselect commands in the tutor= ial. I think pdb + dcd files will work, you don't need PSF for this par= ticular case



<= div dir=3D"ltr" class=3D"gmail_attr">On Thu, 28 Oct 2021, 11:50 Mi Yang, &l= t;drmiyang2019@gmail.com> wrote:
Dear Colleagues,
We have performed= MD for RMSD and RMSF calculation of Ligand-protein complex using NAMD/VMD.= Now, one reviewer is insisting us to also calculate RMSD and RMSF of Ligan= d only.
Is there a way to extract RMSD and RMSF of Ligand only fr= om a .dcd file or through a separate MD?
I have tried RSMD calcul= ator of VMD after opening the psf,pdb and dcd file but "atom selection= " is giving error. I wrote UNK and/or LIG ETC. as per psf file but non= e worked..

Many thanks in advance1
DR.SH= ABBIR
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boundary="00000000000005d56405cf69ca13" X-Proofpoint-ORIG-GUID: u5kBqYiyosKVRQ57ImsTi2HGoigb-syg X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0TEQpMehcZGBgRCllEF2JbTHBLc2YTWmlPEQpYWBdsH15ZWm5MYWB bQREKeE4XY1Nja3sTWH4aX14RCnlMF2F7QhpgQlISeURPEQpDSBcHGBkfEQpDWRcHGx4fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8TcRkSEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF18fQWhbc0NTRVlhfHh7Hx1jR1l+QxhibUVDTUgHWVNNEQpYXBcfBBoEGBkT BRsaBBsaGgQeEgQYGRAbHhofGhEKXlkXc1lvXH4RCk1cFxgSExEKTFoXf2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxd6UHhka1pSclpGRhEKQ1oXGBoTBBIfBBscHA QeEhEKQl4XGxEKRFgXGBEKREkXGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY 2t7E1h+Gl9eEQpCRRdoWnAYSR9meB5AXhEKQk4XY1Nja3sTWH4aX14RCkJMF2wfXllabkxhYFtB EQpCbBdvQml/bk5bUhl4GhEKQkAXa2dzWn18HU9zaVIRCk1eFxsRClpYFxkRCnlDF2kaHnhGGF5 TRwFNEQpZSxcTHx0ZEQpwZxdvbEBgQAFCTgV7eRAaEQpwaBdrQUhjfBpCG39meBAZGhEKcGgXaF lSY10Fe2R5WF8QGRoRCnBoF2BgXkdfHxlSYhtHEBoRCnBoF2UFWEZHXFITHB9/EBkaEQpwaBdnY UFhc1hHbm5wQBAZGhEKcH0XaF9ncwFeeXlTY2wQGRoRCnB9F2YYWnhyQkREb0QdEBkaEQpwaxdo ZU9NSHxrWEhdGxAZGhEKcEsXb2VfREBLW0xEEnwQGRoRCnBrF2xpaH5MTU9CQFheEBkaEQpwfxd lWHIYHUkYXkZpfBAbGx8RCnBfF2RJfm4cTWBiYhhzEBkaEQpwfxdlGXlmXkdpG2RPcxAdHhEKcF 8XZF9NR0YfQXsbSVsQGRoRCnBsF2d4c3NCR1xbfUZLEB4SEQpwTBdkRmh8b11ySFBBaBAZGhEKb X4XGxEKWE0XSxEg X-Proofpoint-GUID: u5kBqYiyosKVRQ57ImsTi2HGoigb-syg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 suspectscore=0 spamscore=0 mlxscore=0 impostorscore=0 adultscore=0 bulkscore=0 mlxlogscore=999 malwarescore=0 priorityscore=322 clxscore=179 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110280075 domainage_hfrom=9573 X-Spam-Score: 0 X-Spam-OrigSender: drmiyang2019@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mi Yang --00000000000005d56405cf69ca13 Content-Type: multipart/alternative; boundary="00000000000005d56105cf69ca11" --00000000000005d56105cf69ca11 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Natalia, Thanks for your comments. We have slightly revised our script in the light of your comments, which we were using for the Ligand-Protein complex. It worked fine for us now. Please see the attached script in case, if anyone else needs it. One has to change the range of ligand atoms numbers. On Thu, Oct 28, 2021 at 2:42 PM Natalia Ostrowska < n.ostrowska@cent.uw.edu.pl> wrote: > I made like three mistakes in these commands =F0=9F=98=85 I was writing f= rom my > phone. You can email me for the correct version later, but this is > definitely the kind of script you need > > On Thu, 28 Oct 2021, 13:33 Natalia Ostrowska, > wrote: > >> Hi, >> You don't have to run any additional simulations etc >> Let me introduce you to the glorious tk console :P :P >> let's say you have 1000 frames. type something like >> set n 0 >> set ref atomselect ["your ligand" frame 0] >> for {set i 0} {$i<1001} {incr i} { >> set conf [atomselect top "your ligand" frame $i] >> puts "$i [measure rmsd $ref $conf]" } >> >> "Your ligand" will be something like "resid X" or "chain Y and resid 23 >> to 39", have a look at your pdb file, and find how is the ligand called = etc >> and look for the atomselect commands in the tutorial. I think pdb + dcd >> files will work, you don't need PSF for this particular case >> >> How-to: >> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html >> https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html >> >> >> On Thu, 28 Oct 2021, 11:50 Mi Yang, wrote: >> >>> Dear Colleagues, >>> We have performed MD for RMSD and RMSF calculation of Ligand-protein >>> complex using NAMD/VMD. Now, one reviewer is insisting us to also calcu= late >>> RMSD and RMSF of Ligand only. >>> Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file >>> or through a separate MD? >>> I have tried RSMD calculator of VMD after opening the psf,pdb and dcd >>> file but "atom selection" is giving error. I wrote UNK and/or LIG ETC. = as >>> per psf file but none worked.. >>> >>> Many thanks in advance1 >>> DR.SHABBIR >>> >> --00000000000005d56105cf69ca11 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Natalia,
Thanks for your comments. We = have slightly revised our script in the light of your comments, which we we= re using for the Ligand-Protein complex. It worked fine for us now. Please = see the attached script in case, if anyone else needs it.
One has= to change the range of ligand atoms numbers.

On Thu, Oct 28, 2021= at 2:42 PM Natalia Ostrowska <n.ostrowska@cent.uw.edu.pl> wrote:
I made like three mistak= es in these commands =F0=9F=98=85 I was writing from my phone. You can emai= l me for the correct version later, but this is definitely the kind of scri= pt you need

On Thu, 28 Oct 2021, 13:33 Natalia Ostrowska, <n.ostrowska@cent.uw.edu.p= l> wrote:
Hi,
You do= n't have to run any additional simulations etc
Let me introduce yo= u to the glorious tk console :P :P=C2=A0
let's s= ay you have 1000 frames. type something like=C2=A0
set n 0=
set ref atomselect ["your ligand" frame 0]<= /div>
for {set i 0} {$i<1001} {incr i} {
=C2=A0 =C2=A0set conf [atomselect top "your ligand" fra= me $i]
=C2=A0 =C2=A0puts "$i [measure rmsd $ref= $conf]" }

"Yo= ur ligand" will be something like "resid X" or "chain Y= and resid 23 to 39", have a look at your pdb file, and find how is th= e ligand called etc and look for the atomselect commands in the tutorial. I= think pdb + dcd files will work, you don't need PSF for this particula= r case



On Thu, 28 Oct 2021, 11:50 Mi Yang, <drmiyang2019@gmail.com> wrote:
Dear Colleagues,
We= have performed MD for RMSD and RMSF calculation of Ligand-protein complex = using NAMD/VMD. Now, one reviewer is insisting us to also calculate RMSD an= d RMSF of Ligand only.
Is there a way to extract RMSD and RMSF of= Ligand only from a .dcd file or through a separate MD?
I have tr= ied RSMD calculator of VMD after opening the psf,pdb and dcd file but "= ;atom selection" is giving error. I wrote UNK and/or LIG ETC. as per p= sf file but none worked..

Many thanks in advance1<= /div>
DR.SHABBIR
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Fri, 29 Oct 2021 07:40:51 -0700 (PDT) X-Gm-Message-State: AOAM532jca8MyX1PXJi5GrHb++E/b0nSAdIe2LotFhdtsuclX4DYrwdd Ka1hI6F0n49KgaUOtk2PiVPZ3t1HiMsmTQwW+cI= X-Google-Smtp-Source: ABdhPJyH7h9hVsQfezbXYHI81CiRK4Al9QzDjGcUqCS1LDqO59PSRm/WAmr1WDDCc0HGAaOiH10Xltnz3T+QLmf03ek= X-Received: by 2002:a2e:4a0a:: with SMTP id x10mr11809819lja.146.1635518448780; Fri, 29 Oct 2021 07:40:48 -0700 (PDT) MIME-Version: 1.0 From: Monika Kumari Date: Fri, 29 Oct 2021 20:10:13 +0530 X-Gmail-Original-Message-ID: Message-ID: Subject: namd-l: Rattle algorithm failure while restarting metadynamics simulation To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="00000000000029c7d305cf7ed0f1" X-Proofpoint-GUID: TtyzRTbJOKX5LJ4ZRObPHdCFf-wWJ2lf X-Proofpoint-ORIG-GUID: TtyzRTbJOKX5LJ4ZRObPHdCFf-wWJ2lf X-CLX-Shades: MLX X-CLX-Response: 1TFkXGR8SEQpMehcaEQpZRBdkfEN7EmlaWXBhTBEKWFgXY0V7flgfe0kaHlI RCnhOF2RLWmxNbBlhfmFrEQp5TBdlaGhDbVoeflhPHBEKQ0gXBxgdGBEKQ1kXBxsaHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXEh9xGAYSHncGGxwbBh4YQhwGGgYTGgYZGnEbEBp3BhoGBx8aBhoGG gYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThd+XlNQeH5IYGVhch9mYB5w eGVIemJOaWxMB119YBhGTBEKWFwXHwQaBBgZEwUbGgQbGhoEHhIEGBkQGx4aHxoRCl5ZF3NZS1N yEQpNXBcbEhoRCkxaF2lsaU1raxEKTEYXb2tra2trEQpCTxdjRUJpAXxeZRJYGREKQ1oXGxoZBB gdBBsaBB4eEQpCXhcbEQpCXBcbEQpCSxdjYWxcck15WEIZHxEKQkkXZEtabE1sGWF+YWsRCkJFF 2xtXkJGR1pgR09cEQpCThdkS1psTWwZYX5haxEKQkwXY0V7flgfe0kaHlIRCkJsF2tAeGJLbEFP QXBeEQpCQBduQGMeHHwYenpuZxEKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2MSXRJJcHAYch9 JEQpZSxccEhsSEQpwaBdhU09keFtJbmdmGhAaEQpwaBdhYUhlR3h7GkxTehAaEQpwaBdmaWhdc0 1pS3MYcBAaEQpwaBdiWEdCGF1lbRJ+GRAaEQpwaBdhYmNbRwEfHGlwGhAaEQpwbBd6elxrU0V/U mxjehAHGxgRCnBDF2Z6e3xOYnMSZxxDEB4YEQptfhcaEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=801 spamscore=0 clxscore=358 mlxscore=0 lowpriorityscore=0 priorityscore=0 impostorscore=0 adultscore=0 suspectscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110290085 domainage_hfrom=6818 X-Spam-Score: 0 X-Spam-OrigSender: Monika.Kumari@chemistry.iitd.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Monika Kumari --00000000000029c7d305cf7ed0f1 Content-Type: text/plain; charset="UTF-8" Dear all, I am running a well-tempered metadynamics simulation with 2 fs timestep using NAMD which is running fine but when I restart the run, it gives the rattle algorithm error. What can the possible things I might be overlooking. Please suggest. Though after reducing the time step, the error disappears. Also, when I ran two simulations parallelly with exactly same files, the colvar trajectory was different. Being molecular dynamics a deterministic simulation, how could it happen? Thanks Monika --00000000000029c7d305cf7ed0f1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear a= ll,
I am running a well-tempered metadynamics simulation with 2 fs= timestep using NAMD which is running fine but when I restart the run, it g= ives the rattle algorithm error. What can the possible things I might be ov= erlooking.=C2=A0Please suggest.=C2=A0
Though after reducing=C2=A0t= he time step, the error disappears.=C2=A0

Also, when= I ran two simulations parallelly with exactly same files, the colvar traje= ctory was different. Being molecular dynamics a deterministic simulation, h= ow could it happen?=C2=A0

Thanks
Monika
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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hello Monika, On Fri, Oct 29, 2021 at 10:43 AM Monika Kumari < Monika.Kumari@chemistry.iitd.ac.in> wrote: > Dear all, > I am running a well-tempered metadynamics simulation with 2 fs timestep > using NAMD which is running fine but when I restart the run, it gives the > rattle algorithm error. What can the possible things I might be > overlooking. Please suggest. > If the instability is only at the restart, can you confirm that you are also loading the correct .colvars.state file alongside the correct NAMD coor/vel/xsc files? https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!qfab6XpgNYgTnJ0ARPo_= iMUrteSFBGkrjXHO1fvhMZYiWjaaW40sFoUySf5pztCvKA$=20 (If you used a NAMD patched with Plumed, you can follow the corresponding instructions for restarting). > Though after reducing the time step, the error disappears. > > Also, when I ran two simulations parallelly with exactly same files, the > colvar trajectory was different. Being molecular dynamics a deterministic > simulation, how could it happen? > This is false. Even with a completely deterministic set of options, the limited precision of floating-point math adds tiny errors that are completely harmless for the sake of physical accuracy but lead over time to diverging trajectories. And if you use a non-deterministic thermostat or barostat (very common in NAMD) determinism may go out the window from the very first step. Giacomo > > Thanks > Monika > --000000000000a3b95005cf7f1ad4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hello Monika,

On Fri, Oct 29, 2021 at 10:4= 3 AM Monika Kumari <Monika.Kumari@chemistry.iitd.ac.in> wrote:
= Dear all,
I am = running a well-tempered metadynamics simulation with 2 fs timestep using NA= MD which is running fine but when I restart the run, it gives the rattle al= gorithm error. What can the possible things I might be overlooking.=C2=A0Pl= ease suggest.=C2=A0

If the instability is only at the restart, can you confirm that you are a= lso loading the correct .colvars.state file alongside the correct NAMD coor= /vel/xsc files?
(If you used a= NAMD patched with Plumed, you can follow the corresponding instructions fo= r restarting).
=C2=A0
Though after reducing=C2=A0the time s= tep, the error disappears.=C2=A0

Also, when I ran two simulations parallelly with exactly same files= , the colvar trajectory was different. Being molecular dynamics a determini= stic simulation, how could it happen?=C2=A0

This is false.=C2=A0 Even with a completely=C2=A0= deterministic set of options, the limited precision of floating-point math = adds tiny errors that are completely harmless for the sake of physical accu= racy but lead over time to diverging trajectories.=C2=A0 And if you use a n= on-deterministic thermostat or barostat (very common in NAMD) determinism m= ay go out the window from the very first step.

Gia= como
=C2=A0

Thanks
Monika
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Sat, 30 Oct 2021 10:14:34 +0530 (IST) Received: by mail-lf1-f43.google.com with SMTP id y26so25008612lfa.11 for ; Fri, 29 Oct 2021 21:44:34 -0700 (PDT) X-Gm-Message-State: AOAM532elxr9uNtJ8V/6B3IDSah3NhVUER/FsbxI8tC7Pk7u0tN/Gm8v dKCZpS94sU5wI58EENZIdsppmUHEpXFlMp7pyK0= X-Google-Smtp-Source: ABdhPJys56TzP5asNEcVRN5UCNT2CHMXNQJA+F4+WsUnP119ngxj610f3auk0gLvphRkroWY/c3zcQC/kVKrPHe5tkc= X-Received: by 2002:a05:6512:b1f:: with SMTP id w31mr14254606lfu.164.1635569071285; Fri, 29 Oct 2021 21:44:31 -0700 (PDT) References: In-Reply-To: From: Monika Kumari Date: Sat, 30 Oct 2021 10:13:56 +0530 X-Gmail-Original-Message-ID: Message-ID: Subject: Re: namd-l: Rattle algorithm failure while restarting metadynamics simulation To: Giacomo Fiorin Cc: NAMD list Content-Type: multipart/alternative; boundary="0000000000007fe91205cf8a99dc" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRkcEQpMehcaEQpZRBdkfEN7EmlaWXBhTBEKWFgXY0V7flgfe0kaHlI RCnhOF2RLWmxNbBlhfmFrEQp5TBdlaGhDbVoeflhPHBEKQ0gXBx8fGBEKQ1kXBxwaEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcYGHEYBhgbdwYbHx4GHBpCGxsGGgYbGhoGHBpxGRAadwYaBhoGGgYHH BoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XXh0cXVIHUn9vYGNARBtc E2ZMH2lpZR9LHBpeUEsaXmsRClhcFx8EGgQYGRMFGxoEGxsaBB8aBBseHxAbHhofGhEKXlkXc1l EYHIRCk1cFxgaGREKTFoXeGlra2sRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQ pCTxdjRUJpAXxeZRJYGREKQ1oXGxoZBBgdBBMEHh8RCkJeFxsRCkRJFxsRCkJcFxsRCkJLF2Nhb FxyTXlYQhkfEQpCSRdkS1psTWwZYX5haxEKQkUXbG1eQkZHWmBHT1wRCkJOF2RLWmxNbBlhfmFr EQpCTBdjRXt+WB97SRoeUhEKQmwXa0B4YktsQU9BcF4RCkJAF2JNcm5lEkMSEkJnEQpCWBdnc2V zQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXY0lcY059bwFYG1oRCllLFxwSGxMRCnBnF2gfQk5abG x9Gh5YEB4SEQpwaBdpaWEfaBIZcFlFWhAZGhEKcGgXYRxmQWlNSHpofxgQGRoRCnBoF2ISbHJIU 0VFfU5eEBkaEQpwaBdsQlAeHERHfUtDThAZGhEKcGgXZm5eXWhjZRNkX14QHhIRCnB9F2tmf08e fnlvYF0eEBkaEQpwfxdiTgUBcEReaUR7ZRAbGxIRCnBfF2IaX1BMRgFGHBpSEBkaEQpwbBd6elx rU0V/UmxjehAaEQpwTBdtaGUZQVJ9exhFUhAZGhEKcEMXaV9EfE5icBlhH0gQHBoRCm1+FxsRCl hNF0sRIA== X-Proofpoint-ORIG-GUID: t76wx-xUEJIjn1v9Lf5CCO5a60tza0tA X-Proofpoint-GUID: t76wx-xUEJIjn1v9Lf5CCO5a60tza0tA MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 mlxscore=0 impostorscore=0 phishscore=0 adultscore=0 suspectscore=0 mlxlogscore=999 malwarescore=0 clxscore=336 spamscore=0 bulkscore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110300024 domainage_hfrom=6819 X-Spam-Score: 0 X-Spam-OrigSender: Monika.Kumari@chemistry.iitd.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Monika Kumari --0000000000007fe91205cf8a99dc Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Dr. Giacomo Thanks for the clarification regarding the deterministic simulations. For the rattle error issue, I am loading the correct .colvars.state file. The error most of the time disappears while using lower timesteps. Also, this error is mainly encountered while running metadynamics on larger molecules in a densely packed environment (e.g amino acid permeation in lipid bilayer). I remember I never encountered the error while running a metadynamics simulation of sodium ion passing through a pore. Thanks. On Fri, 29 Oct 2021 at 20:31, Giacomo Fiorin wrote: > Hello Monika, > > On Fri, Oct 29, 2021 at 10:43 AM Monika Kumari < > Monika.Kumari@chemistry.iitd.ac.in> wrote: > >> Dear all, >> I am running a well-tempered metadynamics simulation with 2 fs timestep >> using NAMD which is running fine but when I restart the run, it gives the >> rattle algorithm error. What can the possible things I might be >> overlooking. Please suggest. >> > > If the instability is only at the restart, can you confirm that you are > also loading the correct .colvars.state file alongside the correct NAMD > coor/vel/xsc files? > > https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd= /colvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!uQUPilQRiRSQYJfoJo= xMjUbrgPoBlRX3BmtRPnpaP9UAYVb1zRt2D9UC5NaGObuTbg$=20 > (If you used a NAMD patched with Plumed, you can follow the corresponding > instructions for restarting). > > >> Though after reducing the time step, the error disappears. >> >> Also, when I ran two simulations parallelly with exactly same files, the >> colvar trajectory was different. Being molecular dynamics a deterministic >> simulation, how could it happen? >> > > This is false. Even with a completely deterministic set of options, the > limited precision of floating-point math adds tiny errors that are > completely harmless for the sake of physical accuracy but lead over time = to > diverging trajectories. And if you use a non-deterministic thermostat or > barostat (very common in NAMD) determinism may go out the window from the > very first step. > > Giacomo > > >> >> Thanks >> Monika >> > --0000000000007fe91205cf8a99dc Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear Dr. Giacomo
Thank= s for the clarification regarding the deterministic simulations.
For the rattle error issue, I am loading the correct=C2=A0.colvars.state file. The error most of = the time disappears while using lower timesteps. Also, this error is mainly= encountered while running metadynamics on larger molecules in a densely pa= cked environment (e.g amino acid permeation in lipid bilayer). I remember I= never encountered the error while running a metadynamics simulation of sod= ium ion passing through a pore.=C2=A0 =C2=A0

Thanks.

On Fri, 29 Oct 2021 at 20:31, Gi= acomo Fiorin <giacomo.fiorin= @gmail.com> wrote:
Hello Monika,

On Fri, Oct 29, 2= 021 at 10:43 AM Monika Kumari <Monika.Kumari@chemistry.iitd.ac.in> w= rote:
Dear all,
I am running a well-tempered metadynamics simulation with 2 fs time= step using NAMD which is running fine but when I restart the run, it gives = the rattle algorithm error. What can the possible things I might be overloo= king.=C2=A0Please suggest.=C2=A0
=
If the instability is only at the restart, can you confirm t= hat you are also loading the correct .colvars.state file alongside the corr= ect NAMD coor/vel/xsc files?
(= If you used a NAMD patched with Plumed, you can follow the corresponding in= structions for restarting).
=C2=A0
Though after reducing=C2= =A0the time step, the error disappears.=C2=A0

Also, when I ran two simulations parallelly with exact= ly same files, the colvar trajectory was different. Being molecular dynamic= s a deterministic simulation, how could it happen?=C2=A0
=

This is false.=C2=A0 Even with a com= pletely=C2=A0deterministic set of options, the limited precision of floatin= g-point math adds tiny errors that are completely harmless for the sake of = physical accuracy but lead over time to diverging trajectories.=C2=A0 And i= f you use a non-deterministic thermostat or barostat (very common in NAMD) = determinism may go out the window from the very first step.

<= /div>
Giacomo
=C2=A0

Thanks
Monika
--0000000000007fe91205cf8a99dc-- From owner-namd-l@halifax.ks.uiuc.edu Sat Oct 30 02:03:18 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19U73I50020380; Sat, 30 Oct 2021 02:03:18 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19U73HmU020340; Sat, 30 Oct 2021 02:03:18 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19U730lx020193; Sat, 30 Oct 2021 02:03:01 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 19U730cr020186; Sat, 30 Oct 2021 02:03:00 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 19U72rfo020159 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Sat, 30 Oct 2021 02:02:53 -0500 (CDT) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 19U5qJEF031685 for ; Sat, 30 Oct 2021 07:02:52 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=p20190061@hyderabad.bits-pilani.ac.in; dkim=pass header.s=google header.d=hyderabad.bits-pilani.ac.in Received: from mail-pj1-f48.google.com (mail-pj1-f48.google.com [209.85.216.48]) by mx0a-00007101.pphosted.com with ESMTP id 3c0xtmggh7-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Sat, 30 Oct 2021 07:02:52 +0000 Received: by mail-pj1-f48.google.com with SMTP id x33-20020a17090a6c2400b001a63ef25836so2744986pjj.3 for ; Sat, 30 Oct 2021 00:02:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=hyderabad.bits-pilani.ac.in; s=google; h=mime-version:from:date:message-id:subject:to; bh=6wircroJdpF6vV1EXl+MRc74h89bbIqFAvH9Gm1F8vw=; b=q0nxYpILNULVNPbSAFyllO+Hxj56fjjqS0B8RFAG1nlMsdx/q3QKv56yyhNAJLcV3t DE4CmcfbK702mmdcesWQw0k+iz4Q93VzaonznOuK9pGg/HvDQhdKuxYWE5fK+mtyUYmc 6r12RETUp19GxUX7AJw2+IjQz67gu4ekKknn0= X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=6wircroJdpF6vV1EXl+MRc74h89bbIqFAvH9Gm1F8vw=; b=Bi08bUhkgu11jkkkYffDckr/aAwHQoygvu51lVPm4vg9IQmzR6nuu9AKv6YFjXUZ/M DcFkX+1jWe64wbLcUXBbAov4fAFonoG4EL/PQIePgsY1D1X9Lpx0Rqxj863OMqazYBj6 1kM20XLBaPNld8WMbQRS8w7u1QowHbeug10E+u2phmXi8MEWeUwI0QzUkUYf/u5lcC8p uvCFZoOF5Mc9k59qeRim3AtsBKqVMasqRpuugcMXQrWBqsVPxy2uGMomPrDWONTak/7M zk+ZQlZAswQXdP7LiziF7hppdvfCIEEo43I1sigFG8IHyf54WQrIHB5KXBXUqzK84HAq pkbQ== X-Gm-Message-State: AOAM533nOjpp9ZU/I9ffSZHHne8/afGU0bkxZjdCfopwWz4DYh/f0fn3 1hOnQGl+0HeY6Na2ONCg8T9xEB/O+5Z2Ay/7/hz6siDNWbyQcpzzvmxZ5TTEplhatgYWVhGDCSw aSINobrx27fPI6AEPpWY5ZRAqFfxj09s= X-Google-Smtp-Source: ABdhPJyBflfBtiaJE121gXdzpXLgWecWxtj1BAU3PfwTDIrHxZC2vpWYs+gCzSo3x2jnrmCTVwju2wkRm2JBTMXNiqo= X-Received: by 2002:a17:903:248f:b0:141:5a79:ae48 with SMTP id p15-20020a170903248f00b001415a79ae48mr13524577plw.12.1635577371552; Sat, 30 Oct 2021 00:02:51 -0700 (PDT) MIME-Version: 1.0 From: "SYEDA SABIHA SULTANA LUBNA ." Date: Sat, 30 Oct 2021 12:32:39 +0530 Message-ID: Subject: namd-l: Trouble in fep.tcl file for FEP run in NAMD To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000003bfedd05cf8c88b4" X-Proofpoint-GUID: 2hCsfbxnDtcZFiMGF3jWtx0Uq3ePW7L- X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 2hCsfbxnDtcZFiMGF3jWtx0Uq3ePW7L- X-CLX-Response: 1TFkXHBIRCkx6FxoRCllEF3pjbxh+HktfeWh/EQpYWBdgHm9Nbn55ExpwRxE KeE4XbF1bYWVCHXBJTRMRCnlMF2xjGGd/WGVgZn5zEQpDSBcHGx4fEQpDWRcHGBkcEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGHhJxGBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1QkVZX k9OEQpDThcYQmlZTEhSRG5eSXBsQ2dtbBlAfV5SGn9bGU96fR1mBxEKWFwXHwQaBBgZEwUbGgQb GhoEHhIEGBgQGx4aHxoRCl5ZF3NZWmEZEQpNXBcYEhIRCkxaF3hpTWtrEQpFWRdvEQpMXxd6BQU FBQUFBQUFQxEKTEYXb2tra2trEQpCTxdkflhPZm5zSXBbTxEKQ1oXGBoTBBIfBBgbHAQeEhEKQl 4XGxEKQlwXGxEKQksXYF1IWVsTAVgbQVARCkJJF2xdW2FlQh1wSU0TEQpCRRdtZHp5e2Z8Y11uT REKQk4XbF1bYWVCHXBJTRMRCkJMF2Aeb01ufnkTGnBHEQpCbBdgQFNhb0djWUhOQBEKQkAXbBJi EklAXGMBfk0RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcbEQp5QxdoYGFiYX1iQ15QfBEKWUs XHBIbExEKcGgXYB5eUBIZbE1nbxoQGRoRCnBoF2ZhXHMSWURTeUBhEBkaEQpwaBdsbXtOc1xhSG JyaBAZGhEKcGgXb3hrHl1DU2xmZWYQGRoRCnBoF2VifGJ5fWBQHB0FEBkaEQpwbBdjf2Jhb2dlX EtrTRAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=68 suspectscore=0 adultscore=0 mlxscore=0 mlxlogscore=915 spamscore=0 phishscore=0 bulkscore=0 lowpriorityscore=0 impostorscore=0 malwarescore=0 priorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110300037 domainage_hfrom=6819 X-Spam-Score: 0 X-Spam-OrigSender: p20190061@hyderabad.bits-pilani.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "SYEDA SABIHA SULTANA LUBNA ." --0000000000003bfedd05cf8c88b4 Content-Type: text/plain; charset="UTF-8" Hi, Can someone help me in understanding why I am getting this error message? This is when i am trying to run my FEP calculation on centose 8 version. where as the same script is working on ubuntu 20 version. Info: Based on Charm++/Converse 61002 for charmpp-6.10.2-rcdhh4jp7pfjtdz5hragsqhs5elcvieh Info: Built Mon Jan 11 20:27:40 IST 2021 by root on sharanga Info: 1 NAMD 2.14 linux-x86_64-netlrts 64 node4 2032 Info: Running on 64 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0428052 s CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification) Info: 4681.57 MB of memory in use based on /proc/self/stat Info: Configuration file is rest-01.namd Info: Working in the current directory /home/debashreeb/FEP_complex Info: Sourcing fep.tcl Warning: Couldn't parse line 105 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 117 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 124 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 137 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 138 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 238 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 246 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 247 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 258 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 271 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 276 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 277 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 278 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 281 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 294 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 297 in configuration file fep.tcl. The line was: } Warning: Couldn't parse line 299 in configuration file fep.tcl. The line was: } ERROR: Expecting value and optional units for option 'langevinTemp' ERROR: Multiple definitions of 'alchLambda' ERROR: in the configuration file are not allowed ERROR: Expecting value and optional units for option 'alchLambda' ERROR: Multiple definitions of 'alchLambda2' ERROR: in the configuration file are not allowed ERROR: Expecting value and optional units for option 'alchLambda2' ERROR: Multiple definitions of 'alchLambdaIDWS' ERROR: in the configuration file are not allowed ERROR: Expecting value and optional units for option 'alchLambdaIDWS' ERROR: Expecting value and optional units for option 'LangevinPistonTemp' ERROR: 'LangevinPistonTemp' was set to 0 but it should be positive ERROR: Multiple definitions of 'firsttimestep' ERROR: in the configuration file are not allowed ERROR: The following variables were set in the ERROR: configuration file but are NOT VALID ERROR: runFEP ERROR: runTIlist ERROR: reinitvels ERROR: minimize ERROR: return ERROR: lappend ERROR: while ERROR: } ERROR: runFEPlist ERROR: incr ERROR: run ERROR: $win ERROR: print ERROR: foreach ERROR: if Thanks for the help. -- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani. --0000000000003bfedd05cf8c88b4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
Can someone help me in understanding wh= y I am getting this error message? This is when i am trying to run my FEP c= alculation on centose 8 version. where as the same script is working on ubu= ntu 20 version.

Info: Based on Charm++/Convers= e 61002 for charmpp-6.10.2-rcdhh4jp7pfjtdz5hragsqhs5elcvieh
Info: Built = Mon Jan 11 20:27:40 IST 2021 by root on sharanga
Info: 1 NAMD =C2=A02.14= =C2=A0linux-x86_64-netlrts =C2=A064 =C2=A0 =C2=A0node4 =C2=A02032
Info:= Running on 64 processors, 1 nodes, 1 physical nodes.
Info: CPU topology= information available.
Info: Charm++/Converse parallel runtime startup = completed at 0.0428052 s
CkLoopLib is used in SMP with simple dynamic sc= heduling (converse-level notification)
Info: 4681.57 MB of memory in use= based on /proc/self/stat
Info: Configuration file is rest-01.namd
In= fo: Working in the current directory /home/debashreeb/FEP_complex
Info: = Sourcing fep.tcl
Warning: Couldn't parse line 105 in configuration f= ile fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 }
Warning: Couldn't p= arse line 117 in configuration file fep.tcl.=C2=A0 The line was: =C2=A0 =C2= =A0 =C2=A0 }
Warning: Couldn't parse line 124 in configuration file = fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 }
Warning: Couldn't parse= line 137 in configuration file fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 = }
Warning: Couldn't parse line 138 in configuration file fep.tcl.=C2= =A0 The line was: }
Warning: Couldn't parse line 238 in c= onfiguration file fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 }
Warning: = Couldn't parse line 246 in configuration file fep.tcl.=C2=A0 The line w= as: =C2=A0 =C2=A0 }
Warning: Couldn't parse line 247 in configuratio= n file fep.tcl.=C2=A0 The line was: }
Warning: Couldn't parse line 2= 58 in configuration file fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 }
Wa= rning: Couldn't parse line 271 in configuration file fep.tcl.=C2=A0 The= line was: =C2=A0 =C2=A0 =C2=A0 =C2=A0 }
Warning: Couldn't parse lin= e 276 in configuration file fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 =C2= =A0 =C2=A0 }
Warning: Couldn't parse line 277 in configuration file = fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 =C2=A0 }
Warning: Couldn'= t parse line 278 in configuration file fep.tcl.=C2=A0 The line was: =C2=A0 = =C2=A0 }
Warning: Couldn't parse line 281 in configuration file fep.= tcl.=C2=A0 The line was: }
Warning: Couldn't parse line 294 in confi= guration file fep.tcl.=C2=A0 The line was: =C2=A0 =C2=A0 }
Warning: Coul= dn't parse line 297 in configuration file fep.tcl.=C2=A0 The line was: = =C2=A0 =C2=A0 }
Warning: Couldn't parse line 299 in configuration fi= le fep.tcl.=C2=A0 The line was: }
ERROR: Expecting value and optional un= its for option 'langevinTemp'
ERROR: Multiple definitions of = 9;alchLambda'
ERROR: =C2=A0 in the configuration file are not allowe= d
ERROR: Expecting value and optional units for option 'alchLambda&#= 39;
ERROR: Multiple definitions of 'alchLambda2'
ERROR: =C2= =A0 in the configuration file are not allowed
ERROR: Expecting value and= optional units for option 'alchLambda2'
ERROR: Multiple definit= ions of 'alchLambdaIDWS'
ERROR: =C2=A0 in the configuration file= are not allowed
ERROR: Expecting value and optional units fo= r option 'alchLambdaIDWS'
ERROR: Expecting value and optional un= its for option 'LangevinPistonTemp'
ERROR: 'LangevinPistonTe= mp' was set to 0 but it should be positive
ERROR: Multiple definitio= ns of 'firsttimestep'
ERROR: =C2=A0 in the configuration file ar= e not allowed
ERROR: The following variables were set in the
ERROR: c= onfiguration file but are NOT VALID
ERROR: =C2=A0 =C2=A0runFEP
ERROR:= =C2=A0 =C2=A0runTIlist
ERROR: =C2=A0 =C2=A0reinitvels
ERROR: =C2=A0 = =C2=A0minimize
ERROR: =C2=A0 =C2=A0return
ERROR: =C2=A0 =C2=A0lappend=
ERROR: =C2=A0 =C2=A0while
ERROR: =C2=A0 =C2=A0}
ERROR: =C2=A0 =C2= =A0runFEPlist
ERROR: =C2=A0 =C2=A0incr
ERROR: =C2=A0 =C2=A0run
ERR= OR: =C2=A0 =C2=A0$win
ERROR: =C2=A0 =C2=A0print
ERROR: =C2=A0 =C2=A0f= oreach
ERROR: =C2=A0 =C2=A0if

Thanks for the he= lp.

The information contained in this electronic communication is intended sole= ly for the individual(s) or entity to which it is addressed. It may contain= proprietary, confidential and/or legally privileged information. Any revie= w, retransmission, dissemination, printing, copying or other use of, or tak= ing any action in reliance on the contents of this information by person(s)= or entities other than the intended recipient is strictly prohibited and m= ay be unlawful. If you have received this communication in error, please no= tify us by responding to this email or telephone and immediately and perman= ently delete all copies of this message and any attachments from your syste= m(s). The contents of this message do not necessarily represent the views o= r policies of BITS Pilani.
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charset="UTF-8" Hi, I managed to set up a QM/MM simulation with QwikMD. I am running a MPI version of NAMD and ORCA 5.0.1. Because the cluster where I run uses SLURM, the way I am running NAMD using the following batch script: --------------------------------------------------------- #SBATCH -n 4 module load OpenMPI module load NAMD/2.14 module load ORCA/5.0.1 export PATH="OpenMPI/bin/:$PATH" export LD_LIBRARY_PATH="OpenMPI/lib/:$LD_LIBRARY_PATH" mpirun -np 1 namd2 QMMM-Min.conf #using 1 MPI only for NAMD --------------------------------------------------------- The simulation runs well when I use 1 processor only in ORCA which means for me that in the QMMM-Min.conf script I use the options (without any reference to PAL): qmConfigLine "!B3LYP 6-31G* " qmConfigLine "!EnGrad NOSOSCF But, when I try to use more than 1 processor by using PAL4: qmConfigLine "!B3LYP 6-31G* " qmConfigLine "!EnGrad NOSOSCF PAL4" the simulation doesn't run. NAMD logfile only says: ERROR: Could not find QM output file! FATAL ERROR: (unknown error): No such file or directory while the logfile of ORCA says: ORCA finished by error termination in GTOInt Calling Command: mpirun -np 4 /bin/orca_gtoint_mpi /0/qmmm_0.input.int.tmp /0/qmmm_0.input [file orca_tools/qcmsg.cpp, line 458]: .... aborting the run I think I am missing something in the way I need to run the NAMD+ORCA. Any comments will be highly appreciated, Thanks --000000000000a80b1105cf95d864 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I managed to set up a QM/MM simulat= ion with QwikMD.=C2=A0 I am running a MPI
version of NAMD and ORC= A 5.0.1. Because the cluster where I run uses=C2=A0
SLURM, the wa= y I am running NAMD using the following batch script:

<= div>---------------------------------------------------------
#SB= ATCH -n 4
=C2=A0=C2=A0
module load OpenMPI
module load NAMD/2.14module load ORCA/5.0.1
=C2=A0
export PATH=3D"OpenMPI/bin/:$PAT= H" =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
export LD_LIBRARY_= PATH=3D"OpenMPI/lib/:$LD_LIBRARY_PATH"
=C2=A0
mpirun -np 1 = namd2 QMMM-Min.conf=C2=A0 =C2=A0#using 1 MPI only for NAMD
---------------------------------------------------------

The simulation runs well wh= en I use 1 processor only in ORCA which means
for me that in the = QMMM-Min.conf=C2=A0script I use the options (without any
referenc= e to PAL):

qmConfigLine "!B3LYP 6-31G* "=
qmConfigLine "!EnGrad NOSOSCF

But, wh= en I try to use more than 1 processor by using PAL4:

qmConfigLine "!B3LYP 6-31G* "
qmConfigLine "!EnGrad = NOSOSCF PAL4"

the simulation doesn't run. NAMD = logfile only says:=C2=A0

ERROR: Could not find QM = output file!
FATAL ERROR: (unknown error): No such file or directory
=

while the logfile of ORCA says:

ORCA finished by error termination in GTOInt =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0
=C2=A0 Calling Command: mpirun -np 4 =C2=A0= /bin/orca_gtoint_mpi=C2=A0/0/qmmm_0.input.int.tmp /0/qmmm_0.input [file orc= a_tools/qcmsg.cpp, line 458]: =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0
=C2=A0 =C2=A0 .... aborting the run
<= div>
I think I am missing something in the way I need to run = the NAMD+ORCA.
Any comments will be highly appreciated,

Thanks
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Sun, 31 Oct 2021 12:10:15 -0700 (PDT) From: =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= Content-Type: multipart/alternative; boundary="Apple-Mail=_035E29C4-405F-47C2-A380-90C02A13060A" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.7\)) Subject: namd-l: CONVERT PSF to TOP grimaces Message-Id: <93211902-9B7D-4BB4-9E19-F1E853677AED@gmail.com> Date: Sun, 31 Oct 2021 14:10:14 -0500 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3608.120.23.2.7) X-CLX-Response: 1TFkXGx0YEQpMehcZHxsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGxMSEQpDWRcHGx4fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8YcRkYEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1xGRhpARBh7R25bSUFpHl9nR0tMW0FQeh8bE2hEQEVZEQpYXBcfBBoEGBkT BRsaBBsbGgQfGgQbHhgQGx4aHxoRCl5ZF3NeYxwaEQpNXBcbGx0RCkxaF2loaU1NaxEKTEYXb2t ra2trEQpCTxdtUnMSQVtpRBMeTBEKQ1oXGBoTBBIfBBgbEwQeExEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdjbHljfXp+YUZPZhEKQk4XY1Nja 3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdvT2RBWkJQbWZrWREKQkAXaxxCb3BteRt6Y1gR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5Qxdpc2leQEgFR119YhEKWUsXEx8dHBEKcGg XZWYcBXgbG0NYRFMQGhEKcGgXellmUhxubmJ7E2wQGhEKcGgXaBl/b0Vlbml5ZxwQGhEKcGwXaW EBf0lme0IZeh4QGRoRCnBDF2dfZntmf1MFYB1CEBoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: vll0jn2QmDqckC4uMmafqkzP519Bnjos X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: vll0jn2QmDqckC4uMmafqkzP519Bnjos X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 adultscore=0 malwarescore=0 phishscore=0 clxscore=172 mlxscore=0 priorityscore=351 mlxlogscore=448 lowpriorityscore=0 impostorscore=0 spamscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2110310120 domainage_hfrom=9576 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= --Apple-Mail=_035E29C4-405F-47C2-A380-90C02A13060A Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Users,=20 Based in rigid characteristics of gromacs (pdb2gmx) for manipule and = build complex system, I=E2=80=99ve used PSFgen embebed into VMD to build = my system. Now I like convert PSF to Top gromacs, using TopoGromacs = tool.=20 My question is: It is right pathway to perform md simulations with = gromacs?=20 Best,=20 Geo.=20= --Apple-Mail=_035E29C4-405F-47C2-A380-90C02A13060A Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear Users, 

Based in rigid characteristics of gromacs = (pdb2gmx) for manipule and build complex system, I=E2=80=99ve used = PSFgen embebed into VMD to build my system. Now I like convert PSF = to Top gromacs, using TopoGromacs tool. 

My question is: It is right = pathway to perform md simulations with gromacs? 

Best, 

Geo. 
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ABdhPJyTO7owD7ukoLDc50u4mS+gBgAhlM7eOVN8WpanfMbZhFYbfq11hTapZ7i4DXPQy3yFrQlPWM41O+9wSM61sW4= X-Received: by 2002:a63:8ac2:: with SMTP id y185mr10081828pgd.205.1635802391868; Mon, 01 Nov 2021 14:33:11 -0700 (PDT) MIME-Version: 1.0 From: David Tang Date: Mon, 1 Nov 2021 16:33:01 -0500 Message-ID: Subject: namd-l: Error Tolerance To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000007d99a705cfc0ec7f" X-Proofpoint-ORIG-GUID: vonHRu_d9_F3XClbIDim9ofrY8xe8p9w X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwbEQpMehceEhEKWUQXZl1cYG9HGExPWl8RClhYF2MFTnBATVIBTmM SEQp4ThdoYwFMf0V/QkFlQBEKeUwXZgFsH1scGRtAG2kRCkNIFwcbGBoRCkNZFwcbGhkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhtxHxsQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04XXEVEYnhfdU4TdWwZcmlGSGNuQ0cTRUxYcxJSTxJaE10RClhcFx8EGgQYGRMF GxoEGxoaBB4SBBsTEBseGh8aEQpeWRdzXk1tGhEKTVwXGxwfEQpMWhdoaU1NaxEKQk8XbRNgEwF hWmttQBIRCkNaFxgaEwQSHwQYGx8EGx0YEQpCXhcbEQpCRRdgfH9uTmIdGFJFYhEKQk4XaGMBTH 9Ff0JBZUARCkJMF2MFTnBATVIBTmMSEQpCbBdlX3BfY3hsHBMfBREKQkAXbHlyWW9dcn1rHlMRC kJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdnS0hhWx58ZnlITREKcGgXb1keUFISb2Vi RG8QGRoRCnBoF2BkXkh9SxkbY2VjEBkaEQpwaBdnXG5FbhsBHUMeXRAZGhEKcGgXa2ZicFtQGkF CRmwQGRoRCnBoF21TQXpFThwBWGtbEBkaEQpwbBdpUx1PX2kec0RhcxAdGhEKbX4XGxEKWE0XSx Eg X-Proofpoint-GUID: vonHRu_d9_F3XClbIDim9ofrY8xe8p9w X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=498 lowpriorityscore=0 spamscore=0 malwarescore=0 impostorscore=0 mlxscore=0 adultscore=0 priorityscore=48 clxscore=161 bulkscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111010111 X-Spam-Score: 0 X-Spam-OrigSender: davidtang@uchicago.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Tang --0000000000007d99a705cfc0ec7f Content-Type: text/plain; charset="UTF-8" Hello, I am running the BEUS simulation and I keep seeing the error tolerance parameter in my log files. From what I understand, this shouldn't be too concerning, but I was just wondering if someone could elaborate on what this parameter means as I do not explicitly set it anywhere in my configuration files. Regards, David --0000000000007d99a705cfc0ec7f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
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boundary="00000000000008443705d0744472" X-Proofpoint-GUID: 6rlha3VNPrWe8kSZap_0h2_7ZfLCNAdr X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 6rlha3VNPrWe8kSZap_0h2_7ZfLCNAdr X-CLX-Response: 1TFkXHh4eEQpMehcZGRMRCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHHhISEQpDWRcHGxgbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcYGhpxHQYfE3cGGxgeBhkaQh0GGgYbGhoGGxoacRMQGncGGgYHH xoGGgYHHBoGGgYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XHFhGQksZfGR6 WH1PEkF5cEtadRpCGHUdcExmaWRrTlgRClhcFx8EGgQYHhsFGxoEGxoaBB0EGx4YEBseGh8aEQp eWRdzXUlheBEKTVwXHxsfEQpMWhdpfGlra00RCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2 trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGwQeExEKQl4XGxEKRF4XGhEKREkXG xEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdmWH1Ya0Aa BXJEaBEKQk4XY1Nja3sTWH4aX14RCkJMF2MfWXl5aR1PfFpaEQpCbBdvUmccckNJT1p+XREKQkA Xa29CaxxHT0l9aAERCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxdnemx9ZR9IZkkdYxEKWUsXEx 8SHBEKcGcXbkF7f35ZQkYBZmYQGhEKcGgXYVhLZX5pe3gTaXIQGhEKcGgXZU4beWIfQgEFE10QG hEKcGgXY1pnYkh6HlN8fkcQGhEKcGgXZB5sekN6bnpeQn0QGhEKcGgXem5iQW17GG9DenwQGhEK cGcXbV1yY3hjQxNwHlwQGRoRCnBsF2hzUllyZ3sfe3lJEBkaEQpwTBdtaGUZQVJ9exhFUhAaEQp tfhcaEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=444 lowpriorityscore=0 adultscore=0 mlxlogscore=999 priorityscore=339 bulkscore=0 mlxscore=0 phishscore=0 suspectscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100095 domainage_hfrom=9586 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --00000000000008443705d0744472 Content-Type: text/plain; charset="UTF-8" I also tried to increase harmonic restraints along the gz path from 0.5 to 5 but the problem still persists. I switched off usesecondclosestframe off but it says Error: keyword "usesecondclosestframe" is not supported, or not recognized in this context On Wed, Nov 10, 2021 at 2:23 PM Ashutosh Shandilya wrote: > I am getting this type of warning > > After running for 30000 steps it shows > TIMING: 30700 CPU: 579.654, 0.0178402/step Wall: 583.7, 0.0179331/step, > 0.126628 hours remaining, 0.000000 MB of memory in use. > ENERGY: 30700 226234.5860 33319.1606 51301.2627 > 0.0000 -1814027.4858 224995.9113 0.0000 21.0432 > 376517.3497 -901638.1722 299.8428 -1278155.5219 > -899427.3684 299.5875 1354.4689 44.7734 > 4458307.8773 0.5178 1.7157 > > *Warning: Geometrical pathCV relies on the assumption that the second > closest frame is the neighbouring frame* > *Please check your configuration or increase restraint on z (*This > warning comes earlier as well > *)* > Frame index: 49 ; optimal RMSD = 0.975194 > Frame index: 51 ; optimal RMSD = 0.975811 > Frame index: 50 ; optimal RMSD = 0.977496 > Frame index: 47 ; optimal RMSD = 0.994026 > Frame index: 48 ; optimal RMSD = 0.995694 > Frame index: 44 ; optimal RMSD = 1.00065 > Frame index: 43 ; optimal RMSD = 1.00377 > Frame index: 42 ; optimal RMSD = 1.00561 > Frame index: 46 ; optimal RMSD = 1.00608 > Frame index: 41 ; optimal RMSD = 1.0122 > Frame index: 45 ; optimal RMSD = 1.01242 > Frame index: 39 ; optimal RMSD = 1.02401 > Frame index: 40 ; optimal RMSD = 1.02975 > Frame index: 52 ; optimal RMSD = 1.03208 > Frame index: 36 ; optimal RMSD = 1.03932 > Frame index: 37 ; optimal RMSD = 1.04629 > ............. > ................. > Frame index: 88 ; optimal RMSD = 3.32354 > Frame index: 89 ; optimal RMSD = 3.75411 > Frame index: 90 ; optimal RMSD = 3.7904 > Frame index: 91 ; optimal RMSD = 3.80612 > Frame index: 92 ; optimal RMSD = 3.8282 > Frame index: 93 ; optimal RMSD = 3.83528 > Frame index: 94 ; optimal RMSD = 3.84841 > Frame index: 95 ; optimal RMSD = 3.86218 > Frame index: 96 ; optimal RMSD = 3.89656 > Frame index: 97 ; optimal RMSD = 3.97904 > Frame index: 98 ; optimal RMSD = 4.16712 > Frame index: 99 ; optimal RMSD = 4.18738 > > The error file gave following error > User defined signal 2 > ERROR: One or more process (first noticed rank 8) terminated with signal > 12 > > Kindly suggest, > Ashutosh > > > > > On Wed, Nov 10, 2021 at 12:11 PM Giacomo Fiorin > wrote: > >> Hi Ashutosh, the "colvars" keyword is an ordinary NAMD configuration >> keyword, not a Tcl command. It's a bit like "constraints" in this regard, >> which would give you a similar error message if you added it late in the >> NAMD script. >> >> Just put "colvars on" early in the NAMD script before any run command, or >> other commands that trigger the Tcl interpreter. You're not required to >> add any Colvars configuration even with "colvars on". >> >> Giacomo >> >> On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya >> wrote: >> >>> Thanks for all your help. In the slurm output I am getting the following >>> error which I am unable to understand. I have been trying several changes >>> in input files to get the job running but still getting some errors. If you >>> have some insight kindly suggest. >>> >>> FATAL ERROR: Setting parameter colvars from script failed! >>> >>> FATAL ERROR: Setting parameter colvars from script failed! >>> >>> The output file ends like this >>> TCL: Running for 20 steps >>> ENERGY: 6100 228438.5351 32958.7464 51721.4945 >>> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 >>> 374233.1041 -936367.4549 298.0237 -1310600.5589 >>> -934162.1854 295.8515 1073.5139 16.7110 >>> 4799315.6868 55.7822 1.3010 >>> >>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100 >>> WRITING COORDINATES TO RESTART FILE AT STEP 6100 >>> FINISHED WRITING RESTART COORDINATES >>> WRITING VELOCITIES TO RESTART FILE AT STEP 6100 >>> FINISHED WRITING RESTART VELOCITIES >>> TCL: Setting parameter langevinTemp to 300 >>> REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN. >>> TCL: Running for 20 steps >>> ENERGY: 6100 228438.5351 32958.7464 51721.4945 >>> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 >>> 377307.1621 -933293.3968 300.4717 -1310600.5589 >>> -931093.1616 300.4717 1103.2400 25.8758 >>> 4799315.6868 1103.2400 25.8758 >>> >>> TCL: Setting parameter colvars to on >>> FATAL ERROR: Setting parameter colvars from script failed! >>> >>> >>> Many thanks, >>> Ashutosh >>> >>> On Thu, Nov 4, 2021 at 11:43 PM Michael Robinson < >>> michael.robinson1@monash.edu> wrote: >>> >>>> Hi Ashutosh, >>>> >>>> I suspect that won't be the first error in the log file - that's >>>> normally something that happens after an initial error. If that's not the >>>> case, look at the output of the supercomputer you were using to run it >>>> (something like a SLURM output) to see if that caused it. >>>> >>>> Cheers, >>>> Michael >>>> >>>> On Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, >>>> wrote: >>>> >>>>> I am running ABF with namd but it stopped abruptly after some thousand >>>>> steps. The error file gave following error. I looked online but didn't find >>>>> any conclusive answer. >>>>> >>>>> User defined signal 2 >>>>> ERROR: One or more process (first noticed rank 8) terminated with >>>>> signal 12 >>>>> >>>>> What could be the problem? >>>>> >>>>> Many thanks, >>>>> Ashutosh >>>>> >>>>> On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya < >>>>> scfbioiitd@gmail.com> wrote: >>>>> >>>>>> Many thanks, it works now. >>>>>> >>>>>> Regards, >>>>>> Ashutosh >>>>>> >>>>>> On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson < >>>>>> michael.robinson1@monash.edu> wrote: >>>>>> >>>>>>> Hi Ashutosh, >>>>>>> >>>>>>> Your input file has a line break between 'abf' and the curly bracket >>>>>>> '{' that opens the configuration block - this is causing the ABF >>>>>>> configuration block to be skipped, and so your input file is failing. I >>>>>>> can't test your given file without the associated system, but I >>>>>>> double-checked that this would occur with one of my own ABF input files, >>>>>>> and this caused the same error. >>>>>>> >>>>>>> Hopefully that helps, >>>>>>> Regards, >>>>>>> Michael Robinson >>>>>>> >>>>>>> On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya < >>>>>>> scfbioiitd@gmail.com> wrote: >>>>>>> >>>>>>>> Hi All >>>>>>>> I want to run eABF with namd and I am getting following errors >>>>>>>> >>>>>>>> colvars: Collective variables initialized, 2 in total. >>>>>>>> colvars: Error: keyword "abf" found without configuration. >>>>>>>> FATAL ERROR: Error in the collective variables module (see above >>>>>>>> for details) >>>>>>>> FATAL ERROR: Error in the collective variables module (see above >>>>>>>> for details). >>>>>>>> >>>>>>>> I was able to run collective variables but when trying to run eABF >>>>>>>> it gives an error. Kindly have a look at the attached input file and >>>>>>>> suggest. >>>>>>>> >>>>>>>> Many thanks >>>>>>>> >>>>>>>> --00000000000008443705d0744472 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I also tried to increase harmonic restraints along th= e gz path from 0.5 to 5 but the problem still persists.
I switche= d off usesecondclosestframe off but it says

Error:= keyword "usesecondclosestframe" is not supported, or not recogni= zed in this context

On Wed, Nov 10, 2021 at 2:23 PM Ashutosh Shandilya= <scfbioiitd@gmail.com> w= rote:
I am getting this type of warning

After running= for 30000 steps it shows
TIMING: 30700 =C2=A0CPU: 579.654, 0.017= 8402/step =C2=A0Wall: 583.7, 0.0179331/step, 0.126628 hours remaining, 0.00= 0000 MB of memory in use.
ENERGY: =C2=A0 30700 =C2=A0 =C2=A0226234.5860 = =C2=A0 =C2=A0 33319.1606 =C2=A0 =C2=A0 51301.2627 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1814027.4858 =C2=A0 =C2=A0224995.9113 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A021.0432 =C2=A0 = =C2=A0376517.3497 =C2=A0 =C2=A0 =C2=A0 =C2=A0-901638.1722 =C2=A0 =C2=A0 =C2= =A0 299.8428 =C2=A0-1278155.5219 =C2=A0 -899427.3684 =C2=A0 =C2=A0 =C2=A0 2= 99.5875 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1354.4689 =C2=A0 =C2=A0 =C2=A0 = =C2=A044.7734 =C2=A0 4458307.8773 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.5178 =C2=A0= =C2=A0 =C2=A0 =C2=A0 1.7157

Warning: Geom= etrical pathCV relies on the assumption that the second closest frame is th= e neighbouring frame
Please check your configuration or in= crease restraint on z (This warning comes earlier as well)
Frame index: 49 ; optimal RMSD =3D 0.975194
Frame index: = 51 ; optimal RMSD =3D 0.975811
Frame index: 50 ; optimal RMSD =3D 0.9774= 96
Frame index: 47 ; optimal RMSD =3D 0.994026
Frame index: 48 ; opti= mal RMSD =3D 0.995694
Frame index: 44 ; optimal RMSD =3D 1.00065
Fram= e index: 43 ; optimal RMSD =3D 1.00377
Frame index: 42 ; optimal RMSD = =3D 1.00561
Frame index: 46 ; optimal RMSD =3D 1.00608
Frame index: 4= 1 ; optimal RMSD =3D 1.0122
Frame index: 45 ; optimal RMSD =3D 1.01242Frame index: 39 ; optimal RMSD =3D 1.02401
Frame index: 40 ; optimal R= MSD =3D 1.02975
Frame index: 52 ; optimal RMSD =3D 1.03208
Frame inde= x: 36 ; optimal RMSD =3D 1.03932
Frame index: 37 ; optimal RMSD =3D 1.04= 629
.............
.................
Frame index: 88 ; optimal RMSD =3D 3.32354
Frame index: 89 ; optim= al RMSD =3D 3.75411
Frame index: 90 ; optimal RMSD =3D 3.7904
Frame i= ndex: 91 ; optimal RMSD =3D 3.80612
Frame index: 92 ; optimal RMSD =3D 3= .8282
Frame index: 93 ; optimal RMSD =3D 3.83528
Frame index: 94 ; op= timal RMSD =3D 3.84841
Frame index: 95 ; optimal RMSD =3D 3.86218
Fra= me index: 96 ; optimal RMSD =3D 3.89656
Frame index: 97 ; optimal RMSD = =3D 3.97904
Frame index: 98 ; optimal RMSD =3D 4.16712
Frame index: 9= 9 ; optimal RMSD =3D 4.18738

The error file gave f= ollowing error
User defined signal 2
ERROR: =C2=A0= One or more process (first noticed rank 8) terminated with signal 12
<= div>
Kindly suggest,
Ashutosh



On Wed, Nov 10, 2021 at 12:11 PM Gi= acomo Fiorin <giacomo.fiorin@gmail.com> wrote:
Hi Ashutosh, the "colvars= " keyword=C2=A0is an ordinary NAMD configuration keyword, not a Tcl co= mmand.=C2=A0 It's a bit like "constraints" in this regard, wh= ich would=C2=A0give you a similar error message if you added it late in the= NAMD script.

Just put "colvars on" early in t= he NAMD script before any run command, or other commands that trigger the T= cl interpreter.=C2=A0 You're not required to add any Colvars configurat= ion even with "colvars on".

Giacomo

On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:=
Thanks for all your help. In the slurm output I am getting the follo= wing error which I am unable to understand. I have been trying several chan= ges in input files to get the job running but still getting some errors. If= you have some insight kindly suggest.

FATAL E= RROR: Setting parameter colvars from script failed!
=C2=A0
FATAL ERR= OR: Setting parameter colvars from script failed!

= The output file ends like this
TCL: Running for 20 steps
ENERG= Y: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2=A0 32958.7464 =C2= =A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2= =A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.00= 00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0374233.1041 =C2=A0 =C2= =A0 =C2=A0 =C2=A0-936367.4549 =C2=A0 =C2=A0 =C2=A0 298.0237 =C2=A0-1310600.= 5589 =C2=A0 -934162.1854 =C2=A0 =C2=A0 =C2=A0 295.8515 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 1073.5139 =C2=A0 =C2=A0 =C2=A0 =C2=A016.7110 =C2=A0 4799315.= 6868 =C2=A0 =C2=A0 =C2=A0 =C2=A055.7822 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.3010<= br>
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100
WRITING COOR= DINATES TO RESTART FILE AT STEP 6100
FINISHED WRITING RESTART COORDINATE= S
WRITING VELOCITIES TO RESTART FILE AT STEP 6100
FINISHED WRITING RE= START VELOCITIES
TCL: Setting parameter langevinTemp to 300
REINITIAL= IZING VELOCITIES AT STEP 6100 TO 300 KELVIN.
TCL: Running for 20 stepsENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2=A0 32958.74= 64 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0377307.1621 =C2= =A0 =C2=A0 =C2=A0 =C2=A0-933293.3968 =C2=A0 =C2=A0 =C2=A0 300.4717 =C2=A0-1= 310600.5589 =C2=A0 -931093.1616 =C2=A0 =C2=A0 =C2=A0 300.4717 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 1103.2400 =C2=A0 =C2=A0 =C2=A0 =C2=A025.8758 =C2=A0 4= 799315.6868 =C2=A0 =C2=A0 =C2=A01103.2400 =C2=A0 =C2=A0 =C2=A0 =C2=A025.875= 8

TCL: Setting parameter colvars to on
FATAL ERROR: Setting param= eter colvars from script failed!


Ma= ny thanks,
Ashutosh

On Thu, Nov 4, 2021 at 11:43 PM Mich= ael Robinson <michael.robinson1@monash.edu> wrote:
Hi Ashutosh,

I suspect that won't be the first= error in the log file - that's normally something that happens after a= n initial error. If that's not the case, look at the output of the supe= rcomputer you were using to run it (something like a SLURM output) to see i= f that caused it.

Cheers= ,=C2=A0
Michael

On Thu, 4 Nov. 2021, 2:38 am As= hutosh Shandilya, <scfbioiitd@gmail.com> wrote:
I am running ABF with namd b= ut it stopped abruptly after some thousand steps. The error file gave follo= wing error. I looked online but didn't find any conclusive answer.
=

User defined signal 2
ERROR: =C2=A0One = or more process (first noticed rank 8) terminated with signal 12
=
What could be the problem?

Many tha= nks,
Ashutosh

On Thu, Oct 28, 2021 at 2:20 PM Ashutosh S= handilya <scfbioiitd@gmail.com> wrote:
Many thanks, it wo= rks now.

Regards,
Ashutosh

On W= ed, Oct 27, 2021 at 8:28 PM Michael Robinson <michael.robinson= 1@monash.edu> wrote:
Hi Ashutosh,

You= r input file has a line break between 'abf' and the curly bracket &= #39;{' that opens the configuration block - this is causing the ABF con= figuration block to be skipped, and so your input file is failing. I can= 9;t test your given file without the associated system, but I double-checke= d that this would occur with one of my own ABF input files, and this caused= the same error.

Hopefully that helps,
<= div>Regards,
Michael Robinson

On Thu, 28 Oct 2021 at 06:= 56, Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex">
Hi A= ll
I want to run eABF with namd and I am getting following errors=

colvars: Collective variables initialized, 2= in total.
colvars: Error: keyword "abf" found without configu= ration.
FATAL ERROR: Error in the collective variables module (see above= for details)
FATAL ERROR: Error in the collective variables module (see= above for details).

I was able to run collective = variables but when trying to run eABF it gives an error. Kindly have a look= at the attached input file and suggest.

Many than= ks

Hello,

I am running the BEUS simulation= and I keep seeing the error tolerance parameter in my log files. From what= I understand, this shouldn't be too concerning, but I was just wonderi= ng if someone could elaborate on what this parameter means as I do not expl= icitly set it anywhere in my configuration files.=C2=A0

Regards,
David
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Message-ID: <695316540.4074965.1635852821865.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: Re: namd-l: Trouble in fep.tcl file for FEP run in NAMD MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_d66f2b4d-e44f-4e20-827a-c2bce714edf4" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Trouble in fep.tcl file for FEP run in NAMD Thread-Index: 7619fKNS/yPEuzAhI4/Gt1I9QxCVZw== X-Proofpoint-ORIG-GUID: gZAPX0qoDxK2pXxOXEDnTo1W5NMfeahI X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxMaEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxsdGREKQ1kXBxsfGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsdGnEeExAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdNcGt6chpbRW5SYRhaclJlcm9uRH5FG30fZGdMT0tCYxEKWFwXHwQaBBgZEwUb GgQbGhoEHhIEGBgQGx4aHxoRCl5ZF3NeWUsZEQpNXBcbEhgRCkxaF3hta01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XaEBFSBgYfGtbehkRCkNaFxsTGQQeEwQYGR4EGBgbEQ pCXhcbEQpEXhcYEQpCRRdkWFxcTX5SSRtlSREKQk4XZU9+EkNpZlkcAWkRCkJMF3oSZ2lgWXlGQ U9lEQpCbBdhEhJPT0xNf08eBREKQkAXZ3lHWXNSeVJ9WH0RCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcYEQp5Qxd6bVx/AWxZU2FAYxEKcGcXbHNgfn9cX2NwRWkQGRoRCnBoF2dgQ35oT0wfYHN lEBkaEQpwaBdlSRpdWGZ8XhNdeRAZGhEKcGgXbRhpel1SE1ATZnkQGRoRCnBoF2ZTf2dSW2lJeW haEBkaEQpwaBd6aEd4YnhaeE0fehAZGhEKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17G EVSEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: gZAPX0qoDxK2pXxOXEDnTo1W5NMfeahI X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=894 lowpriorityscore=0 spamscore=0 malwarescore=0 impostorscore=0 mlxscore=0 adultscore=0 priorityscore=0 clxscore=190 bulkscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111020068 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_d66f2b4d-e44f-4e20-827a-c2bce714edf4 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Hi, Can you double-check that fep.tcl is identical to the one shipped with NAMD? Also, try removing the line "source fep.tcl" and see if any syntax error shows up, besides the missing alchemical parameters. Jerome ----- On 30 Oct 21, at 9:02, SYEDA SABIHA SULTANA LUBNA . wrote: > Hi, > Can someone help me in understanding why I am getting this error message? This > is when i am trying to run my FEP calculation on centose 8 version. where as > the same script is working on ubuntu 20 version. > Info: Based on Charm++/Converse 61002 for > charmpp-6.10.2-rcdhh4jp7pfjtdz5hragsqhs5elcvieh > Info: Built Mon Jan 11 20:27:40 IST 2021 by root on sharanga > Info: 1 NAMD 2.14 linux-x86_64-netlrts 64 node4 2032 > Info: Running on 64 processors, 1 nodes, 1 physical nodes. > Info: CPU topology information available. > Info: Charm++/Converse parallel runtime startup completed at 0.0428052 s > CkLoopLib is used in SMP with simple dynamic scheduling (converse-level > notification) > Info: 4681.57 MB of memory in use based on /proc/self/stat > Info: Configuration file is rest-01.namd > Info: Working in the current directory /home/debashreeb/FEP_complex > Info: Sourcing fep.tcl > Warning: Couldn't parse line 105 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 117 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 124 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 137 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 138 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 238 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 246 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 247 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 258 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 271 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 276 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 277 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 278 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 281 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 294 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 297 in configuration file fep.tcl. The line was: } > Warning: Couldn't parse line 299 in configuration file fep.tcl. The line was: } > ERROR: Expecting value and optional units for option 'langevinTemp' > ERROR: Multiple definitions of 'alchLambda' > ERROR: in the configuration file are not allowed > ERROR: Expecting value and optional units for option 'alchLambda' > ERROR: Multiple definitions of 'alchLambda2' > ERROR: in the configuration file are not allowed > ERROR: Expecting value and optional units for option 'alchLambda2' > ERROR: Multiple definitions of 'alchLambdaIDWS' > ERROR: in the configuration file are not allowed > ERROR: Expecting value and optional units for option 'alchLambdaIDWS' > ERROR: Expecting value and optional units for option 'LangevinPistonTemp' > ERROR: 'LangevinPistonTemp' was set to 0 but it should be positive > ERROR: Multiple definitions of 'firsttimestep' > ERROR: in the configuration file are not allowed > ERROR: The following variables were set in the > ERROR: configuration file but are NOT VALID > ERROR: runFEP > ERROR: runTIlist > ERROR: reinitvels > ERROR: minimize > ERROR: return > ERROR: lappend > ERROR: while > ERROR: } > ERROR: runFEPlist > ERROR: incr > ERROR: run > ERROR: $win > ERROR: print > ERROR: foreach > ERROR: if > Thanks for the help. > The information contained in this electronic communication is intended solely > for the individual(s) or entity to which it is addressed. It may contain > proprietary, confidential and/or legally privileged information. Any review, > retransmission, dissemination, printing, copying or other use of, or taking any > action in reliance on the contents of this information by person(s) or entities > other than the intended recipient is strictly prohibited and may be unlawful. > If you have received this communication in error, please notify us by > responding to this email or telephone and immediately and permanently delete > all copies of this message and any attachments from your system(s). The > contents of this message do not necessarily represent the views or policies of > BITS Pilani. --=_d66f2b4d-e44f-4e20-827a-c2bce714edf4 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi,

Can you double-check that fep.tcl is identical to the one shipp= ed with NAMD?

Also, try remov= ing the line "source fep.tcl" and see if any syntax error shows up, besides= the missing alchemical parameters.

Jerome


= ----- On 30 Oct 21, at 9:02,= SYEDA SABIHA SULTANA LUBNA . <p20190061@hyderabad.bits-pilani.ac.in>= wrote:
Hi,
Can someone help me in understanding why I am getting this error mess= age? This is when i am trying to run my FEP calculation on centose 8 versio= n. where as the same script is working on ubuntu 20 version.

<= div>Info: Based on Charm++/Converse 61002 for charmpp-6.10.2-rcdhh4jp7pfjtd= z5hragsqhs5elcvieh
Info: Built Mon Jan 11 20:27:40 IST 2021 by root on s= haranga
Info: 1 NAMD  2.14  linux-x86_64-netlrts  64 &nbs= p;  node4  2032
Info: Running on 64 processors, 1 nodes, 1 phy= sical nodes.
Info: CPU topology information available.
Info: Charm++/= Converse parallel runtime startup completed at 0.0428052 s
CkLoopLib is = used in SMP with simple dynamic scheduling (converse-level notification)Info: 4681.57 MB of memory in use based on /proc/self/stat
Info: Config= uration file is rest-01.namd
Info: Working in the current directory /hom= e/debashreeb/FEP_complex
Info: Sourcing fep.tcl
Warning: Couldn't par= se line 105 in configuration file fep.tcl.  The line was:    = ; }
Warning: Couldn't parse line 117 in configuration file fep.tcl. = ; The line was:       }
Warning: Couldn't parse line 124 = in configuration file fep.tcl.  The line was:     }
Warni= ng: Couldn't parse line 137 in configuration file fep.tcl.  The line w= as:     }
Warning: Couldn't parse line 138 in configuration fi= le fep.tcl.  The line was: }
Warning: Couldn't parse lin= e 238 in configuration file fep.tcl.  The line was:     }Warning: Couldn't parse line 246 in configuration file fep.tcl.  The = line was:     }
Warning: Couldn't parse line 247 in configurat= ion file fep.tcl.  The line was: }
Warning: Couldn't parse line 258= in configuration file fep.tcl.  The line was:     }
Warn= ing: Couldn't parse line 271 in configuration file fep.tcl.  The line = was:         }
Warning: Couldn't parse line 276 in c= onfiguration file fep.tcl.  The line was:         = }
Warning: Couldn't parse line 277 in configuration file fep.tcl.  = The line was:       }
Warning: Couldn't parse line 278 in= configuration file fep.tcl.  The line was:     }
Warning= : Couldn't parse line 281 in configuration file fep.tcl.  The line was= : }
Warning: Couldn't parse line 294 in configuration file fep.tcl. = ; The line was:     }
Warning: Couldn't parse line 297 in conf= iguration file fep.tcl.  The line was:     }
Warning: Cou= ldn't parse line 299 in configuration file fep.tcl.  The line was: }ERROR: Expecting value and optional units for option 'langevinTemp'
ER= ROR: Multiple definitions of 'alchLambda'
ERROR:   in the configura= tion file are not allowed
ERROR: Expecting value and optional units for = option 'alchLambda'
ERROR: Multiple definitions of 'alchLambda2'
ERRO= R:   in the configuration file are not allowed
ERROR: Expecting val= ue and optional units for option 'alchLambda2'
ERROR: Multiple definitio= ns of 'alchLambdaIDWS'
ERROR:   in the configuration file are not a= llowed
ERROR: Expecting value and optional units for option '= alchLambdaIDWS'
ERROR: Expecting value and optional units for option 'La= ngevinPistonTemp'
ERROR: 'LangevinPistonTemp' was set to 0 but it should= be positive
ERROR: Multiple definitions of 'firsttimestep'
ERROR: &n= bsp; in the configuration file are not allowed
ERROR: The following vari= ables were set in the
ERROR: configuration file but are NOT VALID
ERR= OR:    runFEP
ERROR:    runTIlist
ERROR:   &= nbsp;reinitvels
ERROR:    minimize
ERROR:    retu= rn
ERROR:    lappend
ERROR:    while
ERROR: &n= bsp;  }
ERROR:    runFEPlist
ERROR:    incr<= br>ERROR:    run
ERROR:    $win
ERROR:   &nb= sp;print
ERROR:    foreach
ERROR:    if

=
Thanks for the help.

The information contained in this electronic communication is intended sole= ly for the individual(s) or entity to which it is addressed. It may contain= proprietary, confidential and/or legally privileged information. Any revie= w, retransmission, dissemination, printing, copying or other use of, or tak= ing any action in reliance on the contents of this information by person(s)= or entities other than the intended recipient is strictly prohibited and m= ay be unlawful. If you have received this communication in error, please no= tify us by responding to this email or telephone and immediately and perman= ently delete all copies of this message and any attachments from your syste= m(s). The contents of this message do not necessarily represent the views o= r policies of BITS Pilani.
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boundary="00000000000009682105cfd5b7a1" X-Proofpoint-ORIG-GUID: 41uFQjizNPJoITeXCutmyybzgw20YJ9D X-CLX-Response: 1TFkXGxIbEQpMehcZHxoRCllEF2hBb0V/U2YSa2tCEQpYWBdlAU1/ZX1MYRN mHREKeE4XY1Nja3sTWH4aX14RCnlMF3pGWl0eaHp8AWdfEQpDSBcHGx8TEQpDWRcHGxgbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwbcR4aEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx4bX2x7QENQZHpgRWN+T3JpX15HU1NIUE1dGBpzYBNuEQpYXBcfBBoEGBkT BRsaBBsbGgQfGgQbHh8QGx4aHxoRCl5ZF3NeGxxsEQpNXBcYHhoRCkxaF2hpa01rEQpMRhdva2t ra2sRCkJPF20TYBMBYVprbUASEQpDWhcYGhMEEh8EGBsfBBsdHBEKQl4XGxEKQlwXGxEKXk4XGx EKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdtBUFnQn5kYXJoSREKQk4XY1Nja 3sTWH4aX14RCkJMF2UBTX9lfUxhE2YdEQpCbBdpRVtBckVhSU1uQREKQkAXaFJmREhNHhNsaRoR CkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdtW2AcQn9CbkEYTBEKWUsXEx8dEhEKcGg XaVtDSFMcel1TWxoQGRoRCnBoF21saE9EZV5IXB9AEBkaEQpwaBdofmxNTF1nexxhaBAZGhEKcG gXZ1Nza2JhaBgdE0YQGRoRCnBoF20ca1tJXVIfaGNdEBkaEQpwbBdpfkQYBX8bWWRJGxAZGhEKc EwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: 41uFQjizNPJoITeXCutmyybzgw20YJ9D X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=181 phishscore=0 mlxlogscore=512 suspectscore=0 malwarescore=0 mlxscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 impostorscore=0 spamscore=0 priorityscore=350 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111020116 domainage_hfrom=9578 X-Spam-Score: 0 X-Spam-OrigSender: ecroitoru1@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ethan Croitoru --00000000000009682105cfd5b7a1 Content-Type: text/plain; charset="UTF-8" Hi all, I am running a REST2 simulation and am trying to get a uniform distribution for the exchange rates between replicas. To do so I am hard coding the soluteScalingFactor for each replica and I realized that the soluteScalingFactor was fluctuating between runs for each replica (looking at the log file for each replica and seeing what it is setting the soluteScalingFactor to for each run that has a non-zero number of steps). I am hard coding the scoluteScalingFactor so I am confused as to why there are fluctuations, any clarification would be appreciated. Thanks, Ethan Croitoru --00000000000009682105cfd5b7a1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,

I am running a REST2 simulation= and am trying to get a uniform distribution for the exchange rates between= replicas. To do so I am hard coding the soluteScalingFactor for each repli= ca and I realized that the soluteScalingFactor=C2=A0was fluctuating between= runs for each replica (looking at the log file for each replica and seeing= what it is setting the soluteScalingFactor to for each run that has a non-= zero number of steps). I am hard coding the scoluteScalingFactor so I am co= nfused as to why there are fluctuations, any clarification would be appreci= ated.

Thanks,
Ethan Croitoru
--00000000000009682105cfd5b7a1-- From owner-namd-l@halifax.ks.uiuc.edu Fri Nov 5 11:12:38 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A5GCbNi004819; Fri, 5 Nov 2021 11:12:37 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1A5GCbdN004818; Fri, 5 Nov 2021 11:12:37 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A5GCbnV004812; Fri, 5 Nov 2021 11:12:37 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1A5GCbrD004811; Fri, 5 Nov 2021 11:12:37 -0500 (CDT) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A5GCPSJ004791 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 5 Nov 2021 11:12:26 -0500 (CDT) Received: from pps.filterd (m0272704.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1A5CsbGw014011 for ; Fri, 5 Nov 2021 16:12:24 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0b-00007101.pphosted.com with ESMTP id 3c4t3hn83n-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 05 Nov 2021 16:12:24 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 44C5F1E40E6A for ; Fri, 5 Nov 2021 17:12:21 +0100 (CET) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id 4Qo5DpY1s0QB for ; Fri, 5 Nov 2021 17:12:19 +0100 (CET) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 4A7ED1E40E6E for ; Fri, 5 Nov 2021 17:12:19 +0100 (CET) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id ANw8vg5QlnXl for ; Fri, 5 Nov 2021 17:12:19 +0100 (CET) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id DFFBF1E40E6A for ; Fri, 5 Nov 2021 17:12:18 +0100 (CET) Date: Fri, 5 Nov 2021 17:12:18 +0100 (CET) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list Message-ID: <1834646094.5234069.1636128738554.JavaMail.zimbra@ibpc.fr> Subject: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_e7ebe930-80f5-41ca-bd29-40b04a776c0d" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Index: YL4cq1P0/9BcLKTuVzHfLn+LuXYAVg== Thread-Topic: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies X-Proofpoint-GUID: UFxY87ZMSkFXd9lgR97zZEh3EYR05jby X-CLX-Response: 1TFkXGx0SEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxscHxEKQ1kXBxgZEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfEnEZHRAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThd/bFJzEh1wZ3lBbHJOE0ZNeBMdUHBvQhlvc3gaH0BIUxEKWFwXHwQaBBgeGwUb GgQbGhoEHQQbHh4QGx4aHxoRCl5ZF3NfXFNuEQpNXBcbGRoRCkxaF2hta01NEQpCTxdoQEVIGBh 8a1t6GREKQ1oXGxMZBB4TBBgZHgQYGBsRCkJeFxsRCkJFF2RYXFxNflJJG2VJEQpCThdlT34SQ2 lmWRwBaREKQkwXehJnaWBZeUZBT2URCkJsF2ESEk9PTE1/Tx4FEQpCQBdpcl4BG3BlQwVBZBEKQ lgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2tGX294bnpsU2BjEQpwaBdtUxNYT2JjG3lf EhAZGhEKcGgXYn1rb11wcBNfH2EQGRoRCnBoF25ZR0QTS2IBaF5IEBkaEQpwaBdtH0VNEnoYXkN YRBAZGhEKcGgXZmhDGhkcAXphXWsQGRoRCnBsF2ZgE2RcTRpnT3pQEBkaEQpwTBdtaGUZQVJ9ex hFUhAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: UFxY87ZMSkFXd9lgR97zZEh3EYR05jby X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 bulkscore=0 phishscore=0 impostorscore=0 adultscore=0 suspectscore=0 mlxlogscore=933 mlxscore=0 lowpriorityscore=0 priorityscore=0 clxscore=178 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111050092 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_e7ebe930-80f5-41ca-bd29-40b04a776c0d Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi all,=20 Please be aware of a bug in current NAMD versions that can affect alchemica= l free energies computed using IDWS-style alchemical perturbations. Below I= give workarounds to get correct free energy values from existing data affe= cted by the issue, and to make any new simulation exempt from the issue.=20 Affected versions of NAMD:=20 2.14, 3.x (non-CUDA version), and development versions until now.=20 Condition triggering the issue:=20 The issue occurs if multiple time-step is used and alchOutFreq is greater t= han, but not a multiple of, fullElectFreq.=20 Unfortunately, the current default value of alchOutFreq (5) is likely to fu= lfill this condition.=20 Symptoms:=20 In this situation, some of the energy differences are computed erroneously = - specifically, dE values computed at time steps that are not multiples of = the outer time step include long-range dE values for the wrong target lambd= a.=20 More generally, even without IDWS, alchOutFreq should probably always be a = multiple of fullElectFreq to ensure that comparison energies are as accurat= e as possible, and do not include stale long-range terms.=20 Fix and workaround:=20 For future simulations: define alchOutFreq as either 1 or a multiple of ful= lElectFreq.=20 For existing simulations: re-analyze, discarding any data point from the fe= pout file where the time step number is not a multiple of fullElectFreq.=20 Diagnosis:=20 In doubt, the issue can be diagnosed for a specific dataset by histogrammin= g forward and backward values of the electrostatic dE for an individual IDW= S window. The bug will result in a characteristic bimodal distribution.=20 I will submit a code patch very soon to fix this in a final way. In the mea= ntime, please circulate the information to users who might be affected.=20 Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for reporting= the issue.=20 J=C3=A9r=C3=B4me=20 --=_e7ebe930-80f5-41ca-bd29-40b04a776c0d Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi all,

=
Please be aware of a bug in current NAMD versions that can affec= t alchemical free energies computed using IDWS-style alchemical perturbatio= ns. Below I give workarounds to get correct free energy values from= existing data affected by the issue, and to make any new simulati= on exempt from the issue.

Affected versions of NAMD:
2.14, 3.x (non-CUDA vers= ion), and development versions until now.

Condition triggering the issue:
The= issue occurs if multiple time-step is used and alchOutFreq is grea= ter than, but not a multiple of, fullElectFreq.
Unfortun= ately, the current default value of alchOutFreq (5) is likely to fulfill th= is condition.

Symptom= s:
In this situation, some of the energy differences are= computed erroneously - specifically, dE values computed at time steps that= are not multiples of the outer time step include long-range dE values for = the wrong target lambda.
More generally, even without IDWS, = alchOutFreq should probably always be a multiple of fullElect= Freq to ensure that comparison energies are as accurate as possible, and do= not include stale long-range terms.

Fix and workaround:
For future simulatio= ns: define alchOutFreq as either 1 or a multiple of fullElectFreq= .
For existing simulations: re-analyze, discarding any data point= from the fepout file where the time step number is not a multiple of = fullElectFreq.

Diagno= sis:
In doubt, the issue can be diagnosed for a specific= dataset by histogramming forward and backward values of the electrostatic = dE for an individual IDWS window. The bug will result in a characteristic b= imodal distribution.


I will submit a code patch very soon to fix thi= s in a final way. In the meantime, please circulate the information to user= s who might be affected.
Thanks to Ezry St. Iago-McRae (Brannigan= lab, Rutgers Camden) for reporting the issue.

J=C3=A9r=C3=B4me
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Fri, 05 Nov 2021 09:53:11 -0700 (PDT) Content-Type: multipart/alternative; boundary="------------xhO7eEULZTEXFV7S0rM0M0jZ" Message-ID: Date: Fri, 5 Nov 2021 11:53:09 -0500 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.3.0 Subject: Re: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies Content-Language: en-US To: namd-l@ks.uiuc.edu, =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= References: <1834646094.5234069.1636128738554.JavaMail.zimbra@ibpc.fr> From: yjcoshc In-Reply-To: <1834646094.5234069.1636128738554.JavaMail.zimbra@ibpc.fr> X-Proofpoint-ORIG-GUID: zbHB1RM6D3mdzU9XeO57DYM12aXemMO_ X-Proofpoint-GUID: zbHB1RM6D3mdzU9XeO57DYM12aXemMO_ X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIdEQpMehcZHxoRCllEF2ZkX1pvRRJLb1hmEQpYWBdmW3x/R0hvHwV PZREKeE4XY1Nja3sTWH4aX14RCkNIFwcYHx4RCkNZFwcbGRIRCkNJFxoEGhoaEQpZTRdnZnIRCl lJFxpxGhAadwYbHB1xHhwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XUEhia Bt4ZxxuGUdOUH8Tck9lHx1uc2cbGEtyT0dnZXURClhcFx8EGgQYHhsFGxoEGxsaBB0EGxkYEBse Gh8aEQpeWRdzX11zfxEKTVwXGBoaEQpMWhd4aU1NTREKRVkXb2sRCkxfF3oFBQUFBQUFBQVvEQp MRhdva2tsa2sRCkJPF24cZx1ZcmdmXkhyEQpDWhcYGhMEEh8EGBoSBB8aEQpCXhcbEQpEXhcYEQ pCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2RSQgUaWBpee 0N4EQpCThdjU2NrexNYfhpfXhEKQkwXZlt8f0dIbx8FT2URCkJsF2JPYkQaS0AbUl9dEQpCQBdi HEtbXnxBSHsSWhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2tnTE54cnxdb1xQEQp ZSxcTHxIbEQpwZxdgZkVGEnNraUIdWRAZGhEKcGgXbUVZeXlFTXJvYn0QGRoRCnBoF2h+ZxNIbl lBSRJEEBkaEQpwaBdlQlJJQxIaG2FQXhAZGhEKcGgXbmB4WHJ5TlJ8XU0QGRoRCnBoF2NAWx4bZ F56Gm1wEBkaEQpwfRdkGhtNcG1ccGFEWhAZGhEKcH8XZEhCYhpBfFBoTWsQExgRCnBfF2BkUn4b G3JuHE5dEBkaEQpwbBdmHmlFG0hITWRoXxAZGhEKcEMXbFBcZ1lvTE0YSVkQGRoRCm1+FxsRClh NF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 priorityscore=350 phishscore=0 spamscore=0 malwarescore=0 mlxlogscore=999 adultscore=0 mlxscore=0 clxscore=187 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111050094 domainage_hfrom=9581 X-Spam-Score: 0 X-Spam-OrigSender: yjcoshc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, yjcoshc This is a multi-part message in MIME format. --------------xhO7eEULZTEXFV7S0rM0M0jZ Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Hi Jérôme, In the development branch, I submitted a patch adding an option "computeEnergies" to control the period of computing energy terms, which defaults to be the "outputEnergies", so if someone uses outputenergies          20 fullElectFrequency      4 and that will trigger an error to stop the simulation at start. You may see https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 for more details. As for alchOutFreq, I personally agree to enforce it to be some multiple of "outputenergies" for the GPU version, but I am not sure whether the .fepout file will be deprecated since some people are in favor of the log from stdout. In the case that alchOutFreq is not some multiples ofcomputeEnergies, NAMD3 will show a warning like this: Warning: The period of outputting energies relating to alchemical transformations (alchOutFreq = 10) is not a multiple of the period of computing energies (computeEnergies = 20). If alchOutFreq is smaller than outputEnergies and computeEnergies is not defined, a better solution is to set comp uteEnergies explicitly and keep it the same as alchOutFreq. The simulation will use the greatest common divisor of computeEnergies and alchOutFreq as the period of energy evaluation. I don't know whether the NAMD should just stop here or not, since the greatest common divisor of "alchOutFreq" and "computeEnergies" is 10, not a multiple of "fullElectFrequency". Hopefully you may propose a better solution to this mess. Thanks, Haochuan Chen On 11/5/21 11:12, Jérôme Hénin wrote: > Hi all, > > Please be aware of a bug in current NAMD versions that can affect > alchemical free energies computed using IDWS-style alchemical > perturbations. Below I give workarounds to *get correct free energy > values from existing data* affected by the issue, and to make any new > simulation exempt from the issue. > > *Affected versions of NAMD:* > 2.14, 3.x (non-CUDA version), and development versions until now. > > *Condition triggering the issue:* > The issue occurs if multiple time-step is used and *alchOutFreq is > greater than, but not a multiple of, fullElectFreq.* > Unfortunately, the current default value of alchOutFreq (5) is likely > to fulfill this condition. > > *Symptoms:* > In this situation, some of the energy differences are computed > erroneously - specifically, dE values computed at time steps that are > not multiples of the outer time step include long-range dE values for > the wrong target lambda. > More generally, even without IDWS, alchOutFreq should probably > /always/ be a multiple of fullElectFreq to ensure that comparison > energies are as accurate as possible, and do not include stale > long-range terms. > > *Fix and workaround:* > For future simulations: define alchOutFreq as either 1 or a multiple > of fullElectFreq. > For existing simulations: re-analyze, discarding any data point from > the fepout file where the time step number is not a multiple > of fullElectFreq. > > *Diagnosis:* > In doubt, the issue can be diagnosed for a specific dataset by > histogramming forward and backward values of the electrostatic dE for > an individual IDWS window. The bug will result in a characteristic > bimodal distribution. > > > I will submit a code patch very soon to fix this in a final way. In > the meantime, please circulate the information to users who might be > affected. > Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for > reporting the issue. > > Jérôme --------------xhO7eEULZTEXFV7S0rM0M0jZ Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit

Hi Jérôme,

In the development branch, I submitted a patch adding an option "computeEnergies" to control the period of computing energy terms, which defaults to be the "outputEnergies", so if someone uses

outputenergies          20
fullElectFrequency      4

and that will trigger an error to stop the simulation at start. You may see https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 for more details.

As for alchOutFreq, I personally agree to enforce it to be some multiple of "outputenergies" for the GPU version, but I am not sure whether the .fepout file will be deprecated since some people are in favor of the log from stdout. In the case that alchOutFreq is not some multiples of computeEnergies, NAMD3 will show a warning like this:

Warning: The period of outputting energies relating to alchemical transformations (alchOutFreq = 10) is not a multiple of the period of computing energies (computeEnergies = 20). If alchOutFreq is smaller than outputEnergies and computeEnergies is not defined, a better solution is to set comp
uteEnergies explicitly and keep it the same as alchOutFreq. The simulation will use the greatest common divisor of computeEnergies and alchOutFreq as the period of energy evaluation.

I don't know whether the NAMD should just stop here or not, since the greatest common divisor of "alchOutFreq" and "computeEnergies" is 10, not a multiple of "fullElectFrequency". Hopefully you may propose a better solution to this mess.

Thanks,

Haochuan Chen


On 11/5/21 11:12, Jérôme Hénin wrote:
Hi all,

Please be aware of a bug in current NAMD versions that can affect alchemical free energies computed using IDWS-style alchemical perturbations. Below I give workarounds to get correct free energy values from existing data affected by the issue, and to make any new simulation exempt from the issue.

Affected versions of NAMD:
2.14, 3.x (non-CUDA version), and development versions until now.

Condition triggering the issue:
The issue occurs if multiple time-step is used and alchOutFreq is greater than, but not a multiple of, fullElectFreq.
Unfortunately, the current default value of alchOutFreq (5) is likely to fulfill this condition.

Symptoms:
In this situation, some of the energy differences are computed erroneously - specifically, dE values computed at time steps that are not multiples of the outer time step include long-range dE values for the wrong target lambda.
More generally, even without IDWS, alchOutFreq should probably always be a multiple of fullElectFreq to ensure that comparison energies are as accurate as possible, and do not include stale long-range terms.

Fix and workaround:
For future simulations: define alchOutFreq as either 1 or a multiple of fullElectFreq.
For existing simulations: re-analyze, discarding any data point from the fepout file where the time step number is not a multiple of fullElectFreq.

Diagnosis:
In doubt, the issue can be diagnosed for a specific dataset by histogramming forward and backward values of the electrostatic dE for an individual IDWS window. The bug will result in a characteristic bimodal distribution.


I will submit a code patch very soon to fix this in a final way. In the meantime, please circulate the information to users who might be affected.
Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for reporting the issue.

Jérôme
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Fri, 5 Nov 2021 18:10:36 +0100 (CET) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id 469391E414F7; Fri, 5 Nov 2021 18:10:36 +0100 (CET) Date: Fri, 5 Nov 2021 18:10:35 +0100 (CET) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: yjcoshc Cc: NAMD list Message-ID: <1884500734.5239443.1636132235679.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: <1834646094.5234069.1636128738554.JavaMail.zimbra@ibpc.fr> Subject: Re: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies Content-Type: multipart/alternative; boundary="=_cfeea412-2cb7-4593-bc79-0a47d980d6d5" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies Thread-Index: MEtt7IpAVW7j3I6J8eI6+ClOlx4vJw== X-Proofpoint-ORIG-GUID: 6BZ9Y10tbF09VEl2guFi57A90vY5KTL6 X-Proofpoint-GUID: 6BZ9Y10tbF09VEl2guFi57A90vY5KTL6 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwSEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxkdGBEKQ1kXBxsZEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseEnEYExAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThccaHATcxsaXkhsGhN8b0YYTV9sQx8daxMaXHMfYX5mHBEKWFwXHwQaBBgeGwUb GgQbGxoEHQQbGRsQGx4aHxoRCl5ZF3NfXUVYEQpNXBcYEhMRCkxaF2l4bWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2hARUgYGHxrW3oZEQpDWhcbExkEHhMEGBkeBBgYGx EKQl4XGxEKREkXGxEKQkUXZFhcXE1+UkkbZUkRCkJOF2VPfhJDaWZZHAFpEQpCTBd6EmdpYFl5R kFPZREKQmwXYRIST09MTX9PHgURCkJAF2IcS1tefEFIexJaEQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXHhEKeUMXa2dMTnhyfF1vXFARCnBoF2tDWk9gYUwBHEgaEBoRCnBoF2BfaV9zZmdDekh IEBoRCnBoF2dYSGRlTUVCHkdDEBoRCnBoF2VCc3oFUGVZUG9eEBoRCnBoF2wBUHheQxIBcmcZEB oRCnB9F21JWX1abBlcTBMBEBoRCnB9F2QaG01wbVxwYURaEBkaEQpwfxdgQlN6bm1YemQBExAbG x4RCnBfF2ZgQksBX1BfemlQEBoRCnB/F2RIQmIaQXxQaE1rEBITEQpwXxdgZFJ+GxtybhxOXRAZ GhEKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17GEVSEBoRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 priorityscore=0 phishscore=0 spamscore=0 malwarescore=0 mlxlogscore=999 adultscore=0 mlxscore=0 clxscore=168 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111050095 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_cfeea412-2cb7-4593-bc79-0a47d980d6d5 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Haochuan,=20 I think your patch is extremely useful, performance-wise. This raises the q= uestion: when doing MTS, does it make sense to compute (and output) energie= s at steps that are not multiples of fullElectFrequency? Should computeEner= gies be mandated to be a multiple of fullElectFrequency, similar to the tes= t I just proposed for alchoutFreq ( [ https://urldefense.com/v3/__https://g= itlab.com/tcbgUIUC/namd/-/merge_requests/99__;!!DZ3fjg!svAWPsI-po1zufW5U2-o= kMFQQ0MohRSuWLldZQNzCMg9GL2HgmLRP_etGXips2Edxw$ | https://urldefense.com/v= 3/__https://gitlab.com/tcbgUIUC/namd/-/merge_requests/99__;!!DZ3fjg!svAWPsI= -po1zufW5U2-okMFQQ0MohRSuWLldZQNzCMg9GL2HgmLRP_etGXips2Edxw$ ] )?=20 About fepout files vs. standard output, I think the main benefit of a separ= ate file is to have a large number of samples in a compact file. Right now = the fepout format is too verbose. I am thinking of what would be a desirabl= e new format for the fepout, which would be smaller and easier to parse. Th= is could be introduced as an option, keeping the default to the legacy file= format for compatibility. If you have ideas about desirable properties for= such a format, I'd be interested in hearing them.=20 Best,=20 J=C3=A9r=C3=B4me=20 ----- On 5 Nov 21, at 17:53, yjcoshc wrote:=20 > Hi J=C3=A9r=C3=B4me, > In the development branch, I submitted a patch adding an option " > computeEnergies " to control the period of computing energy terms, which > defaults to be the " outputEnergies ", so if someone uses outputenergies = 20 > fullElectFrequency 4 > and that will trigger an error to stop the simulation at start. You may s= ee [ > https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 | > https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 ] for more details. > As for alchOutFreq , I personally agree to enforce it to be some multiple= of " > outputenergies " for the GPU version, but I am not sure whether the .fepo= ut > file will be deprecated since some people are in favor of the log from st= dout. > In the case that alchOutFreq is not some multiples of computeEnergies , N= AMD3 > will show a warning like this: > Warning: The period of outputting energies relating to alchemical > transformations (alchOutFreq =3D 10) is not a multiple of the period of c= omputing > energies (computeEnergies =3D 20). If alchOutFreq is smaller than outputE= nergies > and computeEnergies is not defined, a better solution is to set comp > uteEnergies explicitly and keep it the same as alchOutFreq. The simulatio= n will > use the greatest common divisor of computeEnergies and alchOutFreq as the > period of energy evaluation. > I don't know whether the NAMD should just stop here or not, since the gre= atest > common divisor of " alchOutFreq " and " computeEnergies " is 10, not a mu= ltiple > of " fullElectFrequency ". Hopefully you may propose a better solution to= this > mess. > Thanks, > Haochuan Chen > On 11/5/21 11:12, J=C3=A9r=C3=B4me H=C3=A9nin wrote: >> Hi all, >> Please be aware of a bug in current NAMD versions that can affect alchem= ical >> free energies computed using IDWS-style alchemical perturbations. Below = I give >> workarounds to get correct free energy values from existing data affecte= d by >> the issue, and to make any new simulation exempt from the issue. >> Affected versions of NAMD: >> 2.14, 3.x (non-CUDA version), and development versions until now. >> Condition triggering the issue: >> The issue occurs if multiple time-step is used and alchOutFreq is greate= r than, >> but not a multiple of, fullElectFreq. >> Unfortunately, the current default value of alchOutFreq (5) is likely to= fulfill >> this condition. >> Symptoms: >> In this situation, some of the energy differences are computed erroneous= ly - >> specifically, dE values computed at time steps that are not multiples of= the >> outer time step include long-range dE values for the wrong target lambda. >> More generally, even without IDWS, alchOutFreq should probably always be= a >> multiple of fullElectFreq to ensure that comparison energies are as accu= rate as >> possible, and do not include stale long-range terms. >> Fix and workaround: >> For future simulations: define alchOutFreq as either 1 or a multiple of >> fullElectFreq. >> For existing simulations: re-analyze, discarding any data point from the= fepout >> file where the time step number is not a multiple of fullElectFreq. >> Diagnosis: >> In doubt, the issue can be diagnosed for a specific dataset by histogram= ming >> forward and backward values of the electrostatic dE for an individual ID= WS >> window. The bug will result in a characteristic bimodal distribution. >> I will submit a code patch very soon to fix this in a final way. In the >> meantime, please circulate the information to users who might be affecte= d. >> Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for report= ing the >> issue. >> J=C3=A9r=C3=B4me --=_cfeea412-2cb7-4593-bc79-0a47d980d6d5 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Hi Haochuan,

I think your patch is extremely useful, performance-wise.= This raises the question: when doing MTS, does it make sense to compute (a= nd output) energies at steps that are not multiples of fullElectFrequency? = Should computeEnergies be mandated to be a multiple of fullElectF= requency, similar to the test I just proposed for alchoutFreq (https://gitlab.com/tcbgUIUC/namd/-/merge_requests/99)?
=
About fepout files vs. standard output,= I think the main benefit of a separate file is to have a large number of s= amples in a compact file. Right now the fepout format is too verbose. I am = thinking of what would be a desirable new format for the fepout, which woul= d be smaller and easier to parse. This could be introduced as an option, ke= eping the default to the legacy file format for compatibility. If you have = ideas about desirable properties for such a format, I'd be interested in he= aring them.

Best,
J= =C3=A9r=C3=B4me


----- On 5 Nov 21, at 17:5= 3, yjcoshc <yjcoshc@gmail.com> wrote:

Hi J=C3=A9r=C3=B4me,

In the development branch, I submitted a patch adding an option "computeEnergies" to control the period of computing energy terms, which defaults to be the "outputEnergies", so if someone uses

outputenergies     &n= bsp;    20
fullElectFrequency      4

and that will trigger an error to stop the simulation at start. You may see https://charm.= cs.illinois.edu/gerrit/c/namd/+/5514 for more details.

As for alchOutFreq, I personally agree to enforce it to be some multiple of "= outputenergies" for the GPU version, but I am not sure whether the .fepout file will be deprecated since some people are in favor of the log from stdout. In the case that alchOutFreq = is not some multiples of computeEnergies, NAMD3 will show a warning like this:

Warning: The period of outputting energies relating to alchemical transformations (alchOutFreq =3D 10) is not a multiple of the period of computing energies (computeEnergies =3D 20). If alchOutFreq is smaller than outputEnergies and computeEnergies is not defined, a better solution is to set computeEnergies explicitly and keep it the same as alchO= utFreq. The simulation will use the greatest common divisor of computeEnergies and alchOutFreq as the period of energy evaluation.

I don't know whether the NAMD should just stop here or not, since the greatest common divisor of "alchOutFreq" and "<= span style=3D"color:#000000;background-color:#ffffff">computeEnergies" is 10, not a multiple of "fullElectFrequency= ". Hopefully you may propose a better solution to this mess.

Thanks,

Haochuan Chen


On 11/5/21 11:12, J=C3=A9r=C3=B4me H=C3= =A9nin wrote:
=20=20=20=20=20=20
Hi all,

Please be aware of a bug in current NAMD versions that can affect alchemical free energies computed using IDWS-style alchemical perturbations. Below I give workarounds to get correct free energy values from existing data affected by the issue, and to make any new simulation exempt from the issue.

Affected versions of NAMD:
2.14, 3.x (non-CUDA version), and development versions until now.

Condition triggering the issue:
The issue occurs if multiple time-step is used and alc= hOutFreq is greater than, but not a multiple of, fullElectFreq.=
Unfortunately, the current default value of alchOutFreq (5) is likely to fulfill this condition.

Symptoms:
In this situation, some of the energy differences are computed erroneously - specifically, dE values computed at time steps that are not multiples of the outer time step include long-range dE values for the wrong target lambda.
More generally, even without IDWS, alchOutFreq should probably always be a multiple of fullElectFreq to ensure that comparison energies are as accurate as possible, and do not include stale long-range terms.

Fix and workaround:
For future simulations: define alchOutFreq as either 1 or= a multiple of fullElectFreq.
For existing simulations: re-analyze, discarding any data point from the fepout file where the time step number is not a multiple of fullElectFreq.

Diagnosis:
In doubt, the issue can be diagnosed for a specific dataset by histogramming forward and backward values of the electrostatic dE for an individual IDWS window. The bug will result in a characteristic bimodal distribution.


I will submit a code patch very soon to fix this in a final way. In the meantime, please circulate the information to users who might be affected.
Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for reporting the issue.

J=C3=A9r=C3=B4me

= --=_cfeea412-2cb7-4593-bc79-0a47d980d6d5-- From owner-namd-l@halifax.ks.uiuc.edu Fri Nov 5 12:14:04 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A5HE4ao013650; Fri, 5 Nov 2021 12:14:04 -0500 (CDT) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1A5HE4Vx013647; Fri, 5 Nov 2021 12:14:04 -0500 (CDT) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A5HE3di013637; Fri, 5 Nov 2021 12:14:03 -0500 (CDT) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1A5HE21j013634; Fri, 5 Nov 2021 12:14:02 -0500 (CDT) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A5HDqKs013521 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Fri, 5 Nov 2021 18:13:48 +0100 (CET) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id A02481E415F0 for ; Fri, 5 Nov 2021 18:13:48 +0100 (CET) Date: Fri, 5 Nov 2021 18:13:48 +0100 (CET) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list Message-ID: <1118965384.5239557.1636132427923.JavaMail.zimbra@ibpc.fr> In-Reply-To: <1884500734.5239443.1636132235679.JavaMail.zimbra@ibpc.fr> References: <1834646094.5234069.1636128738554.JavaMail.zimbra@ibpc.fr> <1884500734.5239443.1636132235679.JavaMail.zimbra@ibpc.fr> Subject: Re: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies Content-Type: multipart/alternative; boundary="=_0ad69afe-149b-45be-a2c4-e4aac9d5f8e9" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies Thread-Index: MEtt7IpAVW7j3I6J8eI6+ClOlx4vJzl6kqkD X-Proofpoint-GUID: nSS3m8PVjhibL1wOUwQaYz25Q53RpWfY X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxITEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxkSHBEKQ1kXBxsZEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscE3EeEhAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdEeXkZRxJ6fEBCQ0hmG11lf117S3NQGB97Hxl4Wn1McxEKWFwXHwQaBBgeGwUb GgQbGxoEHQQbGRgQGx4aHxoRCl5ZF3NfXVhYEQpNXBcZGBoRCkxaF2l7bWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2hARUgYGHxrW3oZEQpDWhcbExkEHhMEGBkeBBgYGx EKQl4XGxEKQkUXZFhcXE1+UkkbZUkRCkJOF2VPfhJDaWZZHAFpEQpCTBd6EmdpYFl5RkFPZREKQ mwXYRIST09MTX9PHgURCkJAF2IcS1tefEFIexJaEQpCWBdnc2VzQG5hYUxdYhEKWlgXHhEKeUMX a2dMTnhyfF1vXFARCnBnF21OU2xZSxNTUB1yEBoRCnBoF2ZaGxMaRl9aHBphEBoRCnBoF2JYUk1 8UAVFS3leEBoRCnBoF2tDWk9gYUwBHEgaEBoRCnBoF2x4Ql5/W0lwE3lAEBoRCnBoF3oYW1t9Yh 8dGEF9EBoRCnB9F21JWX1abBlcTBMBEBoRCnB9F2QaG01wbVxwYURaEBkaEQpwfxdgQlN6bm1Ye mQBExAbGxsRCnBfF2ZgQksBX1BfemlQEBoRCnB/F2RIQmIaQXxQaE1rEBMZEQpwXxdgZFJ+Gxty bhxOXRAZGhEKcGwXZmATZFxNGmdPelAQHBoRCnBMF21oZRlBUn17GEVSEBoRCm1+FxoRClhNF0s RIA== X-Proofpoint-ORIG-GUID: nSS3m8PVjhibL1wOUwQaYz25Q53RpWfY MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 malwarescore=0 priorityscore=0 mlxlogscore=999 clxscore=189 impostorscore=0 bulkscore=0 spamscore=0 suspectscore=0 adultscore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111050096 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_0ad69afe-149b-45be-a2c4-e4aac9d5f8e9 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi all,=20 A small correction to my previous message: when fullElectFrequency > 1, I d= o not recommend setting alchOutFreq to 1, but only to a multiple of fullEle= ctFrequency . The code patch I have submitted, unless it changes before it = gets merged, will enforce that condition.=20 J=C3=A9r=C3=B4me=20 ----- On 5 Nov 21, at 18:10, J=C3=A9r=C3=B4me H=C3=A9nin wrote:=20 > Hi Haochuan, > I think your patch is extremely useful, performance-wise. This raises the > question: when doing MTS, does it make sense to compute (and output) ener= gies > at steps that are not multiples of fullElectFrequency? Should computeEner= gies > be mandated to be a multiple of fullElectFrequency, similar to the test I= just > proposed for alchoutFreq ( [ > https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd/-/merge_requ= ests/99__;!!DZ3fjg!vFZPYdHhusXHdpcWSVMHgH5J_bjge4nWDIAE05KzMvAge9CYXjVaND5w= o2TX36QAMA$ | > https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd/-/merge_requ= ests/99__;!!DZ3fjg!vFZPYdHhusXHdpcWSVMHgH5J_bjge4nWDIAE05KzMvAge9CYXjVaND5w= o2TX36QAMA$ ] )? > About fepout files vs. standard output, I think the main benefit of a sep= arate > file is to have a large number of samples in a compact file. Right now the > fepout format is too verbose. I am thinking of what would be a desirable = new > format for the fepout, which would be smaller and easier to parse. This c= ould > be introduced as an option, keeping the default to the legacy file format= for > compatibility. If you have ideas about desirable properties for such a fo= rmat, > I'd be interested in hearing them. > Best, > J=C3=A9r=C3=B4me > ----- On 5 Nov 21, at 17:53, yjcoshc wrote: >> Hi J=C3=A9r=C3=B4me, >> In the development branch, I submitted a patch adding an option " >> computeEnergies " to control the period of computing energy terms, which >> defaults to be the " outputEnergies ", so if someone uses outputenergies= 20 >> fullElectFrequency 4 >> and that will trigger an error to stop the simulation at start. You may = see [ >> https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 | >> https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 ] for more details. >> As for alchOutFreq , I personally agree to enforce it to be some multipl= e of " >> outputenergies " for the GPU version, but I am not sure whether the .fep= out >> file will be deprecated since some people are in favor of the log from s= tdout. >> In the case that alchOutFreq is not some multiples of computeEnergies , = NAMD3 >> will show a warning like this: >> Warning: The period of outputting energies relating to alchemical >> transformations (alchOutFreq =3D 10) is not a multiple of the period of = computing >> energies (computeEnergies =3D 20). If alchOutFreq is smaller than output= Energies >> and computeEnergies is not defined, a better solution is to set comp >> uteEnergies explicitly and keep it the same as alchOutFreq. The simulati= on will >> use the greatest common divisor of computeEnergies and alchOutFreq as the >> period of energy evaluation. >> I don't know whether the NAMD should just stop here or not, since the gr= eatest >> common divisor of " alchOutFreq " and " computeEnergies " is 10, not a m= ultiple >> of " fullElectFrequency ". Hopefully you may propose a better solution t= o this >> mess. >> Thanks, >> Haochuan Chen >> On 11/5/21 11:12, J=C3=A9r=C3=B4me H=C3=A9nin wrote: >>> Hi all, >>> Please be aware of a bug in current NAMD versions that can affect alche= mical >>> free energies computed using IDWS-style alchemical perturbations. Below= I give >>> workarounds to get correct free energy values from existing data affect= ed by >>> the issue, and to make any new simulation exempt from the issue. >>> Affected versions of NAMD: >>> 2.14, 3.x (non-CUDA version), and development versions until now. >>> Condition triggering the issue: >>> The issue occurs if multiple time-step is used and alchOutFreq is great= er than, >>> but not a multiple of, fullElectFreq. >>> Unfortunately, the current default value of alchOutFreq (5) is likely t= o fulfill >>> this condition. >>> Symptoms: >>> In this situation, some of the energy differences are computed erroneou= sly - >>> specifically, dE values computed at time steps that are not multiples o= f the >>> outer time step include long-range dE values for the wrong target lambd= a. >>> More generally, even without IDWS, alchOutFreq should probably always b= e a >>> multiple of fullElectFreq to ensure that comparison energies are as acc= urate as >>> possible, and do not include stale long-range terms. >>> Fix and workaround: >>> For future simulations: define alchOutFreq as either 1 or a multiple of >>> fullElectFreq. >>> For existing simulations: re-analyze, discarding any data point from th= e fepout >>> file where the time step number is not a multiple of fullElectFreq. >>> Diagnosis: >>> In doubt, the issue can be diagnosed for a specific dataset by histogra= mming >>> forward and backward values of the electrostatic dE for an individual I= DWS >>> window. The bug will result in a characteristic bimodal distribution. >>> I will submit a code patch very soon to fix this in a final way. In the >>> meantime, please circulate the information to users who might be affect= ed. >>> Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for repor= ting the >>> issue. >>> J=C3=A9r=C3=B4me --=_0ad69afe-149b-45be-a2c4-e4aac9d5f8e9 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable
Hi all,

=
A small correction to my previous message: when fullElectFr= equency > 1, I do not recommend setting alchOutFreq to 1, but on= ly to a multiple of fullElectFrequency. The code patch I have subm= itted, unless it changes before it gets merged, will enforce that condition= .

J=C3=A9r=C3=B4me

----- On 5 No= v 21, at 18:10, J=C3=A9r=C3=B4me H=C3=A9nin <jerome.henin@ibpc.fr> wr= ote:
Hi Haochuan,=

I think your patch is extremely useful, performance-wise. Th= is raises the question: when doing MTS, does it make sense to compute (and = output) energies at steps that are not multiples of fullElectFrequency? Sho= uld computeEnergies be mandated to be a multiple of fullElectFreq= uency, similar to the test I just proposed for alchoutFreq (https://gitla= b.com/tcbgUIUC/namd/-/merge_requests/99)?

About fepout fi= les vs. standard output, I think the main benefit of a separate file is to = have a large number of samples in a compact file. Right now the fepout form= at is too verbose. I am thinking of what would be a desirable new format fo= r the fepout, which would be smaller and easier to parse. This could be int= roduced as an option, keeping the default to the legacy file format for com= patibility. If you have ideas about desirable properties for such a format,= I'd be interested in hearing them.

Best,
J=C3=A9r= =C3=B4me


----- On 5 Nov 21, at 17:53, = yjcoshc <yjcoshc@gmail.com> wrote:

Hi J=C3=A9r=C3=B4me= ,

In the development branch, I submitted a patch adding an option "computeEnergies" to control the period of computing energy terms, which defaults to be the "outputEnergies", so if someone uses

outputenergies     &n= bsp;    20
fullElectFrequency      4

and that will trigger an error to stop the simulation at start. You may see https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 for more details.

As for alchOutFreq, I personally agree to enforce it to be some multiple of "= outputenergies" for the GPU version, but I am not sure whether the .fepout file will be deprecated since some people are in favor of the log from stdout. In the case that alchOutFreq = is not some multiples of computeEnergies, NAMD3 will show a warning like this:

Warning: The period of outputting energies relating to alchemical transformations (alchOutFreq =3D 10) is not a multiple of the period of computing energies (computeEnergies =3D 20). If alchOutFreq is smaller than outputEnergies and computeEnergies is not defined, a better solution is to set computeEnergies explicitly and keep it the same as alchO= utFreq. The simulation will use the greatest common divisor of computeEnergies and alchOutFreq as the period of energy evaluation.

I don't know whether the NAMD should just stop here or not, since the greatest common divisor of "alchOutFreq" and "<= span style=3D"color:#000000;background-color:#ffffff">computeEnergies" is 10, not a multiple of "fullElectFrequency= ". Hopefully you may propose a better solution to this mess.

Thanks,

Haochuan Chen


On 11/5/21 11:12, J=C3=A9r=C3=B4me H=C3= =A9nin wrote:
=20=20=20=20=20=20
Hi all,

Please be aware of a bug in current NAMD versions that can affect alchemical free energies computed using IDWS-style alchemical perturbations. Below I give workarounds to get correct free energy values from existing data affected by the issue, and to make any new simulation exempt from the issue.

Affected versions of NAMD:
2.14, 3.x (non-CUDA version), and development versions until now.

Condition triggering the issue:
The issue occurs if multiple time-step is used and alc= hOutFreq is greater than, but not a multiple of, fullElectFreq.=
Unfortunately, the current default value of alchOutFreq (5) is likely to fulfill this condition.

Symptoms:
In this situation, some of the energy differences are computed erroneously - specifically, dE values computed at time steps that are not multiples of the outer time step include long-range dE values for the wrong target lambda.
More generally, even without IDWS, alchOutFreq should probably always be a multiple of fullElectFreq to ensure that comparison energies are as accurate as possible, and do not include stale long-range terms.

Fix and workaround:
For future simulations: define alchOutFreq as either 1 or= a multiple of fullElectFreq.
For existing simulations: re-analyze, discarding any data point from the fepout file where the time step number is not a multiple of fullElectFreq.

Diagnosis:
In doubt, the issue can be diagnosed for a specific dataset by histogramming forward and backward values of the electrostatic dE for an individual IDWS window. The bug will result in a characteristic bimodal distribution.


I will submit a code patch very soon to fix this in a final way. In the meantime, please circulate the information to users who might be affected.
Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for reporting the issue.

J=C3=A9r=C3=B4me

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Fri, 05 Nov 2021 14:21:01 -0700 (PDT) Content-Type: multipart/alternative; boundary="------------D2a0d9CzXk0Je0KHJea31tp3" Message-ID: Date: Fri, 5 Nov 2021 16:20:59 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.3.0 Subject: Re: namd-l: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies Content-Language: en-US To: =?UTF-8?B?SsOpcsO0bWUgSMOpbmlu?= Cc: NAMD list References: <1834646094.5234069.1636128738554.JavaMail.zimbra@ibpc.fr> <1884500734.5239443.1636132235679.JavaMail.zimbra@ibpc.fr> From: yjcoshc In-Reply-To: <1884500734.5239443.1636132235679.JavaMail.zimbra@ibpc.fr> X-Proofpoint-ORIG-GUID: GcqDE5KL2wVc6qpRFxeSZikwlorScbDy X-Proofpoint-GUID: GcqDE5KL2wVc6qpRFxeSZikwlorScbDy X-CLX-Response: 1TFkXGxIZEQpMehcZHx0RCllEF2ZkX1pvRRJLb1hmEQpYWBdmW3x/R0hvHwV PZREKeE4XY1Nja3sTWH4aX14RCkNIFwceHxwRCkNZFwcbGRIRCkNJFxoEGhoaEQpZTRdnZnIRCl lJFxpxGhAadwYbHBlxHhgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XbUlbb m8fYWYYXXxJHFtaeGxST3lwQ0FdRkVYeUlIblMRClhcFx8EGgQYHhsFGxoEGxoaBB0EGx4ZEBse Gh8aEQpeWRdzXxp+SBEKTVwXGB8SEQpMWhdpeGlrTU0RCkVZF29rEQpMXxd6BQUFBQUFBQUFbxE KTEYXb2trbGtrEQpCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQQeExEKQl4XGxEKREkXGx EKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdkUkIFGlgaX ntDeBEKQk4XY1Nja3sTWH4aX14RCkJMF2ZbfH9HSG8fBU9lEQpCbBdiT2JEGktAG1JfXREKQkAX YhxLW158QUh7EloRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBceEQp5QxdrZ0xOeHJ8XW9cUBE KWUsXEx8SGxEKcGcXYGZFRhJza2lCHVkQGRoRCnBoF2tDWk9gYUwBHEgaEBoRCnBoF2teaENIQW F+SAFSEBoRCnBoF2dYSGRlTUVCHkdDEBoRCnBoF29oYQFAH05ZRXtYEBoRCnBoF2kdHB5FTW5oB W1oEBoRCnB9F2Zbb3tTa2BmTBsdEBoRCnB9F2QaG01wbVxwYURaEBkaEQpwfRdtSVl9WmwZXEwT ARAaEQpwfxdgQlN6bm1YemQBExAbGhwRCnBfF2ZgQksBX1BfemlQEBoRCnB/F2RIQmIaQXxQaE1 rEB8eEQpwXxdgZFJ+GxtybhxOXRAZGhEKcGwXZh5pRRtISE1kaF8QGRoRCnBMF21oZRlBUn17GE VSEBoRCnBDF2JYG0xYRBxESFlyEBoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 spamscore=0 mlxlogscore=999 mlxscore=0 suspectscore=0 bulkscore=0 clxscore=183 adultscore=0 malwarescore=0 phishscore=0 priorityscore=357 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111050115 domainage_hfrom=9581 X-Spam-Score: 0 X-Spam-OrigSender: yjcoshc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, yjcoshc This is a multi-part message in MIME format. --------------D2a0d9CzXk0Je0KHJea31tp3 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: Quoted-printable Hi J=C3=A9r=C3=B4me, I think your patch is good and also the simplest way to solve the issue. Thanks, Haochuan Chen On 11/5/21 12:10, J=C3=A9r=C3=B4me H=C3=A9nin wrote: > Hi Haochuan, > > I think your patch is extremely useful, performance-wise. This raises=20 > the question: when doing MTS, does it make sense to compute (and=20 > output) energies at steps that are not multiples of=20 > fullElectFrequency? Should=C2=A0computeEnergies be mandated to be a=20 > multiple of=C2=A0fullElectFrequency, similar to the test I just proposed= =20 > for alchoutFreq (https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/= namd/-/merge_requests/99)?__;!!DZ3fjg!rMuJ8NvKcGZ_jindodF2gHzmdu4-yQVg-AES4= N4MfSOvqXlY-cwvcy_5TUFD16dSbA$=20 > > About fepout files vs. standard output, I think the main benefit of a=20 > separate file is to have a large number of samples in a compact file.=20 > Right now the fepout format is too verbose. I am thinking of what=20 > would be a desirable new format for the fepout, which would be smaller=20 > and easier to parse. This could be introduced as an option, keeping=20 > the default to the legacy file format for compatibility. If you have=20 > ideas about desirable properties for such a format, I'd be interested=20 > in hearing them. > > Best, > J=C3=A9r=C3=B4me > > > ----- On 5 Nov 21, at 17:53, yjcoshc wrote: > > Hi J=C3=A9r=C3=B4me, > > In the development branch, I submitted a patch adding an option > "computeEnergies" to control the period of computing energy terms, > which defaults to be the "outputEnergies", so if someone uses > > outputenergies=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 20 > fullElectFrequency=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 4 > > and that will trigger an error to stop the simulation at start. > You may see https://charm.cs.illinois.edu/gerrit/c/namd/+/5514 for > more details. > > As for alchOutFreq, I personally agree to enforce it to be some > multiple of "outputenergies" for the GPU version, but I am not > sure whether the .fepout file will be deprecated since some people > are in favor of the log from stdout. In the case that alchOutFreq > is not some multiples ofcomputeEnergies, NAMD3 will show a warning > like this: > > Warning: The period of outputting energies relating to alchemical > transformations (alchOutFreq =3D 10) is not a multiple of the period > of computing energies (computeEnergies =3D 20). If alchOutFreq is > smaller than outputEnergies and computeEnergies is not defined, a > better solution is to set computeEnergies explicitly and keep it > the same as alchOutFreq. The simulation will use the greatest > common divisor of computeEnergies and alchOutFreq as the period of > energy evaluation. > > I don't know whether the NAMD should just stop here or not, since > the greatest common divisor of "alchOutFreq" and "computeEnergies" > is 10, not a multiple of "fullElectFrequency". Hopefully you may > propose a better solution to this mess. > > Thanks, > > Haochuan Chen > > > On 11/5/21 11:12, J=C3=A9r=C3=B4me H=C3=A9nin wrote: > > Hi all, > > Please be aware of a bug in current NAMD versions that can > affect alchemical free energies computed using IDWS-style > alchemical perturbations. Below I give workarounds to *get > correct free energy values from existing data* affected by the > issue, and to make any new simulation exempt from the issue. > > *Affected versions of NAMD:* > 2.14, 3.x (non-CUDA version), and development versions until now. > > *Condition triggering the issue:* > The issue occurs if multiple time-step is used and > *alchOutFreq is greater than, but not a multiple of, > fullElectFreq.* > Unfortunately, the current default value of alchOutFreq (5) is > likely to fulfill this condition. > > *Symptoms:* > In this situation, some of the energy differences are computed > erroneously - specifically, dE values computed at time steps > that are not multiples of the outer time step include > long-range dE values for the wrong target lambda. > More generally, even without IDWS,=C2=A0alchOutFreq should probab= ly > /always/ be a multiple of=C2=A0fullElectFreq to ensure that > comparison energies are as accurate as possible, and do not > include stale long-range terms. > > *Fix and workaround:* > For future simulations: define=C2=A0alchOutFreq as either 1 or a > multiple of=C2=A0fullElectFreq. > For existing simulations: re-analyze, discarding any data > point from the fepout file where the time step number is not a > multiple of=C2=A0fullElectFreq. > > *Diagnosis:* > In doubt, the issue can be diagnosed for a specific dataset by > histogramming forward and backward values of the electrostatic > dE for an individual IDWS window. The bug will result in a > characteristic bimodal distribution. > > > I will submit a code patch very soon to fix this in a final > way. In the meantime, please circulate the information to > users who might be affected. > Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) > for reporting the issue. > > J=C3=A9r=C3=B4me > >= --------------D2a0d9CzXk0Je0KHJea31tp3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: Quoted-printable

Hi J=C3=A9r=C3=B4me,

I think your patch is good and also the simplest way to solve the issue.

Thanks,

Haochuan Chen


On 11/5/21 12:10, J=C3=A9r=C3=B4me H=C3= =A9nin wrote:
Hi Haochuan,

I think your patch is extremely useful, performance-wise. This raises the question: when doing MTS, does it make sense to compute (and output) energies at steps that are not multiples of fullElectFrequency? Should=C2=A0computeEnergies be mandated to be a multiple of=C2=A0fullElectFrequency, similar to the test I just proposed for alchoutFreq (https://gitlab.com/tcbg= UIUC/namd/-/merge_requests/99)?

About fepout files vs. standard output, I think the main benefit of a separate file is to have a large number of samples in a compact file. Right now the fepout format is too verbose. I am thinking of what would be a desirable new format for the fepout, which would be smaller and easier to parse. This could be introduced as an option, keeping the default to the legacy file format for compatibility. If you have ideas about desirable properties for such a format, I'd be interested in hearing them.

Best,
J=C3=A9r=C3=B4me


----- On 5 Nov 21, at 17:53, yjcoshc <yjcoshc@gmail.com> wrote:

Hi J=C3=A9r=C3=B4me,

In the development branch, I submitted a patch adding an option "computeEnergies" to control the period of computing energy terms, which defaults to be the "outputEnergies", so if someone uses

outputenergies=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 20
fullElectFrequency=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 4

and that will trigger an error to stop the simulation at start. You may see ht= tps://charm.cs.illinois.edu/gerrit/c/namd/+/5514 for more details.

As for alchOutFreq, I personally agree to enforce it to be some multiple of "outputenergies" for the GPU version, but I am not sure whether the .fepout file will be deprecated since some people are in favor of the log from stdout. In the case that alchOu= tFreq is not some multiples of computeEnergies, NAMD3 will show a warning like this:

Warnin= g: The period of outputting energies relating to alchemical transformations (alchOutFreq =3D 10) is not a multiple of the period of computing energies (computeEnergies =3D 20). If alchOutFreq is smaller than outputEnergies and computeEnergies is not defined, a better solution is to set computeEner= gies explicitly and keep it the same as alchOutFreq. The simulation will use the greatest common divisor of computeEnergies and alchOutFreq as the period of energy evaluation.

I don't know whether the NAMD should just stop here or not, since the greatest common divisor of "al= chOutFreq" and "comput= eEnergies" is 10, not a multiple of "fullElectF= requency". Hopefully you may propose a better solution to this mess.

Thanks,

Haochuan Chen


On 11/5/21 11:12, J=C3=A9r=C3=B4= me H=C3=A9nin wrote:
Hi all,

Please be aware of a bug in current NAMD versions that can affect alchemical free energies computed using IDWS-style alchemical perturbations. Below I give workarounds to get correct free energy values from existing data affected by the issue, and to make any new simulation exempt from the issue.

Affected versions of NAMD:
2.14, 3.x (non-CUDA version), and development versions until now.

Condition triggering the issue:
The issue occurs if multiple time-step is used and alchOutFreq is greater than, but not a multiple of, fullElectFreq.
Unfortunately, the current default value of alchOutFreq (5) is likely to fulfill this condition.

Symptoms:
In this situation, some of the energy differences are computed erroneously - specifically, dE values computed at time steps that are not multiples of the outer time step include long-range dE values for the wrong target lambda.
More generally, even without IDWS,=C2=A0alchOutFreq should probably always be a multiple of=C2=A0fullElectFreq to ensure that comparison energies are as accurate as possible, and do not include stale long-range terms.

Fix and workaround:
For future simulations: define=C2=A0alchOutFreq as either 1 or a multiple of=C2=A0fullElectFreq.
For existing simulations: re-analyze, discarding any data point from the fepout file where the time step number is not a multiple of=C2=A0fullElectFreq.

Diagnosis:
In doubt, the issue can be diagnosed for a specific dataset by histogramming forward and backward values of the electrostatic dE for an individual IDWS window. The bug will result in a characteristic bimodal distribution.


I will submit a code patch very soon to fix this in a final way. In the meantime, please circulate the information to users who might be affected.
Thanks to Ezry St. Iago-McRae (Brannigan lab, Rutgers Camden) for reporting the issue.

J=C3=A9r=C3=B4me

= --------------D2a0d9CzXk0Je0KHJea31tp3-- From owner-namd-l@halifax.ks.uiuc.edu Mon Nov 8 19:31:38 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A91Vc3F018586; Mon, 8 Nov 2021 19:31:38 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1A91VcsM018585; Mon, 8 Nov 2021 19:31:38 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A91VbdQ018581; Mon, 8 Nov 2021 19:31:37 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1A91Vb7m018580; Mon, 8 Nov 2021 19:31:37 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1A91VPSR018572 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 8 Nov 2021 19:31:25 -0600 (CST) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1A91C7O7025595 for ; Tue, 9 Nov 2021 01:31:24 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=zebamir85@gmail.com; dkim=pass header.d=gmail.com header.s=20210112 Received: from mail-io1-f47.google.com (mail-io1-f47.google.com [209.85.166.47]) by mx0b-00007101.pphosted.com with ESMTP id 3c7388eu3u-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Tue, 09 Nov 2021 01:31:24 +0000 Received: by mail-io1-f47.google.com with SMTP id e144so21232249iof.3 for ; Mon, 08 Nov 2021 17:31:24 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:from:date:message-id:subject:to; bh=eMqtBcSpXnWzn213/1Ibz02sry5V1og7Utw8k1bp81w=; b=MOka8smY4ULD+SK5/6IiFVaPGg6typAaHbgiVaYtJ1nSOLL6eSatLkIti+fAFpNgpz 17RYUKFXyxGMtU2Aw/N3V2ONi0UaPiD0xL/78KddvY6NIjXF0KaykR4/DmF9kAZT8ZKI ViukHCdqfnOzOrjI9p/8yr35m40zkHAusu+yrqSt1bBuWrOzh3QYGCOn8LfHosmH90Kw Ingz67cEXB8UjyzFf1EYxksSH0RLJ0POTRl5nBDxE1bTbDw2JqSNc+LX+Y6RDt11GFac s6V4fICMm7KQeWsTOBGHNECMzaTnS5fffQ6v6q1vHTBtZEgSlIRkruBAK6aB4AovccYv PXEQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=eMqtBcSpXnWzn213/1Ibz02sry5V1og7Utw8k1bp81w=; b=BUAwoiI6CEKwdfEdN8bv7/PAZxZ0wAjWBFgwr77fEgtJoOBpPW4bFAEyhhH0YUVCGA dRI2Q5O+GzjYBfALr5pjds1tLfdPYt5bTFzz50kzGcIqmFJD1Nn8G4UT0jRQ/CNgc1Qw 0ucAMdV3GLtGVVPSp8azhNNUXt0wfpCYIBuyT67YaWl2U2QSHZqGHiioSRHxtCGFNARQ uKnf/F4uRhWaCWgmDhUtZ+9D1M8Xyqxxrgg5QYunp/O5KKZLFwpdbVdFj+fYlvO0iy0H ic8rfW/ZZjf6nTD/6EBa0dL9GRpglSiWDIG9EQOLAn+m+icp0UdRee85yKDHS+3sUTDe Ukxw== X-Gm-Message-State: AOAM531BCOoLz2c3VvwwuiIVpOcobJMvqowZj8v/WLeRAphaYfSxcx0S ENXWWNjDPoP7C2a5Yq8xznv8oTnOKRhsDoNGxxhLUYM+f2s= X-Google-Smtp-Source: ABdhPJzIdG6L4MydgwFEIP+vjw6P9a60JgJp+GFwcHpeBsE6V2oL5eC2IO29FEj+LZX5p1A+WfFo5IF6uo39KoUzdd4= X-Received: by 2002:a05:6638:358b:: with SMTP id v11mr2541745jal.53.1636421483671; Mon, 08 Nov 2021 17:31:23 -0800 (PST) MIME-Version: 1.0 From: Amir Zeb Date: Tue, 9 Nov 2021 10:31:12 +0900 Message-ID: Subject: namd-l: Why simulation running on linux is damn slow?? To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000003cb88e05d05111ff" X-CLX-Response: 1TFkXGxwbEQpMehcZHxkRCllEF3prYB9EQ0wbfEtPEQpYWBdoWUcSGQF8ZXJ HQREKeE4XY1Nja3sTWH4aX14RCnlMF2FLBR17fENHZGdHEQpDSBcHGxgdEQpDWRcHGB8bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4bcR8aEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3VQR0hoRml9c0FBaGNeXnUHbG9LeR5+dVBvHRxGRB58EQpYXBcfBBoEGB4b BRsaBBsbGgQdBBsZGRAbHhofGhEKXlkXc1wZe2IRCk1cFxsdGBEKTFoXaGlNTWsRCkxGF29ra2t raxEKQk8XelB4ZGtaUnJaRkYRCkNaFxgaEwQSHwQbHBwEHh0RCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXa0RzbhsYGWREX2gRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdoWUcSGQF8ZXJHQREKQmwXbnoYcHxFfGJ/G2kRCkJAF25QfGxLWxxvekNyEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXYGhFbVlBH3tLR1MRCllLFxMfEh8RCnBoF20 fRRh7WnNHTkcfEBkaEQpwaBdkAWlJSEhdchlmWRAZGhEKcGgXZk9NfF0aTGlDE1gQGRoRCnBoF2 BYZFofYX1Da39MEBkaEQpwaBdlZBt5QHNPcmtYTxAZGhEKcGwXZkVYaBpuXU5wbUQQGRoRCm1+F xsRClhNF0sRIA== X-Proofpoint-GUID: _zmbBlCWYkkBItt_-FEaS4T_zE76ln4V X-Proofpoint-ORIG-GUID: _zmbBlCWYkkBItt_-FEaS4T_zE76ln4V X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=161 mlxscore=0 lowpriorityscore=0 phishscore=0 impostorscore=0 suspectscore=0 bulkscore=0 spamscore=0 mlxlogscore=872 priorityscore=353 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111090004 domainage_hfrom=9585 X-Spam-Score: 0 X-Spam-OrigSender: zebamir85@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Amir Zeb --0000000000003cb88e05d05111ff Content-Type: text/plain; charset="UTF-8" Hello NAMD users, I have a system of ~250000 atoms and I want to run simulation for 100 ns. The time step is 2, so I put run = 50000000 in config file. It took 4 days and hardly completed 6400000 steps, this means it'll take >20 days to complete 100 ns simulation with this speed. The command I used is: namd2 +idle poll +p10 +devices 0 config. namd > xxx.log Details of my system: Linux, Ubuntu CPU(s) 40, online cups list 0-39, Core(s) per socket 10, Sockets 2, NVIDIA GM206 [GeForce GTX 960] (rev a1). but when I put the command nvidia-smi, it prints 'not found', but can be installed with: sudo aor install nvidia-340 and many others. Please let me know what should I do to speed up the simulation? kind regards Amir --0000000000003cb88e05d05111ff Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello NAMD users,
I have a system of ~25= 0000 atoms and I want to run simulation for 100 ns. The time step is 2, so = I put run =3D 50000000 in config file. It took 4 days and hardly completed = 6400000 steps, this means it'll take >20 days to complete 100 ns sim= ulation with this speed. The command I used is:=C2=A0
namd2 +idle poll +p10 +devices 0 config.
namd >= xxx.log
Details of my system:
Linux, Ubuntu
CPU(s) 40, online cups list 0-39, Co= re(s) per socket 10, Sockets 2,
=C2=A0NVIDIA GM206 [= GeForce GTX 960] (rev a1).
but when I put the comman= d nvidia-smi,
it prints 'not found', but can= be installed with: sudo aor install nvidia-340
and = many others.
Please let me know what should I do to = speed up the simulation?
kind regards

Amir

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Thread-Topic: namd-l: Why simulation running on linux is damn slow?? 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CH2PR11MB4342.namprd11.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 25c8465e-17bc-40ad-a56e-08d9a337e7c8 X-MS-Exchange-CrossTenant-originalarrivaltime: 09 Nov 2021 04:17:55.5931 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 5217e0e7-539d-4563-b1bf-7c6dcf074f91 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 1Ck+suqMHBvJLvGPo3SilEHFw9581UhmkH3uYZd0jWt3CX1wDEYCi4GIcfdD7z1I8RAdDAot8lnG7NaEs2mn8A== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR11MB4342 X-OriginatorOrg: utah.edu X-CFilter-Loop: Reflected X-CLX-Response: 1TFkXGxwcEQpMehcaEQpZRBdmXHxfXmEFehhbHhEKWFgXYWlneEx7f0h7WVI RCnhOF3p9S3NEf1xTXEcZEQp5TBd6QUxSXB1TGloFYxEKQ0gXBxsfGxEKQ1kXBxsdGBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseHHEfHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdOR10TT01EE2laQGhjTEhpbmlgXwdGYV14bU1QGlpldREKWFwXHwQaBBgeGwUb GgQbGxoEHQQbGRgQGx4aHxoRCl5ZF3NcH1l5EQpNXBcHHxkRCkxaF3xpTU1NEQpFWRdvEQpMXxd 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definitions=main-2111090022 domainage_hfrom=12747 X-Spam-Score: 0 X-Spam-OrigSender: u1304129@utah.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, HANNAH MARIE BURTON --_000_CH2PR11MB4342E257A22B0DDDCAA7E723E1929CH2PR11MB4342namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I have inherited an old system with preconfigured windows for that system, = where the previous owner is unsure how they generated these windows. I alre= ady have the windows I would like configured based on a previous simulation= but now have an updated starting structure. How would I go about making th= is starting structure to work with my current window configurations? I saw = that: The most common approach is to use an initial SMD pull to cover your reacti= on coordinate space (center =3D initial value, targetCenter =3D final value= ), and then pick frames from that pull to seed your umbrellas. But I cannot do this option, it would be far too difficult to implement as = there is a certain order of binding that needs to occur, and I am going to = be sampling roughly 400 different configurations. Essentially can I take my starting structure, apply a quick pulling simulat= ion to get my chlorides in the right position? How would I go about this? T= he tutorial files only have you pulling one thing all the way through via S= MD and that will not work for my system. I just want a way to pull the star= ting equlibrated structure into the window, and then be able to run product= ion on it after running a quick pulling simulation to get my chlorides in t= he right spot. Thanks, Hannah --_000_CH2PR11MB4342E257A22B0DDDCAA7E723E1929CH2PR11MB4342namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello, 
I have inherited an old system with preconfigured windows for that system, = where the previous owner is unsure how they generated these windows. I alre= ady have the windows I would like configured based on a previous simulation= but now have an updated starting structure. How would I go about making this starting structure to work wit= h my current window configurations? I saw that: 

The most common approach is to= use an initial SMD pull to cover your reaction coordinate space (center = =3D initial value, targetCenter =3D final value), and then pick frames from that pull to seed your umbrellas. 

But I cannot do this option, it would be far too difficult to implement as = there is a certain order of binding that needs to occur, and I am going to = be sampling roughly 400 different configurations. 
Essentially can I take my starting structure, apply a quick pulling simulat= ion to get my chlorides in the right position? How would I go about this? T= he tutorial files only have you pulling one thing all the way through via S= MD and that will not work for my system. I just want a way to pull the starting equlibrated structure into = the window, and then be able to run production on it after running a quick = pulling simulation to get my chlorides in the right spot. 

Thanks,
Hannah
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Thread-Topic: namd-l: Why simulation running on linux is damn slow?? 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X-Google-Smtp-Source: ABdhPJwpT8PqYV7b385ZC+qj98/38nJJ7mIEAgUwNfERaDE+Vigm3pvB8I/emULwLg3RQMR71N0klpFtoqj2taG56AQ= X-Received: by 2002:ac2:4bc1:: with SMTP id o1mr253825lfq.553.1636556534236; Wed, 10 Nov 2021 07:02:14 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: Natalia Ostrowska Date: Wed, 10 Nov 2021 16:02:01 +0100 Message-ID: Subject: Re: namd-l: Why simulation running on linux is damn slow?? To: NAMD Mailing-list , Amir Zeb Content-Type: multipart/alternative; boundary="000000000000e0e8a505d0708219" X-CLX-Response: 1TFkXGxIZEQpMehcbHBwRCllEF21fHUlIHGdCR0JiEQpYWBdte3J+Z2VZQmh nRREKeE4XYxNfR2R6Y3tEbmwRCnlMF2xQSRMBT2RmRh9mEQpDSBcHGRMbEQpDWRcHGxkdEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwZcR4YEBp3BhgaBhoRClleF2hjeREKSUYXX0NfS XVCRVleT04RCkNOF31ZEml1RGFwT3hNUhppcBhwbBsHG3MeQ2dLS0tAH2dsEQpYXBcfBBoEGB4b BRsaBBsaGgQdBBseGRAbHhofGhEKXlkXc11zZXwRCk1cFxgeEQpMWhd/aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2JkT10eZHxNX1JcEQpDWhcYGhMEEh8EGxwdBB4bEQ pCXhcbEQpEXhcYEQpCRRdnZR8eGUhIGWh5YREKQk4XYxNfR2R6Y3tEbmwRCkJMF217cn5nZVlCa GdFEQpCbBdkG2hARn9NWxxIYREKQkAXYE9kRBtPeFhbeWQRCkJYF2dzZXNAbmFhTF1iEQpNXhcb EQpaWBcbEQp5QxdgQV1oUEAZGGJMSBEKcGcXbmJFG3gZclBgSEgQHhIRCnBoF29jaV5zTnlIW0B dEBkaEQpwaBdkAWlJSEhdchlmWRAZGhEKcGgXZk9NfF0aTGlDE1gQGRoRCnBoF2ZgZEZBb01CEk YcEBkaEQpwaBdhUE9MRx0fTlxAHhAZGhEKcGwXaWR6f0weQxhpThIQGRoRCnBMF2RGaHxvXXJIU EFoEBkaEQptfhcbEQpYTRdLESA= X-Proofpoint-GUID: Ws8C_nKZeRgx0CZ2ZF1-1Y4iMaaaj5MF X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: Ws8C_nKZeRgx0CZ2ZF1-1Y4iMaaaj5MF X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 impostorscore=0 malwarescore=0 bulkscore=0 priorityscore=166 mlxscore=0 spamscore=0 mlxlogscore=999 clxscore=183 phishscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100079 X-Spam-Score: 0 X-Spam-OrigSender: n.ostrowska@cent.uw.edu.pl X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Natalia Ostrowska --000000000000e0e8a505d0708219 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi, I have ran simulations of around this size on comparable setup and >20 days is completely normal - use this time to do stuff that you will have to do anyway, like writing analysis scripts etc. (applying for a grant at the supercomputing center would be a good idea too :P) Remember to download fragments of the trajectory every once in a while and have a look at the system in vmd - so if something goes wrong you would spot it as early as possible Regards, Natalia Ostrowska Univeristy of Warsaw, Poland Centre of New Technologies Biomolecular Machines Laboratory wt., 9 lis 2021 o 02:33 Amir Zeb napisa=C5=82(a): > Hello NAMD users, > I have a system of ~250000 atoms and I want to run simulation for 100 ns. > The time step is 2, so I put run =3D 50000000 in config file. It took 4 d= ays > and hardly completed 6400000 steps, this means it'll take >20 days to > complete 100 ns simulation with this speed. The command I used is: > namd2 +idle poll +p10 +devices 0 config. > namd > xxx.log > Details of my system: > Linux, Ubuntu > CPU(s) 40, online cups list 0-39, Core(s) per socket 10, Sockets 2, > NVIDIA GM206 [GeForce GTX 960] (rev a1). > but when I put the command nvidia-smi, > it prints 'not found', but can be installed with: sudo aor install > nvidia-340 > and many others. > Please let me know what should I do to speed up the simulation? > kind regards > > Amir > > --000000000000e0e8a505d0708219 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
I have ran simulations of around this siz= e on comparable setup and >20 days is completely normal - use this time = to do stuff that you will have to do anyway, like writing analysis scripts = etc. (applying for a grant at the supercomputing center would be a good ide= a too :P)

Remember to download fragments of the trajectory eve= ry once in a while and have a look at the system in vmd - so if something g= oes wrong you would spot it as early as possible

Regards,
Natalia Ostrowska=
Univeristy of Warsaw, Poland
Centre of New Technologies
Biomolecular Machines Laboratory


wt., 9 lis 2021 o 02:33=C2=A0Amir Zeb <zebamir85@gmail.com> napisa=C5=82(a):
Hello NAMD users,I have a system of ~250000 atoms and I want to run simulati= on for 100 ns. The time step is 2, so I put run =3D 50000000 in config file= . It took 4 days and hardly completed 6400000 steps, this means it'll t= ake >20 days to complete 100 ns simulation with this speed. The command = I used is:=C2=A0
namd2 +idle poll +p10 +devices 0 co= nfig.
namd > xxx.log
Detai= ls of my system:
Linux, Ubuntu
CPU(s) 40, online cups list 0-39, Core(s) per socket 10, Sockets 2,
=
=C2=A0NVIDIA GM206 [GeForce GTX 960] (rev a1).
but when I put the command nvidia-smi,
= it prints 'not found', but can be installed with: sudo aor install = nvidia-340
and many others.
P= lease let me know what should I do to speed up the simulation?
kind regards

= Amir

--000000000000e0e8a505d0708219-- From owner-namd-l@halifax.ks.uiuc.edu Wed Nov 10 10:26:18 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AAGQI6a017154; Wed, 10 Nov 2021 10:26:18 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AAGQH1C017153; Wed, 10 Nov 2021 10:26:17 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AAGQHOP017149; Wed, 10 Nov 2021 10:26:17 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AAGQHvX017148; Wed, 10 Nov 2021 10:26:17 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AAGQ8eT017141 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 10 Nov 2021 10:26:09 -0600 (CST) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AAGKQaQ022814 for ; Wed, 10 Nov 2021 16:26:08 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=fcoppo3@uic.edu; dkim=pass header.s=google header.d=uic.edu Received: from mail-ed1-f46.google.com (mail-ed1-f46.google.com [209.85.208.46]) by mx0a-00007101.pphosted.com with ESMTP id 3c8drjt4w2-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 10 Nov 2021 16:26:08 +0000 Received: by mail-ed1-f46.google.com with SMTP id r12so12817243edt.6 for ; Wed, 10 Nov 2021 08:26:07 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=uic.edu; s=google; h=mime-version:from:date:message-id:subject:to; bh=GpKVQBr0MJjNHa2zFwFYttWVFw38+UCaAc/CNRWSj/4=; b=BtHS/boFpZHm8//R3hz8WAo7dcIjSE0FY22I8SzHYBWEUgujypD4NLRhJNYyZLPl/I 5n2P9mAE9sLdK45+7I0HYukFiZBdZq1wmN8MZEkBEd5Wgq0pJtWVUcTsOMKiAHDHcEa0 RTaVzMDlG37k8PVpKLS7pYRdqH3y3bJgtCIUWznFoZXiHd/kpqE39NCpdfHpsm+vjobB t6H9W30aZuEfJe7nR4H/X60K05lnFOeIDFFIq0xO14GmiNEYPDl6aeZHEEH9hRdWytXl 9YNWnKXuExZS8cg3Y9JhNtKOEYGIelcZzl6XU6YZFV181JqKQkPurVWSr5ueMI1InzFy rInA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=GpKVQBr0MJjNHa2zFwFYttWVFw38+UCaAc/CNRWSj/4=; b=Zg4ih8rENKgiZ0VhFjhwMYz2vnNref4KRZFE/aJLg7TXjVIXiTRWsxsQF2JBp2wHOr x8jLuXf2uUjvkuOIH6yUgGzHiJDkomx9s+ggVUsl4eOujjxpCcP+EYPwnQj1vf15RZwo 5CAQV2irIT1B9NsENK8787QcWbv5ldPyAIgCr7fYAu6hk3UpRsUp1MHSlpHyteJAWVQ/ rBZfEIAijzCfIp7GLpWJPWM2vGB7IWUb6Bpy+p7Eq2cpc0I5hIrqcU2fTV0zDSwcrTvE fGM2QmdlJF3uPSi5XI8XWFCH4MtoyCNDifcLsezzZZT//uTTSmfT6EOx882vcPBDAFBl dnfQ== X-Gm-Message-State: AOAM531VKbqfukRS4mFc+UyVWZxjzKgDP8NISK4G9pt55QU0MF92pnjN YpKGrIVOGOsa8v3jQky4R5zTZBHEYsgDdVUZD335mbibCLMJNQ== X-Google-Smtp-Source: ABdhPJy0epLGpQp01/FCOWMJKy2H5WmzeuVuGOOugONp7MrjmZzqvj8Le4mRhOkxguDilddtsuEbOF8aP9nkdu/mWXs= X-Received: by 2002:a17:906:2749:: with SMTP id a9mr341330ejd.471.1636561558895; Wed, 10 Nov 2021 08:25:58 -0800 (PST) MIME-Version: 1.0 From: Francesco Coppola Date: Wed, 10 Nov 2021 10:25:47 -0600 Message-ID: Subject: namd-l: Protein simulations: why does the structure change so much? To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000005f16f705d071ae2e" X-CLX-Response: 1TFkXGBofEQpMehcbGBkRCllEF2ZDWV5fTGxae2ABEQpYWBdkekBYbVJNRUV FWhEKeE4Xbh1yGWIeYF1pUksRCnlMF2d9TnhgQXJeEnNZEQpDSBcHGBgcEQpDWRcHGxwcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIfcRsZEhAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThd9fm1+YhgSThleSWdoeFpeW39raWtEe3pTZnh5HwceXhEKWFwXHwQaBBge GwUbGgQbGhoEHQQbHhkQGx4aHxoRCl5ZF3NdcEkdEQpNXBcbGRkRCkxaF2xpTU1rEQpMRhdva2t ra2sRCkJPF24cZx1ZcmdmXkhyEQpDWhcYGhMEEh8EGBoSBB4cEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxduHXIZYh5gXWlSSxEKQkkXbh1yGWIeYF1pUksRCkJFF25cBVNOaVIcck4dEQpCThduHXIZY h5gXWlSSxEKQkwXZHpAWG1STUVFRVoRCkJsF3pmGVNFTUdnBV56EQpCQBdlaW1lS09keFsTcBEK QlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2lTWmh8X31/BXNyEQpwaBdpE01peGxjTkE bHxAZGhEKcGgXYU1mU3tAUxpJa2cQGRoRCnBoF2hsBUMYRhNaAWsdEBkaEQpwaBdvehwZWXBBZR pvfRAZGhEKcGgXbkJzcB9Zb0RIRkQQGRoRCnBsF2Zyc017X3xyRh99EBkaEQptfhcbEQpYTRdLE SA= X-Proofpoint-GUID: WTGTH28d3tcMBRptqUACAnQPyLRS5-4t X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: WTGTH28d3tcMBRptqUACAnQPyLRS5-4t X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 impostorscore=0 malwarescore=0 bulkscore=0 priorityscore=123 mlxscore=0 spamscore=0 mlxlogscore=422 clxscore=205 phishscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100084 X-Spam-Score: 0 X-Spam-OrigSender: fcoppo3@uic.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Coppola --0000000000005f16f705d071ae2e Content-Type: text/plain; charset="UTF-8" Hi, I am writing to understand if it is normal that from the crystallographic structure (pdb structure on protein data bank) to the final structure after my simulation, that the protein changes conformation without returning to the initial one. I tried to change damping in my parameter file, but this doesn't seem to change the result much, as well as the timestep to 1fs instead of 2. There are some parameters that I particularly need to keep in mind when simulating proteins that can affect and create errors in my simulation? In particular the problem is related to a binding pocket that I am trying to examine since I would like to combine them with docking analysis (where the simulation conditions are very different). Thank you so much for your attention and time! Have a good day! Best regards, Francesco Coppola --0000000000005f16f705d071ae2e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I am writing to understand if it is normal= that from the crystallographic structure (pdb structure on protein data ba= nk) to the final structure after my simulation, that the protein changes co= nformation without returning to the initial one. I tried to change damping = in my parameter file, but this doesn't seem to change the result much, = as well as the timestep to 1fs instead of 2.

= There are some parameters that I particularly need to keep in mind when sim= ulating proteins that can affect and create errors in my simulation?
<= br>
In particular the problem is related to a binding pocket that I am = trying to examine since I would like to combine them with docking analysis = (where the simulation conditions are very different).

Thank you so much for your attention and time!
Have a go= od day!

Best regards,
Francesco Coppola<= /div>
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charset="UTF-8" Thanks for all your help. In the slurm output I am getting the following error which I am unable to understand. I have been trying several changes in input files to get the job running but still getting some errors. If you have some insight kindly suggest. FATAL ERROR: Setting parameter colvars from script failed! FATAL ERROR: Setting parameter colvars from script failed! The output file ends like this TCL: Running for 20 steps ENERGY: 6100 228438.5351 32958.7464 51721.4945 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 374233.1041 -936367.4549 298.0237 -1310600.5589 -934162.1854 295.8515 1073.5139 16.7110 4799315.6868 55.7822 1.3010 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100 WRITING COORDINATES TO RESTART FILE AT STEP 6100 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 6100 FINISHED WRITING RESTART VELOCITIES TCL: Setting parameter langevinTemp to 300 REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN. TCL: Running for 20 steps ENERGY: 6100 228438.5351 32958.7464 51721.4945 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 377307.1621 -933293.3968 300.4717 -1310600.5589 -931093.1616 300.4717 1103.2400 25.8758 4799315.6868 1103.2400 25.8758 TCL: Setting parameter colvars to on FATAL ERROR: Setting parameter colvars from script failed! Many thanks, Ashutosh On Thu, Nov 4, 2021 at 11:43 PM Michael Robinson < michael.robinson1@monash.edu> wrote: > Hi Ashutosh, > > I suspect that won't be the first error in the log file - that's normally > something that happens after an initial error. If that's not the case, look > at the output of the supercomputer you were using to run it (something like > a SLURM output) to see if that caused it. > > Cheers, > Michael > > On Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, > wrote: > >> I am running ABF with namd but it stopped abruptly after some thousand >> steps. The error file gave following error. I looked online but didn't find >> any conclusive answer. >> >> User defined signal 2 >> ERROR: One or more process (first noticed rank 8) terminated with signal >> 12 >> >> What could be the problem? >> >> Many thanks, >> Ashutosh >> >> On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya >> wrote: >> >>> Many thanks, it works now. >>> >>> Regards, >>> Ashutosh >>> >>> On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson < >>> michael.robinson1@monash.edu> wrote: >>> >>>> Hi Ashutosh, >>>> >>>> Your input file has a line break between 'abf' and the curly bracket >>>> '{' that opens the configuration block - this is causing the ABF >>>> configuration block to be skipped, and so your input file is failing. I >>>> can't test your given file without the associated system, but I >>>> double-checked that this would occur with one of my own ABF input files, >>>> and this caused the same error. >>>> >>>> Hopefully that helps, >>>> Regards, >>>> Michael Robinson >>>> >>>> On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya >>>> wrote: >>>> >>>>> Hi All >>>>> I want to run eABF with namd and I am getting following errors >>>>> >>>>> colvars: Collective variables initialized, 2 in total. >>>>> colvars: Error: keyword "abf" found without configuration. >>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>> details) >>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>> details). >>>>> >>>>> I was able to run collective variables but when trying to run eABF it >>>>> gives an error. Kindly have a look at the attached input file and suggest. >>>>> >>>>> Many thanks >>>>> >>>>> --000000000000a3eb3805d071ee7c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thanks for all your help. In the slurm output I am ge= tting the following error which I am unable to understand. I have been tryi= ng several changes in input files to get the job running but still getting = some errors. If you have some insight kindly suggest.

FATAL ERROR: Setting parameter colvars from script failed!
=C2= =A0
FATAL ERROR: Setting parameter colvars from script failed!

The output file ends like this
TCL: Running for = 20 steps
ENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2= =A0 32958.7464 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 = =C2=A0 =C2=A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0374233= .1041 =C2=A0 =C2=A0 =C2=A0 =C2=A0-936367.4549 =C2=A0 =C2=A0 =C2=A0 298.0237= =C2=A0-1310600.5589 =C2=A0 -934162.1854 =C2=A0 =C2=A0 =C2=A0 295.8515 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1073.5139 =C2=A0 =C2=A0 =C2=A0 =C2=A016.711= 0 =C2=A0 4799315.6868 =C2=A0 =C2=A0 =C2=A0 =C2=A055.7822 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 1.3010

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 61= 00
WRITING COORDINATES TO RESTART FILE AT STEP 6100
FINISHED WRITING = RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 6100
F= INISHED WRITING RESTART VELOCITIES
TCL: Setting parameter langevinTemp t= o 300
REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN.
TCL: Runn= ing for 20 steps
ENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2= =A0 =C2=A0 32958.7464 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = 0.0000 =C2=A0 =C2=A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0377307.1621 =C2=A0 =C2=A0 =C2=A0 =C2=A0-933293.3968 =C2=A0 =C2=A0 =C2=A0= 300.4717 =C2=A0-1310600.5589 =C2=A0 -931093.1616 =C2=A0 =C2=A0 =C2=A0 300.= 4717 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1103.2400 =C2=A0 =C2=A0 =C2=A0 =C2= =A025.8758 =C2=A0 4799315.6868 =C2=A0 =C2=A0 =C2=A01103.2400 =C2=A0 =C2=A0 = =C2=A0 =C2=A025.8758

TCL: Setting parameter colvars to on
FATAL E= RROR: Setting parameter colvars from script failed!


Many thanks,
Ashutosh

On Thu, Nov 4, 20= 21 at 11:43 PM Michael Robinson <michael.robinson1@monash.edu> wrote:
Hi Ashutosh,

I suspect that won't be the first= error in the log file - that's normally something that happens after a= n initial error. If that's not the case, look at the output of the supe= rcomputer you were using to run it (something like a SLURM output) to see i= f that caused it.

Cheers= ,=C2=A0
Michael

On Thu, 4 Nov. 2021, 2:38 am As= hutosh Shandilya, <scfbioiitd@gmail.com> wrote:
I am running ABF with namd b= ut it stopped abruptly after some thousand steps. The error file gave follo= wing error. I looked online but didn't find any conclusive answer.
=

User defined signal 2
ERROR: =C2=A0One = or more process (first noticed rank 8) terminated with signal 12
=
What could be the problem?

Many tha= nks,
Ashutosh

On Thu, Oct 28, 2021 at 2:20 PM Ashutosh S= handilya <scfbioiitd@gmail.com> wrote:
Many thanks, it wo= rks now.

Regards,
Ashutosh

On W= ed, Oct 27, 2021 at 8:28 PM Michael Robinson <michael.robinson= 1@monash.edu> wrote:
Hi Ashutosh,

You= r input file has a line break between 'abf' and the curly bracket &= #39;{' that opens the configuration block - this is causing the ABF con= figuration block to be skipped, and so your input file is failing. I can= 9;t test your given file without the associated system, but I double-checke= d that this would occur with one of my own ABF input files, and this caused= the same error.

Hopefully that helps,
<= div>Regards,
Michael Robinson

On Thu, 28 Oct 2021 at 06:= 56, Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex">
Hi A= ll
I want to run eABF with namd and I am getting following errors=

colvars: Collective variables initialized, 2= in total.
colvars: Error: keyword "abf" found without configu= ration.
FATAL ERROR: Error in the collective variables module (see above= for details)
FATAL ERROR: Error in the collective variables module (see= above for details).

I was able to run collective = variables but when trying to run eABF it gives an error. Kindly have a look= at the attached input file and suggest.

Many than= ks

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charset="UTF-8" Hi Ashutosh, the "colvars" keyword is an ordinary NAMD configuration keyword, not a Tcl command. It's a bit like "constraints" in this regard, which would give you a similar error message if you added it late in the NAMD script. Just put "colvars on" early in the NAMD script before any run command, or other commands that trigger the Tcl interpreter. You're not required to add any Colvars configuration even with "colvars on". Giacomo On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya wrote: > Thanks for all your help. In the slurm output I am getting the following > error which I am unable to understand. I have been trying several changes > in input files to get the job running but still getting some errors. If you > have some insight kindly suggest. > > FATAL ERROR: Setting parameter colvars from script failed! > > FATAL ERROR: Setting parameter colvars from script failed! > > The output file ends like this > TCL: Running for 20 steps > ENERGY: 6100 228438.5351 32958.7464 51721.4945 > 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 > 374233.1041 -936367.4549 298.0237 -1310600.5589 > -934162.1854 295.8515 1073.5139 16.7110 > 4799315.6868 55.7822 1.3010 > > WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100 > WRITING COORDINATES TO RESTART FILE AT STEP 6100 > FINISHED WRITING RESTART COORDINATES > WRITING VELOCITIES TO RESTART FILE AT STEP 6100 > FINISHED WRITING RESTART VELOCITIES > TCL: Setting parameter langevinTemp to 300 > REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN. > TCL: Running for 20 steps > ENERGY: 6100 228438.5351 32958.7464 51721.4945 > 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 > 377307.1621 -933293.3968 300.4717 -1310600.5589 > -931093.1616 300.4717 1103.2400 25.8758 > 4799315.6868 1103.2400 25.8758 > > TCL: Setting parameter colvars to on > FATAL ERROR: Setting parameter colvars from script failed! > > > Many thanks, > Ashutosh > > On Thu, Nov 4, 2021 at 11:43 PM Michael Robinson < > michael.robinson1@monash.edu> wrote: > >> Hi Ashutosh, >> >> I suspect that won't be the first error in the log file - that's normally >> something that happens after an initial error. If that's not the case, look >> at the output of the supercomputer you were using to run it (something like >> a SLURM output) to see if that caused it. >> >> Cheers, >> Michael >> >> On Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, >> wrote: >> >>> I am running ABF with namd but it stopped abruptly after some thousand >>> steps. The error file gave following error. I looked online but didn't find >>> any conclusive answer. >>> >>> User defined signal 2 >>> ERROR: One or more process (first noticed rank 8) terminated with >>> signal 12 >>> >>> What could be the problem? >>> >>> Many thanks, >>> Ashutosh >>> >>> On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya >>> wrote: >>> >>>> Many thanks, it works now. >>>> >>>> Regards, >>>> Ashutosh >>>> >>>> On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson < >>>> michael.robinson1@monash.edu> wrote: >>>> >>>>> Hi Ashutosh, >>>>> >>>>> Your input file has a line break between 'abf' and the curly bracket >>>>> '{' that opens the configuration block - this is causing the ABF >>>>> configuration block to be skipped, and so your input file is failing. I >>>>> can't test your given file without the associated system, but I >>>>> double-checked that this would occur with one of my own ABF input files, >>>>> and this caused the same error. >>>>> >>>>> Hopefully that helps, >>>>> Regards, >>>>> Michael Robinson >>>>> >>>>> On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya >>>>> wrote: >>>>> >>>>>> Hi All >>>>>> I want to run eABF with namd and I am getting following errors >>>>>> >>>>>> colvars: Collective variables initialized, 2 in total. >>>>>> colvars: Error: keyword "abf" found without configuration. >>>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>>> details) >>>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>>> details). >>>>>> >>>>>> I was able to run collective variables but when trying to run eABF it >>>>>> gives an error. Kindly have a look at the attached input file and suggest. >>>>>> >>>>>> Many thanks >>>>>> >>>>>> --0000000000008a788305d0725097 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Ashutosh, the "colvars" keyword=C2=A0is an or= dinary NAMD configuration keyword, not a Tcl command.=C2=A0 It's a bit = like "constraints" in this regard, which would=C2=A0give you a si= milar error message if you added it late in the NAMD script.

=
Just put "colvars on" early in the NAMD script before any ru= n command, or other commands that trigger the Tcl interpreter.=C2=A0 You= 9;re not required to add any Colvars configuration even with "colvars = on".

Giacomo

On Wed, Nov 10, 2021 at 11:= 45 AM Ashutosh Shandilya <scfbio= iitd@gmail.com> wrote:
Thanks for all your help. In the slurm = output I am getting the following error which I am unable to understand. I = have been trying several changes in input files to get the job running but = still getting some errors. If you have some insight kindly suggest.

FATAL ERROR: Setting parameter colvars from script fa= iled!
=C2=A0
FATAL ERROR: Setting parameter colvars from script fail= ed!

The output file ends like this
TCL: = Running for 20 steps
ENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 = =C2=A0 =C2=A0 32958.7464 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 = =C2=A0374233.1041 =C2=A0 =C2=A0 =C2=A0 =C2=A0-936367.4549 =C2=A0 =C2=A0 =C2= =A0 298.0237 =C2=A0-1310600.5589 =C2=A0 -934162.1854 =C2=A0 =C2=A0 =C2=A0 2= 95.8515 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1073.5139 =C2=A0 =C2=A0 =C2=A0 = =C2=A016.7110 =C2=A0 4799315.6868 =C2=A0 =C2=A0 =C2=A0 =C2=A055.7822 =C2=A0= =C2=A0 =C2=A0 =C2=A0 1.3010

WRITING EXTENDED SYSTEM TO RESTART FILE= AT STEP 6100
WRITING COORDINATES TO RESTART FILE AT STEP 6100
FINISH= ED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STE= P 6100
FINISHED WRITING RESTART VELOCITIES
TCL: Setting parameter lan= gevinTemp to 300
REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN.TCL: Running for 20 steps
ENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A022843= 8.5351 =C2=A0 =C2=A0 32958.7464 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.20= 61 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 = =C2=A0 =C2=A0377307.1621 =C2=A0 =C2=A0 =C2=A0 =C2=A0-933293.3968 =C2=A0 =C2= =A0 =C2=A0 300.4717 =C2=A0-1310600.5589 =C2=A0 -931093.1616 =C2=A0 =C2=A0 = =C2=A0 300.4717 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1103.2400 =C2=A0 =C2=A0 = =C2=A0 =C2=A025.8758 =C2=A0 4799315.6868 =C2=A0 =C2=A0 =C2=A01103.2400 =C2= =A0 =C2=A0 =C2=A0 =C2=A025.8758

TCL: Setting parameter colvars to on=
FATAL ERROR: Setting parameter colvars from script failed!

Many thanks,
Ashutosh
=
On Thu= , Nov 4, 2021 at 11:43 PM Michael Robinson <michael.robinson1@monash.edu> = wrote:
Hi Ashutosh,

I suspe= ct that won't be the first error in the log file - that's normally = something that happens after an initial error. If that's not the case, = look at the output of the supercomputer you were using to run it (something= like a SLURM output) to see if that caused it.

=
Cheers,=C2=A0
Michael
<= /div>
O= n Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, <scfbioiitd@gmail.com> wrote:
<= /div>
I am running ABF with namd but it stopped abruptly after some thousand st= eps. The error file gave following error. I looked online but didn't fi= nd any conclusive answer.

User defined signal= 2
ERROR: =C2=A0One or more process (first noticed rank 8) termin= ated with signal 12

What could be the problem?

Many thanks,
Ashutosh

On Thu, Oct = 28, 2021 at 2:20 PM Ashutosh Shandilya <scfbioiitd@gmail.com> w= rote:
Many thanks, it works now.

Regards,<= /div>
Ashutosh

On Wed, Oct 27, 2021 at 8:28 PM Michael Robin= son <michael.robinson1@monash.edu> wrote:
Hi Ashu= tosh,

Your input file has a line break between = 9;abf' and the curly bracket '{' that opens the configuration b= lock - this is causing the ABF configuration block to be skipped, and so yo= ur input file is failing. I can't test your given file without the asso= ciated system, but I double-checked that this would occur with one of my ow= n ABF input files, and this caused the same error.

Hopefully that helps,
Regards,
Michael Robinson

On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya <scfbioiitd@g= mail.com> wrote:
Hi All
I want to run eABF with namd= and I am getting following errors

colvars: C= ollective variables initialized, 2 in total.
colvars: Error: keyword &qu= ot;abf" found without configuration.
FATAL ERROR: Error in the coll= ective variables module (see above for details)
FATAL ERROR: Error in th= e collective variables module (see above for details).

=
I was able to run collective variables but when trying to run eABF it = gives an error. Kindly have a look at the attached input file and suggest.<= /div>

Many thanks

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([2001:1388:3cc2:65a1:100b:b46f:23bb:2ab6]) by smtp.gmail.com with ESMTPSA id t1sm463092vkl.56.2021.11.10.10.59.14 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Wed, 10 Nov 2021 10:59:15 -0800 (PST) From: =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= Content-Type: multipart/alternative; boundary="Apple-Mail=_CA1F8318-CB92-41A2-BD86-35AEA7C7A0C9" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.7\)) Subject: namd-l: Colvar Flat-bottom potential "distanceXY" Message-Id: <2D9EC077-4DAD-41F8-80F1-9A3903BC81FE@gmail.com> Date: Wed, 10 Nov 2021 13:59:45 -0500 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3608.120.23.2.7) X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcZHxkRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGR4TEQpDWRcHEh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxtxGRsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWhJdR2ZGZBtTf3JnRUVHUBhiWBJ8c019TU1sEkBJR3ARClhcFx8EGgQYHhsF GxoEGxsaBB0EGxkZEBseGh8aEQpeWRdzXUhZTBEKTVwXGxISEQpMWhdoaU1NaxEKTEYXb29ra2t raxEKQk8XYGRrH2dEGHBmGFoRCkNaFxgaEwQSHwQYGBgEHhMRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXY2x5Y316fmFGT2YRCkJOF2NTY2t7E 1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwXb09kQVpCUG1ma1kRCkJAF2VcZ1BpWxt7ZVl6EQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXZRtNfWd7SWVPHH8RCllLFxMfEhwRCnBoF2M eRR9kSWITXWQfEBkaEQpwaBdnHFoYeh8bQF1sYBAZGhEKcGgXb0RlRRpNW1lDW3kQGRoRCnBoF2 FceG5AT2QYYmZAEBkaEQpwaBdnaGBzYnlHeV19UBAZGhEKcGwXaWEBf0lme0IZeh4QGRoRCm1+F xsRClhNF0sRIA== X-Proofpoint-GUID: p8wmLlN1yUXMoomz2Hr8VYgWggF8jcmZ X-Proofpoint-ORIG-GUID: p8wmLlN1yUXMoomz2Hr8VYgWggF8jcmZ X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 mlxscore=0 clxscore=171 priorityscore=353 bulkscore=0 impostorscore=0 lowpriorityscore=0 mlxlogscore=462 spamscore=0 phishscore=0 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100094 domainage_hfrom=9586 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= --Apple-Mail=_CA1F8318-CB92-41A2-BD86-35AEA7C7A0C9 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear users, I'm pulling in the direction of Z, so I want to apply harmicWalls so = that the protein confines in a certain radius, but I don't really = understand what values =E2=80=8B=E2=80=8Bto give to lowwall and = upperwall my protein has as COM in Z 6.4 nm and as maximum length in xy and 6.2 = nm, and my colvar is "distanceXY" the radius could be 5.7 nm (0.5 nm less than the original length) best, Geo.= --Apple-Mail=_CA1F8318-CB92-41A2-BD86-35AEA7C7A0C9 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Dear users,

I'm pulling in the direction of Z, so I want to apply = harmicWalls so that the protein confines in a certain radius, but I = don't really understand what values =E2=80=8B=E2=80=8Bto give to lowwall = and upperwall

my protein has as = COM in Z 6.4 nm and as maximum length in xy and 6.2 nm, and my colvar is = "distanceXY"

the radius could = be 5.7 nm (0.5 nm less than the original length)

best,

Geo.
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boundary="000000000000e46dd205d07439ee" X-Proofpoint-GUID: Ttt2GAP7Hd5JP_pOuPQrif4WXRsbxdFa X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: Ttt2GAP7Hd5JP_pOuPQrif4WXRsbxdFa X-CLX-Response: 1TFkXGxIbEQpMehcZGxgRCllEF2B/WlpNSHwbGhNrEQpYWBdpRxgaGmldZWJ 8ZhEKeE4XY1Nja3sTWH4aX14RCnlMF2RoSEhPHV9Zb0McEQpDSBcHExMRCkNZFwcfHhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscG3EeGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThd+Xl4YbWt6HWJOH2B6dVplX3p7WENMHn1yeFlIUk5sSxEKWFwXHwQaBBgeGwUb GgQbGhoEHQQbHh4QGx4aHxoRCl5ZF3NdSWJHEQpNXBcbGRMRCkxaF2xpTU1rEQpMRhdva2tra2s RCkJPF2Bkax9nRBhwZhhaEQpDWhcYGhMEEh8EGBgYBB4fEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2BlBW9tRk8SQXBOEQpCThdjU2NrexNYf hpfXhEKQkwXaUcYGhppXWVifGYRCkJsF29vc2B4TH59R1AfEQpCQBd6XG1Scn1PX0BwTREKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxkRCnlDF2d7R19ba2dCclMYEQpZSxcTHxIcEQpwaBdsUmd LWkNYfWJvaBAZGhEKcGgXaB5PHEMYeG1ub0IQGRoRCnBoF29HYElyBW9pHEQSEBkaEQpwaBdjf1 h4HW1gWh4FZxAZGhEKcGgXbHpee1hSQVpiE0EQGRoRCnB9F3oSflleZV1FZmFjEBkaEQpwfRdjb HlpXE18f0xMfhAZGhEKcH0XYFNfSQEZb1wBTVsQGRoRCnB/F25uaBoTHUNgH11tEBwfEQpwXxdh XhpBbFNZHhoZGRAZGhEKcF8XY054Y0lnT1ptcGkQGRoRCnBsF2F9cGF5AV5cQBtPEBkaEQptfhc bEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=2 malwarescore=0 clxscore=181 lowpriorityscore=0 adultscore=0 mlxlogscore=164 priorityscore=312 bulkscore=0 mlxscore=2 phishscore=0 suspectscore=0 impostorscore=0 spamscore=2 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100095 domainage_hfrom=9586 X-Spam-Score: 2 X-Spam-OrigSender: scinikhil@gmail.com X-Spam-Bar: * Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nikhil Maroli --000000000000e46dd205d07439ee Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear NAMD experts, Anyone can guide me on the precompiled version of namd Fujitsu A64FX CPU processor to use through MPI across the nodes? (https://urldefense.com/v3/__https://en.wikipedia.or= g/wiki/Fugaku_(supercomputer)__;!!DZ3fjg!pim3UankaL0dNIPeVC0BvToKoRx40dMykY= rHGMEK_sR2j5UF19CGZw_atGcH2xVy3A$ ). Or do i need to compile it from source? --=20 *Regards,* *-nikhil* --000000000000e46dd205d07439ee Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear NAMD experts,
Anyone can guide me on the pr= ecompiled version of namd Fujitsu=C2=A0A64FX=C2=A0CPU=C2=A0 processor to use through MPI = across the nodes?=C2=A0 (https://en.wikipedia.org/wik= i/Fugaku_(supercomputer)). Or do i need to compile it from source?=C2= =A0

--
Regards,
-nikhil
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boundary="0000000000004a11c505d0743988" X-Proofpoint-GUID: MzogJb7n_Zg85AoYpK8QgdSHAnuYbgsg X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: MzogJb7n_Zg85AoYpK8QgdSHAnuYbgsg X-CLX-Response: 1TFkXHhwZEQpMehcZGR0RCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHHx8bEQpDWRcHGxgbEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRccGXEZHAYZdwYbHxoGHhJCHgYaBhsaGgYbHBlxHhgQGncGGgYaB hoGBxwaBhoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF2dQRU1gSB1EdXBN Eh9rRXNaYRJ7TU55YmtEX3NITVlNEQpYXBcfBBoEGB4bBRsaBBsaGgQdBBseGRAbHhofGhEKXlk Xc11JYkkRCk1cFx8fGhEKTFoXe2lrTU0RCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbG trEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGwQeHBEKQl4XGxEKREkXGxEKQlwXGxEKX k4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdmWH1Ya0AaBXJEaBEKQk4X Y1Nja3sTWH4aX14RCkJMF2MfWXl5aR1PfFpaEQpCbBdvUmccckNJT1p+XREKQkAXa29CaxxHT0l 9aAERCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5Qxdnemx9ZR9IZkkdYxEKWUsXEx8SHBEKcGcXbV 1yY3hjQxNwHlwQHhIRCnBoF2ZfemBYch5bRUBYEBoRCnBoF25oW0YYHRtQX2EBEBoRCnBoF2VOG 3liH0IBBRNdEBkaEQpwaBdkWktpQ30daWlNSRAeEhEKcGgXem5iQW17GG9DenwQGhEKcGwXaHNS WXJnex97eUkQGRoRCnBMF21oZRlBUn17GEVSEBoRCm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=463 lowpriorityscore=0 adultscore=0 mlxlogscore=999 priorityscore=337 bulkscore=0 mlxscore=0 phishscore=0 suspectscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100095 domainage_hfrom=9586 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --0000000000004a11c505d0743988 Content-Type: text/plain; charset="UTF-8" I am getting this type of warning After running for 30000 steps it shows TIMING: 30700 CPU: 579.654, 0.0178402/step Wall: 583.7, 0.0179331/step, 0.126628 hours remaining, 0.000000 MB of memory in use. ENERGY: 30700 226234.5860 33319.1606 51301.2627 0.0000 -1814027.4858 224995.9113 0.0000 21.0432 376517.3497 -901638.1722 299.8428 -1278155.5219 -899427.3684 299.5875 1354.4689 44.7734 4458307.8773 0.5178 1.7157 *Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame* *Please check your configuration or increase restraint on z (*This warning comes earlier as well *)* Frame index: 49 ; optimal RMSD = 0.975194 Frame index: 51 ; optimal RMSD = 0.975811 Frame index: 50 ; optimal RMSD = 0.977496 Frame index: 47 ; optimal RMSD = 0.994026 Frame index: 48 ; optimal RMSD = 0.995694 Frame index: 44 ; optimal RMSD = 1.00065 Frame index: 43 ; optimal RMSD = 1.00377 Frame index: 42 ; optimal RMSD = 1.00561 Frame index: 46 ; optimal RMSD = 1.00608 Frame index: 41 ; optimal RMSD = 1.0122 Frame index: 45 ; optimal RMSD = 1.01242 Frame index: 39 ; optimal RMSD = 1.02401 Frame index: 40 ; optimal RMSD = 1.02975 Frame index: 52 ; optimal RMSD = 1.03208 Frame index: 36 ; optimal RMSD = 1.03932 Frame index: 37 ; optimal RMSD = 1.04629 ............ ................ Frame index: 88 ; optimal RMSD = 3.32354 Frame index: 89 ; optimal RMSD = 3.75411 Frame index: 90 ; optimal RMSD = 3.7904 Frame index: 91 ; optimal RMSD = 3.80612 Frame index: 92 ; optimal RMSD = 3.8282 Frame index: 93 ; optimal RMSD = 3.83528 Frame index: 94 ; optimal RMSD = 3.84841 Frame index: 95 ; optimal RMSD = 3.86218 Frame index: 96 ; optimal RMSD = 3.89656 Frame index: 97 ; optimal RMSD = 3.97904 Frame index: 98 ; optimal RMSD = 4.16712 Frame index: 99 ; optimal RMSD = 4.18738 The error file gave following error User defined signal 2 ERROR: One or more process (first noticed rank 8) terminated with signal 12 Kindly suggest, Ashutosh On Wed, Nov 10, 2021 at 12:11 PM Giacomo Fiorin wrote: > Hi Ashutosh, the "colvars" keyword is an ordinary NAMD configuration > keyword, not a Tcl command. It's a bit like "constraints" in this regard, > which would give you a similar error message if you added it late in the > NAMD script. > > Just put "colvars on" early in the NAMD script before any run command, or > other commands that trigger the Tcl interpreter. You're not required to > add any Colvars configuration even with "colvars on". > > Giacomo > > On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya > wrote: > >> Thanks for all your help. In the slurm output I am getting the following >> error which I am unable to understand. I have been trying several changes >> in input files to get the job running but still getting some errors. If you >> have some insight kindly suggest. >> >> FATAL ERROR: Setting parameter colvars from script failed! >> >> FATAL ERROR: Setting parameter colvars from script failed! >> >> The output file ends like this >> TCL: Running for 20 steps >> ENERGY: 6100 228438.5351 32958.7464 51721.4945 >> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 >> 374233.1041 -936367.4549 298.0237 -1310600.5589 >> -934162.1854 295.8515 1073.5139 16.7110 >> 4799315.6868 55.7822 1.3010 >> >> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100 >> WRITING COORDINATES TO RESTART FILE AT STEP 6100 >> FINISHED WRITING RESTART COORDINATES >> WRITING VELOCITIES TO RESTART FILE AT STEP 6100 >> FINISHED WRITING RESTART VELOCITIES >> TCL: Setting parameter langevinTemp to 300 >> REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN. >> TCL: Running for 20 steps >> ENERGY: 6100 228438.5351 32958.7464 51721.4945 >> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 >> 377307.1621 -933293.3968 300.4717 -1310600.5589 >> -931093.1616 300.4717 1103.2400 25.8758 >> 4799315.6868 1103.2400 25.8758 >> >> TCL: Setting parameter colvars to on >> FATAL ERROR: Setting parameter colvars from script failed! >> >> >> Many thanks, >> Ashutosh >> >> On Thu, Nov 4, 2021 at 11:43 PM Michael Robinson < >> michael.robinson1@monash.edu> wrote: >> >>> Hi Ashutosh, >>> >>> I suspect that won't be the first error in the log file - that's >>> normally something that happens after an initial error. If that's not the >>> case, look at the output of the supercomputer you were using to run it >>> (something like a SLURM output) to see if that caused it. >>> >>> Cheers, >>> Michael >>> >>> On Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, >>> wrote: >>> >>>> I am running ABF with namd but it stopped abruptly after some thousand >>>> steps. The error file gave following error. I looked online but didn't find >>>> any conclusive answer. >>>> >>>> User defined signal 2 >>>> ERROR: One or more process (first noticed rank 8) terminated with >>>> signal 12 >>>> >>>> What could be the problem? >>>> >>>> Many thanks, >>>> Ashutosh >>>> >>>> On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya < >>>> scfbioiitd@gmail.com> wrote: >>>> >>>>> Many thanks, it works now. >>>>> >>>>> Regards, >>>>> Ashutosh >>>>> >>>>> On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson < >>>>> michael.robinson1@monash.edu> wrote: >>>>> >>>>>> Hi Ashutosh, >>>>>> >>>>>> Your input file has a line break between 'abf' and the curly bracket >>>>>> '{' that opens the configuration block - this is causing the ABF >>>>>> configuration block to be skipped, and so your input file is failing. I >>>>>> can't test your given file without the associated system, but I >>>>>> double-checked that this would occur with one of my own ABF input files, >>>>>> and this caused the same error. >>>>>> >>>>>> Hopefully that helps, >>>>>> Regards, >>>>>> Michael Robinson >>>>>> >>>>>> On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya < >>>>>> scfbioiitd@gmail.com> wrote: >>>>>> >>>>>>> Hi All >>>>>>> I want to run eABF with namd and I am getting following errors >>>>>>> >>>>>>> colvars: Collective variables initialized, 2 in total. >>>>>>> colvars: Error: keyword "abf" found without configuration. >>>>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>>>> details) >>>>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>>>> details). >>>>>>> >>>>>>> I was able to run collective variables but when trying to run eABF >>>>>>> it gives an error. Kindly have a look at the attached input file and >>>>>>> suggest. >>>>>>> >>>>>>> Many thanks >>>>>>> >>>>>>> --0000000000004a11c505d0743988 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I am getting this type of warning

After= running for 30000 steps it shows
TIMING: 30700 =C2=A0CPU: 579.65= 4, 0.0178402/step =C2=A0Wall: 583.7, 0.0179331/step, 0.126628 hours remaini= ng, 0.000000 MB of memory in use.
ENERGY: =C2=A0 30700 =C2=A0 =C2=A02262= 34.5860 =C2=A0 =C2=A0 33319.1606 =C2=A0 =C2=A0 51301.2627 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1814027.4858 =C2=A0 =C2=A0224995.91= 13 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A021.0432 = =C2=A0 =C2=A0376517.3497 =C2=A0 =C2=A0 =C2=A0 =C2=A0-901638.1722 =C2=A0 =C2= =A0 =C2=A0 299.8428 =C2=A0-1278155.5219 =C2=A0 -899427.3684 =C2=A0 =C2=A0 = =C2=A0 299.5875 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1354.4689 =C2=A0 =C2=A0 = =C2=A0 =C2=A044.7734 =C2=A0 4458307.8773 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.5178= =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.7157

Warnin= g: Geometrical pathCV relies on the assumption that the second closest fram= e is the neighbouring frame
Please check your configuratio= n or increase restraint on z (This warning comes earlier as well)
Frame index: 49 ; optimal RMSD =3D 0.975194
Frame = index: 51 ; optimal RMSD =3D 0.975811
Frame index: 50 ; optimal RMSD =3D= 0.977496
Frame index: 47 ; optimal RMSD =3D 0.994026
Frame index: 48= ; optimal RMSD =3D 0.995694
Frame index: 44 ; optimal RMSD =3D 1.00065<= br>Frame index: 43 ; optimal RMSD =3D 1.00377
Frame index: 42 ; optimal = RMSD =3D 1.00561
Frame index: 46 ; optimal RMSD =3D 1.00608
Frame ind= ex: 41 ; optimal RMSD =3D 1.0122
Frame index: 45 ; optimal RMSD =3D 1.01= 242
Frame index: 39 ; optimal RMSD =3D 1.02401
Frame index: 40 ; opti= mal RMSD =3D 1.02975
Frame index: 52 ; optimal RMSD =3D 1.03208
Frame= index: 36 ; optimal RMSD =3D 1.03932
Frame index: 37 ; optimal RMSD =3D= 1.04629
.............
.................
=
Frame index: 88 ; optimal RMSD =3D 3.32354
Frame index: 89 ; = optimal RMSD =3D 3.75411
Frame index: 90 ; optimal RMSD =3D 3.7904
Fr= ame index: 91 ; optimal RMSD =3D 3.80612
Frame index: 92 ; optimal RMSD = =3D 3.8282
Frame index: 93 ; optimal RMSD =3D 3.83528
Frame index: 94= ; optimal RMSD =3D 3.84841
Frame index: 95 ; optimal RMSD =3D 3.86218Frame index: 96 ; optimal RMSD =3D 3.89656
Frame index: 97 ; optimal R= MSD =3D 3.97904
Frame index: 98 ; optimal RMSD =3D 4.16712
Frame inde= x: 99 ; optimal RMSD =3D 4.18738

The error file ga= ve following error
User defined signal 2
ERROR: = =C2=A0One or more process (first noticed rank 8) terminated with signal 12<= /div>

Kindly suggest,
Ashutosh
<= br>


On Wed, Nov 10, 2021 at 12:11= PM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
Hi Ashutosh, the "= ;colvars" keyword=C2=A0is an ordinary NAMD configuration keyword, not = a Tcl command.=C2=A0 It's a bit like "constraints" in this re= gard, which would=C2=A0give you a similar error message if you added it lat= e in the NAMD script.

Just put "colvars on" ea= rly in the NAMD script before any run command, or other commands that trigg= er the Tcl interpreter.=C2=A0 You're not required to add any Colvars co= nfiguration even with "colvars on".

Giac= omo

On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya <scfbioiitd@gmail.com>= ; wrote:
Thanks for all your help. In the slurm output I am getting t= he following error which I am unable to understand. I have been trying seve= ral changes in input files to get the job running but still getting some er= rors. If you have some insight kindly suggest.

FATAL ERROR: Setting parameter colvars from script failed!
=C2=A0
F= ATAL ERROR: Setting parameter colvars from script failed!

The output file ends like this
TCL: Running for 20 steps<= br>ENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2=A0 32958.7= 464 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0374233.1041 =C2= =A0 =C2=A0 =C2=A0 =C2=A0-936367.4549 =C2=A0 =C2=A0 =C2=A0 298.0237 =C2=A0-1= 310600.5589 =C2=A0 -934162.1854 =C2=A0 =C2=A0 =C2=A0 295.8515 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 1073.5139 =C2=A0 =C2=A0 =C2=A0 =C2=A016.7110 =C2=A0 4= 799315.6868 =C2=A0 =C2=A0 =C2=A0 =C2=A055.7822 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = 1.3010

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100
WRITI= NG COORDINATES TO RESTART FILE AT STEP 6100
FINISHED WRITING RESTART COO= RDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 6100
FINISHED WRI= TING RESTART VELOCITIES
TCL: Setting parameter langevinTemp to 300
RE= INITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN.
TCL: Running for 20 = steps
ENERGY: =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2=A0 3= 2958.7464 =C2=A0 =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2= =A0 =C2=A0 =C2=A0 -1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0377307.16= 21 =C2=A0 =C2=A0 =C2=A0 =C2=A0-933293.3968 =C2=A0 =C2=A0 =C2=A0 300.4717 = =C2=A0-1310600.5589 =C2=A0 -931093.1616 =C2=A0 =C2=A0 =C2=A0 300.4717 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1103.2400 =C2=A0 =C2=A0 =C2=A0 =C2=A025.875= 8 =C2=A0 4799315.6868 =C2=A0 =C2=A0 =C2=A01103.2400 =C2=A0 =C2=A0 =C2=A0 = =C2=A025.8758

TCL: Setting parameter colvars to on
FATAL ERROR: S= etting parameter colvars from script failed!


<= /div>
Many thanks,
Ashutosh

On Thu, Nov 4, 2021 at 1= 1:43 PM Michael Robinson <michael.robinson1@monash.edu> wrote:
Hi Ashuto= sh,

I suspect that won't b= e the first error in the log file - that's normally something that happ= ens after an initial error. If that's not the case, look at the output = of the supercomputer you were using to run it (something like a SLURM outpu= t) to see if that caused it.

Cheers,=C2=A0
Michael

On Thu, 4 Nov. 2021,= 2:38 am Ashutosh Shandilya, <scfbioiitd@gmail.com> wrote:
I am running ABF = with namd but it stopped abruptly after some thousand steps. The error file= gave following error. I looked online but didn't find any conclusive a= nswer.

User defined signal 2
ERROR:= =C2=A0One or more process (first noticed rank 8) terminated with signal 12=

What could be the problem?

Many thanks,
Ashutosh

On Thu, Oct 28, 2021 at 2:20 PM= Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
Many th= anks, it works now.

Regards,
Ashutosh

On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson <micha= el.robinson1@monash.edu> wrote:
Hi Ashutosh,

Your input file has a line break between 'abf' and the curl= y bracket '{' that opens the configuration block - this is causing = the ABF configuration block to be skipped, and so your input file is failin= g. I can't test your given file without the associated system, but I do= uble-checked that this would occur with one of my own ABF input files, and = this caused the same error.

Hopefully that he= lps,
Regards,
Michael Robinson

On Thu, 28 Oct = 2021 at 06:56, Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:=
Hi All
I want to run eABF with namd and I am getting follo= wing errors

colvars: Collective variables ini= tialized, 2 in total.
colvars: Error: keyword "abf" found with= out configuration.
FATAL ERROR: Error in the collective variables module= (see above for details)
FATAL ERROR: Error in the collective variables = module (see above for details).

I was able to run = collective variables but when trying to run eABF it gives an error. Kindly = have a look at the attached input file and suggest.

Many thanks

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boundary="_000_D001A37A5AF54A13AD638689EC00DABCmsuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: c7187e95-9fa8-4cc6-c742-08d9a484dc8f X-MS-Exchange-CrossTenant-originalarrivaltime: 10 Nov 2021 20:01:19.1937 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: kEG7h3Zc0D7hQAYM7F8+Mo8/00qwmNq8058e4eXraprLJ/6F1nkWXNW84WE6//Ab7ueKWZdHmXDJKvOc+dltLQ== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB5002 X-CLX-Response: 1TFkXGxwcEQpMehcdGhEKWUQXaXtSfmRsGVBgYWQRClhYF29hWBMaS10bQ0F lEQp4Thdob0xmAXJmZEtdEhEKeUwXYGVTYE0dTx5nGFwRCkNIFwcbExgRCkNZFwceGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhseHHEfHRAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdMXGB/T0ZOQmh7Gmh7fF9eW19vWU1/eX9iU35iX05hWhEKWFwXHwQaBBgeGwUb GgQbGhoEHQQbHhkQGx4aHxoRCl5ZF3NdSUdZEQpNXBcYGx8RCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2tsa2sRCkJPF3oef2ZvQh9Tcmt9EQpDWhceGgQbGh0EGB4ZBB IeEQpCXhcbEQpEXhcZEQpCRRdobWtgeRJLQFoefREKQk4XaG9MZgFyZmRLXRIRCkJMF29hWBMaS 10bQ0FlEQpCbBdheRwfElx7T1ppQhEKQkAXYh1iZU4be0cTbWIRCkJYF2dzZXNAbmFhTF1iEQpN XhcbEQpaWBcdEQp5QxdkS1JhH0NBawV9ThEKWUsXGxgcGh0RCnBnF21HYWtNYxlMU2luEBkaEQp waBdvaWZGWntpRkxafhAZGhEKcGgXY3sdQxMaHF5uTXsQGRoRCnBoF2B8HG4dWmgde1h4EBMeEQ pwaBdrf0lgSFgdbExtQRAZGhEKcGgXYVxrZHofWGtFY3IQGxkaEQpwZxdpQ25QAVlzRwEeUxAZG hEKcH0XbRhiZXJocG5JaGEQGRoRCnB9F2dBGlhseGVOHR9OEBkaEQpwfxdhZm9bGmdkQkgdWxAb GBwRCnBfF2BaHW5CRX9sUklTEBsZEhEKcH8Xbm5oGhMdQ2AfXW0QHBwRCnBfF2kfTE1pUnIeTGc eEBkaEQpwbBdneBpAYhhJGn55TRAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: fvJUeldhBQ0BQVutquEsgUSUHyTHudKp X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: fvJUeldhBQ0BQVutquEsgUSUHyTHudKp MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 impostorscore=0 malwarescore=0 bulkscore=0 priorityscore=70 mlxscore=0 spamscore=0 mlxlogscore=560 clxscore=166 phishscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100097 domainage_hfrom=12607 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_D001A37A5AF54A13AD638689EC00DABCmsuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Nikhil, If its Fugaku specifically, I=E2=80=99m betting they already compiled it, a= nd it wouldn=E2=80=99t hurt to ask. Otherwise, I think its just a Linux-ARM= system, and other than changing the architecture, you would be able to com= pile NAMD no problem. -Josh From: on behalf of Nikhil Maroli Reply-To: "namd-l@ks.uiuc.edu" , Nikhil Maroli Date: Wednesday, November 10, 2021 at 2:37 PM To: "namd-l@ks.uiuc.edu" Subject: namd-l: Fujitsu A64FX CPU processor-suitable NAMD Dear NAMD experts, Anyone can guide me on the precompiled version of namd Fujitsu A64FX CPU = processor to use through MPI across the nodes? (https://urldefense.com/v3/= __https://en.wikipedia.org/wiki/Fugaku_(supercomputer)__;!!DZ3fjg!oCyTHeN3K= 6d0O1fiNm-hXAqyWYjyatcM_cGH3OGu3z23WssmnzHYVfKAbVw5k6-DoA$ ). Or = do i need to compile it from source? -- Regards, -nikhil --_000_D001A37A5AF54A13AD638689EC00DABCmsuedu_ Content-Type: text/html; charset="utf-8" Content-ID: <539A3585DF62014EBA7653445A9CA4F7@namprd12.prod.outlook.com> Content-Transfer-Encoding: base64 PGh0bWwgeG1sbnM6bz0idXJuOnNjaGVtYXMtbWljcm9zb2Z0LWNvbTpvZmZpY2U6b2ZmaWNlIiB4 bWxuczp3PSJ1cm46c2NoZW1hcy1taWNyb3NvZnQtY29tOm9mZmljZTp3b3JkIiB4bWxuczptPSJo dHRwOi8vc2NoZW1hcy5taWNyb3NvZnQuY29tL29mZmljZS8yMDA0LzEyL29tbWwiIHhtbG5zPSJo dHRwOi8vd3d3LnczLm9yZy9UUi9SRUMtaHRtbDQwIj4NCjxoZWFkPg0KPG1ldGEgaHR0cC1lcXVp dj0iQ29udGVudC1UeXBlIiBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9dXRmLTgiPg0KPG1l dGEgbmFtZT0iR2VuZXJhdG9yIiBjb250ZW50PSJNaWNyb3NvZnQgV29yZCAxNSAoZmlsdGVyZWQg bWVkaXVtKSI+DQo8c3R5bGU+PCEtLQ0KLyogRm9udCBEZWZpbml0aW9ucyAqLw0KQGZvbnQtZmFj ZQ0KCXtmb250LWZhbWlseToiQ2FtYnJpYSBNYXRoIjsNCglwYW5vc2UtMToyIDQgNSAzIDUgNCA2 IDMgMiA0O30NCkBmb250LWZhY2UNCgl7Zm9udC1mYW1pbHk6Q2FsaWJyaTsNCglwYW5vc2UtMToy 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namd-l: Water molecules "flying away" in Gaussian calculation of "water int" step in FFTK To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="0000000000009dd40705d0758aba" X-Proofpoint-GUID: fidfyrfETsd1533QMFaI4nzIz9Z82wDt X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: fidfyrfETsd1533QMFaI4nzIz9Z82wDt X-CLX-Response: 1TFkXGx0YEQpMehcaEQpZRBduUlNdUFtNZFlwEhEKWFgXZwVQRnNtHBlvexs RCnhOF2xuR2BiX3tgfx5QEQp5TBd6UkgeaXJba0AeeREKQ0gXBxgeGREKQ1kXBxscGxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGHEZGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdMQ05MU1hMb35ZThsfGRl7Z2xLYx5EUGNQE3ASGF1uXhEKWFwXHwQaBBgeGwUb GgQbGhoEHQQbHhkQGx4aHxoRCl5ZF3NdTkwdEQpNXBcfHxEKTFoXaU1NTREKQk8XYVkceRhIBRI bQngRCkNaFxgaEwQSHwQYGxMEGx0fEQpCXhcbEQpCRRd6UhtLemBzUk9rRhEKQk4XbG5HYGJfe2 B/HlARCkJMF2cFUEZzbRwZb3sbEQpCbBdmbFt+Tk9FaG9lYBEKQkAXYm1Nf0dYGH9gR2IRCkJYF 2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxduXntnWEVFYllcbxEKcGgXbkNEH3lZbRNGQ1sQ GhEKcGgXZmhhbG5rQGBiHUMQGhEKcGgXelgfUF54aE5uXRIQGhEKcGgXZ3IcYlpdYRthU2UQGhE KcGgXZGBkYnocGxscZQUQGhEKcGwXaBteHVpQeB4cSWMQGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=172 lowpriorityscore=0 adultscore=0 mlxlogscore=502 priorityscore=0 bulkscore=0 mlxscore=0 phishscore=0 suspectscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111100099 X-Spam-Score: 0 X-Spam-OrigSender: alexandre.suman@unesp.br X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?Q?Alexandre_Suman_de_Ara=C3=BAjo?= --0000000000009dd40705d0758aba Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi all I am modeling a ligand using FFTK and I am observing a strange behavior in the water interaction step. In FFTK I define hydrogen bond acceptors and donors. and water molecules are placed in an initial conformation for Gaussian energy calculation. I run the Gaussian calculations and the results for interactions where my ligand is a hydrogen bond ACCEPTOR (oxygen atoms from ligand interacting with hydrogen from water) are ok, with the system finding the minimum energy distance as a few Angstroms. However, the results in which my ligand is hydrogen bond DONOR (hydrogen atom from ligand interacting with oxygen from water), the water molecules go far away, not finding a near energy minimum. Does someone who faces this problem sometimes could help me? Regards --=20 Prof. Dr. Alexandre Suman de Araujo Departamento de F=C3=ADsica Instituto de Bioci=C3=AAncias, Letras e Ci=C3=AAncias Exatas - IBILCE Universidade Estadual Paulista e-mail: alexandre.suman@unesp.br Phone: +55 (17) 3221-2566/3221-2240 --0000000000009dd40705d0758aba Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all

I am modeling a ligand using FFT= K and I am observing a strange behavior in the water interaction step.=C2= =A0

In FFTK I define hydrogen bond acceptors and d= onors. and water molecules are placed in an initial conformation for Gaussi= an energy calculation.

I run the Gaussian calculat= ions and the results for interactions where my ligand is a hydrogen bond AC= CEPTOR (oxygen atoms from ligand interacting with hydrogen from water) are = ok, with the system finding the minimum energy distance as a few Angstroms.= However, the results in which my ligand is hydrogen bond DONOR (hydrogen a= tom from ligand interacting with oxygen from water), the water molecules go= far away, not finding a near energy minimum.=C2=A0

Does someone who faces this problem sometimes could help me?
Regards
--=20
Prof. Dr. Alexandre Suman de Araujo
Departamento de F=C3=ADsica
Instituto de Bioci=C3=AAncias, Letras e Ci=C3=AAncias Exatas - IBILCE
Universidade Estadual Paulista
e-mail: alexa=
ndre.suman@unesp.br
Phone: +55 (17) 3221-2566/3221-2240
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charset="UTF-8" I am getting this type of warning After running for 30000 steps it shows TIMING: 30700 CPU: 579.654, 0.0178402/step Wall: 583.7, 0.0179331/step, 0.126628 hours remaining, 0.000000 MB of memory in use. ENERGY: 30700 226234.5860 33319.1606 51301.2627 0.0000 -1814027.4858 224995.9113 0.0000 21.0432 376517.3497 -901638.1722 299.8428 -1278155.5219 -899427.3684 299.5875 1354.4689 44.7734 4458307.8773 0.5178 1.7157 *Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame* *Please check your configuration or increase restraint on z (*This warning comes earlier as well *)* I tried to increase *harmonic restraints* along the gz path from 0.5 to 5 but the problem still persists. Frame index: 49 ; optimal RMSD = 0.975194 Frame index: 51 ; optimal RMSD = 0.975811 Frame index: 50 ; optimal RMSD = 0.977496 Frame index: 47 ; optimal RMSD = 0.994026 Frame index: 48 ; optimal RMSD = 0.995694 Frame index: 44 ; optimal RMSD = 1.00065 Frame index: 43 ; optimal RMSD = 1.00377 Frame index: 42 ; optimal RMSD = 1.00561 Frame index: 46 ; optimal RMSD = 1.00608 Frame index: 41 ; optimal RMSD = 1.0122 Frame index: 45 ; optimal RMSD = 1.01242 Frame index: 39 ; optimal RMSD = 1.02401 Frame index: 40 ; optimal RMSD = 1.02975 Frame index: 52 ; optimal RMSD = 1.03208 Frame index: 36 ; optimal RMSD = 1.03932 Frame index: 37 ; optimal RMSD = 1.04629 ............ ................ Frame index: 88 ; optimal RMSD = 3.32354 Frame index: 89 ; optimal RMSD = 3.75411 Frame index: 90 ; optimal RMSD = 3.7904 Frame index: 91 ; optimal RMSD = 3.80612 Frame index: 92 ; optimal RMSD = 3.8282 Frame index: 93 ; optimal RMSD = 3.83528 Frame index: 94 ; optimal RMSD = 3.84841 Frame index: 95 ; optimal RMSD = 3.86218 Frame index: 96 ; optimal RMSD = 3.89656 Frame index: 97 ; optimal RMSD = 3.97904 Frame index: 98 ; optimal RMSD = 4.16712 Frame index: 99 ; optimal RMSD = 4.18738 The error file gave following error User defined signal 2 ERROR: One or more process (first noticed rank 8) terminated with signal 12 Kindly suggest, Ashutosh On Wed, Nov 10, 2021 at 12:11 PM Giacomo Fiorin wrote: > Hi Ashutosh, the "colvars" keyword is an ordinary NAMD configuration > keyword, not a Tcl command. It's a bit like "constraints" in this regard, > which would give you a similar error message if you added it late in the > NAMD script. > > Just put "colvars on" early in the NAMD script before any run command, or > other commands that trigger the Tcl interpreter. You're not required to > add any Colvars configuration even with "colvars on". > > Giacomo > > On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya > wrote: > >> Thanks for all your help. In the slurm output I am getting the following >> error which I am unable to understand. I have been trying several changes >> in input files to get the job running but still getting some errors. If you >> have some insight kindly suggest. >> >> FATAL ERROR: Setting parameter colvars from script failed! >> >> FATAL ERROR: Setting parameter colvars from script failed! >> >> The output file ends like this >> TCL: Running for 20 steps >> ENERGY: 6100 228438.5351 32958.7464 51721.4945 >> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 >> 374233.1041 -936367.4549 298.0237 -1310600.5589 >> -934162.1854 295.8515 1073.5139 16.7110 >> 4799315.6868 55.7822 1.3010 >> >> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100 >> WRITING COORDINATES TO RESTART FILE AT STEP 6100 >> FINISHED WRITING RESTART COORDINATES >> WRITING VELOCITIES TO RESTART FILE AT STEP 6100 >> FINISHED WRITING RESTART VELOCITIES >> TCL: Setting parameter langevinTemp to 300 >> REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN. >> TCL: Running for 20 steps >> ENERGY: 6100 228438.5351 32958.7464 51721.4945 >> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000 >> 377307.1621 -933293.3968 300.4717 -1310600.5589 >> -931093.1616 300.4717 1103.2400 25.8758 >> 4799315.6868 1103.2400 25.8758 >> >> TCL: Setting parameter colvars to on >> FATAL ERROR: Setting parameter colvars from script failed! >> >> >> Many thanks, >> Ashutosh >> >> On Thu, Nov 4, 2021 at 11:43 PM Michael Robinson < >> michael.robinson1@monash.edu> wrote: >> >>> Hi Ashutosh, >>> >>> I suspect that won't be the first error in the log file - that's >>> normally something that happens after an initial error. If that's not the >>> case, look at the output of the supercomputer you were using to run it >>> (something like a SLURM output) to see if that caused it. >>> >>> Cheers, >>> Michael >>> >>> On Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, >>> wrote: >>> >>>> I am running ABF with namd but it stopped abruptly after some thousand >>>> steps. The error file gave following error. I looked online but didn't find >>>> any conclusive answer. >>>> >>>> User defined signal 2 >>>> ERROR: One or more process (first noticed rank 8) terminated with >>>> signal 12 >>>> >>>> What could be the problem? >>>> >>>> Many thanks, >>>> Ashutosh >>>> >>>> On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya < >>>> scfbioiitd@gmail.com> wrote: >>>> >>>>> Many thanks, it works now. >>>>> >>>>> Regards, >>>>> Ashutosh >>>>> >>>>> On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson < >>>>> michael.robinson1@monash.edu> wrote: >>>>> >>>>>> Hi Ashutosh, >>>>>> >>>>>> Your input file has a line break between 'abf' and the curly bracket >>>>>> '{' that opens the configuration block - this is causing the ABF >>>>>> configuration block to be skipped, and so your input file is failing. I >>>>>> can't test your given file without the associated system, but I >>>>>> double-checked that this would occur with one of my own ABF input files, >>>>>> and this caused the same error. >>>>>> >>>>>> Hopefully that helps, >>>>>> Regards, >>>>>> Michael Robinson >>>>>> >>>>>> On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya < >>>>>> scfbioiitd@gmail.com> wrote: >>>>>> >>>>>>> Hi All >>>>>>> I want to run eABF with namd and I am getting following errors >>>>>>> >>>>>>> colvars: Collective variables initialized, 2 in total. >>>>>>> colvars: Error: keyword "abf" found without configuration. >>>>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>>>> details) >>>>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>>>> details). >>>>>>> >>>>>>> I was able to run collective variables but when trying to run eABF >>>>>>> it gives an error. Kindly have a look at the attached input file and >>>>>>> suggest. >>>>>>> >>>>>>> Many thanks >>>>>>> >>>>>>> --00000000000052602205d085b536 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

I am = getting this type of warning

After running for 30000 steps it= shows
TIMING: 30700 =C2=A0CPU: 579.654, 0.0178402/step =C2=A0Wal= l: 583.7, 0.0179331/step, 0.126628 hours remaining, 0.000000 MB of memory i= n use.
ENERGY: =C2=A0 30700 =C2=A0 =C2=A0226234.5860 =C2=A0 =C2=A0 33319= .1606 =C2=A0 =C2=A0 51301.2627 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 = =C2=A0 =C2=A0 -1814027.4858 =C2=A0 =C2=A0224995.9113 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A021.0432 =C2=A0 =C2=A0376517.3497 = =C2=A0 =C2=A0 =C2=A0 =C2=A0-901638.1722 =C2=A0 =C2=A0 =C2=A0 299.8428 =C2= =A0-1278155.5219 =C2=A0 -899427.3684 =C2=A0 =C2=A0 =C2=A0 299.5875 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 1354.4689 =C2=A0 =C2=A0 =C2=A0 =C2=A044.7734 = =C2=A0 4458307.8773 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.5178 =C2=A0 =C2=A0 =C2=A0= =C2=A0 1.7157

Warning: Geometrical pathCV= relies on the assumption that the second closest frame is the neighbouring= frame
Please check your configuration or increase restrai= nt on z (This warning comes earlier as well)
I=C2= =A0 tried to increase harmonic restraints along the gz path from 0.5= to 5 but the problem still persists.

Frame index: 49 ; optimal RMSD =3D 0.975194
Frame index: 51 ; optimal R= MSD =3D 0.975811
Frame index: 50 ; optimal RMSD =3D 0.977496
Frame in= dex: 47 ; optimal RMSD =3D 0.994026
Frame index: 48 ; optimal RMSD =3D 0= .995694
Frame index: 44 ; optimal RMSD =3D 1.00065
Frame index: 43 ; = optimal RMSD =3D 1.00377
Frame index: 42 ; optimal RMSD =3D 1.00561
F= rame index: 46 ; optimal RMSD =3D 1.00608
Frame index: 41 ; optimal RMSD= =3D 1.0122
Frame index: 45 ; optimal RMSD =3D 1.01242
Frame index: 3= 9 ; optimal RMSD =3D 1.02401
Frame index: 40 ; optimal RMSD =3D 1.02975<= br>Frame index: 52 ; optimal RMSD =3D 1.03208
Frame index: 36 ; optimal = RMSD =3D 1.03932
Frame index: 37 ; optimal RMSD =3D 1.04629
..= ..........
.................
Frame inde= x: 88 ; optimal RMSD =3D 3.32354
Frame index: 89 ; optimal RMSD =3D 3.75= 411
Frame index: 90 ; optimal RMSD =3D 3.7904
Frame index: 91 ; optim= al RMSD =3D 3.80612
Frame index: 92 ; optimal RMSD =3D 3.8282
Frame i= ndex: 93 ; optimal RMSD =3D 3.83528
Frame index: 94 ; optimal RMSD =3D 3= .84841
Frame index: 95 ; optimal RMSD =3D 3.86218
Frame index: 96 ; o= ptimal RMSD =3D 3.89656
Frame index: 97 ; optimal RMSD =3D 3.97904
Fr= ame index: 98 ; optimal RMSD =3D 4.16712
Frame index: 99 ; optimal RMSD = =3D 4.18738

The error file gave following error
User defined signal 2
ERROR: =C2=A0One or more proce= ss (first noticed rank 8) terminated with signal 12

Kindly suggest,
Ashutosh




On Wed, Nov 10, 2021 at 12:11 PM Giacomo Fiorin <= giacomo.fiori= n@gmail.com> wrote:
Hi Ashutosh, the "colvars" keyword=C2= =A0is an ordinary NAMD configuration keyword, not a Tcl command.=C2=A0 It&#= 39;s a bit like "constraints" in this regard, which would=C2=A0gi= ve you a similar error message if you added it late in the NAMD script.
Just put "colvars on" early in the NAMD script be= fore any run command, or other commands that trigger the Tcl interpreter.= =C2=A0 You're not required to add any Colvars configuration even with &= quot;colvars on".

Giacomo

On Wed, Nov 10= , 2021 at 11:45 AM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
Thanks f= or all your help. In the slurm output I am getting the following error whic= h I am unable to understand. I have been trying several changes in input fi= les to get the job running but still getting some errors. If you have some = insight kindly suggest.

FATAL ERROR: Setting p= arameter colvars from script failed!
=C2=A0
FATAL ERROR: Setting par= ameter colvars from script failed!

The output file= ends like this
TCL: Running for 20 steps
ENERGY: =C2=A0 =C2= =A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2=A0 32958.7464 =C2=A0 =C2=A0 517= 21.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1882555.54= 10 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0374233.1041 =C2=A0 =C2=A0 =C2=A0 =C2= =A0-936367.4549 =C2=A0 =C2=A0 =C2=A0 298.0237 =C2=A0-1310600.5589 =C2=A0 -9= 34162.1854 =C2=A0 =C2=A0 =C2=A0 295.8515 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 1073.5139 =C2=A0 =C2=A0 =C2=A0 =C2=A016.7110 =C2=A0 4799315.6868 =C2=A0 = =C2=A0 =C2=A0 =C2=A055.7822 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.3010

WRITI= NG EXTENDED SYSTEM TO RESTART FILE AT STEP 6100
WRITING COORDINATES TO R= ESTART FILE AT STEP 6100
FINISHED WRITING RESTART COORDINATES
WRITING= VELOCITIES TO RESTART FILE AT STEP 6100
FINISHED WRITING RESTART VELOCI= TIES
TCL: Setting parameter langevinTemp to 300
REINITIALIZING VELOCI= TIES AT STEP 6100 TO 300 KELVIN.
TCL: Running for 20 steps
ENERGY: = =C2=A0 =C2=A06100 =C2=A0 =C2=A0228438.5351 =C2=A0 =C2=A0 32958.7464 =C2=A0 = =C2=A0 51721.4945 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -= 1882555.5410 =C2=A0 =C2=A0258836.2061 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0377307.1621 =C2=A0 =C2=A0 = =C2=A0 =C2=A0-933293.3968 =C2=A0 =C2=A0 =C2=A0 300.4717 =C2=A0-1310600.5589= =C2=A0 -931093.1616 =C2=A0 =C2=A0 =C2=A0 300.4717 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 1103.2400 =C2=A0 =C2=A0 =C2=A0 =C2=A025.8758 =C2=A0 4799315.6868= =C2=A0 =C2=A0 =C2=A01103.2400 =C2=A0 =C2=A0 =C2=A0 =C2=A025.8758

TC= L: Setting parameter colvars to on
FATAL ERROR: Setting parameter colvar= s from script failed!


Many thanks,<= /div>
Ashutosh

On Thu, Nov 4, 2021 at 11:43 PM Michael Robin= son <m= ichael.robinson1@monash.edu> wrote:
Hi Ashutosh,
=
I suspect that won't be the first error in = the log file - that's normally something that happens after an initial = error. If that's not the case, look at the output of the supercomputer = you were using to run it (something like a SLURM output) to see if that cau= sed it.

Cheers,=C2=A0
Michael

On Thu, 4 Nov. 2021, 2:38 am Ashutosh Sha= ndilya, <scfbi= oiitd@gmail.com> wrote:
I am running ABF with namd but it stop= ped abruptly after some thousand steps. The error file gave following error= . I looked online but didn't find any conclusive answer.

User defined signal 2
ERROR: =C2=A0One or more pr= ocess (first noticed rank 8) terminated with signal 12

=
What could be the problem?

Many thanks,
=
Ashutosh

On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya &= lt;scfbioiitd@gmail.com> wrote:
Many thanks, it works now.

Regards,
Ashutosh

On Wed, Oct 27= , 2021 at 8:28 PM Michael Robinson <michael.robinson1@monash.e= du> wrote:
Hi Ashutosh,

Your input fi= le has a line break between 'abf' and the curly bracket '{'= that opens the configuration block - this is causing the ABF configuration= block to be skipped, and so your input file is failing. I can't test y= our given file without the associated system, but I double-checked that thi= s would occur with one of my own ABF input files, and this caused the same = error.

Hopefully that helps,
Regard= s,
Michael Robinson

On Thu, 28 Oct 2021 at 06:56, Ashuto= sh Shandilya <scfbioiitd@gmail.com> wrote:
Hi All
I want to run eABF with namd and I am getting following errors

colvars: Collective variables initialized, 2 in total.=
colvars: Error: keyword "abf" found without configuration.FATAL ERROR: Error in the collective variables module (see above for detai= ls)
FATAL ERROR: Error in the collective variables module (see above for= details).

I was able to run collective variables = but when trying to run eABF it gives an error. Kindly have a look at the at= tached input file and suggest.

Many thanks

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nonbonded=20 parameters for atom type N238. How to fix it depends on how there came=20 to be atoms with type N238. I don't recognize it as being in the=20 standard CHARMM parameter sets. Does your system have an components that=20 you needed to parameterize (like whatever needs the UNK_DEF6D6.prm file)? -Josh On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote: > Hello! > An error occured when I run a molecular dynamic using NAMD3, > > FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 > > > I don't know how to solve it, any suggestion will be much appreciate. > > The following parameters were used, > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_all36_prot.prm > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_all36_carb.prm > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_all36_cgenff.prm > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_all36_lipid.prm > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_all36_na.prm > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/UNK_DEF6D6.prm > parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/toppar_water_ions_n= amd.str > #parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/toppar_water_ions.= mod.str (don't works) > > > > > Thanks, > > Zhihong xin > > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!uVsOD3CDQs066tBFC3xROQI0suhEylSkTmazy6rOp51OzxR7wZIqqHY= UPYVE0lv21w$=20 --------------C924472B6D783EE97F20F98D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable Hi Zhihong,

What this means is that the parameter set doesn't have nonbonded parameters for atom type N238. How to fix it depends on how there came to be atoms with type N238. I don't recognize it as being in the standard CHARMM parameter sets. Does your system have an components that you needed to parameterize (like whatever needs the UNK_DEF6D6.prm file)?

-Josh

On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97= =E5=AE=8F wrote:
=20=20=20=20=20=20
Hello!
An error occured when I run a molecular dynamic using NAMD3, 

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238


I don't know how to solve it, any suggestion will be much appreciate.

The following parameters were used,
parameters          ./common/par_al= l36_prot.prm
parameters          ./common/par_al= l36_carb.prm
parameters          ./common/par_al= l36_cgenff.prm
parameters          ./common/par_al= l36_lipid.prm
parameters          ./common/par_al= l36_na.prm
parameters          ./common/UNK_DE= F6D6.prm
parameters          ./common/toppar= _water_ions_namd.str
#parameters          ./common/toppa= r_water_ions.mod.str (don't works)




Thanks,

Zhihong xin



--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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boundary="0000000000007a8dcb05d098fb59" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx4ZEQpMehcZHhgRCllEF3poR1wfbxtYXF5jEQpYWBdoWXhyHl5raGE TehEKeE4XY1Nja3sTWH4aX14RCnlMF2lZAW1lHW1wSWxaEQpDSBcHEx8RCkNZFwcTHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsYGXEbHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdLb2dGbWFMTh18TG5JZ14ee1lER3tgS3thb2dSdRxochEKWFwXHwQaBBgeGwUb GgQbGhoEHQQbHhkQGx4aHxoRCl5ZF3NSaVt7EQpNXBcZGRkRCkxaF3tpTWtNEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGxMEGx IYEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF29PeEMdZl5NY0JOEQpCThdjU2NrexNYfhpfXhEKQkwXaFl4ch5ea2hhE3oRCkJsF2Ff QEZGf11LaGRGEQpCQBdoBRsbSVpvREN5eREKQlgXZ3Nlc0BuYWFMXWIRClpYFx8RCnlDF2xdSHh mGk4aYGQaEQpZSxcTHxISEQpwaBdjRWhjYm9maH19fBAZGhEKcGgXYFJcfX9cQFkSG14QGRoRCn BoF2QfZk1hfBhhTl8cEBkaEQpwaBdiG39rZHldfmZIRxAZGhEKcGgXenl9a3BMUmFTW0kQGRoRC nB9F2t6HGBTGRhvUEVgEB4SEQpwfRdmQV9NUFxOaxlgaxAZGhEKcH8Xbh9nXX1eQBN4ZHkQGxsa EQpwXxdkY2htHn1Qa0xQYBAeEhEKcH8XYWZvWxpnZEJIHVsQGxkYEQpwXxdjYhJQSGN4H3xCfRA bGhgRCnBsF2R/aGlhU2JoQht/EB4SEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: aEMlGKfd7VfDcMt4QsnmQJaQKEMx_6BX X-Proofpoint-ORIG-GUID: aEMlGKfd7VfDcMt4QsnmQJaQKEMx_6BX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 adultscore=0 lowpriorityscore=0 phishscore=0 mlxscore=0 suspectscore=0 clxscore=143 impostorscore=0 spamscore=0 priorityscore=342 mlxlogscore=618 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111120088 domainage_hfrom=9588 X-Spam-Score: 0 X-Spam-OrigSender: kushalrajroyfc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kushal Raj Roy --0000000000007a8dcb05d098fb59 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi, Instead of mod.str try to use toppar_water_ions_namd.str. Hopefully, it will work. Best, Kushal On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas, wrote: > Hi Zhihong, > > What this means is that the parameter set doesn't have nonbonded > parameters for atom type N238. How to fix it depends on how there came to > be atoms with type N238. I don't recognize it as being in the standard > CHARMM parameter sets. Does your system have an components that you neede= d > to parameterize (like whatever needs the UNK_DEF6D6.prm file)? > > -Josh > > On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote: > > Hello! > An error occured when I run a molecular dynamic using NAMD3, > > FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 > > > I don't know how to solve it, any suggestion will be much appreciate. > > The following parameters were used, > parameters ./common/par_all36_prot.prm > parameters ./common/par_all36_carb.prm > parameters ./common/par_all36_cgenff.prm > parameters ./common/par_all36_lipid.prm > parameters ./common/par_all36_na.prm > parameters ./common/UNK_DEF6D6.prm > parameters ./common/toppar_water_ions_namd.str > #parameters ./common/toppar_water_ions.mod.str (don't works) > > > > > Thanks, > > Zhihong xin > > > > -- > Josh Vermaas > vermaasj@msu.edu > Assistant Professor, Plant Research Laboratory and Biochemistry and Molec= ular Biology > Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-v= ermaas/ > > --0000000000007a8dcb05d098fb59 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,=C2=A0

In= stead of mod.str try to use=C2=A0toppar_water_ions_namd.str. Hopefully, it = will work.=C2=A0

Bes= t,

Kushal
On Fri, 1= 2 Nov, 2021, 9:01 pm Josh Vermaas, <= vermaasj@msu.edu> wrote:
=20
Hi Zhihong,

What this means is that the parameter set doesn't have nonbonded parameters for atom type N238. How to fix it depends on how there came to be atoms with type N238. I don't recognize it as being in the standard CHARMM parameter sets. Does your system have an components that you needed to parameterize (like whatever needs the UNK_DEF6D6.prm file)?

-Josh

On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote:
=20
Hello!
An error occured when I run a molecular dynamic using NAMD3,=C2=A0

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N23= 8


I don't know how to solve it, any suggestion will be much appreciate.

The following parameters were used,
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_prot.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_carb.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_cgenff.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_lipid.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_na.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/UNK_DE= F6D6.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/toppar= _water_ions_namd.str
#parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/toppa= r_water_ions.mod.str (don't works)




Thanks,

Zhihong xin



--=20
Josh Vermaas

ve=
rmaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.n=
atsci.msu.edu/people/faculty/josh-vermaas/
--0000000000007a8dcb05d098fb59-- From owner-namd-l@halifax.ks.uiuc.edu Fri Nov 12 10:16:40 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ACGGeQf000890; Fri, 12 Nov 2021 10:16:40 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ACGGeTl000889; Fri, 12 Nov 2021 10:16:40 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ACGGdR5000885; Fri, 12 Nov 2021 10:16:39 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ACGGds5000884; Fri, 12 Nov 2021 10:16:39 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ACGG2ZN000145 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 12 Nov 2021 10:16:03 -0600 (CST) Received: from pps.filterd (m0166258.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1ACFo0e9020747 for ; Fri, 12 Nov 2021 16:16:02 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=xzhfood@njau.edu.cn Received: from mail-m176238.qiye.163.com (mail-m176238.qiye.163.com [59.111.176.238]) by mx0b-00007101.pphosted.com with ESMTP id 3c9rvh2084-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Fri, 12 Nov 2021 16:16:01 +0000 Received: from njau.edu.cn (localhost [127.0.0.1]) by mail-m176238.qiye.163.com (Hmail) with ESMTP id 3A195F60274; Sat, 13 Nov 2021 00:15:57 +0800 (CST) Content-Type: multipart/alternative; BOUNDARY="=_Part_313359_1938748691.1636733757230" Message-ID: To: namd-l@ks.uiuc.edu, Kushal Raj Roy Subject: namd-l: =?UTF-8?B?UmU6UmU6IG5hbWQtbDogRkFUQUwgRVJST1I6IERJRE4nVCBGSU5EIHZkVyBQQVJBTUVURVIgRk9SIEFUT00gVFlQRSBOMjM4?= X-Priority: 3 X-Mailer: HMail Webmail Server V2.0 Copyright (c) 2016-163.com X-Originating-IP: 202.195.247.243 In-Reply-To: Received: from xzhfood@njau.edu.cn( [202.195.247.243) ] by ajax-webmail ( [127.0.0.1] ) ; Sat, 13 Nov 2021 00:15:57 +0800 (GMT+08:00) From: =?UTF-8?B?6L6b5b+X5a6P?= Date: Sat, 13 Nov 2021 00:15:57 +0800 (GMT+08:00) X-HM-Spam-Status: e1kfGhgUHx5ZQUtXWQgPGg8OCBgUHx5ZQUlOS1dZCBgUCR5ZQVlLVUtZV1 kWDxoPAgseWUFZKDYvK1lXWShZQUhPN1dZLVlBSVdZDwkaFQgSH1lBWUJNHk5WGR5KGRlITEhPSB lNVRMBExYaEhckFA4PWVdZFhoPEhUdFFlBWVVLWQY+ X-HM-Sender-Digest: e1kJHlYWEh9ZQUNKQ0pJSEhIT0pDN1dZDB4ZWUEPCQ4eV1kSHx4VD1lB WUc6PBA6Lww5Sz5WPjYVPEkIFS0ILkpPCjFVSVVKTUhNTEhITE5MT09NVTMWGhIXVQMBEx0UFB87 FREaDlUeHw5VGBVFWVdZEgtZQVlJS0lVSkJOVUlPTFVJT0hZV1kIAVlBSktMT0w3Bg++ X-HM-Tid: 0a7d14ead183d9b0kuws17cff2e64bd X-Proofpoint-ORIG-GUID: T38hgytC0UADmChMdkqov38x7ey4OQlR X-CLX-Response: 1TFkXGxIZEQpMehcaEQpZRBdrSBpwYXxYaG1OXBEKWFgXZ3ocGFJJYm4ecE4 RCnhOF2dsb0tEZ3kTYhpjEQp5TBdlZUNwYW0dbF1NEhEKQ0gXBxgYGBEKQ1kXBxsaGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscGXEeGBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThd+GRJCTVNeaRp/a25HaUJnTkFbRVwZElIdT1MeZXtGeBEKWFwXHwQaBBgeGwUb GgQbGxoEHQQbGRkQGx4aHxoRCl5ZF3NSbkxJEQpNXBceHx0RCkxaF2xpQk1NEQpFWRdpa2sRCk1 OF2gRCkxGF2hraxEKQk8XZE1gX0xfckEefF4RCkNaFx8TBBsbGwQbHRwEGBkSEQpCXhcbEQpEXh cYEQpCRRdkeWJHGGV4QB5AXxEKQk4XZ2xvS0RneRNiGmMRCkJMF2d6HBhSSWJuHnBOEQpCbBdpa EwYBW9DHVhoAREKQkAXb0teZX5Af3p5S0ERCkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5QxdsXUh4 ZhpOGmBkGhEKcGcXaUNuUAFZc0cBHlMQGhEKcGgXYFJcfX9cQFkSG14QGhEKcGgXenl9a3BMUmF TW0kQGhEKcGgXaGIZeAV8e39If18QGhEKcGgXYXpYZ3BtGURefUIQGhEKcGgXaH5HckBJclt7XG UQGhEKcH0XaxMaYHwFYWxsfx8QGhEKcGcXZX1dQRpcfkRrRWsQGhEKcH0Xa3ocYFMZGG9QRWAQG hEKcH8XbHAfcmhfGUN6Gx8QGx4cEQpwXxdnSGRsXllkSERBWBAaEQpwfxduH2ddfV5AE3hkeRAb GxsRCnBfF2RjaG0efVBrTFBgEBoRCnBsF29pX39dWmccT0kTEB4SEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: T38hgytC0UADmChMdkqov38x7ey4OQlR X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 phishscore=0 spamscore=0 adultscore=0 impostorscore=0 mlxlogscore=832 mlxscore=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 clxscore=183 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111120093 X-Spam-Score: 0 X-Spam-OrigSender: xzhfood@njau.edu.cn X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?UTF-8?B?6L6b5b+X5a6P?= --=_Part_313359_1938748691.1636733757230 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks Josh and Kushal. The ligand parameter(UNK_DEF6D6.prm) was generated by Ligpargen( https://ur= ldefense.com/v3/__http://zarbi.chem.yale.edu/ligpargen/__;!!DZ3fjg!ph09oszz= US7UYHmeDfrR2wr2796iFD0r0PWWcnbJXZ4ZB1HiXNPvCOw8iX8LuzE6JA$ ), also I try u= se toppar_water_ions_namd.str. instead, but it failure. zhihong =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9AKushal Raj Roy =E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A2021-11-12 23:20:20 =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9Anamd-l@ks.uiuc.edu,Josh Vermaas =E4=B8=BB=E9=A2=98=EF=BC=9ARe: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMET= ER FOR ATOM TYPE N238 Hi,=20 Instead of mod.str try to use toppar_water_ions_namd.str. Hopefully, it wil= l work.=20 Best, Kushal On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas, wrote: Hi Zhihong, What this means is that the parameter set doesn't have nonbonded parameter= s for atom type N238. How to fix it depends on how there came to be atoms w= ith type N238. I don't recognize it as being in the standard CHARMM paramet= er sets. Does your system have an components that you needed to parameteriz= e (like whatever needs the UNK_DEF6D6.prm file)? -Josh On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote: Hello! An error occured when I run a molecular dynamic using NAMD3,=20 FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 I don't know how to solve it, any suggestion will be much appreciate. The following parameters were used, parameters ./common/par_all36_prot.prm parameters ./common/par_all36_carb.prm parameters ./common/par_all36_cgenff.prm parameters ./common/par_all36_lipid.prm parameters ./common/par_all36_na.prm parameters ./common/UNK_DEF6D6.prm parameters ./common/toppar_water_ions_namd.str #parameters ./common/toppar_water_ions.mod.str (don't works) Thanks, Zhihong xin --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!ph09oszzUS7UYHmeDfrR2wr2796iFD0r0PWWcnbJXZ4ZB1HiXNPvCOw= 8iX_ASHUGFQ$=20 --=_Part_313359_1938748691.1636733757230 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

Thanks Josh and Kushal.

The ligand= parameter(UNK_DEF6D6.prm) was generated by Ligpargen( http://zarbi.chem.yale.edu/lig= pargen/), also I try use toppar_water_ions_namd.str. instead,= but it failure.

zhihong



=

=E5=8F=91=E4=BB=B6=E4= =BA=BA=EF=BC=9AKushal Raj Roy <kushalrajroyfc@gmail.com>
=E5=8F= =91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A2021-11-12 23:20:20
=E6=94=B6= =E4=BB=B6=E4=BA=BA=EF=BC=9Anamd-l@ks.uiuc.edu,Josh Vermaas <vermaasj@msu= .edu>
=E4=B8=BB=E9=A2=98=EF=BC=9ARe: namd-l: FATAL ERROR: DIDN'T FI= ND vdW PARAMETER FOR ATOM TYPE N238
Hi, 

Instead of mod.str try to use toppar_water_ions_namd.str. Ho= pefully, it will work. 

Best,

Kus= hal

On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas, <vermaasj@msu.edu> wrote:
=20=20
Hi Zhihong,

What this means is that the parameter set doesn't have nonbonded parameters for atom type N238. How to fix it depends on how there came to be atoms with type N238. I don't recognize it as being in the standard CHARMM parameter sets. Does your system have an components that you needed to parameterize (like whatever needs the UNK_DEF6D6.prm file)?

-Josh

On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote:
=20=20=20=20=20=20
Hello!
An error occured when I run a molecular dynamic using NAMD3, 

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238


I don't know how to solve it, any suggestion will be much appreciate.

The following parameters were used,
parameters          ./common/par_al= l36_prot.prm
parameters          ./common/par_al= l36_carb.prm
parameters          ./common/par_al= l36_cgenff.prm
parameters          ./common/par_al= l36_lipid.prm
parameters          ./common/par_al= l36_na.prm
parameters          ./common/UNK_DE= F6D6.prm
parameters          ./common/toppar= _water_ions_namd.str
#parameters          ./common/toppa= r_water_ions.mod.str (don't works)




Thanks,

Zhihong xin



--=20
Josh Vermaas

ve=
rmaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.n=
atsci.msu.edu/people/faculty/josh-vermaas/

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boundary="00000000000031d63605d09a8f9a" X-Proofpoint-ORIG-GUID: Ih-GHHC2GjanW1rPWxwZqwLWGts4ENlS X-CLX-Response: 1TFkXGxIdEQpMehcZGBMRCllEF3poR1wfbxtYXF5jEQpYWBdoWXhyHl5raGE TehEKeE4XY1Nja3sTWH4aX14RCnlMF2lZAW1lHW1wSWxaEQpDSBcHGBwcEQpDWRcHGxkcEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwdcR4cEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2NCB21iYmkYbUBLRH0bWHp9Ul1wW11mfW1eWR5vZEZ5EQpYXBcfBBoEGB4b BRsaBBsbGgQdBBsZGRAbHhofGhEKXlkXc1Jvf2wRCk1cFxsZHBEKTFoXaXxpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGx0ZEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF29PeEMdZl5NY0JOEQpCThdjU2NrexNYfhpfXhEKQkwXaFl4ch5ea2hhE3oRCkJs F2FfQEZGf11LaGRGEQpCQBdiRH1gWEdJRV9IYREKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxI RCnlDF2VmHEt+QRlFZxhBEQpZSxcTHxISEQpwZxdifxoeRElJH2MfHhAaEQpwaBdlHUZ4TExvb0 VmYhAaEQpwaBdgUlx9f1xAWRIbXhAaEQpwaBdrRVtwQm16SHtYXhAaEQpwaBd6eX1rcExSYVNbS RAaEQpwaBdnWktNWBpdQ1xkcxAaEQpwfRdrExpgfAVhbGx/HxAaEQpwfRdibGBOR2dSeGh9RBAa EQpwZxdpQ25QAVlzRwEeUxAaEQpwZxdlfV1BGlx+RGtFaxAaEQpwfRdrehxgUxkYb1BFYBAaEQp wfRdmQV9NUFxOaxlgaxAbEhEKcH0XbmRHa2l5Ex5eRU0QGhEKcH8XbHAfcmhfGUN6Gx8QGx4TEQ pwXxdnSGRsXllkSERBWBAaEQpwfxdtRF9GRW19SHkZbhAbHxoRCnBfF2tGSxN5aGlufBN4EBsbH hEKcH8Xbh9nXX1eQBN4ZHkQGxsYEQpwXxdkY2htHn1Qa0xQYBAaEQpwfxdhZm9bGmdkQkgdWxAb GRkRCnBfF2NiElBIY3gffEJ9EBsaHhEKcGwXZH9oaWFTYmhCG38QGxIRCm1+FxsRClhNF0sRIA= = X-Proofpoint-GUID: Ih-GHHC2GjanW1rPWxwZqwLWGts4ENlS X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=329 phishscore=0 spamscore=0 adultscore=0 impostorscore=0 mlxlogscore=865 mlxscore=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 clxscore=187 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111120096 domainage_hfrom=9588 X-Spam-Score: 0 X-Spam-OrigSender: kushalrajroyfc@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Kushal Raj Roy --00000000000031d63605d09a8f9a Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi, I think you didn=E2=80=99t get what prof. Vermaas trying to anecdote about = your unknown compound's (UNK_DEF6D6.prm) prm file. For instance, I would like to suggest you generate all the parameter files by using charmm-gui rather than LigPargen. Best, Kushal On Fri, 12 Nov, 2021, 10:18 pm =E8=BE=9B=E5=BF=97=E5=AE=8F, wrote: > > Thanks Josh and Kushal. > > The ligand parameter(UNK_DEF6D6.prm) was generated by Ligpargen( > https://urldefense.com/v3/__http://zarbi.chem.yale.edu/ligpargen/__;!!DZ3= fjg!q7EpUSeNyEAA-BfOaFAH-SQ-L1v7EEU_87H40lpitko2_O1t9Zzw6RKsXSN8VAoWbw$ ), > = also > I try use toppar_water_ions_namd.str. instead, but it failure. > > zhihong > > > > > =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9AKushal Raj Roy > =E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A2021-11-12 23:20:20 > =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9Anamd-l@ks.uiuc.edu,Josh Vermaas > =E4=B8=BB=E9=A2=98=EF=BC=9ARe: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAM= ETER FOR ATOM TYPE N238 > > Hi, > > Instead of mod.str try to use toppar_water_ions_namd.str. Hopefully, it > will work. > > Best, > > Kushal > > On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas, wrote: > >> Hi Zhihong, >> >> What this means is that the parameter set doesn't have nonbonded >> parameters for atom type N238. How to fix it depends on how there came to >> be atoms with type N238. I don't recognize it as being in the standard >> CHARMM parameter sets. Does your system have an components that you need= ed >> to parameterize (like whatever needs the UNK_DEF6D6.prm file)? >> >> -Josh >> >> On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote: >> >> Hello! >> An error occured when I run a molecular dynamic using NAMD3, >> >> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 >> >> >> I don't know how to solve it, any suggestion will be much appreciate. >> >> The following parameters were used, >> parameters ./common/par_all36_prot.prm >> parameters ./common/par_all36_carb.prm >> parameters ./common/par_all36_cgenff.prm >> parameters ./common/par_all36_lipid.prm >> parameters ./common/par_all36_na.prm >> parameters ./common/UNK_DEF6D6.prm >> parameters ./common/toppar_water_ions_namd.str >> #parameters ./common/toppar_water_ions.mod.str (don't works) >> >> >> >> >> Thanks, >> >> Zhihong xin >> >> >> >> -- >> Josh Vermaas >> vermaasj@msu.edu >> Assistant Professor, Plant Research Laboratory and Biochemistry and Mole= cular Biology >> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-= vermaas/ >> >> > --00000000000031d63605d09a8f9a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,=C2=A0

I = think you didn=E2=80=99t get what prof. Vermaas trying to anecdote about yo= ur unknown compound's (UNK_DEF6D6.prm)=C2=A0prm file. For instance,=C2=A0 I would like to = suggest you generate all the parameter files by using charmm-gui rather tha= n LigPargen.=C2=A0

Best,=

Kushal=C2=A0

On Fr= i, 12 Nov, 2021, 10:18 pm =E8=BE=9B=E5=BF=97=E5=AE=8F, <xzhf= ood@njau.edu.cn> wrote:
<= br>
Thanks Josh and Kushal.

The ligand paramet= er(UNK_DEF6D6.prm) was generated by Ligpargen(=C2=A0http://zarbi.chem.yale.edu/lig= pargen/),=C2=A0also I try use=C2=A0toppar_water_ions_namd.str. instead,= but it failure.

zhihong




=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9AKushal Raj Roy = <kushalrajroyfc@gmail.com>
=E5=8F= =91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A2021-11-12 23:20:20
=E6=94=B6=E4= =BB=B6=E4=BA=BA=EF=BC=9Anamd-l@ks.uiuc.edu,Josh V= ermaas <vermaasj@msu.edu>
=E4=B8=BB=E9=A2= =98=EF=BC=9ARe: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM= TYPE N238
Hi,=C2=A0

Instead of mod.str try to use=C2=A0to= ppar_water_ions_namd.str. Hopefully, it will work.=C2=A0

Best,

Kushal

On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas,= <vermaasj@msu.edu> wrote:
=20
Hi Zhihong,

What this means is that the parameter set doesn't have nonbonded parameters for atom type N238. How to fix it depends on how there came to be atoms with type N238. I don't recognize it as being in the standard CHARMM parameter sets. Does your system have an components that you needed to parameterize (like whatever needs the UNK_DEF6D6.prm file)?

-Josh

On 11/12/21 9:35 AM, =E8=BE=9B=E5=BF=97=E5=AE=8F wrote:
=20
Hello!
An error occured when I run a molecular dynamic using NAMD3,=C2=A0

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N23= 8


I don't know how to solve it, any suggestion will be much appreciate.

The following parameters were used,
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_prot.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_carb.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_cgenff.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_lipid.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/par_al= l36_na.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/UNK_DE= F6D6.prm
parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/toppar= _water_ions_namd.str
#parameters=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./common/toppa= r_water_ions.mod.str (don't works)




Thanks,

Zhihong xin



--=20
Josh Vermaas

vermaasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci.msu.edu/people/faculty/josh-vermaas/=

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([2001:1388:3cc3:2da9:308c:f0e6:4fd5:fa39]) by smtp.gmail.com with ESMTPSA id x9sm10583831vkn.36.2021.11.16.09.24.54 for (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Tue, 16 Nov 2021 09:24:55 -0800 (PST) From: =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= Content-Type: multipart/alternative; boundary="Apple-Mail=_4752EB4D-63C3-4320-A658-FB229A45BB96" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.7\)) Subject: namd-l: Gallium parameters Message-Id: Date: Tue, 16 Nov 2021 12:25:32 -0500 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3608.120.23.2.7) X-Proofpoint-ORIG-GUID: 1C_Fn4wb0tlD4F4mQ4xZJM1c7mdLECm_ X-CLX-Response: 1TFkXGx0YEQpMehcZHhsRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHEhsRCkNZFxoRCkNJFxoEGh oaEQpZTRdnZnIRCllJFxpxGhAadwYbHxhxGRgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XG2l1bEQeXUgaXkZuHmweR3seUnBgZxtJHUdOZm9pR3URClhcFx8EGgQYHhsFGxoE GxsaBB0EGxkZEBseGh8aEQpeWRdzU3MebhEKTVwXGB4eEQpMWhdsaU1NaxEKTEYXb29ra2traxE KQk8XekBaf1pYS3AfcF0RCkNaFxgaEwQSHwQYGBsEGx0dEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2NseWN9en5hRk9mEQpCThdjU2NrexNYf hpfXhEKQkwXeh5jQR5eXBwfcksRCkJsF29PZEFaQlBtZmtZEQpCQBdpXh9Oc3NFRUZZHhEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2F/AXMZWR5lYhgFEQpZSxcTHxMYEQpwaBdjfn1 iXmRIZB9SWRAZGhEKcGgXYERIQlJ8cxhATB0QGRoRCnBoF2hJHW8ZXUJAHkVZEBkaEQpwbBdpYQ F/SWZ7Qhl6HhAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: 1C_Fn4wb0tlD4F4mQ4xZJM1c7mdLECm_ X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 spamscore=0 priorityscore=341 impostorscore=0 adultscore=0 clxscore=172 phishscore=0 lowpriorityscore=0 mlxscore=0 malwarescore=0 mlxlogscore=629 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111160085 domainage_hfrom=9592 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?IlJPUMOTTi1QQUxBQ0lPUyBHLiI=?= --Apple-Mail=_4752EB4D-63C3-4320-A658-FB229A45BB96 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear users, I have an organic molecule that is coordinated by gallium, and I would = like to know where I can find parameters for these or how I can generate = them. best, geo.= --Apple-Mail=_4752EB4D-63C3-4320-A658-FB229A45BB96 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
Dear users,

I have an organic molecule that is coordinated by gallium, and I would like to know where I can find parameters for these or how I can generate them.

best,

geo.
--Apple-Mail=_4752EB4D-63C3-4320-A658-FB229A45BB96-- From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 16 15:39:48 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AGLdmod005289; Tue, 16 Nov 2021 15:39:48 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AGLdm9j005288; Tue, 16 Nov 2021 15:39:48 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AGLdlQv005284; Tue, 16 Nov 2021 15:39:47 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AGLdlnH005283; Tue, 16 Nov 2021 15:39:47 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AGLdTN1004638 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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Tue, 16 Nov 2021 14:39:26 -0700 Received: from localhost (localhost [127.0.0.1]) by mailrelay2.lanl.gov (Postfix) with ESMTP id 358CD100DED4 for ; Tue, 16 Nov 2021 14:39:26 -0700 (MST) X-NIE-2-Virus-Scanner: amavisd-new at mailrelay2.lanl.gov Received: from EXG16-P-MBX01.win.lanl.gov (exg16-p-mbx01.win.lanl.gov [128.165.106.181]) by mailrelay2.lanl.gov (Postfix) with ESMTP id 24789100DECF for ; Tue, 16 Nov 2021 14:39:26 -0700 (MST) Received: from EXG16-P-MBX04.win.lanl.gov (128.165.106.184) by EXG16-P-MBX01.win.lanl.gov (128.165.106.181) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2242.12; Tue, 16 Nov 2021 14:39:25 -0700 Received: from EXG16-P-MBX04.win.lanl.gov ([::1]) by EXG16-P-MBX04.win.lanl.gov ([fe80::989b:b4f9:e658:5526%6]) with mapi id 15.01.2242.012; Tue, 16 Nov 2021 14:39:25 -0700 From: "Wall, Michael E" To: "namd-l@ks.uiuc.edu" Subject: namd-l: QMMM latency in PME correction Thread-Topic: QMMM latency in PME correction Thread-Index: AQHX2yTBpMV6vb3JLUyapJPRRxwbMg== Date: Tue, 16 Nov 2021 21:39:25 +0000 Message-ID: <12f06652aed04c9aad76cbe0f0e504a5@lanl.gov> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [128.165.106.146] Content-Type: multipart/alternative; boundary="_000_12f06652aed04c9aad76cbe0f0e504a5lanlgov_" X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:6.0.425,18.0.790 definitions=2021-11-16_06:2021-11-16,2021-11-16 signatures=0 X-Proofpoint-Spam-Reason: safe X-Proofpoint-GUID: _Xs51nuH5G5tU4GXQYt9SP6ICkCIjgOT X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIdEQpMehcZGhEKWUQXY05Iek59emlmfUwRClhYF2BkWhtMZm1PUmJ CEQp4ThdvZ3hmbWtiBXlTHxEKeUwXaU0cTBNAYBwTU18RCkNIFwcfGB4RCkNZFwcbGBsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB1xExkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XdXJZHxtEX2IfbR9efx5tcntzXhN5ehxjaUFpY0BNZX4RClhcFx8EGgQYHhsF GxoEGxoaBB0EGx4eEBseGh8aEQpeWRdzU0lHWxEKTVwXGxsZEQpMWhdsaU1NaxEKTEYXb29ra2t paxEKQk8XaEAdYF1aZWNuX04RCkNaFxgaHgQbGBsEGQQeHREKQl4XGxEKRF4XGBEKQlwXGxEKXk 4XGxEKQksXb2d4Zm1rYgV5Ux8RCkJJF29neGZta2IFeVMfEQpCRRdjGnMaAXNMa3laWxEKQk4Xb 2d4Zm1rYgV5Ux8RCkJMF2BkWhtMZm1PUmJCEQpCbBdpW35bQ0lyWFxuGhEKQkAXel95TkxIWRh+ fGcRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdlZ29aXBJlWRp6fREKcGgXbEBGHm0 aS1xrGk8QGRoRCnBoF2toSWtwRFBYTnp/EBkaEQpwaBdgHnAfAXpEeWlHTBAZGhEKcGgXaX0BBV 16RHNSSEIQGRoRCnBoF29dex5ecnpmaGRLEBkaEQpwfRdmQRNDaFN7TEFJSBAZGhEKcH0XZWR/X GVeBVtdTEMQGRoRCnB9F2JOZlBickhoQ0JoEBkaEQpwfxdrHWseU3tnY0ttehAcHxEKcF8XYk5m UGJySGhDQmgQGRoRCnB/F2NiXAFAW15Me01YEBsYHBEKcF8XZm1lZGNuaGBaYBIQGRoRCnBsF2x 8XVJDHG9meFhuEBkaEQpwQxdmQltac2lMHENjHBASHxEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: _Xs51nuH5G5tU4GXQYt9SP6ICkCIjgOT MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=187 suspectscore=0 malwarescore=0 mlxlogscore=865 phishscore=0 spamscore=0 mlxscore=0 priorityscore=30 impostorscore=0 bulkscore=0 lowpriorityscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111160097 X-Spam-Score: 0 X-Spam-OrigSender: mewall@lanl.gov X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Wall, Michael E" --_000_12f06652aed04c9aad76cbe0f0e504a5lanlgov_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Hello NAMD-L, I'm using NAMD to perform QMMM using a large QM region, using LATTE as a QM= solver (https://urldefense.com/v3/__https://github.com/lanl/latte__;!!DZ3f= jg!sF2-qGbr94sZuQylawLrZXrTe3zqvOL5SUo1Po3pBtX5gf_92TKt2iTMDez8dOCyhg$ ). I= 'm seeing some latency on the NAMD side that I'm trying to address. I've done some profiling and found that most of the latency is associated w= ith a PME correction in src/ComputeQM.C (line 5033 in the NAMD_2.14b2_Sourc= e version, about 6-9 seconds required for the system I'm currently looking = at). I had a conversation with Marcelo Melo about strategies for addressing this= issue by parallelizing the PME correction (along with a couple of other ca= lculations). He shared his thoughts and also suggested I post to this maili= ng list to share the observation more broadly and to see whether one of the= other developers might have any insights. Thank you for considering this issue. Sincerely, Michael Wall --- Michael Wall mewall@lanl.gov https://urldefense.com/v3/__http://public.lanl.gov/mewall__;!!DZ3fjg!sF2-qG= br94sZuQylawLrZXrTe3zqvOL5SUo1Po3pBtX5gf_92TKt2iTMDeyDZi9pJQ$=20 --_000_12f06652aed04c9aad76cbe0f0e504a5lanlgov_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable

Hello NAMD-L,

I'm using NAMD to perform QMMM using a large QM region, using LATTE as= a QM solver (https://github.com/lanl/latte). I'm seeing some latency on the N= AMD side that I'm trying to address.

I've done some profiling and found that most of the latency is associa= ted with a PME correction in src/ComputeQM.C (line 5033 in the NAMD_2.14b2_Source version, about 6-9 seconds req= uired for the system I'm currently looking at).

I had a conversation with Marcelo Melo about strategies for a= ddressing this issue by parallelizing the PME correction (along w= ith a couple of other calculations). He shared his thoughts and also = suggested I post to this mailing list to share the observation more broadly and to see whether one of the othe= r developers might have any insights. 

Thank you for considering this issue.

Sincerely,

Michael Wall


---
Michael Wall
mewall@lanl.gov
h= ttp://public.lanl.gov/mewall

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boundary="00000000000017939205d0fd7aef" X-CLX-Response: 1TFkXGxgSEQpMehcYExkRCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHGBkfEQpDWRcHGx0fEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxoScRsbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxtZf2keUB1ecxoeWV0eWmxAR1hze0N6TER4Xnp1SFMZEQpYXBcfBBoEGB4b BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXc1NZaX0RCk1cFxkYGBEKTFoXbGlra2sRCkxGF29ra2t raxEKQk8XaFheUEkFElx7ZHsRCkNaFxgaEwQSHwQYGBsEHxkRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZlh9WGtAGgVyRGgRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdjH1l5eWkdT3xaWhEKQmwXb1JnHHJDSU9afl0RCkJAF2lBX158XWVjGB5zEQpC WBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXeh4cGX8BH15+Rn8RCllLFxMfExkRCnBoF2VMa0JgcBo caRtBEBkaEQpwaBdhZHpPQ2BmU19OSxAZGhEKcGgXbwFcZ3tybkUZUlAQGRoRCnBoF2JfZ2Jzfk lMQHpdEBkaEQpwaBdhYX5TGEV/bWhMcBAZGhEKcGwXaHNSWXJnex97eUkQGRoRCnBMF21oZRlBU n17GEVSEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 1sUC4z7tY04sw4pFjmrYQiPfnRtP_by3 X-Proofpoint-GUID: 1sUC4z7tY04sw4pFjmrYQiPfnRtP_by3 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 clxscore=128 adultscore=0 mlxscore=0 suspectscore=0 bulkscore=0 spamscore=0 impostorscore=0 lowpriorityscore=0 priorityscore=293 mlxlogscore=905 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170074 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --00000000000017939205d0fd7aef Content-Type: text/plain; charset="UTF-8" I am getting this error all the time however looking at the log file it I can't see any problem, Can someone guide me through this? TIMING: 140000 CPU: 582.638, 0.00415636/step Wall: 588.943, 0.00420159/step, 0.0700266 hours remaining, 0.000000 MB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 140000 223373.9499 31849.0499 51029.8752 0.0000 -1835084.0187 226095.3588 0.0000 0.0000 375499.3782 -927236.4068 299.0321 -1302735.7850 -925060.6627 298.8982 1333.1145 -117.7176 4325123.9157 32.4425 35.0408 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 140000 WRITING COORDINATES TO DCD FILE npt.dcd AT STEP 140000 WRITING COORDINATES TO RESTART FILE AT STEP 140000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 140000 FINISHED WRITING RESTART VELOCITIES TIMING: 140100 CPU: 583.073, 0.00434618/step Wall: 589.384, 0.00440529/step, 0.0732991 hours remaining, 0.000000 MB of memory in use. ENERGY: 140100 223597.4105 31606.3767 51068.4535 0.0000 -1836648.9281 227931.4741 0.0000 0.0000 375223.0652 -927222.1480 298.8121 -1302445.2132 -925055.2839 298.7649 1523.2635 38.9990 4320494.5662 14.3267 11.1725 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 140100 WRITING COORDINATES TO RESTART FILE AT STEP 140100 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 140100 FINISHED WRITING RESTART VELOCITIES TIMING: 140200 CPU: 583.481, 0.00408428/step Wall: 589.798, 0.00414259/step, 0.068813 hours remaining, 0.000000 MB of memory in use. ENERGY: 140200 224237.8163 31792.6069 51139.2750 0.0000 -1837442.9612 228065.3755 0.0000 0.0000 375097.6231 -927110.2645 298.7122 -1302207.8876 -924947.7198 298.7550 1461.2544 28.8577 4319731.6498 -38.1838 -36.6981 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 140200 WRITING COORDINATES TO RESTART FILE AT STEP 140200 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 140200 FINISHED WRITING RESTART VELOCITIES The file ends like this without writing further energies. The errorfile says one or more process terminated. Many thanks, Ashutosh --00000000000017939205d0fd7aef Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I am getting this error all the time however looking = at the log file it I can't see any problem, Can someone guide me throug= h this?

TIMING: 140000 =C2=A0CPU: 582.638, 0.0= 0415636/step =C2=A0Wall: 588.943, 0.00420159/step, 0.0700266 hours remainin= g, 0.000000 MB of memory in use.
ETITLE: =C2=A0 =C2=A0 =C2=A0TS =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 BOND =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0ANGLE = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0DIHED =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0I= MPRP =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ELECT =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0VDW =C2=A0 =C2=A0 =C2=A0 BOUNDARY =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 MISC =C2=A0 =C2=A0 =C2=A0 =C2=A0KINETIC =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 TOTAL =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= TEMP =C2=A0 =C2=A0 =C2=A0POTENTIAL =C2=A0 =C2=A0 =C2=A0 =C2=A0 TOTAL3 =C2= =A0 =C2=A0 =C2=A0 =C2=A0TEMPAVG =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0PR= ESSURE =C2=A0 =C2=A0 =C2=A0GPRESSURE =C2=A0 =C2=A0 =C2=A0 =C2=A0 VOLUME =C2= =A0 =C2=A0 =C2=A0 PRESSAVG =C2=A0 =C2=A0 =C2=A0GPRESSAVG

ENERGY: =C2= =A0140000 =C2=A0 =C2=A0223373.9499 =C2=A0 =C2=A0 31849.0499 =C2=A0 =C2=A0 5= 1029.8752 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1835084.= 0187 =C2=A0 =C2=A0226095.3588 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0375499.3782 =C2=A0 =C2=A0 =C2=A0 =C2= =A0-927236.4068 =C2=A0 =C2=A0 =C2=A0 299.0321 =C2=A0-1302735.7850 =C2=A0 -9= 25060.6627 =C2=A0 =C2=A0 =C2=A0 298.8982 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 1333.1145 =C2=A0 =C2=A0 =C2=A0-117.7176 =C2=A0 4325123.9157 =C2=A0 =C2=A0 = =C2=A0 =C2=A032.4425 =C2=A0 =C2=A0 =C2=A0 =C2=A035.0408

WRITING EXTE= NDED SYSTEM TO RESTART FILE AT STEP 140000
WRITING COORDINATES TO DCD FI= LE npt.dcd AT STEP 140000
WRITING COORDINATES TO RESTART FILE AT STEP 14= 0000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTA= RT FILE AT STEP 140000
FINISHED WRITING RESTART VELOCITIES
TIMING: 14= 0100 =C2=A0CPU: 583.073, 0.00434618/step =C2=A0Wall: 589.384, 0.00440529/st= ep, 0.0732991 hours remaining, 0.000000 MB of memory in use.
ENERGY: =C2= =A0140100 =C2=A0 =C2=A0223597.4105 =C2=A0 =C2=A0 31606.3767 =C2=A0 =C2=A0 5= 1068.4535 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 -1836648.= 9281 =C2=A0 =C2=A0227931.4741 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0375223.0652 =C2=A0 =C2=A0 =C2=A0 =C2= =A0-927222.1480 =C2=A0 =C2=A0 =C2=A0 298.8121 =C2=A0-1302445.2132 =C2=A0 -9= 25055.2839 =C2=A0 =C2=A0 =C2=A0 298.7649 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 1523.2635 =C2=A0 =C2=A0 =C2=A0 =C2=A038.9990 =C2=A0 4320494.5662 =C2=A0 = =C2=A0 =C2=A0 =C2=A014.3267 =C2=A0 =C2=A0 =C2=A0 =C2=A011.1725

WRITI= NG EXTENDED SYSTEM TO RESTART FILE AT STEP 140100
WRITING COORDINATES TO= RESTART FILE AT STEP 140100
FINISHED WRITING RESTART COORDINATES
WRI= TING VELOCITIES TO RESTART FILE AT STEP 140100
FINISHED WRITING RESTART = VELOCITIES
TIMING: 140200 =C2=A0CPU: 583.481, 0.00408428/step =C2=A0Wall= : 589.798, 0.00414259/step, 0.068813 hours remaining, 0.000000 MB of memory= in use.
ENERGY: =C2=A0140200 =C2=A0 =C2=A0224237.8163 =C2=A0 =C2=A0 317= 92.6069 =C2=A0 =C2=A0 51139.2750 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 = =C2=A0 =C2=A0 -1837442.9612 =C2=A0 =C2=A0228065.3755 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0.0000 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A0375097.6231 = =C2=A0 =C2=A0 =C2=A0 =C2=A0-927110.2645 =C2=A0 =C2=A0 =C2=A0 298.7122 =C2= =A0-1302207.8876 =C2=A0 -924947.7198 =C2=A0 =C2=A0 =C2=A0 298.7550 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 1461.2544 =C2=A0 =C2=A0 =C2=A0 =C2=A028.8577 = =C2=A0 4319731.6498 =C2=A0 =C2=A0 =C2=A0 -38.1838 =C2=A0 =C2=A0 =C2=A0 -36.= 6981

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 140200
WRITI= NG COORDINATES TO RESTART FILE AT STEP 140200
FINISHED WRITING RESTART C= OORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 140200
FIN= ISHED WRITING RESTART VELOCITIES

=C2=A0The file en= ds like this without writing further energies. The errorfile says one or mo= re process terminated.

Many thanks,
Ashu= tosh
--00000000000017939205d0fd7aef-- From owner-namd-l@halifax.ks.uiuc.edu Wed Nov 17 10:02:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHG2aWe007598; Wed, 17 Nov 2021 10:02:36 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHG2aBh007597; Wed, 17 Nov 2021 10:02:36 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHG2ZAU007593; Wed, 17 Nov 2021 10:02:35 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHG2ZpF007592; Wed, 17 Nov 2021 10:02:35 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHG2QTk007584 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 17 Nov 2021 10:02:27 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AHFs13U013717 for ; Wed, 17 Nov 2021 16:02:26 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=scfbioiitd@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-wr1-f42.google.com (mail-wr1-f42.google.com [209.85.221.42]) by mx0a-00007101.pphosted.com with ESMTP id 3cctsn3g0j-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 17 Nov 2021 16:02:25 +0000 Received: by mail-wr1-f42.google.com with SMTP id a9so5640747wrr.8 for ; Wed, 17 Nov 2021 08:02:25 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:from:date:message-id:subject:to; bh=x+xm+U6A3ycjbeNxcFqwVrinn/II6l+8eEGt7kI0Xhk=; b=F5cZz+At+yXaLH/63eKPDSCdOGDNT1RW9FBMUZeRRIL5hlt2uGX8KMKX0WSe8nX1Q2 5n3CpdlcpWZ9dP337XIMVp01tpLvT9gK+vcLW0QxIeCKK2STblYoc1vbm1zB9z4yiA84 8BWWj/fAzDAPaWLYI9q9X7MrQ1fqss87I3yM3lwGQdkqw2mKJZjXyb3eq+3WPYZF6qFU vuhPn57mQat/Yp6+NryYhajE7nnPe+7ViLCr36RX2oaZTHsUuSNiK8jA1dRprAFnEXQW 69KVgJbqL/cfFX1KcvgCal5OBB+MkcxWHM2sz3zQZ27t6h0ZCkAKk222GvysGt5to+0H PzNA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=x+xm+U6A3ycjbeNxcFqwVrinn/II6l+8eEGt7kI0Xhk=; b=66Pfx7hpPjg/dHq7byXMqjCWSKH44V18N+y/Su04XNOzTDcRTbqAzgxMmybsTOonRU e4vw14amPvvj0e0ZtX4Kt25BPJz4JQyuDlht0jICxEUnCIkc5I8o1Z9rVbRw5UogUBcR ulgYbvi01x2muJHk1XS0G0W484PahXjm3yAhcpeW7Xt5YqD4Sm7cOBoVGkitkyrA13da CEtGeol8F+KWZdLAenBw8Y+5DYHkXkMklMOOXV7oOsi2tqQWwQSVJwrMcJg92L27VFj5 jByQLoFODsurbkQXes0Kc5hqHONOeKdtJrg9v8CSQlK8u5fv0+SJVsar74GiAh30jcdf HsDw== X-Gm-Message-State: AOAM530ImOtPCsN4/WeDdMDiEZY6V9arRWI/H+LwgKWJHY9Ef+nA0Gfo edUx5DZSm/WMwEXSaomrheR4fbXHGbdmSiZcDimTz2uN6tQ= X-Google-Smtp-Source: ABdhPJyy1TsAsBk9orE1/xP2QWEATOu90NVTlDOBqDLAQbldhP9b0q2xthQ55YZzHCDp0JxUzd5Z3BPgV+GcAVIE2q8= X-Received: by 2002:a5d:6843:: with SMTP id o3mr21146398wrw.174.1637164943593; Wed, 17 Nov 2021 08:02:23 -0800 (PST) MIME-Version: 1.0 From: Ashutosh Shandilya Date: Wed, 17 Nov 2021 10:58:33 -0500 Message-ID: Subject: namd-l: colvars: Too many iterations in routine jacobi. To: NAMD list Content-Type: multipart/mixed; boundary="000000000000e6f1c205d0fe2ab8" X-Proofpoint-ORIG-GUID: eUjtSI5cAz0ATzpJCG17Lp6zYpy5CiYD X-CLX-Shades: MLX X-CLX-Response: 1TFkXGRITEQpMehcZGhkRCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHGR4aEQpDWRcHGxgZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcfHnESBhsZdwYbGx8GGRpCHQYaBhwTBhsYGnEbHxAadwYaBhoGG gYaBhoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF09/QF55Yx9Ja1Aaa35Q WmBpbRsdZlocUHNaUx9pQ3NuEQpYXBcfBBoEGB4bBRsaBBsaGgQdBBseHhAbHhofGhEKXlkXc1N ZXV4RCk1cFxsZExEKTFoXaGlra00RCkxGF29ra2traxEKQk8XaFheUEkFElx7ZHsRCkNaFxgaEw QSHwQYGBsEHhgRCkJeFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZlh9WGtAGgVyRGgRCkJOF2NTY2t7E1h+Gl9eEQpCTBdjH1l5eWkdT3xaWhEKQmwX b1JnHHJDSU9afl0RCkJAF2FITEQbRFtQbWYFEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXaFtZfVhAGGhjb2gRCllLFxMfExkRCnBoF2lCRkxyRXBQXBJsEBkaEQpwaBdkZkBiQUNdHX 1ZXhAZGhEKcGgXaR9eGGNBTgFJbEMQGRoRCnBoF29mch1HbGhuQ3BNEBkaEQpwaBdjb2dDQE5MG R9JHRAZGhEKcGsXZht+Y0VzXQVSQlsQGRoRCnBLF2NMBWRPbXhkUkhcEBkaEQpwbBdoc1JZcmd7 H3t5SRAeEhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: eUjtSI5cAz0ATzpJCG17Lp6zYpy5CiYD X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 impostorscore=0 mlxlogscore=977 spamscore=0 clxscore=389 lowpriorityscore=0 malwarescore=0 priorityscore=303 bulkscore=0 suspectscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170076 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --000000000000e6f1c205d0fe2ab8 Content-Type: multipart/alternative; boundary="000000000000e6f1c005d0fe2ab6" --000000000000e6f1c005d0fe2ab6 Content-Type: text/plain; charset="UTF-8" I am running ABF and getting this error. Frame index: 32 ; optimal RMSD = 4.87456 Frame index: 31 ; optimal RMSD = 4.87456 Frame index: 30 ; optimal RMSD = 4.87456 Frame index: 29 ; optimal RMSD = 4.87456 Frame index: 28 ; optimal RMSD = 4.87456 colvars: Prepared sample and gradient buffers at step 0. colvars: Too many iterations in routine jacobi. colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc). colvars: Too many PFATAL ERROR: Error in the collective variables module (see above for details) FATAL ERROR: Error in the collective variables module (see above for details) I have used different timesteps but still I am getting this error. Any suggestions? Many thanks --000000000000e6f1c005d0fe2ab6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I am=C2=A0 running ABF and getting this error.
<= div>
Frame index: 32 ; optimal RMSD =3D 4.87456
Frame inde= x: 31 ; optimal RMSD =3D 4.87456
Frame index: 30 ; optimal RMSD =3D 4.87= 456
Frame index: 29 ; optimal RMSD =3D 4.87456
Frame index: 28 ; opti= mal RMSD =3D 4.87456
colvars: =C2=A0 Prepared sample and gradient buffer= s at step 0.
colvars: Too many iterations in routine jacobi.
colvars:= This is usually the result of an ill-defined set of atoms for rotational a= lignment (RMSD, rotateReference, etc).
colvars: Too many PFATAL ERROR: E= rror in the collective variables module (see above for details)
FATAL ER= ROR: Error in the collective variables module (see above for details)
=

I have used different timesteps but still I am getting = this error. Any suggestions?

Many thanks
=
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To: NAMD list , Ashutosh Shandilya Content-Type: multipart/alternative; boundary="00000000000063d3a305d0fe87f7" X-CLX-Shades: MLX X-Proofpoint-GUID: 94-bQobogGdCXbmJdyGf95GEHuM1j9Tb X-Proofpoint-ORIG-GUID: 94-bQobogGdCXbmJdyGf95GEHuM1j9Tb X-CLX-Response: 1TFkXGBkaEQpMehcZGxgRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGBIeEQpDWRcHHx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYYGxpxGB4TEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxMeB0h7RUhFTW1OaXJIR2BOU21MEx9tb2JfZxtAE35IEQpYXBcfBBoEGB4b BRsaBBsbGgQdBBsZGxAbHhofGhEKXlkXc1NeYx0RCk1cFxscGxEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHBMRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2dcfgFYXRlsbWMFEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXZEBFGFAcZxxvQGwRCllLFxMfExkRCnBoF2RmQGJBQ10dfVleEBkaEQpwaBducxJhZn9CfE NjTxAZGhEKcGgXb3xTXBtIE0FCclIQGRoRCnBoF2dLW3lkS0FoGl9tEBkaEQpwaBdpGUcST2VpS 11AUxAZGhEKcGwXZh97WFxiBUtYZB8QGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdL ESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 phishscore=0 lowpriorityscore=0 clxscore=230 spamscore=0 bulkscore=0 priorityscore=312 malwarescore=0 impostorscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170077 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000063d3a305d0fe87f7 Content-Type: text/plain; charset="UTF-8" This message is the key: colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc). If the structure of the group of atoms changes too much, it becomes possible that a pure rotation is not the transformation that minimizes the RMSD, but another transformation does (e.g. rotation + reflection across a plane). You do not need to change the time step, but instead pick a selection that is guaranteed to have only moderate changes in structure. Practically speaking, the RMSD should remain much lower than the radius of gyration. If you compute that RMSD in VMD you will have a similar problem, just with a different outcome because the numerical algorithm is different. Giacomo On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya wrote: > I am running ABF and getting this error. > > Frame index: 32 ; optimal RMSD = 4.87456 > Frame index: 31 ; optimal RMSD = 4.87456 > Frame index: 30 ; optimal RMSD = 4.87456 > Frame index: 29 ; optimal RMSD = 4.87456 > Frame index: 28 ; optimal RMSD = 4.87456 > colvars: Prepared sample and gradient buffers at step 0. > colvars: Too many iterations in routine jacobi. > colvars: This is usually the result of an ill-defined set of atoms for > rotational alignment (RMSD, rotateReference, etc). > colvars: Too many PFATAL ERROR: Error in the collective variables module > (see above for details) > FATAL ERROR: Error in the collective variables module (see above for > details) > > I have used different timesteps but still I am getting this error. Any > suggestions? > > Many thanks > --00000000000063d3a305d0fe87f7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
This message is the key:
colvars: This is usually the result of an ill-defined set of atoms for = rotational alignment (RMSD, rotateReference, etc).

<= div>If the structure of the group of atoms= changes too much, it becomes possible that a pure rotation is not the tran= sformation that minimizes the RMSD, but another transformation does (e.g. r= otation=C2=A0+ reflection across a plane).

You do not need to change= the time step, but instead pick a selection that is guaranteed to have onl= y moderate changes in structure.=C2=A0 Practically speaking, the RMSD shoul= d=C2=A0remain much lower than the radius of gyration.

If you compute that RMSD in VMD you will have a similar problem, j= ust with a different outcome because the numerical algorithm is different.<= /span>

Giacomo

On Wed, Nov 17, 2021 at 1= 1:03 AM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
I am=C2=A0 running = ABF and getting this error.

Frame index: 32 ; opti= mal RMSD =3D 4.87456
Frame index: 31 ; optimal RMSD =3D 4.87456
Frame= index: 30 ; optimal RMSD =3D 4.87456
Frame index: 29 ; optimal RMSD =3D= 4.87456
Frame index: 28 ; optimal RMSD =3D 4.87456
colvars: =C2=A0 P= repared sample and gradient buffers at step 0.
colvars: Too many iterati= ons in routine jacobi.
colvars: This is usually the result of an ill-def= ined set of atoms for rotational alignment (RMSD, rotateReference, etc).colvars: Too many PFATAL ERROR: Error in the collective variables module (= see above for details)
FATAL ERROR: Error in the collective variables mo= dule (see above for details)

I have used different= timesteps but still I am getting this error. Any suggestions?
Many thanks
--00000000000063d3a305d0fe87f7-- From owner-namd-l@halifax.ks.uiuc.edu Wed Nov 17 11:55:35 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHHtZc5012712; Wed, 17 Nov 2021 11:55:35 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHHtYER012711; Wed, 17 Nov 2021 11:55:34 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHHtY2v012707; Wed, 17 Nov 2021 11:55:34 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHHtYwW012706; Wed, 17 Nov 2021 11:55:34 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHHtO7P012697 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 17 Nov 2021 11:55:24 -0600 (CST) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AHFtHnR028025 for ; Wed, 17 Nov 2021 17:55:24 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=scfbioiitd@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-wm1-f45.google.com (mail-wm1-f45.google.com [209.85.128.45]) by mx0b-00007101.pphosted.com with ESMTP id 3cd4t899yu-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 17 Nov 2021 17:55:23 +0000 Received: by mail-wm1-f45.google.com with SMTP id p18so2983672wmq.5 for ; Wed, 17 Nov 2021 09:55:23 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=55dU1uZrTPEZ0yE/jlyfG8bx5hqDUgBU/1ooI08Iysw=; b=S/wWTjjLYIkXvfbdHSs8cydcMAhxrpm2jG8Xd75T+G6lzzcKYcCQiMTD6pqgX1K2BL qBLGxVFmRp7uWF/bDj8TN72XYLH7mANd0YnSPP8JrRFmwWHCem1wsq+Ue2ubkypIOzzl 4D4n4xrWYvB0Wdx3KoyD6FYZFgLaXiDHHmlA1X40aXyevrGRGsTp8wZirI2g1v5gV6CJ CglbV4i+qSqP8QjPsd6notl3qh1m7y9F808RmqNh0zX/P0InGhp3yAWCQpxUWLPqiKRR MlPel9yp4fnJI/THu7nZX+sHSQmCfDdip9A1dgxgAEIIgw8XdahiW9KDSlyIFk+4s8sD 3k0g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=55dU1uZrTPEZ0yE/jlyfG8bx5hqDUgBU/1ooI08Iysw=; b=1jF54c8W4MWT1LKoBthWzBaj124q1OIAlS/4DqIH3poRkCyKSAycQYd9vHf9HAt/Jc TimdRC1TzedLTlVf/WwI79ThUu4IgBAziL5IYPnE58+kbRY4M54aXIBkJlQswjDG6/qh 4ohRP7wsS4xfDQDC6RYrR2HY82NzZDwEpN9+xqAYmrAxpoB6jD61P5UQXumRBC7Pvd4n uvlj+do3BfA+UvS4tjd+O0tV/Ho9Hig7wbvynUoE1J62Oqnxwthk1yoZR11vTvP7IuMd N//JivPdZVoJmrNTcY/OaYfmX3pwfINwWEtvDUwAlEw2jRerutyPGiRxEk8L+nIJFgRI aGNQ== X-Gm-Message-State: AOAM533rC9wc94g2GcrRa0ooPP1zhLrzg+14FyLE84YFmW1i8Wf1Vpwe lHF4jqn0dN2snizU31O1m0ktWN+S/mxfXHd77Qw= X-Google-Smtp-Source: ABdhPJxrQ7HQ52NzB3xuAzfes5QDH3/ObxOOXlU9/0zlIiIwzlkEr/Yq3tf+fxvY13o2Bzglar7CMxx0j26Q8eJ7Y0Y= X-Received: by 2002:a05:600c:4153:: with SMTP id h19mr1859411wmm.142.1637171722271; Wed, 17 Nov 2021 09:55:22 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: Ashutosh Shandilya Date: Wed, 17 Nov 2021 12:51:32 -0500 Message-ID: Subject: Re: namd-l: colvars: Too many iterations in routine jacobi. To: Giacomo Fiorin Cc: NAMD list Content-Type: multipart/alternative; boundary="000000000000f13e0905d0ffbe2f" X-CLX-Response: 1TFkXGxkbEQpMehcZGBkRCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHGR4TEQpDWRcHHxkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGxtxGxgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XQhhoGh9/UFAfRlNZeEh1eUNYbFpLbUtbWE5saBtLSVkRClhcFx8EGgQYHhsF GxoEGxsaBB0EGxkYEBseGh8aEQpeWRdzU19LRxEKTVwXGR4eEQpMWhd4aWtrTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2h9QWBDWn1zR0ETEQpDWhcYGhMEEh8EGxgSBB 4fEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2ZYfVhrQBoFckRoEQpCThdjU2NrexNYfhpfXhEKQkwXYx9ZeXlpHU98WloRCkJsF29S ZxxyQ0lPWn5dEQpCQBdnXH4BWF0ZbG1jBREKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2RARRh QHGccb0BsEQpZSxcTHxMZEQpwaBdkQVJSXlpTARh8fxAZGhEKcGgXZX5TRRJiYWVmU10QGRoRCn BoF2RmQGJBQ10dfVleEB4SEQpwaBdvfFNcG0gTQUJyUhAeEhEKcGgXaRlHEk9laUtdQFMQHhIRC nBsF2hzUllyZ3sfe3lJEBsSEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: h2B05Uzz5lysRb_SirFpaGaqrdFB1acs X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: h2B05Uzz5lysRb_SirFpaGaqrdFB1acs X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 adultscore=0 spamscore=0 lowpriorityscore=0 mlxlogscore=999 malwarescore=0 mlxscore=0 phishscore=0 bulkscore=0 clxscore=131 suspectscore=0 priorityscore=323 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170081 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --000000000000f13e0905d0ffbe2f Content-Type: text/plain; charset="UTF-8" Thanks for your reply, As I understand I should consider the selection which has only moderate change. First step itself gives this problem so I have not calculated the RMSD. I have a string of pdbs from PNEB path and I want to have a pmf that's why I am using abf. So the selected atoms have lots of transformation. So what are the options. Many thanks, Ashutosh On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin wrote: > This message is the key: > colvars: This is usually the result of an ill-defined set of atoms for > rotational alignment (RMSD, rotateReference, etc). > > If the structure of the group of atoms changes too much, it becomes > possible that a pure rotation is not the transformation that minimizes the > RMSD, but another transformation does (e.g. rotation + reflection across a > plane). > > You do not need to change the time step, but instead pick a selection that > is guaranteed to have only moderate changes in structure. Practically > speaking, the RMSD should remain much lower than the radius of gyration. > > If you compute that RMSD in VMD you will have a similar problem, just with > a different outcome because the numerical algorithm is different. > > Giacomo > > On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya > wrote: > >> I am running ABF and getting this error. >> >> Frame index: 32 ; optimal RMSD = 4.87456 >> Frame index: 31 ; optimal RMSD = 4.87456 >> Frame index: 30 ; optimal RMSD = 4.87456 >> Frame index: 29 ; optimal RMSD = 4.87456 >> Frame index: 28 ; optimal RMSD = 4.87456 >> colvars: Prepared sample and gradient buffers at step 0. >> colvars: Too many iterations in routine jacobi. >> colvars: This is usually the result of an ill-defined set of atoms for >> rotational alignment (RMSD, rotateReference, etc). >> colvars: Too many PFATAL ERROR: Error in the collective variables module >> (see above for details) >> FATAL ERROR: Error in the collective variables module (see above for >> details) >> >> I have used different timesteps but still I am getting this error. Any >> suggestions? >> >> Many thanks >> > --000000000000f13e0905d0ffbe2f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thanks for your reply, As I understand I should consi= der the selection which has only moderate change. First step itself gives t= his problem so I have not calculated the RMSD. I have a string of pdbs from= PNEB path and I want to have a pmf that's why I am using abf. So the s= elected atoms have lots of transformation. So what are the options.

Many thanks,
Ashutosh

On Wed, Nov = 17, 2021 at 11:28 AM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
This message is the key:<= div>colvars: This is usually the result of= an ill-defined set of atoms for rotational alignment (RMSD, rotateReferenc= e, etc).

If th= e structure of the group of atoms changes too much, it becomes possible tha= t a pure rotation is not the transformation that minimizes the RMSD, but an= other transformation does (e.g. rotation=C2=A0+ reflection across a plane).=

You do not need to change the time step, but instead pick a selecti= on that is guaranteed to have only moderate changes in structure.=C2=A0 Pra= ctically speaking, the RMSD should=C2=A0remain much lower than the radius o= f gyration.

If you compute that RMSD in VMD y= ou will have a similar problem, just with a different outcome because the n= umerical algorithm is different.

Giacomo

On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya <scfbioiitd@gmail.com>= wrote:
I am=C2=A0 running ABF and getting this error.

=
Frame index: 32 ; optimal RMSD =3D 4.87456
Frame index: 31 ; = optimal RMSD =3D 4.87456
Frame index: 30 ; optimal RMSD =3D 4.87456
F= rame index: 29 ; optimal RMSD =3D 4.87456
Frame index: 28 ; optimal RMSD= =3D 4.87456
colvars: =C2=A0 Prepared sample and gradient buffers at ste= p 0.
colvars: Too many iterations in routine jacobi.
colvars: This is= usually the result of an ill-defined set of atoms for rotational alignment= (RMSD, rotateReference, etc).
colvars: Too many PFATAL ERROR: Error in = the collective variables module (see above for details)
FATAL ERROR: Err= or in the collective variables module (see above for details)
I have used different timesteps but still I am getting this err= or. Any suggestions?

Many thanks
--000000000000f13e0905d0ffbe2f-- From owner-namd-l@halifax.ks.uiuc.edu Wed Nov 17 12:32:38 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHIWca9014871; Wed, 17 Nov 2021 12:32:38 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHIWcmR014870; Wed, 17 Nov 2021 12:32:38 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHIWbN4014866; Wed, 17 Nov 2021 12:32:37 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHIWbgw014865; Wed, 17 Nov 2021 12:32:37 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHIWOWd014857 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 17 Nov 2021 12:32:25 -0600 (CST) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AHFs1bi028634 for ; Wed, 17 Nov 2021 18:32:24 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=giacomo.fiorin@gmail.com; dkim=pass header.d=gmail.com header.s=20210112 Received: from mail-yb1-f176.google.com (mail-yb1-f176.google.com [209.85.219.176]) by mx0b-00007101.pphosted.com with ESMTP id 3cd152ubbu-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 17 Nov 2021 18:32:24 +0000 Received: by mail-yb1-f176.google.com with SMTP id s186so10185176yba.12 for ; Wed, 17 Nov 2021 10:32:24 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=zsnVWjIBY+NpbXQDi1X9KWDrQUCtmQdflsxX6t7In44=; b=WXEqrZx2ovLyPxeEQBzGpyg/hLOSvkaX73IsB2wyLvu11k+QXI9BfTVt9ooCgYJoBQ z4xbKb38Mcia0XPLshLc8F1cwQSsCgpjJx/F5ZXDUp9yAZ5qqko6//IB0rk0JJdjJolg ogEJNhayhi8madJrhZCOz++i070yerUA37cQTsgUGuSg2B9MoPBb0yrU12XVTkpFM4MW k6hG5fv81ZsdZakXBx0JzX23xE2TnRB3yvR2eJxDUe/9FIfTjcaKaT6QhzTxletbuJ95 n8rH5n/lDH7xONf1Ituj2KpL4+uAnz0VoDeGAEZO7RsNb9dtHmuxwIZDri40EiWbySJE 44RQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=zsnVWjIBY+NpbXQDi1X9KWDrQUCtmQdflsxX6t7In44=; b=XQ01wM1H0Bv64wLlXXMLTJVZ6iYApnV1ZDh+ycmVEZuNFs9BbN/TnorEjVmjgViCO1 AmnHSsATt1FITNvMLytg/I7nwIKkgBdks7YVWFJQX4KlNj5rno9omd0BWA+vtjbEeIrY 2zE4SZjOUltW64dBOg4IpNoU9uk0UGSkT3/ai8UJGhHu0qrCnTP+8aVVizLMlhRJignk dgEu8kP9YZ+pRsgT8izpvPfAC18ufVtl6rntMeFGYJa+CXnIFqS5mzSX3pMuA254aq+r MTmm4J7zMnf+5KoskYx2DLue558ZXnszr5IXWsCi7c3G5U5xpNoN7xZhvdBHV6GARc7F XCCQ== X-Gm-Message-State: AOAM532SQoXOrHjAxsI+pFZdMt6U0beQREY8lmKrs/5Sls9h2il+pzAr dyOGF5BcEo3IaR0zTnTXzOQCiXpm0SdUXrmLE6U= X-Google-Smtp-Source: ABdhPJxS6GbKF68SZTSsxjtTwLjnaeDvbhUKVdr3p661CW0Kvlz/oNpGCMmJW4kIng54m2Mr8CFCtKkh0PF01GhReUw= X-Received: by 2002:a25:cb46:: with SMTP id b67mr21362552ybg.517.1637173943627; Wed, 17 Nov 2021 10:32:23 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: Giacomo Fiorin Date: Wed, 17 Nov 2021 13:31:47 -0500 Message-ID: Subject: Re: namd-l: colvars: Too many iterations in routine jacobi. To: Ashutosh Shandilya Cc: NAMD list Content-Type: multipart/alternative; boundary="00000000000058756a05d10043b8" X-CLX-Shades: MLX X-Proofpoint-GUID: 8RF4PxmFgtOOMOGGeb7kB0HmuJwzLfaR X-Proofpoint-ORIG-GUID: 8RF4PxmFgtOOMOGGeb7kB0HmuJwzLfaR X-CLX-Response: 1TFkXGxMcEQpMehcZGhsRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHh4YEQpDWRcHHxkRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHRxxHx0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XEnhsHnpSR2xNXmVlZ2VtbU9IHUFoGmJHX2BdUGZMS3gRClhcFx8EGgQYHhsF GxoEGxsaBB0EGxkYEBseGh8aEQpeWRdzU18TfhEKTVwXBxkRCkxaF2l7aWtNTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2FZHHkYSAUSG0J4EQpDWhcYGhMEEh8EGBsTBB sdHBEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdsZUBSSxtyZXlOTREKQk4XY1Nja3sTWH4aX14RCkJMF2ddW3IdbmxPWHhgEQpCbBdh X3pTGUNEGnobfhEKQkAXZ1x+AVhdGWxtYwURCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5QxdkQEUYUBxnHG9AbBEKWUsXEx8TGREKcGgXZGZAYkFDXR19WV4QHhIRCnBoF298U1wbSBNBQn JSEB4SEQpwaBdhHXppHh0fZ3NAfBAaEQpwaBdjH0J6TVxecmgTeBAaEQpwaBdpGUcST2VpS11AU xAeEhEKcGwXZh97WFxiBUtYZB8QGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 suspectscore=0 phishscore=0 lowpriorityscore=0 clxscore=196 spamscore=0 bulkscore=0 priorityscore=301 malwarescore=0 impostorscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170083 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000058756a05d10043b8 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable There *were* multiple RMSD computations, because that's how the distances between path frames are computed. You are also omitting several warnings above, btw. One was "Please check your configuration or increase restraint on z(=CF=83)". What did you do th= ere? I don't know where you got the PDB structures from, but I recommend that you load them in VMD and compute the RMSD of the coordinates of your simulation with respect to each. All RMSDs need to be well defined in order to be able to compute the path variable derived from them. Giacomo On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya wrote: > Thanks for your reply, As I understand I should consider the selection > which has only moderate change. First step itself gives this problem so I > have not calculated the RMSD. I have a string of pdbs from PNEB path and = I > want to have a pmf that's why I am using abf. So the selected atoms have > lots of transformation. So what are the options. > > Many thanks, > Ashutosh > > On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin > wrote: > >> This message is the key: >> colvars: This is usually the result of an ill-defined set of atoms for >> rotational alignment (RMSD, rotateReference, etc). >> >> If the structure of the group of atoms changes too much, it becomes >> possible that a pure rotation is not the transformation that minimizes t= he >> RMSD, but another transformation does (e.g. rotation + reflection across= a >> plane). >> >> You do not need to change the time step, but instead pick a selection >> that is guaranteed to have only moderate changes in structure. Practica= lly >> speaking, the RMSD should remain much lower than the radius of gyration. >> >> If you compute that RMSD in VMD you will have a similar problem, just >> with a different outcome because the numerical algorithm is different. >> >> Giacomo >> >> On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya >> wrote: >> >>> I am running ABF and getting this error. >>> >>> Frame index: 32 ; optimal RMSD =3D 4.87456 >>> Frame index: 31 ; optimal RMSD =3D 4.87456 >>> Frame index: 30 ; optimal RMSD =3D 4.87456 >>> Frame index: 29 ; optimal RMSD =3D 4.87456 >>> Frame index: 28 ; optimal RMSD =3D 4.87456 >>> colvars: Prepared sample and gradient buffers at step 0. >>> colvars: Too many iterations in routine jacobi. >>> colvars: This is usually the result of an ill-defined set of atoms for >>> rotational alignment (RMSD, rotateReference, etc). >>> colvars: Too many PFATAL ERROR: Error in the collective variables modul= e >>> (see above for details) >>> FATAL ERROR: Error in the collective variables module (see above for >>> details) >>> >>> I have used different timesteps but still I am getting this error. Any >>> suggestions? >>> >>> Many thanks >>> >> --00000000000058756a05d10043b8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
There were multiple RMSD computati= ons, because that's how the distances between path frames are computed.=

You are also omitting sev= eral warnings above, btw.=C2=A0 One was "Please check your configurati= on or increase restraint on z(=CF=83)".=C2=A0 What did you do there?

I don't know where you got the PDB = structures from, but I recommend that you load them in VMD and compute the = RMSD of the coordinates of your simulation with respect to each.=C2=A0 All = RMSDs need to be well defined in order to be able to compute the path varia= ble derived from them.

Giacomo


On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya <scfbioiitd@gmail.com> = wrote:
Thanks for your reply, As I understand I should consider the = selection which has only moderate change. First step itself gives this prob= lem so I have not calculated the RMSD. I have a string of pdbs from PNEB pa= th and I want to have a pmf that's why I am using abf. So the selected = atoms have lots of transformation. So what are the options.
<= br>
Many thanks,
Ashutosh

On Wed, Nov 17, 2021= at 11:28 AM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
This message is= the key:
colvars: This is usually the= result of an ill-defined set of atoms for rotational alignment (RMSD, rota= teReference, etc).

If the structure of the group of atoms changes too much, it becomes po= ssible that a pure rotation is not the transformation that minimizes the RM= SD, but another transformation does (e.g. rotation=C2=A0+ reflection across= a plane).

You do not need to change the time step, but instead pick= a selection that is guaranteed to have only moderate changes in structure.= =C2=A0 Practically speaking, the RMSD should=C2=A0remain much lower than th= e radius of gyration.
If you compute that RMS= D in VMD you will have a similar problem, just with a different outcome bec= ause the numerical algorithm is different.

Gi= acomo

On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya <<= a href=3D"mailto:scfbioiitd@gmail.com" target=3D"_blank">scfbioiitd@gmail.c= om> wrote:
I am=C2=A0 running ABF and getting this error.

Frame index: 32 ; optimal RMSD =3D 4.87456
Frame in= dex: 31 ; optimal RMSD =3D 4.87456
Frame index: 30 ; optimal RMSD =3D 4.= 87456
Frame index: 29 ; optimal RMSD =3D 4.87456
Frame index: 28 ; op= timal RMSD =3D 4.87456
colvars: =C2=A0 Prepared sample and gradient buff= ers at step 0.
colvars: Too many iterations in routine jacobi.
colvar= s: This is usually the result of an ill-defined set of atoms for rotational= alignment (RMSD, rotateReference, etc).
colvars: Too many PFATAL ERROR:= Error in the collective variables module (see above for details)
FATAL = ERROR: Error in the collective variables module (see above for details)

I have used different timesteps but still I am gettin= g this error. Any suggestions?

Many thanks
--00000000000058756a05d10043b8-- From owner-namd-l@halifax.ks.uiuc.edu Wed Nov 17 13:12:38 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHJCcCR016933; Wed, 17 Nov 2021 13:12:38 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHJCb10016932; Wed, 17 Nov 2021 13:12:37 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHJCbER016928; Wed, 17 Nov 2021 13:12:37 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHJCbtX016927; Wed, 17 Nov 2021 13:12:37 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHJCUcA016919 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 17 Nov 2021 13:12:30 -0600 (CST) Received: from pps.filterd (m0272703.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AHJ9D9Y022924 for ; Wed, 17 Nov 2021 19:12:30 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=scfbioiitd@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-wr1-f52.google.com (mail-wr1-f52.google.com [209.85.221.52]) by mx0b-00007101.pphosted.com with ESMTP id 3cckr4g2ju-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 17 Nov 2021 19:12:29 +0000 Received: by mail-wr1-f52.google.com with SMTP id a9so6671866wrr.8 for ; Wed, 17 Nov 2021 11:12:29 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=XZ5g63TqdsdlgON8OYQek58ru7xembsoXlHFFD3YXfI=; b=ohljlfVCOEWjZwbVA1MC4JYjd5S4OFDVA8axxEowmxJz3uwsoe7KpMbr4i7zBVoHGc 2T4Tmf1Fn0w+cmbZ0GgyadVyIkiI6/h3tLf3WKlP2dzwn+kAKBEuV6X5U70FdK+P3Hx8 OvafDybwBF2qFuCJBT7BMQsX6qSqw5ja4mro9m7D9hLanY3L2v02ZEKmoux7lVikKNy0 1nFPZzCHu6j2e/u/SM9PtqeM1W3NyWARfnn4kR7VA88fEzB+h/KpJWWMDVmZkeszUuBM qxyrRIDSeZhqlOtvEDJdXFA+vH3dZHYEPyI3ACdL7Ub8LLEaNarOE4qWusu10m9418+5 OqjQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=XZ5g63TqdsdlgON8OYQek58ru7xembsoXlHFFD3YXfI=; b=Aiez1dIvkbS9Wk2Za/DfKPkkySBzZDPGPF81O/uE+yBDwZE/NcJ7NYtm2fSnJ6zYUr 97PNMHonosL1G9Tuug9wix+eBGF7BR/I5oQClarWYua5FpHo+xHMzmyGOcUNJM86OSOR IO84ta8NZ5M81OOJoMoZrsIdO3yeYyfi6L874zDZ8xwfL758BP/AKgjw55nAfpsgNcqb 9Z+lXvfjcf6n18k2n+BhOcFtm4nm+CqU+5nyZb+TaEfHvwVlObAWJdlfcKAPobSTmpba biVbrMYuWazumXbO5Gsne5VgzDa1QEwB4zwy1NWh/YLkQUM08U1FnCc1JpJNQ9csaRIg RXaw== X-Gm-Message-State: AOAM5326SvBINdDR8GaiJsQ/5L/DW9AXj9H8OtXjmwwbbFvMmiLvad35 54xF35SLAz7ABM02PY9K9jn8wm+Y8tPAL8JCnfc= X-Google-Smtp-Source: ABdhPJywhAlGp5TumqFua7mEQmWwkwBGUdVxJj9Su0aRlXy/nBBa+udybdLiQR3ephCi07l1GrS0NGg1xpQRJzMHfbk= X-Received: by 2002:a5d:6843:: with SMTP id o3mr22750853wrw.174.1637176348135; Wed, 17 Nov 2021 11:12:28 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: Ashutosh Shandilya Date: Wed, 17 Nov 2021 14:08:38 -0500 Message-ID: Subject: Re: namd-l: colvars: Too many iterations in routine jacobi. To: Giacomo Fiorin Cc: NAMD list Content-Type: multipart/alternative; boundary="000000000000aa525805d100d26a" X-Proofpoint-GUID: N9RHEFciWpwD_B6LYVs6xFp35VZVjy1l X-CLX-Response: 1TFkXGx0bEQpMehcZGRwRCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHGBIYEQpDWRcHHx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxtxGRsQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XZBN4Ym9sSUN9Wl1udWgcZnN8WRxSbFoZH3xwfEBTG0YRClhcFx8EGgQYHhsF GxoEGxsaBB0EGxkZEBseGh8aEQpeWRdzU1xDHhEKTVwXGRsSEQpMWhdpeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGw QfGBEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmWH1Ya0AaBXJEaBEKQk4XY1Nja3sTWH4aX14RCkJMF2MfWXl5aR1PfFpaEQpCbBdv UmccckNJT1p+XREKQkAXZ1x+AVhdGWxtYwURCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdkQEU YUBxnHG9AbBEKWUsXEx8TGREKcGgXaBpaTBxgSU57enMQGhEKcGgXb3B6fE1ZfGgaYnMQGhEKcG gXYR16aR4dH2dzQHwQGhEKcGgXYx9Cek1cXnJoE3gQGhEKcGgXY3lIbHJpX3tta2MQGhEKcGwXa HNSWXJnex97eUkQGxIRCnBMF21oZRlBUn17GEVSEBoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: N9RHEFciWpwD_B6LYVs6xFp35VZVjy1l X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 malwarescore=0 lowpriorityscore=0 phishscore=0 spamscore=0 priorityscore=336 impostorscore=0 clxscore=171 suspectscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170085 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --000000000000aa525805d100d26a Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I increased harmonic restrain to 5.0 using command abf { colvars gs fullSamples 1000 historyfreq 100000 hidejacobian off } harmonic { colvars gs centers 0.0 forceconstant 5.0 } Output file shows the same RMSD for all the structures something like this which should not be the case. Is it because i switched off *usesecondclosestframe* off. I have been trying to change several parameters in the input but still getting some kind of error. Frame index: 67 ; optimal RMSD =3D 0.985712 Frame index: 80 ; optimal RMSD =3D 0.985712 Frame index: 79 ; optimal RMSD =3D 0.985712 Frame index: 78 ; optimal RMSD =3D 0.985712 Frame index: 77 ; optimal RMSD =3D 0.985712 Frame index: 76 ; optimal RMSD =3D 0.985712 Frame index: 75 ; optimal RMSD =3D 0.985712 Frame index: 74 ; optimal RMSD =3D 0.985712 Frame index: 73 ; optimal RMSD =3D 0.985712 Frame index: 72 ; optimal RMSD =3D 0.985712 Frame index: 71 ; optimal RMSD =3D 0.985712 Frame index: 70 ; optimal RMSD =3D 0.985712 Frame index: 69 ; optimal RMSD =3D 0.985712 Frame index: 68 ; optimal RMSD =3D 0.985712 Frame index: 81 ; optimal RMSD =3D 0.985712 Frame index: 66 ; optimal RMSD =3D 0.985712 Frame index: 65 ; optimal RMSD =3D 0.985712 Frame index: 64 ; optimal RMSD =3D 0.985712 Frame index: 63 ; optimal RMSD =3D 0.985712 Frame index: 62 ; optimal RMSD =3D 0.985712 Frame index: 61 ; optimal RMSD =3D 0.985712 Frame index: 60 ; optimal RMSD =3D 0.985712 Frame index: 59 ; optimal RMSD =3D 0.985712 Frame index: 58 ; optimal RMSD =3D 0.985712 Frame index: 57 ; optimal RMSD =3D 0.985712 Frame index: 56 ; optimal RMSD =3D 0.985712 Frame index: 55 ; optimal RMSD =3D 0.985712 Frame index: 94 ; optimal RMSD =3D 0.985712 Frame index: 107 ; optimal RMSD =3D 0.985712 108 PDB structures were obtained from the PNEB path. I computed RMSD with VMD which is mentioned below. Kindly have a look and suggest. My actual RMSD varies like this. 1 0.5520958304405212 2 0.6408998370170593 3 0.7004873752593994 4 0.7478375434875488 5 0.7849769592285156 6 0.8124300241470337 7 0.829501748085022 8 0.8617943525314331 9 0.8889437317848206 10 0.9140389561653137 11 0.925011396408081 12 0.931750476360321 13 0.9490005373954773 14 0.9639561176300049 15 0.9865623712539673 16 1.0129530429840088 17 1.017659068107605 18 1.0304405689239502 19 1.05254328250885 20 1.0523943901062012 21 1.0497472286224365 22 1.0674532651901245 23 1.0869779586791992 24 1.1080254316329956 25 1.1066851615905762 26 1.1148474216461182 27 1.1117987632751465 28 1.1251643896102905 29 1.1315655708312988 30 1.1351579427719116 31 1.1500359773635864 32 1.1598128080368042 33 1.1690787076950073 34 1.1832456588745117 35 1.190578579902649 36 1.1949034929275513 37 1.2126442193984985 38 1.2073010206222534 39 1.2080799341201782 40 1.2127560377120972 41 1.2220537662506104 42 1.2297075986862183 43 1.2463030815124512 44 1.258796215057373 45 1.2574396133422852 46 1.2649439573287964 Kindly suggest. Thanks, Ashutosh On Wed, Nov 17, 2021 at 1:32 PM Giacomo Fiorin wrote: > There *were* multiple RMSD computations, because that's how the distances > between path frames are computed. > > You are also omitting several warnings above, btw. One was "Please check > your configuration or increase restraint on z(=CF=83)". What did you do = there? > > I don't know where you got the PDB structures from, but I recommend that > you load them in VMD and compute the RMSD of the coordinates of your > simulation with respect to each. All RMSDs need to be well defined in > order to be able to compute the path variable derived from them. > > Giacomo > > > On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya > wrote: > >> Thanks for your reply, As I understand I should consider the selection >> which has only moderate change. First step itself gives this problem so = I >> have not calculated the RMSD. I have a string of pdbs from PNEB path and= I >> want to have a pmf that's why I am using abf. So the selected atoms have >> lots of transformation. So what are the options. >> >> Many thanks, >> Ashutosh >> >> On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin >> wrote: >> >>> This message is the key: >>> colvars: This is usually the result of an ill-defined set of atoms for >>> rotational alignment (RMSD, rotateReference, etc). >>> >>> If the structure of the group of atoms changes too much, it becomes >>> possible that a pure rotation is not the transformation that minimizes = the >>> RMSD, but another transformation does (e.g. rotation + reflection acros= s a >>> plane). >>> >>> You do not need to change the time step, but instead pick a selection >>> that is guaranteed to have only moderate changes in structure. Practic= ally >>> speaking, the RMSD should remain much lower than the radius of gyration= --000000000000aa525805d100d26a-- From owner-namd-l@halifax.ks.uiuc.edu Wed Nov 17 13:43:09 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHJh8kA018882; Wed, 17 Nov 2021 13:43:09 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHJh8TA018881; Wed, 17 Nov 2021 13:43:08 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHJh8Y7018877; Wed, 17 Nov 2021 13:43:08 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AHJh87P018876; Wed, 17 Nov 2021 13:43:08 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AHJgqBV018867 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 17 Nov 2021 13:42:53 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AHJGTLt013207 for ; Wed, 17 Nov 2021 19:42:52 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=giacomo.fiorin@gmail.com; dkim=pass header.s=20210112 header.d=gmail.com Received: from mail-yb1-f169.google.com (mail-yb1-f169.google.com [209.85.219.169]) by mx0a-00007101.pphosted.com with ESMTP id 3cctsn5k0c-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 17 Nov 2021 19:42:51 +0000 Received: by mail-yb1-f169.google.com with SMTP id s186so10739464yba.12 for ; Wed, 17 Nov 2021 11:42:51 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=k+vmp3wiBf5kRT5XlTJanvPTxTZchnDx9OFhRn3WVX4=; b=jgA3zzLcbABBUr9PDYtLGgZXWI3yiTYs1Lac8NKKnLz9LMCgyAxztHNou9mDmQm7q6 dmejdnELZ0M5ZNGC+eBQxwy0khw4nu99OZpZ0pV6Ot3eXDwMWYqXDfxX7o/NEzQv6dUv azMQbrhZd0Z35GhT2EiFB0X7u8CI4UB/SYj1FOAQjXA7ENLf44eCnVU4c+v77FIbR0Qf wIss7nNciJbJEvXccDRTQNfNzCFmoAnlvm/v8s1RotIM+0JCUY2RHLDEJWxzg1L1uS13 +fdldkZ/ycutCpC+CHMWfdLMy8LpvQcOAZRMpmQMR6Zbp1t2tNxxVdMCQJa56Ye8vfj/ KPzg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=k+vmp3wiBf5kRT5XlTJanvPTxTZchnDx9OFhRn3WVX4=; b=JFZSulALtq+mvsQkVbVITLjTpmIf4nPVbDkdv3U+OhkKlABxOf7cN1RNbDCSlR9M21 tVftD/wasaVrjHjpfT0Ko7VL8uLXz4GvNk6Y7ktp9bq7rs6EItrmT9CqSFpeuzZ3vdOs 4RiOU+uWGU6NLkHs7a+ltrp2hXKJMuE4tpApXlc8AE5Kk/6iEdNg6kMlhOv/CyjTGGtT bctCKD2hU0Y5iiGmGiEcLkGeYxxLpl7S/t9sK9sfhenODoLNqFgG3lG09qrR2CB2+Y/H lJHVNjgw+A4JkiWcE3k3N3gfn0Edpi2zuf4h9Mh1kggASWpfdd9BS4NRi8dWCK689cax dnOg== X-Gm-Message-State: AOAM530Jpah3+Asupf4/9RXlz72U4yHUigXzGgwihDHe346bbXyw8LBt 8O1phMJqvCmb5B6WzJPWrtGN7wGwawJir1tD/Wc= X-Google-Smtp-Source: ABdhPJzwTvstIUsB9TDh+9VlCFqDr5XYoAgaK9DzWNkRZjCx15e4h09j7W/i8z7uREJEe4e/uc1wN4PewXq8buBQY0k= X-Received: by 2002:a25:e752:: with SMTP id e79mr19864864ybh.377.1637178170793; Wed, 17 Nov 2021 11:42:50 -0800 (PST) References: In-Reply-To: From: Giacomo Fiorin Date: Wed, 17 Nov 2021 14:42:14 -0500 Message-ID: Subject: Re: namd-l: colvars: Too many iterations in routine jacobi. To: Ashutosh Shandilya Cc: NAMD list Content-Type: multipart/alternative; boundary="0000000000004de0f705d1013f92" X-Proofpoint-ORIG-GUID: mojb8ydhbInhkiwuVhhL67ekZEtL1Yw3 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBocEQpMehcZGhIRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHh8bEQpDWRcHHx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEhxxHRgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XR0VASBJTTkJIY0RCQUNdX3xCQmYcHU9BcG9eZhtzXRkRClhcFx8EGgQYHhsF GxoEGxoaBB0EGx4ZEBseGh8aEQpeWRdzU1wFchEKTVwXHh8fEQpMWhdpeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHBMRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2dcfgFYXRlsbWMFEQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXZEB FGFAcZxxvQGwRCllLFxMfExkRCnBoF2h4RElfZ2NbT0JjEBoRCnBoF2tzRl1wGFgSSBN8EBoRCn BoF2hQHWZaQ2t+clJJEBoRCnBoF256eExcU1lzG0EeEBoRCnBoF2dsXGRzXHJlRBpMEBoRCnB9F 20TcHl7fWdAaH1IEBoRCnB9F2EcbFJQTEl6SUN6EBoRCnB9F20bchhkGx57Y38SEBoRCnB/F2JO BQFwRF5pRHtlEBIcEQpwXxdiGl9QTEYBRhwaUhAaEQpwbBdmH3tYXGIFS1hkHxAeEhEKcEwXbWh lGUFSfXsYRVIQGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: mojb8ydhbInhkiwuVhhL67ekZEtL1Yw3 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 mlxscore=0 impostorscore=0 mlxlogscore=999 spamscore=0 clxscore=206 lowpriorityscore=0 malwarescore=0 priorityscore=308 bulkscore=0 suspectscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111170087 domainage_hfrom=9593 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --0000000000004de0f705d1013f92 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Please stop changing your parameters at random: it won't help you either in the short or long term. The best place would be to pick the first of those PDB structures, and compute the RMSD of the chosen atoms in the initial configuration for the NAMD run and the one from the PDB file, e.g. "1.pdb". This can be done by setting a simple rmsd function instead of the path CV: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:cvc_rmsd__;Iw!!DZ3fjg!vKPC7M13JpfoITkSSfCNsSRs4= _ziQtMYbpAAWkgd4La7ChXIFTVJ0p_BEVnaxWFvLQ$=20 Note that the PDB files may contain the whole system or just the selection: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvars_pdb_format__;Iw!!DZ3fjg!vKPC7M13JpfoITk= SSfCNsSRs4_ziQtMYbpAAWkgd4La7ChXIFTVJ0p_BEVm426Z0XQ$=20 but in other contexts (e.g. in VMD) you can only load a PDB file that matches the same molecule. Take this into account. If everything is set up correctly and an optimal rotation is possible, you should be able to compute the same RMSDs using VMD's internal commands and Colvars. When computed over atoms of the same mass, there is an identical match between "measure rmsd" in VMD and the "rmsd" function in Colvars. If they are not the same, something is different in your configuration. Note that you can also use the Colvars Dashboard, included as a plugin in the latest VMD alpha release: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-vmd/co= lvars-refman-vmd.html*sec:dashboard__;Iw!!DZ3fjg!vKPC7M13JpfoITkSSfCNsSRs4_= ziQtMYbpAAWkgd4La7ChXIFTVJ0p_BEVlXCF6u_w$=20 to avoid having to set up a new NAMD run while you're debugging. Once you see that the RMSD can be computed reproducibly between the initial simulation snapshot and the first frame, move over to the other PNEB frames. Giacomo On Wed, Nov 17, 2021 at 2:12 PM Ashutosh Shandilya wrote: > I increased harmonic restrain to 5.0 using command > abf { > colvars gs > fullSamples 1000 > historyfreq 100000 > hidejacobian off > } > harmonic { > colvars gs > centers 0.0 > forceconstant 5.0 > } > > Output file shows the same RMSD for all the structures something like this > which should not be the case. Is it because i switched off > *usesecondclosestframe* off. I have been trying to change several > parameters in the input but still getting some kind of error. > > Frame index: 67 ; optimal RMSD =3D 0.985712 > Frame index: 80 ; optimal RMSD =3D 0.985712 > Frame index: 79 ; optimal RMSD =3D 0.985712 > Frame index: 78 ; optimal RMSD =3D 0.985712 > Frame index: 77 ; optimal RMSD =3D 0.985712 > Frame index: 76 ; optimal RMSD =3D 0.985712 > Frame index: 75 ; optimal RMSD =3D 0.985712 > Frame index: 74 ; optimal RMSD =3D 0.985712 > Frame index: 73 ; optimal RMSD =3D 0.985712 > Frame index: 72 ; optimal RMSD =3D 0.985712 > Frame index: 71 ; optimal RMSD =3D 0.985712 > Frame index: 70 ; optimal RMSD =3D 0.985712 > Frame index: 69 ; optimal RMSD =3D 0.985712 > Frame index: 68 ; optimal RMSD =3D 0.985712 > Frame index: 81 ; optimal RMSD =3D 0.985712 > Frame index: 66 ; optimal RMSD =3D 0.985712 > Frame index: 65 ; optimal RMSD =3D 0.985712 > Frame index: 64 ; optimal RMSD =3D 0.985712 > Frame index: 63 ; optimal RMSD =3D 0.985712 > Frame index: 62 ; optimal RMSD =3D 0.985712 > Frame index: 61 ; optimal RMSD =3D 0.985712 > Frame index: 60 ; optimal RMSD =3D 0.985712 > Frame index: 59 ; optimal RMSD =3D 0.985712 > Frame index: 58 ; optimal RMSD =3D 0.985712 > Frame index: 57 ; optimal RMSD =3D 0.985712 > Frame index: 56 ; optimal RMSD =3D 0.985712 > Frame index: 55 ; optimal RMSD =3D 0.985712 > Frame index: 94 ; optimal RMSD =3D 0.985712 > Frame index: 107 ; optimal RMSD =3D 0.985712 > > > 108 PDB structures were obtained from the PNEB path. I computed RMSD with > VMD which is mentioned below. Kindly have a look and suggest. My actual > RMSD varies like this. > 1 0.5520958304405212 > 2 0.6408998370170593 > 3 0.7004873752593994 > 4 0.7478375434875488 > 5 0.7849769592285156 > 6 0.8124300241470337 > 7 0.829501748085022 > 8 0.8617943525314331 > 9 0.8889437317848206 > 10 0.9140389561653137 > 11 0.925011396408081 > 12 0.931750476360321 > 13 0.9490005373954773 > 14 0.9639561176300049 > 15 0.9865623712539673 > 16 1.0129530429840088 > 17 1.017659068107605 > 18 1.0304405689239502 > 19 1.05254328250885 > 20 1.0523943901062012 > 21 1.0497472286224365 > 22 1.0674532651901245 > 23 1.0869779586791992 > 24 1.1080254316329956 > 25 1.1066851615905762 > 26 1.1148474216461182 > 27 1.1117987632751465 > 28 1.1251643896102905 > 29 1.1315655708312988 > 30 1.1351579427719116 > 31 1.1500359773635864 > 32 1.1598128080368042 > 33 1.1690787076950073 > 34 1.1832456588745117 > 35 1.190578579902649 > 36 1.1949034929275513 > 37 1.2126442193984985 > 38 1.2073010206222534 > 39 1.2080799341201782 > 40 1.2127560377120972 > 41 1.2220537662506104 > 42 1.2297075986862183 > 43 1.2463030815124512 > 44 1.258796215057373 > 45 1.2574396133422852 > 46 1.2649439573287964 > > Kindly suggest. > > Thanks, > Ashutosh > > > On Wed, Nov 17, 2021 at 1:32 PM Giacomo Fiorin > wrote: > >> There *were* multiple RMSD computations, because that's how the >> distances between path frames are computed. >> >> You are also omitting several warnings above, btw. One was "Please check >> your configuration or increase restraint on z(=CF=83)". What did you do= there? >> >> I don't know where you got the PDB structures from, but I recommend that >> you load them in VMD and compute the RMSD of the coordinates of your >> simulation with respect to each. All RMSDs need to be well defined in >> order to be able to compute the path variable derived from them. >> >> Giacomo >> >> >> On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya >> wrote: >> >>> Thanks for your reply, As I understand I should consider the selection >>> which has only moderate change. First step itself gives this problem so= I >>> have not calculated the RMSD. I have a string of pdbs from PNEB path an= d I >>> want to have a pmf that's why I am using abf. So the selected atoms have >>> lots of transformation. So what are the options. >>> >>> Many thanks, >>> Ashutosh >>> >>> On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin < >>> giacomo.fiorin@gmail.com> wrote: >>> >>>> This message is the key: >>>> colvars: This is usually the result of an ill-defined set of atoms for >>>> rotational alignment (RMSD, rotateReference, etc). >>>> >>>> If the structure of the group of atoms changes too much, it becomes >>>> possible that a pure rotation is not the transformation that minimizes= the >>>> RMSD, but another transformation does (e.g. rotation + reflection acro= ss a >>>> plane). >>>> >>>> You do not need to change the time step, but instead pick a selection >>>> that is guaranteed to have only moderate changes in structure. Practi= cally >>>> speaking, the RMSD should remain much lower than the radius of gyratio= n. >>>> >>>> If you compute that RMSD in VMD you will have a similar problem, just >>>> with a different outcome because the numerical algorithm is different. >>>> >>>> Giacomo >>>> >>>> On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya < >>>> scfbioiitd@gmail.com> wrote: >>>> >>>>> I am running ABF and getting this error. >>>>> >>>>> Frame index: 32 ; optimal RMSD =3D 4.87456 >>>>> Frame index: 31 ; optimal RMSD =3D 4.87456 >>>>> Frame index: 30 ; optimal RMSD =3D 4.87456 >>>>> Frame index: 29 ; optimal RMSD =3D 4.87456 >>>>> Frame index: 28 ; optimal RMSD =3D 4.87456 >>>>> colvars: Prepared sample and gradient buffers at step 0. >>>>> colvars: Too many iterations in routine jacobi. >>>>> colvars: This is usually the result of an ill-defined set of atoms for >>>>> rotational alignment (RMSD, rotateReference, etc). >>>>> colvars: Too many PFATAL ERROR: Error in the collective variables >>>>> module (see above for details) >>>>> FATAL ERROR: Error in the collective variables module (see above for >>>>> details) >>>>> >>>>> I have used different timesteps but still I am getting this error. Any >>>>> suggestions? >>>>> >>>>> Many thanks >>>>> >>>> --0000000000004de0f705d1013f92 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Please stop changing your parameters at r= andom: it won't help you either in the short or long term.

The best place would be to pick the fi= rst of those PDB structures, and compute the RMSD of the chosen atoms in th= e initial configuration for the NAMD run and the one from the PDB file, e.g= . "1.pdb".=C2=A0 This can be done by setting a simple rmsd functi= on instead of the path CV:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd= .html#sec:cvc_rmsd

Note that the PDB file= s may contain the whole system or just the selection:
but in other contexts (e.g. in VMD) you can onl= y load a PDB file that matches the same molecule.=C2=A0 Take this into acco= unt.

If everything is set up correctly and a= n optimal rotation is possible, you should be able to compute the same RMSD= s using VMD's internal commands and Colvars.=C2=A0 When computed over a= toms of the same mass, there is an identical match between "measure rm= sd" in VMD and the "rmsd" function in Colvars.=C2=A0 If they= are not the same, something is different in your configuration.
=
Note that you can also use the Colvars Dashboard, included a= s a plugin in the latest VMD alpha release:
to avoid having = to set up a new NAMD run while you're debugging.

Once you see that the RMSD can be computed reproducibly between the init= ial simulation snapshot and the first frame, move over to the other PNEB fr= ames.

Giacomo


<= /div>
O= n Wed, Nov 17, 2021 at 2:12 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
I increased ha= rmonic restrain to 5.0 using command
abf {
=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 colvars = gs
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 fullSamples 1000
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 historyfreq 100000
=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 hidejacobian off
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 }
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 harmonic {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 colvars gs
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 c= enters 0.0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 force= constant 5.0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0}

Output file shows the same RMSD for all the structur= es something like this which should not be the case. Is it because i switch= ed off usesecondclosestframe off. I have been trying to change sever= al parameters in the input but still getting some kind of error.
<= div>
Frame index: 67 ; optimal RMSD =3D 0.985712
Frame ind= ex: 80 ; optimal RMSD =3D 0.985712
Frame index: 79 ; optimal RMSD =3D 0.= 985712
Frame index: 78 ; optimal RMSD =3D 0.985712
Frame index: 77 ; = optimal RMSD =3D 0.985712
Frame index: 76 ; optimal RMSD =3D 0.985712Frame index: 75 ; optimal RMSD =3D 0.985712
Frame index: 74 ; optimal R= MSD =3D 0.985712
Frame index: 73 ; optimal RMSD =3D 0.985712
Frame in= dex: 72 ; optimal RMSD =3D 0.985712
Frame index: 71 ; optimal RMSD =3D 0= .985712
Frame index: 70 ; optimal RMSD =3D 0.985712
Frame index: 69 ;= optimal RMSD =3D 0.985712
Frame index: 68 ; optimal RMSD =3D 0.985712Frame index: 81 ; optimal RMSD =3D 0.985712
Frame index: 66 ; optimal = RMSD =3D 0.985712
Frame index: 65 ; optimal RMSD =3D 0.985712
Frame i= ndex: 64 ; optimal RMSD =3D 0.985712
Frame index: 63 ; optimal RMSD =3D = 0.985712
Frame index: 62 ; optimal RMSD =3D 0.985712
Frame index: 61 = ; optimal RMSD =3D 0.985712
Frame index: 60 ; optimal RMSD =3D 0.985712<= br>Frame index: 59 ; optimal RMSD =3D 0.985712
Frame index: 58 ; optimal= RMSD =3D 0.985712
Frame index: 57 ; optimal RMSD =3D 0.985712
Frame = index: 56 ; optimal RMSD =3D 0.985712
Frame index: 55 ; optimal RMSD =3D= 0.985712
Frame index: 94 ; optimal RMSD =3D 0.985712
Frame index: 10= 7 ; optimal RMSD =3D 0.985712


108 P= DB structures were obtained from the PNEB path. I computed RMSD with VMD wh= ich is mentioned below. Kindly have a look and suggest. My actual RMSD vari= es like this.
1 0.5520958304405212
2 0.6408998370170593
3 0= .7004873752593994
4 0.7478375434875488
5 0.7849769592285156
6 0.81= 24300241470337
7 0.829501748085022
8 0.8617943525314331
9 0.888943= 7317848206
10 0.9140389561653137
11 0.925011396408081
12 0.9317504= 76360321
13 0.9490005373954773
14 0.9639561176300049
15 0.98656237= 12539673
16 1.0129530429840088
17 1.017659068107605
18 1.030440568= 9239502
19 1.05254328250885
20 1.0523943901062012
21 1.04974722862= 24365
22 1.0674532651901245
23 1.0869779586791992
24 1.10802543163= 29956
25 1.1066851615905762
26 1.1148474216461182
27 1.11179876327= 51465
28 1.1251643896102905
29 1.1315655708312988
30 1.13515794277= 19116
31 1.1500359773635864
32 1.1598128080368042
33 1.16907870769= 50073
34 1.1832456588745117
35 1.190578579902649
36 1.194903492927= 5513
37 1.2126442193984985
38 1.2073010206222534
39 1.208079934120= 1782
40 1.2127560377120972
41 1.2220537662506104
42 1.229707598686= 2183
43 1.2463030815124512
44 1.258796215057373
45 1.2574396133422= 852
46 1.2649439573287964

Kindly suggest.

Thanks,
Ashutosh


On Wed, Nov 17, 2021 at 1:32 PM Giacomo Fiorin <giacomo.fiorin@gmail.com> = wrote:
There were multiple RMSD computations, bec= ause that's how the distances between path frames are computed.

You are also omitting several war= nings above, btw.=C2=A0 One was "Please check your configuration or in= crease restraint on z(=CF=83)".=C2=A0 What did you do there?

I don't know where you got the PDB structur= es from, but I recommend that you load them in VMD and compute the RMSD of = the coordinates of your simulation with respect to each.=C2=A0 All RMSDs ne= ed to be well defined in order to be able to compute the path variable deri= ved from them.

Giacomo

<= /div>
O= n Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
=
Thanks for your reply, As I understand I should consider the selection= which has only moderate change. First step itself gives this problem so I = have not calculated the RMSD. I have a string of pdbs from PNEB path and I = want to have a pmf that's why I am using abf. So the selected atoms hav= e lots of transformation. So what are the options.

=
Many thanks,
Ashutosh

On Wed, Nov 17, 2021 at 11:28= AM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
This message is the ke= y:
colvars: This is usually the result= of an ill-defined set of atoms for rotational alignment (RMSD, rotateRefer= ence, etc).

If= the structure of the group of atoms changes too much, it becomes possible = that a pure rotation is not the transformation that minimizes the RMSD, but= another transformation does (e.g. rotation=C2=A0+ reflection across a plan= e).

You do not need to change the time step, but instead pick a sele= ction that is guaranteed to have only moderate changes in structure.=C2=A0 = Practically speaking, the RMSD should=C2=A0remain much lower than the radiu= s of gyration.

If you compute that RMSD in VM= D you will have a similar problem, just with a different outcome because th= e numerical algorithm is different.

Giacomo

On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya <scfbioiitd@gmail.com= > wrote:
I am=C2=A0 running ABF and getting this error.
=
Frame index: 32 ; optimal RMSD =3D 4.87456
Frame index: 3= 1 ; optimal RMSD =3D 4.87456
Frame index: 30 ; optimal RMSD =3D 4.87456<= br>Frame index: 29 ; optimal RMSD =3D 4.87456
Frame index: 28 ; optimal = RMSD =3D 4.87456
colvars: =C2=A0 Prepared sample and gradient buffers at= step 0.
colvars: Too many iterations in routine jacobi.
colvars: Thi= s is usually the result of an ill-defined set of atoms for rotational align= ment (RMSD, rotateReference, etc).
colvars: Too many PFATAL ERROR: Error= in the collective variables module (see above for details)
FATAL ERROR:= Error in the collective variables module (see above for details)

I have used different timesteps but still I am getting this= error. Any suggestions?

Many thanks
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R. Melo" Date: Wed, 17 Nov 2021 22:01:19 -0500 Message-ID: Subject: Re: namd-l: QMMM latency in PME correction To: NAMD , "Wall, Michael E" Content-Type: multipart/alternative; boundary="00000000000001835305d1076131" X-CLX-Response: 1TFkXGBseEQpMehcZGBwRCllEF21ta2xYEn9bT2ZFEQpYWBdsekNpUlJ7QlN lTBEKeE4XY1Nja3sTWH4aX14RCnlMF28bTHN9E0ZMW0FFEQpDSBcHHxsTEQpDWRcHEhsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbEx5xGx0eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2dNUnASYksZaE1AB21jRmdoX1J4XwcbEkBQf1JyeGxbEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXc1MYSxMRCk1cFxgaGBEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQ QeHBEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdka1pYbl4Bc0VPfxEKQk4XY1Nja3sTWH4aX14RCkJMF2x6Q2lSUntCU2VMEQpCbBdm c2hGGE0TWhIeWxEKQkAXbnpIc09uEnlve2wRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcSEQp 5QxdtRkNHfWtCf3gYaBEKWUsXEx8THhEKcGgXbUdjXhJ6QEJccmYQGRoRCnBoF2BBUm0cRQFSGH tZEBkaEQpwaBdpUkFIWFtDWl8YZBAZGhEKcGgXYGVTZWQZRmJtQWUQGRoRCnBoF2lAc19BRnJ7c kttEBkaEQpwfRdiTmZQYnJIaENCaBAZGhEKcH0XaUl+bwFSYFwFGVgQGRoRCnB9F2Vkf1xlXgVb XUxDEBkaEQpwfRdofE4YRGEbbR8cRRAZGhEKcH0XehgSWxh/GhxJEnMQGRoRCnB/F2sdax5Te2d jS216EBIcEQpwXxdiTmZQYnJIaENCaBAZGhEKcH8XYWZvWxpnZEJIHVsQGxgaEQpwXxdjYhJQSG N4H3xCfRAbGhoRCnB/F2NiXAFAW15Me01YEBsYHBEKcF8XZm1lZGNuaGBaYBIQGRoRCnB/F21EX 0ZFbX1IeRluEBsZGxEKcF8Xa0ZLE3loaW58E3gQGxofEQpwbBdoW3hOemdaQFNQZhAZGhEKbX4X GxEKWE0XSxEg X-Proofpoint-ORIG-GUID: MgxZ8Ha3Bgj-GIlMBuxRu-18jzUxXRFq X-Proofpoint-GUID: MgxZ8Ha3Bgj-GIlMBuxRu-18jzUxXRFq X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 clxscore=214 adultscore=0 mlxscore=0 suspectscore=0 bulkscore=0 spamscore=0 impostorscore=0 lowpriorityscore=0 priorityscore=326 mlxlogscore=999 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111180016 domainage_hfrom=9594 X-Spam-Score: 0 X-Spam-OrigSender: melomcr@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Marcelo C. R. Melo" --00000000000001835305d1076131 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Michael, Thank you for sharing the issue here. To follow up with some specifics, the issue is arising in a system with approximately five thousand QM atoms and 12 thousand point charges (PCs) representing MM atoms. The PME correction is currently executed in a single core and depends on two double loops, one that treats all QM-QM atom pairs and another that treats QM-PC pairs. My thought is that the PME correction could be distributed over all ranks that have relevant QM and/or MM atoms by sharing the positions and charges of QM atoms. Ths would require a couple of extra messages for each QM step, which would not be a problem for a large system like this, but I wonder what that would entail for smaller QM regions. We would welcome any thoughts on this. In the meantime, I'll run some extra timings and benchmarks to see if this approach is feasible. Best, Marcelo On Tue, 16 Nov 2021 at 16:41, Wall, Michael E wrote: > Hello NAMD-L, > > I'm using NAMD to perform QMMM using a large QM region, using LATTE as a > QM solver (https://urldefense.com/v3/__https://github.com/lanl/latte__;!!= DZ3fjg!qbNSrKdN68fL0G2-A-4O-3yn-dd6Pna-RbcGZql0DnmUTI8BFhidjtagkbdT2TV6mQ$= =20 > ). > I'm seeing some latency on the NAMD side that I'm trying to address. > > I've done some profiling and found that most of the latency is associated > with a PME correction in src/ComputeQM.C (line 5033 in the NAMD_2.14b2_So= urce > version, about 6-9 seconds required for the system I'm currently looking > at). > > I had a conversation with Marcelo Melo about strategies for > addressing this issue by parallelizing the PME correction (along with a > couple of other calculations). He shared his thoughts and also suggested > I post to this mailing list to share the observation more broadly and > to see whether one of the other developers might have any insights. > > Thank you for considering this issue. > > Sincerely, > > Michael Wall > > > --- > Michael Wall > mewall@lanl.gov > https://urldefense.com/v3/__http://public.lanl.gov/mewall__;!!DZ3fjg!qbNS= rKdN68fL0G2-A-4O-3yn-dd6Pna-RbcGZql0DnmUTI8BFhidjtagkbeO1dWyTw$=20 > > > --00000000000001835305d1076131 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Michael,
Thank you for sharing the issue here.

To follow up with some specifics, the issue is arising= in a system with approximately five thousand QM atoms and 12 thousand poin= t charges (PCs) representing MM atoms.=C2=A0
The PME correction i= s currently executed in a single core and depends on two double loops, one = that treats all QM-QM atom pairs and another that treats QM-PC pairs.=C2=A0=

My thought is that the PME correction could be di= stributed over all ranks that have relevant QM and/or MM atoms by sharing t= he positions and charges of QM atoms. Ths would require a couple of extra m= essages for each QM step, which would not be a problem for a large system l= ike this, but I wonder what that would entail for smaller QM regions.
=

We would welcome any thoughts on=C2=A0this. In the mean= time, I'll run some extra timings and benchmarks to see if this approac= h is=C2=A0feasible.

Best,
Marcelo
<= /div>
O= n Tue, 16 Nov 2021 at 16:41, Wall, Michael E <mewall@lanl.gov> wrote:

Hello NAMD-L,

I'm using NAMD to perform QMMM using a large=C2=A0QM region, using LATT= E as a QM solver (https://github.com/lanl/latte). I'm= seeing some=C2=A0latency on the NAMD side that I'm trying to address.

I've done some profiling=C2=A0and found that most of the latency is ass= ociated with=C2=A0a PME correction in=C2=A0src/ComputeQM.C=C2=A0(line 5033 in the NAMD_2.14b2_Source version,=C2=A0about 6-9 seconds requ= ired=C2=A0for the system I'm currently looking at).

I had a conversation with Marcelo Melo about strategies for ad= dressing=C2=A0this issue by parallelizing the PME=C2=A0correction (along wi= th a couple of other calculations). He shared his thoughts=C2=A0and also=C2=A0su= ggested I post to this mailing list=C2=A0to share the observation more broadly and to=C2=A0see whether one of the othe= r=C2=A0developers might have any insights.=C2=A0=

Thank you=C2=A0for considering this issue.

Sincerely,

Michael Wall


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charset="UTF-8" While attempting to minimize a CHCL3 box built from CHARMM36-provided toppar_chloroform_dh.str, namd crashes FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4) > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4) > Actually, the prm part of the str (which was read by namd) l correctly furnishes > ANGLES > CLCM CCM CLCM 0.0 111.30 > HCM CCM CLCM 0.0 107.57 > Why is namd looking for those wrong angles? The central atom is carbon not hydrogen. Thanks for advice francesco pietra --000000000000a736aa05d10beee9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
While attempting to minimize a CHCL3 box built from C= HARMM36-provided toppar_chloroform_dh.str, namd crashes

FATAL ERROR: UNABLE= TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4)
FATAL ERROR: UN= ABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4)

Actually, the prm part of the str (which was read b= y namd) l correctly furnishes
ANGLES
CLCM =C2=A0CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2= =A0 =C2=A0111.30
HCM =C2=A0 CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2= =A0107.57

Why is namd looking for tho= se wrong angles? The central atom is carbon not hydrogen.
Thanks for advice
francesco p= ietra
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charset="UTF-8" It seems thatb the str used is inadequate. Alsdo adjusting angles in str, namd assks for dihedrals fp On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra wrote: > While attempting to minimize a CHCL3 box built from CHARMM36-provided > toppar_chloroform_dh.str, namd crashes > > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4) >> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 >> 4) >> > > Actually, the prm part of the str (which was read by namd) l correctly > furnishes > >> ANGLES >> CLCM CCM CLCM 0.0 111.30 >> HCM CCM CLCM 0.0 107.57 >> > > Why is namd looking for those wrong angles? The central atom is carbon not > hydrogen. > > Thanks for advice > francesco pietra > --0000000000002b0e7b05d10d415b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
It seems thatb the str used is inadequate. Alsdo adju= sting angles in str, namd assks for dihedrals
fp
<= br>
On Thu,= Nov 18, 2021 at 9:29 AM Francesco Pietra <chiendarret@gmail.com> wrote:
While attempting to = minimize a CHCL3 box built from CHARMM36-provided toppar_chloroform_dh.str,= namd crashes

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CL= CM (ATOMS 1 5 4)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HC= M CLCM (ATOMS 1 5 4)

Actually, the pr= m part of the str (which was read by namd) l correctly furnishes
<= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex">
ANGLES
CLCM =C2=A0= CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2=A0111.30
HCM =C2=A0 CCM =C2= =A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2=A0107.57

Why is namd looking for those wrong angles? The central atom is car= bon not hydrogen.

Thanks for advice
francesco pietra
--0000000000002b0e7b05d10d415b-- From owner-namd-l@halifax.ks.uiuc.edu Thu Nov 18 08:04:04 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AIE44Ao008988; Thu, 18 Nov 2021 08:04:04 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AIE44s7008987; Thu, 18 Nov 2021 08:04:04 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AIE436u008983; Thu, 18 Nov 2021 08:04:03 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AIE43KE008982; Thu, 18 Nov 2021 08:04:03 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AIE3sDf008935 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Have you looked at the bonds in your psf to make sure they are correct? This looks like you've hydrogen atoms that have two bonds... Best, Peter On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra wrote: > It seems thatb the str used is inadequate. Alsdo adjusting angles in str, > namd assks for dihedrals > fp > > On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra > wrote: > >> While attempting to minimize a CHCL3 box built from CHARMM36-provided >> toppar_chloroform_dh.str, namd crashes >> >> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 >>> 4) >>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 >>> 4) >>> >> >> Actually, the prm part of the str (which was read by namd) l correctly >> furnishes >> >>> ANGLES >>> CLCM CCM CLCM 0.0 111.30 >>> HCM CCM CLCM 0.0 107.57 >>> >> >> Why is namd looking for those wrong angles? The central atom is carbon >> not hydrogen. >> >> Thanks for advice >> francesco pietra >> > --000000000000e687ed05d110a047 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Have you looked at the bonds in your psf to make sure= they are correct? This looks like you've hydrogen atoms that have two = bonds...
Best,
Peter

On Thu, Nov 18, 2021= at 5:42 AM Francesco Pietra <c= hiendarret@gmail.com> wrote:
It seems thatb the str used is in= adequate. Alsdo adjusting angles in str, namd assks for dihedrals
fp

--000000000000e687ed05d110a047-- From owner-namd-l@halifax.ks.uiuc.edu Thu Nov 18 19:41:25 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AJ1fPgo017255; Thu, 18 Nov 2021 19:41:25 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AJ1fPgK017254; Thu, 18 Nov 2021 19:41:25 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AJ1fOgr017250; Thu, 18 Nov 2021 19:41:24 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AJ1fOvW017249; Thu, 18 Nov 2021 19:41:24 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AJ1f9c3017240 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Dear Users, I am running abf simulation with namd and it seems to be running fine generating pmf and gradient files, but colvavrs.traj file is empty. Although output logfile says colvars: This version was built with the C++11 standard or higher. colvars: Using NAMD interface, version "2019-12-04". colvars: The restart output state file will be "prod9-restart.colvars.state". colvars: The final output state file will be "prod9.colvars.state". colvars: Writing to colvar trajectory file "prod9.colvars.traj". but they are empty. My abf input files looks like this colvar { width 0.05 lowerboundary 0 upperboundary 1 extendedlagrangian on extendedfluctuation 0.05 gspath { atoms {atomnumbers { 12961 12975 ..... 61848 61880 }} refPositionsFile1 1.pdb refPositionsFile2 2.pdb refPositionsFile3 3.pdb ........... refPositionsFile102 102.pdb refPositionsFile103 103.pdb refPositionsFile104 104.pdb refPositionsFile105 105.pdb refPositionsFile106 106.pdb refPositionsFile107 107.pdb refPositionsFile108 108.pdb } } abf { colvars gs fullSamples 500 historyfreq 1000 } Conf file inputs: # output outputname ${runnew} outputenergies 500 outputtiming 500 binaryoutput no restartfreq 500 dcdfreq 1000 dcdfile ${runnew}.dcd wrapall off wrapNearest on # for restarting: restartname ${runnew}-restart colvars on cv configfile input_file.tcl run $step Kindly suggest, Thanks --0000000000001012b205d11a5e54 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: base64 PGRpdiBkaXI9Imx0ciI+RGVhciBVc2Vycyw8ZGl2PkkgYW0gcnVubmluZ8KgYWJmIHNpbXVsYXRp b24gd2l0aCBuYW1kIGFuZCBpdCBzZWVtcyB0byBiZSBydW5uaW5nIGZpbmUgZ2VuZXJhdGluZyBw bWYgYW5kIGdyYWRpZW50IGZpbGVzLCBidXQgY29sdmF2cnMudHJhasKgZmlsZSBpcyBlbXB0eS4g QWx0aG91Z2ggb3V0cHV0IGxvZ2ZpbGXCoCBzYXlzPC9kaXY+PGRpdj48YnI+PC9kaXY+PGRpdj5j b2x2YXJzOiBUaGlzIHZlcnNpb24gd2FzIGJ1aWx0IHdpdGggdGhlIEMrKzExIHN0YW5kYXJkIG9y IGhpZ2hlci48YnI+Y29sdmFyczogVXNpbmcgTkFNRCBpbnRlcmZhY2UsIHZlcnNpb24gJnF1b3Q7 MjAxOS0xMi0wNCZxdW90Oy48YnI+Y29sdmFyczogVGhlIHJlc3RhcnQgb3V0cHV0IHN0YXRlIGZp bGUgd2lsbCBiZSAmcXVvdDtwcm9kOS1yZXN0YXJ0LmNvbHZhcnMuc3RhdGUmcXVvdDsuPGJyPmNv bHZhcnM6IFRoZSBmaW5hbCBvdXRwdXQgc3RhdGUgZmlsZSB3aWxsIGJlICZxdW90O3Byb2Q5LmNv bHZhcnMuc3RhdGUmcXVvdDsuPGJyPmNvbHZhcnM6IFdyaXRpbmcgdG8gY29sdmFyIHRyYWplY3Rv cnkgZmlsZSAmcXVvdDtwcm9kOS5jb2x2YXJzLnRyYWomcXVvdDsuPGJyPjwvZGl2PjxkaXY+YnV0 IHRoZXkgYXJlIGVtcHR5LjwvZGl2PjxkaXY+PGJyPjwvZGl2PjxkaXY+TXkgYWJmIGlucHV0IGZp bGVzIGxvb2tzIGxpa2UgdGhpczxicj48L2Rpdj48ZGl2Pjxicj48L2Rpdj48ZGl2Pjxicj48L2Rp dj48ZGl2PsKgY29sdmFyIHs8YnI+wqDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCB3aWR0aCAwLjA1 PGJyPsKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIGxvd2VyYm91bmRhcnkgMDxicj7CoCDCoCDCoCDC oCDCoCDCoCDCoCDCoCB1cHBlcmJvdW5kYXJ5IDE8YnI+wqAgwqAgwqAgwqAgwqAgwqAgwqAgwqAg ZXh0ZW5kZWRsYWdyYW5naWFuIG9uPGJyPsKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIGV4dGVuZGVk Zmx1Y3R1YXRpb24gMC4wNTxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoMKgwqAgZ3NwYXRoIHs8 YnI+wqAgwqAgwqAgwqAgwqAgwqAgwqAgwqBhdG9tcyB7YXRvbW51bWJlcnMgeyAxMjk2MSAxMjk3 NSAuLi4uLiA2MTg0OCA2MTg4MCB9fTxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCByZWZQb3Np dGlvbnNGaWxlMSAxLnBkYjxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCByZWZQb3NpdGlvbnNG aWxlMiAyLnBkYjxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCByZWZQb3NpdGlvbnNGaWxlMyAz LnBkYjxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCAuLi4uLi4uLi4uLjxicj7CoCDCoCDCoCDC oCDCoCDCoCDCoCDCoCByZWZQb3NpdGlvbnNGaWxlMTAyIDEwMi5wZGI8YnI+wqAgwqAgwqAgwqAg wqAgwqAgwqAgwqAgcmVmUG9zaXRpb25zRmlsZTEwMyAxMDMucGRiPGJyPsKgIMKgIMKgIMKgIMKg IMKgIMKgIMKgIHJlZlBvc2l0aW9uc0ZpbGUxMDQgMTA0LnBkYjxicj7CoCDCoCDCoCDCoCDCoCDC oCDCoCDCoCByZWZQb3NpdGlvbnNGaWxlMTA1IDEwNS5wZGI8YnI+wqAgwqAgwqAgwqAgwqAgwqAg wqAgwqAgcmVmUG9zaXRpb25zRmlsZTEwNiAxMDYucGRiPGJyPsKgIMKgIMKgIMKgIMKgIMKgIMKg IMKgIHJlZlBvc2l0aW9uc0ZpbGUxMDcgMTA3LnBkYjxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDC oCByZWZQb3NpdGlvbnNGaWxlMTA4IDEwOC5wZGI8YnI+wqAgwqAgwqAgwqAgwqAgwqAgwqAgwqAg wqAgwqAgwqAgwqAgwqAgwqAgwqAgwqAgwqAgwqAgwqB9PGJyPsKgIMKgIMKgIMKgIMKgIMKgIMKg IMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgfTxicj7CoCDCoCDCoCDCoCDCoCDC oCDCoCDCoCBhYmYgezxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCBjb2x2 YXJzIGdzPGJyPsKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIGZ1bGxTYW1wbGVz IDUwMDxicj7CoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCDCoCBoaXN0b3J5ZnJlcSAx MDAwPGJyPsKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIMKgIH08YnI+PC9kaXY+PGRpdj48YnI+ PC9kaXY+PGRpdj5Db25mIGZpbGUgaW5wdXRzOjwvZGl2PjxkaXY+IyBvdXRwdXQ8YnI+b3V0cHV0 bmFtZSAke3J1bm5ld308YnI+b3V0cHV0ZW5lcmdpZXMgNTAwPGJyPm91dHB1dHRpbWluZyDCoCA1 MDA8YnI+YmluYXJ5b3V0cHV0IMKgIG5vPGJyPnJlc3RhcnRmcmVxIMKgIDUwMDxicj5kY2RmcmVx IMKgIMKgIMKgIDEwMDA8YnI+ZGNkZmlsZSDCoCDCoCDCoCAke3J1bm5ld30uZGNkPGJyPndyYXBh bGwgwqAgwqAgwqAgwqBvZmY8YnI+d3JhcE5lYXJlc3QgwqAgwqBvbjxicj48YnI+IyBmb3IgcmVz dGFydGluZzo8YnI+cmVzdGFydG5hbWUgJHtydW5uZXd9LXJlc3RhcnQ8YnI+Y29sdmFycyBvbjxi cj5jdiBjb25maWdmaWxlIGlucHV0X2ZpbGUudGNsPGJyPnJ1biAkc3RlcDxicj48L2Rpdj48ZGl2 Pjxicj48L2Rpdj48ZGl2PktpbmRseSBzdWdnZXN0LDwvZGl2PjxkaXY+VGhhbmtzPC9kaXY+PC9k aXY+DQo= --0000000000001012b205d11a5e54-- From owner-namd-l@halifax.ks.uiuc.edu Thu Nov 18 21:05:55 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AJ35tQm019512; 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charset="UTF-8" Could be buffering. Try "run 0" or a small number of steps. On Thu, Nov 18, 2021 at 8:42 PM Ashutosh Shandilya wrote: > Dear Users, > I am running abf simulation with namd and it seems to be running fine > generating pmf and gradient files, but colvavrs.traj file is empty. > Although output logfile says > > colvars: This version was built with the C++11 standard or higher. > colvars: Using NAMD interface, version "2019-12-04". > colvars: The restart output state file will be > "prod9-restart.colvars.state". > colvars: The final output state file will be "prod9.colvars.state". > colvars: Writing to colvar trajectory file "prod9.colvars.traj". > but they are empty. > > My abf input files looks like this > > > colvar { > width 0.05 > lowerboundary 0 > upperboundary 1 > extendedlagrangian on > extendedfluctuation 0.05 > gspath { > atoms {atomnumbers { 12961 12975 ..... 61848 61880 }} > refPositionsFile1 1.pdb > refPositionsFile2 2.pdb > refPositionsFile3 3.pdb > ........... > refPositionsFile102 102.pdb > refPositionsFile103 103.pdb > refPositionsFile104 104.pdb > refPositionsFile105 105.pdb > refPositionsFile106 106.pdb > refPositionsFile107 107.pdb > refPositionsFile108 108.pdb > } > } > abf { > colvars gs > fullSamples 500 > historyfreq 1000 > } > > Conf file inputs: > # output > outputname ${runnew} > outputenergies 500 > outputtiming 500 > binaryoutput no > restartfreq 500 > dcdfreq 1000 > dcdfile ${runnew}.dcd > wrapall off > wrapNearest on > > # for restarting: > restartname ${runnew}-restart > colvars on > cv configfile input_file.tcl > run $step > > Kindly suggest, > Thanks > --00000000000002a35f05d11b8db5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Could be buffering.

Try "run 0&quo= t; or a small number of steps.


Dear Users,<= div>I am running=C2=A0abf simulation with namd and it seems to be running f= ine generating pmf and gradient files, but colvavrs.traj=C2=A0file is empty= . Although output logfile=C2=A0 says

colvars: This= version was built with the C++11 standard or higher.
colvars: Using NAM= D interface, version "2019-12-04".
colvars: The restart output= state file will be "prod9-restart.colvars.state".
colvars: Th= e final output state file will be "prod9.colvars.state".
colva= rs: Writing to colvar trajectory file "prod9.colvars.traj".
but they are empty.

My abf input files lo= oks like this


=C2=A0colvar {=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 width 0.05=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 lowerboundary 0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 upperboundary 1=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 extendedlagrangia= n on
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 extendedflu= ctuation 0.05
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2= =A0=C2=A0 gspath {
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0atoms {atomnumbers { 12961 12975 ..... 61848 61880 }}
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositionsFile1 1.pdb
=C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositionsFile2 2.pdb=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositionsFile3= 3.pdb
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 .........= .
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositionsF= ile102 102.pdb
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 r= efPositionsFile103 103.pdb
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 refPositionsFile104 104.pdb
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 refPositionsFile105 105.pdb
=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositionsFile106 106.pdb
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositionsFile107 10= 7.pdb
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 refPositio= nsFile108 108.pdb
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0}
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0}
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 abf {
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 c= olvars gs
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 fullSamples 500
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 historyfreq 1000
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 }

Conf file inputs:
# output
outputname $= {runnew}
outputenergies 500
outputtiming =C2=A0 500
binaryoutput = =C2=A0 no
restartfreq =C2=A0 500
dcdfreq =C2=A0 =C2=A0 =C2=A0 1000dcdfile =C2=A0 =C2=A0 =C2=A0 ${runnew}.dcd
wrapall =C2=A0 =C2=A0 =C2=A0= =C2=A0off
wrapNearest =C2=A0 =C2=A0on

# for restarting:
resta= rtname ${runnew}-restart
colvars on
cv configfile input_file.tcl
r= un $step

Kindly suggest,
Thanks
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boundary="000000000000798b2905d120f514" X-CLX-Response: 1TFkXGxIZEQpMehcZHxgRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHh8eEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwZcR4YEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2BoQG1fQWx1SB1LTBJGQnN1aBNAeRNcfRJsXllmH25/EQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXc1B4ekwRCk1cFxkcGREKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbHR8RCkJeFxsRCkRYFxgRCkRJFxkRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpz HBEKQmwXZRhFRWJHS2FoS2wRCkJAF2N6aWR/Zm9GfXB5EQpaWBcZEQp5QxdtYhhGExtgZRtDYxE KWUsXEx8THxEKcGgXb1hSGX9AYkZ+T2UQGRoRCnBoF2J5XlNTX09fb0EBEBkaEQpwaBd6QHBBE0 58SHoTchAeEhEKcGgXZkF8clJrcm5OHVsQHhIRCnBoF2dyHU8BS0RDYFJvEBkaEQpwfRd6Wx9CX E9/SBMdSBAZGhEKcH8XYR8dZUQZGX56fXgQGRoRCnBfF2VaRhJyfUQBUB5EEBkaEQpwbBdkeX5k WWceU1NpbxAZGhEKcEwXY2hnfWJhEkN9bgUQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: JBjGukF_b7af8lhY_B9jS9vW8FtsL5DU X-Proofpoint-ORIG-GUID: JBjGukF_b7af8lhY_B9jS9vW8FtsL5DU X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 adultscore=0 priorityscore=352 spamscore=0 phishscore=0 mlxscore=0 mlxlogscore=421 suspectscore=0 clxscore=183 lowpriorityscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111190052 domainage_hfrom=9595 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --000000000000798b2905d120f514 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Peter Bonds between all couple of atoms, even CL-CL > 5000 !NBOND: bonds > 1 2 1 4 1 5 1 > 6 > 2 3 7 8 7 10 7 > 11 > 7 12 8 9 13 14 13 > 16 > 13 17 13 18 14 15 19 > 20 > 19 22 19 23 19 24 20 > 21 > where atom numbering is > 5000 !NATOM > 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0 > 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0 > 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0 > 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0 > 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0 > > All such bonding is also evident from loading psf/pdb to vmd. > > I started from a box prepared with packmol, and I tried also adding TER > between residues > HEADER > TITLE Built with Packmol > REMARK Packmol generated pdb file > REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicamp.br= /packmol__;!!DZ3fjg!q3HBReG05vAH7TecnLBopbfTkKXY0lAdye4dyLyj39gbbf1ugnRqvHu= 298tdcTTxSQ$=20 > REMARK > HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00 > CL > HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00 > CL > HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00 > CL > HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00 > C > HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00 > H > TER > HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00 > CL > HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00 > CL > HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00 > CL > HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00 > C > HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00 > H > TER > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx No such problems encountered in making a MEOH box, starting from "RESI MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained, with psf indicating only the correct bonds. With CHARMM36/CGenFF the only source of topology for CHCL3 is toppar_chloroform_dh.str I can't understand where I am wrong with CHCL3 Thanks for advice francesco On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino wrote: > Have you looked at the bonds in your psf to make sure they are correct? > This looks like you've hydrogen atoms that have two bonds... > Best, > Peter > > On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra > wrote: > >> It seems thatb the str used is inadequate. Alsdo adjusting angles in str, >> namd assks for dihedrals >> fp >> >> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra >> wrote: >> >>> While attempting to minimize a CHCL3 box built from CHARMM36-provided >>> toppar_chloroform_dh.str, namd crashes >>> >>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 >>>> 4) >>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 >>>> 5 4) >>>> >>> >>> Actually, the prm part of the str (which was read by namd) l correctly >>> furnishes >>> >>>> ANGLES >>>> CLCM CCM CLCM 0.0 111.30 >>>> HCM CCM CLCM 0.0 107.57 >>>> >>> >>> Why is namd looking for those wrong angles? The central atom is carbon >>> not hydrogen. >>> >>> Thanks for advice >>> francesco pietra >>> >> --000000000000798b2905d120f514 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Peter
Bonds between all couple of atoms,= even CL-CL
500= 0 !NBOND: bonds
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A0= =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 5 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6
=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A02 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 = =C2=A010 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A011
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A07 =C2=A0 =C2=A0 =C2=A0 =C2=A012 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 9 =C2=A0 =C2=A0 =C2=A0 =C2= =A013 =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 = =C2=A0 =C2=A0 =C2=A016
=C2=A0 =C2=A0 =C2=A0 =C2=A0 13 =C2=A0 =C2=A0 =C2= =A0 =C2=A017 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A018 = =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2=A0 =C2=A015 =C2=A0 =C2=A0 = =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A020
=C2=A0 =C2=A0 =C2=A0 =C2= =A0 19 =C2=A0 =C2=A0 =C2=A0 =C2=A022 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 = =C2=A0 =C2=A0 =C2=A023 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 = =C2=A024 =C2=A0 =C2=A0 =C2=A0 =C2=A020 =C2=A0 =C2=A0 =C2=A0 =C2=A021
<= /blockquote>
where atom numbering is
5000 !NATOM
=C2=A0 =C2=A0 =C2=A0 =C2=A01 AO1 = =C2=A01 =C2=A0 =C2=A0CCL3 C =C2=A0 =C2=A0CCM =C2=A0 =C2=A00.179000 =C2=A0 = =C2=A0 =C2=A0 12.0110 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0= =C2=A0 =C2=A02 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL1 =C2=A0CLCM =C2=A0-0.08700= 0 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2= =A0 =C2=A0 =C2=A0 =C2=A03 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL2 =C2=A0CLCM =C2= =A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A04 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL3 =C2= =A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A05 AO1 =C2=A01 =C2=A0 =C2=A0CC= L3 HX =C2=A0 HCM =C2=A0 =C2=A00.082000 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0080 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0

All such bonding is also evident fro= m loading psf/pdb to vmd.

I started from a box= prepared with packmol, and I tried also adding TER between residues
<= div>HEADER
TITLE =C2=A0 =C2=A0 Built with Packmol =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
REMARK =C2= =A0 Packmol generated pdb file
REMARK =C2=A0 Home-Page: http://m3g.i= qm.unicamp.br/packmol
REMARK
HETATM =C2=A0 =C2=A01 CL1 =C2=A0CCL3= A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.522 =C2=A0 5.429 =C2=A0 3.173 =C2=A01.00 = =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2= =A02 CL2 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.670 =C2=A0 3.053 =C2= =A0 4.852 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0=
HETATM =C2=A0 =C2=A03 CL3 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.0= 18 =C2=A0 2.823 =C2=A0 1.969 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A04 C =C2=A0 =C2=A0CCL3A =C2=A0 1 = =C2=A0 =C2=A0 =C2=A031.285 =C2=A0 3.845 =C2=A0 3.391 =C2=A01.00 =C2=A00.00 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2=A0
HETATM =C2=A0 =C2=A05 =C2=A0= HX =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A032.361 =C2=A0 3.996 =C2=A0 3.50= 9 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER<= br>HETATM =C2=A0 =C2=A06 CL1 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.81= 7 =C2=A017.228 =C2=A0 1.210 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A07 CL2 =C2=A0CCL3A =C2=A0 2 =C2= =A0 =C2=A0 =C2=A0 1.496 =C2=A017.919 =C2=A0 2.829 =C2=A01.00 =C2=A00.00 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A08 CL3 =C2= =A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.573 =C2=A016.195 =C2=A0 3.922 =C2= =A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM = =C2=A0 =C2=A09 C =C2=A0 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.231 =C2= =A017.561 =C2=A0 2.849 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 C =C2=A0
HETATM =C2=A0 10 =C2=A0HX =C2=A0CCL3A =C2=A0 2 =C2=A0 = =C2=A0 =C2=A0 3.759 =C2=A018.439 =C2=A0 3.230 =C2=A01.00 =C2=A00.00 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
xxxxxxxx= xxxxxxxxxxxxxxxxxxxxxx
No such problems encountered in making a M= EOH box, starting from "RESI MEOH" in CGenFF. Clear, not interact= ing MEOH molecules where obtained,
with psf indicating only the c= orrect bonds.

With CHARMM36/CGenFF the only so= urce of topology for CHCL3 is toppar_chloroform_dh.str
I can'= t understand where I am wrong with CHCL3
Thanks for advice
francesco

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boundary="000000000000bd634605d124a6b8" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBgZEQpMehcbHhoRCllEF2dMU0cZaBJoR0x7EQpYWBdjWGZBfmxIWGB SexEKeE4XYX5mSUN9fVxYHUARCnlMF29Pf24BGnlLH1NlEQpDSBcHHhofEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGBoZcRgbGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdva1lTRBhiHXtaRltPGGtBbRNkQGtSTmh1R18cXkh5fREKWFwXHwQaBBge GAUbGgQbGxoEHQQbGRkQGx4aHxoRCl5ZF3NQfGJ5EQpNXBceGxsRCkxaF3hpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XbRNgEwFhWmttQBIRCkNaFxgaEwQSHwQYGx 8EGx0SEQpCXhcbEQpESRcZEQpCXBcbEQpeThcbEQpCSxdhfmZJQ319XFgdQBEKQkkXYX5mSUN9f VxYHUARCkJFF2YYHn1uYEhLZkVyEQpCThdhfmZJQ319XFgdQBEKQkwXY1hmQX5sSFhgUnsRCkJs F21vZhxcb35fW2NcEQpCQBdjemlkf2ZvRn1weREKQlgXZ3Nlc0BuYWFMXWIRClpYFxkRCnlDF21 iGEYTG2BlG0NjEQpwaBduZF8fQVtAaUZ6WhAZGhEKcGgXekBwQRNOfEh6E3IQHRoRCnBoF2ZBfH JSa3JuTh1bEBIfEQpwaBdsaX5SbUVpeRJoWBAZGhEKcGgXZ3IdTwFLRENgUm8QGRoRCnB9F3pbH 0JcT39IEx1IEBkaEQpwfxdhHx1lRBkZfnp9eBAeEhEKcF8XZVpGEnJ9RAFQHkQQGRoRCnBsF2ZM YRpIeHAffGJvEBkaEQpwTBdjaGd9YmESQ31uBRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: EAsyn2H7Qplqe2AkG9NjAxdB_mu6tbSW X-Proofpoint-ORIG-GUID: EAsyn2H7Qplqe2AkG9NjAxdB_mu6tbSW MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 phishscore=0 clxscore=223 mlxscore=0 bulkscore=0 adultscore=0 impostorscore=0 lowpriorityscore=0 mlxlogscore=661 malwarescore=0 priorityscore=140 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111190078 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --000000000000bd634605d124a6b8 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Based on the comments in that topology file (which I had to google -- it would really help to include such things in the mailing list discussion), it looks like those CL-CL and other problematic bonds are present only for SHAKE. That suggests to me that this is supposed to be a rigid chloroform model, which might not be possible in NAMD. Did you check the original paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968) for how this is supposed to be implemented? Thanks, Peter On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra wrote: > Hi Peter > Bonds between all couple of atoms, even CL-CL > >> 5000 !NBOND: bonds >> 1 2 1 4 1 5 1 >> 6 >> 2 3 7 8 7 10 7 >> 11 >> 7 12 8 9 13 14 13 >> 16 >> 13 17 13 18 14 15 19 >> 20 >> 19 22 19 23 19 24 20 >> 21 >> > where atom numbering is > >> 5000 !NATOM >> 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0 >> 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0 >> 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0 >> 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0 >> 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0 >> > >> All such bonding is also evident from loading psf/pdb to vmd. >> >> I started from a box prepared with packmol, and I tried also adding TER >> between residues >> HEADER >> TITLE Built with Packmol >> REMARK Packmol generated pdb file >> REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicamp.b= r/packmol__;!!DZ3fjg!rfO_wUWkY1X5XBCTAEnorNJUdxsw_prm7ebIkV8xhw4w-5fPksl3kY= 3o2LgqhQQ8PA$=20 >> REMARK >> HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00 >> CL >> HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00 >> CL >> HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00 >> CL >> HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00 >> C >> HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00 >> H >> TER >> HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00 >> CL >> HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00 >> CL >> HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00 >> CL >> HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00 >> C >> HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00 >> H >> TER >> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > No such problems encountered in making a MEOH box, starting from "RESI > MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained, > with psf indicating only the correct bonds. > > With CHARMM36/CGenFF the only source of topology for CHCL3 is > toppar_chloroform_dh.str > I can't understand where I am wrong with CHCL3 > Thanks for advice > francesco > > On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino > wrote: > >> Have you looked at the bonds in your psf to make sure they are correct? >> This looks like you've hydrogen atoms that have two bonds... >> Best, >> Peter >> >> On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra >> wrote: >> >>> It seems thatb the str used is inadequate. Alsdo adjusting angles in >>> str, namd assks for dihedrals >>> fp >>> >>> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra >>> wrote: >>> >>>> While attempting to minimize a CHCL3 box built from CHARMM36-provided >>>> toppar_chloroform_dh.str, namd crashes >>>> >>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 >>>>> 5 4) >>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 >>>>> 5 4) >>>>> >>>> >>>> Actually, the prm part of the str (which was read by namd) l correctly >>>> furnishes >>>> >>>>> ANGLES >>>>> CLCM CCM CLCM 0.0 111.30 >>>>> HCM CCM CLCM 0.0 107.57 >>>>> >>>> >>>> Why is namd looking for those wrong angles? The central atom is carbon >>>> not hydrogen. >>>> >>>> Thanks for advice >>>> francesco pietra >>>> >>> --000000000000bd634605d124a6b8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Based on the comments in that topology file (which I = had to google -- it would really help to include such things in the mailing= list discussion), it looks like those CL-CL and other problematic bonds ar= e present only for SHAKE. That suggests to me that this is supposed to be a= rigid chloroform model, which might not be possible in NAMD. Did you check= the original paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1= 985, 89, 968) for how this is supposed to be implemented?
Thanks,=
Peter

Hi Peter
Bonds between all couple of atoms, even= CL-CL
5000 !NB= OND: bonds
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 2 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 5 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A02 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2= =A010 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A011
=C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A07 =C2=A0 =C2=A0 =C2=A0 =C2=A012 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 9 =C2=A0 =C2=A0 =C2=A0 =C2=A013= =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 = =C2=A0 =C2=A016
=C2=A0 =C2=A0 =C2=A0 =C2=A0 13 =C2=A0 =C2=A0 =C2=A0 =C2= =A017 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A018 =C2=A0 = =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2=A0 =C2=A015 =C2=A0 =C2=A0 =C2=A0 = =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A020
=C2=A0 =C2=A0 =C2=A0 =C2=A0 19 = =C2=A0 =C2=A0 =C2=A0 =C2=A022 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 = =C2=A0 =C2=A023 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A024= =C2=A0 =C2=A0 =C2=A0 =C2=A020 =C2=A0 =C2=A0 =C2=A0 =C2=A021
where atom numbering is
5000 !NATOM
=C2=A0 =C2=A0 =C2=A0 =C2=A01 AO1 =C2=A01 = =C2=A0 =C2=A0CCL3 C =C2=A0 =C2=A0CCM =C2=A0 =C2=A00.179000 =C2=A0 =C2=A0 = =C2=A0 12.0110 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0= =C2=A02 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL1 =C2=A0CLCM =C2=A0-0.087000 =C2= =A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 = =C2=A0 =C2=A0 =C2=A03 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL2 =C2=A0CLCM =C2=A0-0= .087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0=C2=A0 =C2=A0 =C2=A0 =C2=A04 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL3 =C2=A0CLCM= =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A05 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 HX = =C2=A0 HCM =C2=A0 =C2=A00.082000 =C2=A0 =C2=A0 =C2=A0 =C2=A01.0080 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 0

All such bonding is also evident from loadi= ng psf/pdb to vmd.

I started from a box prepar= ed with packmol, and I tried also adding TER between residues
HEA= DER
TITLE =C2=A0 =C2=A0 Built with Packmol =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
REMARK =C2=A0 Pack= mol generated pdb file
REMARK =C2=A0 Home-Page: ht= tp://m3g.iqm.unicamp.br/packmol
REMARK
HETATM =C2=A0 =C2=A01 CL1 = =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.522 =C2=A0 5.429 =C2=A0 3.173 = =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM= =C2=A0 =C2=A02 CL2 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.670 =C2=A0 = 3.053 =C2=A0 4.852 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= CL =C2=A0
HETATM =C2=A0 =C2=A03 CL3 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 = =C2=A031.018 =C2=A0 2.823 =C2=A0 1.969 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A04 C =C2=A0 =C2=A0CCL3A= =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.285 =C2=A0 3.845 =C2=A0 3.391 =C2=A01.00 = =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2=A0
HETATM =C2=A0 =C2= =A05 =C2=A0HX =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A032.361 =C2=A0 3.996 = =C2=A0 3.509 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2= =A0
TER
HETATM =C2=A0 =C2=A06 CL1 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 = =C2=A0 3.817 =C2=A017.228 =C2=A0 1.210 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A07 CL2 =C2=A0CCL3A =C2= =A0 2 =C2=A0 =C2=A0 =C2=A0 1.496 =C2=A017.919 =C2=A0 2.829 =C2=A01.00 =C2= =A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A0= 8 CL3 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.573 =C2=A016.195 =C2=A0 3= .922 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
H= ETATM =C2=A0 =C2=A09 C =C2=A0 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.2= 31 =C2=A017.561 =C2=A0 2.849 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 C =C2=A0
HETATM =C2=A0 10 =C2=A0HX =C2=A0CCL3A =C2=A0 2 =C2= =A0 =C2=A0 =C2=A0 3.759 =C2=A018.439 =C2=A0 3.230 =C2=A01.00 =C2=A00.00 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
xxxx= xxxxxxxxxxxxxxxxxxxxxxxxxx
No such problems encountered in making= a MEOH box, starting from "RESI MEOH" in CGenFF. Clear, not inte= racting MEOH molecules where obtained,
with psf indicating only t= he correct bonds.

With CHARMM36/CGenFF the onl= y source of topology for CHCL3 is toppar_chloroform_dh.str
I can&= #39;t understand where I am wrong with CHCL3
Thanks for advic= e
francesco

On Thu, Nov 18, 2021 at 3:38 PM Peter Freddo= lino <petefred@u= mich.edu> wrote:
Have you looked at the bonds in your psf to m= ake sure they are correct? This looks like you've hydrogen atoms that h= ave two bonds...
Best,
Peter

On Thu, Nov 1= 8, 2021 at 5:42 AM Francesco Pietra <chiendarret@gmail.com> wrote:
It seems= thatb the str used is inadequate. Alsdo adjusting angles in str, namd assk= s for dihedrals
fp

=
On Thu, Nov 18, 2021 at 9:29 AM Franc= esco Pietra <= chiendarret@gmail.com> wrote:
While attempting to minimize a C= HCL3 box built from CHARMM36-provided toppar_chloroform_dh.str, namd crashe= s

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 = 4)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS = 1 5 4)

Actually, the prm part of the = str (which was read by namd) l correctly furnishes
ANGLES
CLCM =C2=A0CCM =C2=A0CLCM= =C2=A0 =C2=A00.0 =C2=A0 =C2=A0111.30
HCM =C2=A0 CCM =C2=A0CLCM =C2=A0 = =C2=A00.0 =C2=A0 =C2=A0107.57

Why is = namd looking for those wrong angles? The central atom is carbon not hydroge= n.

Thanks for advice
francesco pietra
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Fri, 19 Nov 2021 08:56:11 -0800 (PST) References: In-Reply-To: From: Francesco Pietra Date: Fri, 19 Nov 2021 17:55:59 +0100 Message-ID: Subject: Re: vmd-l: Re: namd-l: namd minimization looking for wrong angle To: Peter Freddolino Cc: "" , VMD Mailing List Content-Type: multipart/mixed; boundary="00000000000000c56705d12727a9" X-Proofpoint-ORIG-GUID: RoZjeh8F0jUBKM7IOL-HE_nBMRQOxcvx X-CLX-Response: 1TFkXGxIcEQpMehcZGh4RCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHh4dEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwccR4fEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3hFcEBPQhJsGkB/aGFnHWNlZgdib3VEaGd4e2VSSVxSEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGRAbHhofGhEKXlkXc1ByUn8RCk1cFx8SExEKTFoXe2lrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGg QbHBMRCkJeFxsRCkRJFxkRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwX ZRhFRWJHS2FoS2wRCkJAF2N6aWR/Zm9GfXB5EQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXbWI YRhMbYGUbQ2MRCllLFxMfEx8RCnBoF2NlZU8fH2xufUlSEBkaEQpwaBdhe157TB9ac3tSWRAZGh EKcGgXZEF4AX9JY21pUGUQGRoRCnBoF3oZXUVvYU1lThwfEBkaEQpwaBdifhJSRQFNYloBYhAZG hEKcH0XelsfQlxPf0gTHUgQHhIRCnB/F2EfHWVEGRl+en14EB4aEQpwXxdlWkYScn1EAVAeRBAe EhEKcGwXZHl+ZFlnHlNTaW8QHRoRCnBMF2NoZ31iYRJDfW4FEB4SEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 4twXgE2FaSxXXNMzgw0WT6YocrUl_otM X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 impostorscore=0 clxscore=186 bulkscore=0 lowpriorityscore=0 mlxscore=0 suspectscore=0 priorityscore=304 phishscore=0 spamscore=0 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=2 engine=8.12.0-2110150000 definitions=main-2111190094 domainage_hfrom=9595 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --00000000000000c56705d12727a9 Content-Type: multipart/alternative; boundary="00000000000000c56605d12727a7" --00000000000000c56605d12727a7 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Unfortunately I have no access to that journal. At any event, I never use SHAKE, so that I parameterized CHCL3 on the MATCH server, getting the attached rtf. On that basis, I first tried to generate psf/pdb for a single CHCL3 molecule. With autopsf the error.log was ERROR: failed on end of segment > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. > ERROR: failed on end of segment > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. > while executing > "segment $segid { > pdb $segfile > # We alias the C-terminal OXT atoms to OT2 so that psfgen has to > guess one atom less. > # Otherwise psf..." > (procedure "psfsegments" line 37) > invoked from within > "psfsegments $logfileout" > (procedure "::autopsf::afterchains_gui" line 66) > invoked from within > "::autopsf::afterchains_gui" > invoked from within > ".autopsf.chains.finish invoke" > ("uplevel" body line 1) > invoked from within > "uplevel #0 [list $w invoke]" > (procedure "tk::ButtonUp" line 22) > invoked from within > "tk::ButtonUp .autopsf.chains.finish" > (command bound to event) while the terminal last lines told segfiles CHCl3_autopsf-temp.pdb_XO1.pdb > CHCl3_autopsf-temp.pdb_XO1.pdb > 1 4 > psfgen) building segment XO1 > psfgen) reading residues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb > psfgen) unknown residue type CCL3 > psfgen) extracted 1 residues from pdb file > psfgen) setting patch for first residue to none > psfgen) setting patch for last residue to none > Info: generating structure... > psfgen) unknown residue type CCL3 > Then, I made recourse to vmd text mode, getting attached chcl3.psf/pdb without any issue. However, I needed psf/pdb for the solvent box, again from the box generated with packmol that I reported previously. In this case I was not aware of any trick to avoid writing 1000-fold inputs on the .gen file, so that I tried with autopsf. The last lines on the terminal were: psfgen) extracted 1000 residues from pdb file > psfgen) setting patch for first residue to none > psfgen) setting patch for last residue to none > Info: generating structure... > psfgen) unknown residue type CCL3 > Segmentation fault > Obviously CCL3 was and is the residue. Probably, without additional information no one will be able to suggest a remedy for autopsf (perhaps, however, suggesting how to deal with vmd text mode for the solvent box, i.e. a shortcut for the onethousand blocks) Thanks for your attention francesco On Fri, Nov 19, 2021 at 2:57 PM Peter Freddolino wrote: > Based on the comments in that topology file (which I had to google -- it > would really help to include such things in the mailing list discussion), > it looks like those CL-CL and other problematic bonds are present only for > SHAKE. That suggests to me that this is supposed to be a rigid chloroform > model, which might not be possible in NAMD. Did you check the original > paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968) > for how this is supposed to be implemented? > Thanks, > Peter > > On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra > wrote: > >> Hi Peter >> Bonds between all couple of atoms, even CL-CL >> >>> 5000 !NBOND: bonds >>> 1 2 1 4 1 5 1 >>> 6 >>> 2 3 7 8 7 10 7 >>> 11 >>> 7 12 8 9 13 14 13 >>> 16 >>> 13 17 13 18 14 15 19 >>> 20 >>> 19 22 19 23 19 24 20 >>> 21 >>> >> where atom numbering is >> >>> 5000 !NATOM >>> 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0 >>> 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0 >>> 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0 >>> 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0 >>> 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0 >>> >> >>> All such bonding is also evident from loading psf/pdb to vmd. >>> >>> I started from a box prepared with packmol, and I tried also adding TER >>> between residues >>> HEADER >>> TITLE Built with Packmol >>> REMARK Packmol generated pdb file >>> REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicamp.= br/packmol__;!!DZ3fjg!s6lbYqArpiNe-Obx81ImBSD98ZIZEvVBLc8BZnnzXEAVk3UpETJeC= 8YQpDdQSBNkdg$=20 >>> REMARK >>> HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00 >>> CL >>> HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00 >>> CL >>> HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00 >>> CL >>> HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00 >>> C >>> HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00 >>> H >>> TER >>> HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00 >>> CL >>> HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00 >>> CL >>> HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00 >>> CL >>> HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00 >>> C >>> HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00 >>> H >>> TER >>> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> No such problems encountered in making a MEOH box, starting from "RESI >> MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained, >> with psf indicating only the correct bonds. >> >> With CHARMM36/CGenFF the only source of topology for CHCL3 is >> toppar_chloroform_dh.str >> I can't understand where I am wrong with CHCL3 >> Thanks for advice >> francesco >> >> On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino >> wrote: >> >>> Have you looked at the bonds in your psf to make sure they are correct? >>> This looks like you've hydrogen atoms that have two bonds... >>> Best, >>> Peter >>> >>> On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra >>> wrote: >>> >>>> It seems thatb the str used is inadequate. Alsdo adjusting angles in >>>> str, namd assks for dihedrals >>>> fp >>>> >>>> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra >>>> wrote: >>>> >>>>> While attempting to minimize a CHCL3 box built from CHARMM36-provided >>>>> toppar_chloroform_dh.str, namd crashes >>>>> >>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 >>>>>> 5 4) >>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS >>>>>> 1 5 4) >>>>>> >>>>> >>>>> Actually, the prm part of the str (which was read by namd) l correctly >>>>> furnishes >>>>> >>>>>> ANGLES >>>>>> CLCM CCM CLCM 0.0 111.30 >>>>>> HCM CCM CLCM 0.0 107.57 >>>>>> >>>>> >>>>> Why is namd looking for those wrong angles? The central atom is carbon >>>>> not hydrogen. >>>>> >>>>> Thanks for advice >>>>> francesco pietra >>>>> >>>> --00000000000000c56605d12727a7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Unfortunately I have no access to that journal. At an= y event, I never use SHAKE, so that I parameterized CHCL3 on the MATCH serv= er, getting the attached rtf. On that basis, I first tried to generate psf/= pdb for a single CHCL3 molecule. With autopsf the error.log was
<= br>

ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR!= =C2=A0 Use resetpsf to start over.
ERROR: failed on end of segment
MO= LECULE DESTROYED BY FATAL ERROR!=C2=A0 Use resetpsf to start over.
=C2= =A0 =C2=A0 while executing
"segment $segid {
=C2=A0 =C2=A0 =C2= =A0 pdb $segfile

=C2=A0 =C2=A0 =C2=A0 # We alias the C-terminal OXT atoms to OT2= so that psfgen has to guess one atom less.
=C2=A0 =C2=A0 =C2=A0 # Other= wise psf..."
=C2=A0 =C2=A0 (procedure "psfsegments" line = 37)
=C2=A0 =C2=A0 invoked from within
"psfsegments $logfileout&q= uot;
=C2=A0 =C2=A0 (procedure "::autopsf::afterchains_gui" lin= e 66)
=C2=A0 =C2=A0 invoked from within
"::autopsf::afterchains_= gui"
=C2=A0 =C2=A0 invoked from within
".autopsf.chains.fin= ish invoke"
=C2=A0 =C2=A0 ("uplevel" body line 1)
=C2= =A0 =C2=A0 invoked from within
"uplevel #0 [list $w invoke]"=C2=A0 =C2=A0 (procedure "tk::ButtonUp" line 22)
=C2=A0 =C2= =A0 invoked from within
"tk::ButtonUp .autopsf.chains.finish"<= br>=C2=A0 =C2=A0 (command bound to event)

=
while the terminal last lines told

segfiles CHCl3_autopsf-temp.pdb_XO1= .pdb
CHCl3_autopsf-temp.pdb_XO1.pdb
1 4
psfgen) building segment X= O1
psfgen) reading residues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb=
psfgen) unknown residue type CCL3
psfgen) extracted 1 residues from = pdb file
psfgen) setting patch for first residue to none
psfgen) sett= ing patch for last residue to none
Info: generating structure...
psfg= en) unknown residue type CCL3

Then, I= made recourse to vmd text mode, getting attached chcl3.psf/pdb without any= issue.

However, I needed psf/pdb for the solvent = box, again from the box generated with packmol that I reported previously. = In this case I was not aware of any trick to avoid writing 1000-fold inputs= on the .gen file, so that I tried with autopsf. The last lines on the term= inal were:

psfgen) extracted 1000 residues from pdb file
psfgen) setting= patch for first residue to none
psfgen) setting patch for last residue = to none
Info: generating structure...
psfgen) unknown residue type CC= L3
Segmentation fault

Obviously CC= L3 was and is the residue. Probably, without additional information no one = will be able to suggest a remedy for autopsf=C2=A0 (perhaps, however, sugge= sting how to deal with vmd text mode for the solvent box, i.e. a shortcut f= or the onethousand blocks)

Thanks for your att= ention
francesco


On Fri, Nov 19, 2021 at = 2:57 PM Peter Freddolino <petefred= @umich.edu> wrote:
Based on the comments in that topology fil= e (which I had to google -- it would really help to include such things in = the mailing list discussion), it looks like those CL-CL and other problemat= ic bonds are present only for SHAKE. That suggests to me that this is suppo= sed to be a rigid chloroform model, which might not be possible in NAMD. Di= d you check the original paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. P= hys. Chem 1985, 89, 968) for how this is supposed to be implemented?
<= div>Thanks,
Peter

On Fri, Nov 19, 2021 at 4:33 AM Fr= ancesco Pietra <chiendarret@gmail.com> wrote:
Hi Peter
Bonds betw= een all couple of atoms, even CL-CL
5000 !NBOND: bonds
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A01 =C2=A0 =C2=A0 =C2=A0 =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 4 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 5 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6
=C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A02 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7= =C2=A0 =C2=A0 =C2=A0 =C2=A010 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 = =C2=A0 =C2=A011
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A07 =C2=A0 =C2=A0 =C2=A0= =C2=A012 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 9 =C2= =A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2= =A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A016
=C2=A0 =C2=A0 =C2=A0 =C2=A0 1= 3 =C2=A0 =C2=A0 =C2=A0 =C2=A017 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0= =C2=A0 =C2=A018 =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2=A0 =C2=A01= 5 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A020
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 19 =C2=A0 =C2=A0 =C2=A0 =C2=A022 =C2=A0 =C2=A0 =C2=A0 =C2= =A019 =C2=A0 =C2=A0 =C2=A0 =C2=A023 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 = =C2=A0 =C2=A0 =C2=A024 =C2=A0 =C2=A0 =C2=A0 =C2=A020 =C2=A0 =C2=A0 =C2=A0 = =C2=A021
where atom numbering is
5000 !NATOM
=C2=A0 =C2=A0 =C2= =A0 =C2=A01 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 C =C2=A0 =C2=A0CCM =C2=A0 =C2=A00= .179000 =C2=A0 =C2=A0 =C2=A0 12.0110 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0=C2=A0 =C2=A0 =C2=A0 =C2=A02 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL1 =C2=A0CLCM= =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A03 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL2 = =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A04 AO1 =C2=A01 =C2=A0 =C2= =A0CCL3 CL3 =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A05 AO1 =C2=A01 = =C2=A0 =C2=A0CCL3 HX =C2=A0 HCM =C2=A0 =C2=A00.082000 =C2=A0 =C2=A0 =C2=A0 = =C2=A01.0080 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0

All such bonding is als= o evident from loading psf/pdb to vmd.

I start= ed from a box prepared with packmol, and I tried also adding TER between re= sidues
HEADER
TITLE =C2=A0 =C2=A0 Built with Packmol =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 <= br>REMARK =C2=A0 Packmol generated pdb file
REMARK =C2=A0 Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
HETAT= M =C2=A0 =C2=A01 CL1 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.522 =C2=A0= 5.429 =C2=A0 3.173 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0CL =C2=A0
HETATM =C2=A0 =C2=A02 CL2 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2= =A0 =C2=A030.670 =C2=A0 3.053 =C2=A0 4.852 =C2=A01.00 =C2=A00.00 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A03 CL3 =C2=A0CCL3A = =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.018 =C2=A0 2.823 =C2=A0 1.969 =C2=A01.00 = =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2= =A04 C =C2=A0 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.285 =C2=A0 3.845 = =C2=A0 3.391 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2= =A0
HETATM =C2=A0 =C2=A05 =C2=A0HX =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 = =C2=A032.361 =C2=A0 3.996 =C2=A0 3.509 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
HETATM =C2=A0 =C2=A06 CL1 =C2=A0CCL= 3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.817 =C2=A017.228 =C2=A0 1.210 =C2=A01.00= =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 = =C2=A07 CL2 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 1.496 =C2=A017.919 = =C2=A0 2.829 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2= =A0
HETATM =C2=A0 =C2=A08 CL3 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 = 3.573 =C2=A016.195 =C2=A0 3.922 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A09 C =C2=A0 =C2=A0CCL3A =C2=A0= 2 =C2=A0 =C2=A0 =C2=A0 3.231 =C2=A017.561 =C2=A0 2.849 =C2=A01.00 =C2=A00.= 00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2=A0
HETATM =C2=A0 10 =C2=A0HX= =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.759 =C2=A018.439 =C2=A0 3.230 = =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
No such probl= ems encountered in making a MEOH box, starting from "RESI MEOH" i= n CGenFF. Clear, not interacting MEOH molecules where obtained,
w= ith psf indicating only the correct bonds.

Wit= h CHARMM36/CGenFF the only source of topology for CHCL3 is toppar_chlorofor= m_dh.str
I can't understand where I am wrong with CHCL3
Thanks for advice
francesco

On Thu, Nov 18, 202= 1 at 3:38 PM Peter Freddolino <petefred@umich.edu> wrote:
Have you looked at t= he bonds in your psf to make sure they are correct? This looks like you'= ;ve hydrogen atoms that have two bonds...
Best,
Pet= er

On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra <chiendarret@gmail.com&= gt; wrote:
It seems thatb the str used is inadequate. Alsdo adjusting= angles in str, namd assks for dihedrals
fp

On Thu, Nov = 18, 2021 at 9:29 AM Francesco Pietra <chiendarret@gmail.com> wrote:
While a= ttempting to minimize a CHCL3 box built from CHARMM36-provided toppar_chlor= oform_dh.str, namd crashes

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR= CCM HCM CLCM (ATOMS 1 5 4)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS= FOR CCM HCM CLCM (ATOMS 1 5 4)

Actua= lly, the prm part of the str (which was read by namd) l correctly furnishes=
ANGLES
= CLCM =C2=A0CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2=A0111.30
HCM =C2= =A0 CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2=A0107.57
<= div>
Why is namd looking for those wrong angles? The central = atom is carbon not hydrogen.

Thanks for advice=
francesco pietra
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Fri, 19 Nov 2021 09:03:10 -0800 (PST) References: In-Reply-To: From: Peter Freddolino Date: Fri, 19 Nov 2021 12:02:59 -0500 Message-ID: Subject: Re: vmd-l: Re: namd-l: namd minimization looking for wrong angle To: Francesco Pietra Cc: "" , VMD Mailing List Content-Type: multipart/alternative; boundary="000000000000f1c72a05d1273f5b" X-Proofpoint-GUID: RgBoiPQIC9_6h6W6SMHE-8JzpLCCBBtd X-CLX-Response: 1TFkXGxMZEQpMehcbHx4RCllEF2dMU0cZaBJoR0x7EQpYWBdjWGZBfmxIWGB SexEKeE4XYX5mSUN9fVxYHUARCnlMF29Pf24BGnlLH1NlEQpDSBcHGRIeEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0ZcRsaHRAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThd4TWhFQ3p7Y2kTdRxCHH0ceWdibwcSYFBaZmlpaGheThEKWFwXHwQaBBge GAUbGgQbGxoEHQQbGRsQGx4aHxoRCl5ZF3NQchtbEQpNXBcfHhwRCkxaF3tpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZH5YT2Zuc0lwW08RCkNaFxgaEwQSHwQYGx wEHh8RCkJeFxsRCkRJFxkRCkJcFxsRCl5OFxsRCkJLF2F+ZklDfX1cWB1AEQpCSRdhfmZJQ319X FgdQBEKQkUXZhgefW5gSEtmRXIRCkJOF2F+ZklDfX1cWB1AEQpCTBdjWGZBfmxIWGBSexEKQmwX bW9mHFxvfl9bY1wRCkJAF2N6aWR/Zm9GfXB5EQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXbWI YRhMbYGUbQ2MRCnBoF2NlZU8fH2xufUlSEB4SEQpwaBdhe157TB9ac3tSWRAeEhEKcGgXZEF4AX 9JY21pUGUQHhIRCnBoF3oZXUVvYU1lThwfEB4SEQpwaBdifhJSRQFNYloBYhAeEhEKcH0XelsfQ lxPf0gTHUgQHhIRCnB/F2EfHWVEGRl+en14EBIfEQpwXxdlWkYScn1EAVAeRBAeEhEKcGwXZkxh Gkh4cB98Ym8QHhIRCnBMF2NoZ31iYRJDfW4FEB4SEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: RgBoiPQIC9_6h6W6SMHE-8JzpLCCBBtd X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=154 bulkscore=0 mlxscore=0 clxscore=193 suspectscore=0 mlxlogscore=999 lowpriorityscore=0 spamscore=0 adultscore=0 phishscore=0 malwarescore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111190094 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --000000000000f1c72a05d1273f5b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable How were you running autopsf, and with what version of vmd? autopsf -mol 0 -top 1009279.rtf (after having loaded chcl3.pdb) works fine for me with the files that you provided, using vmd1.9.4a51 Best, Peter On Fri, Nov 19, 2021 at 11:56 AM Francesco Pietra wrote: > Unfortunately I have no access to that journal. At any event, I never use > SHAKE, so that I parameterized CHCL3 on the MATCH server, getting the > attached rtf. On that basis, I first tried to generate psf/pdb for a sing= le > CHCL3 molecule. With autopsf the error.log was > > > ERROR: failed on end of segment >> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. >> ERROR: failed on end of segment >> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. >> while executing >> "segment $segid { >> pdb $segfile >> > > # We alias the C-terminal OXT atoms to OT2 so that psfgen has to >> guess one atom less. >> # Otherwise psf..." >> (procedure "psfsegments" line 37) >> invoked from within >> "psfsegments $logfileout" >> (procedure "::autopsf::afterchains_gui" line 66) >> invoked from within >> "::autopsf::afterchains_gui" >> invoked from within >> ".autopsf.chains.finish invoke" >> ("uplevel" body line 1) >> invoked from within >> "uplevel #0 [list $w invoke]" >> (procedure "tk::ButtonUp" line 22) >> invoked from within >> "tk::ButtonUp .autopsf.chains.finish" >> (command bound to event) > > > while the terminal last lines told > > segfiles CHCl3_autopsf-temp.pdb_XO1.pdb >> CHCl3_autopsf-temp.pdb_XO1.pdb >> 1 4 >> psfgen) building segment XO1 >> psfgen) reading residues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb >> psfgen) unknown residue type CCL3 >> psfgen) extracted 1 residues from pdb file >> psfgen) setting patch for first residue to none >> psfgen) setting patch for last residue to none >> Info: generating structure... >> psfgen) unknown residue type CCL3 >> > > Then, I made recourse to vmd text mode, getting attached chcl3.psf/pdb > without any issue. > > However, I needed psf/pdb for the solvent box, again from the box > generated with packmol that I reported previously. In this case I was not > aware of any trick to avoid writing 1000-fold inputs on the .gen file, so > that I tried with autopsf. The last lines on the terminal were: > > psfgen) extracted 1000 residues from pdb file >> psfgen) setting patch for first residue to none >> psfgen) setting patch for last residue to none >> Info: generating structure... >> psfgen) unknown residue type CCL3 >> Segmentation fault >> > > Obviously CCL3 was and is the residue. Probably, without additional > information no one will be able to suggest a remedy for autopsf (perhaps, > however, suggesting how to deal with vmd text mode for the solvent box, > i.e. a shortcut for the onethousand blocks) > > Thanks for your attention > francesco > > > On Fri, Nov 19, 2021 at 2:57 PM Peter Freddolino > wrote: > >> Based on the comments in that topology file (which I had to google -- it >> would really help to include such things in the mailing list discussion), >> it looks like those CL-CL and other problematic bonds are present only f= or >> SHAKE. That suggests to me that this is supposed to be a rigid chloroform >> model, which might not be possible in NAMD. Did you check the original >> paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 96= 8) >> for how this is supposed to be implemented? >> Thanks, >> Peter >> >> On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra >> wrote: >> >>> Hi Peter >>> Bonds between all couple of atoms, even CL-CL >>> >>>> 5000 !NBOND: bonds >>>> 1 2 1 4 1 5 1 >>>> 6 >>>> 2 3 7 8 7 10 7 >>>> 11 >>>> 7 12 8 9 13 14 13 >>>> 16 >>>> 13 17 13 18 14 15 19 >>>> 20 >>>> 19 22 19 23 19 24 20 >>>> 21 >>>> >>> where atom numbering is >>> >>>> 5000 !NATOM >>>> 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0 >>>> 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0 >>>> 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0 >>>> 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0 >>>> 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0 >>>> >>> >>>> All such bonding is also evident from loading psf/pdb to vmd. >>>> >>>> I started from a box prepared with packmol, and I tried also adding TER >>>> between residues >>>> HEADER >>>> TITLE Built with Packmol >>>> >>>> REMARK Packmol generated pdb file >>>> REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicamp= .br/packmol__;!!DZ3fjg!pzLUg7caCn0rQ4ggyiu8U1xMUH3XmVVxGpxNymBQjvmFIQCz0sCj= VghQtH93F1XAgw$=20 >>>> REMARK >>>> HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00 >>>> CL >>>> HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00 >>>> CL >>>> HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00 >>>> CL >>>> HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00 >>>> C >>>> HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00 >>>> H >>>> TER >>>> HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00 >>>> CL >>>> HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00 >>>> CL >>>> HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00 >>>> CL >>>> HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00 >>>> C >>>> HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00 >>>> H >>>> TER >>>> >>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >>> No such problems encountered in making a MEOH box, starting from "RESI >>> MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained, >>> with psf indicating only the correct bonds. >>> >>> With CHARMM36/CGenFF the only source of topology for CHCL3 is >>> toppar_chloroform_dh.str >>> I can't understand where I am wrong with CHCL3 >>> Thanks for advice >>> francesco >>> >>> On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino >>> wrote: >>> >>>> Have you looked at the bonds in your psf to make sure they are correct? >>>> This looks like you've hydrogen atoms that have two bonds... >>>> Best, >>>> Peter >>>> >>>> On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra >>>> wrote: >>>> >>>>> It seems thatb the str used is inadequate. Alsdo adjusting angles in >>>>> str, namd assks for dihedrals >>>>> fp >>>>> >>>>> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra < >>>>> chiendarret@gmail.com> wrote: >>>>> >>>>>> While attempting to minimize a CHCL3 box built from CHARMM36-provided >>>>>> toppar_chloroform_dh.str, namd crashes >>>>>> >>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS >>>>>>> 1 5 4) >>>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS >>>>>>> 1 5 4) >>>>>>> >>>>>> >>>>>> Actually, the prm part of the str (which was read by namd) l >>>>>> correctly furnishes >>>>>> >>>>>>> ANGLES >>>>>>> CLCM CCM CLCM 0.0 111.30 >>>>>>> HCM CCM CLCM 0.0 107.57 >>>>>>> >>>>>> >>>>>> Why is namd looking for those wrong angles? The central atom is >>>>>> carbon not hydrogen. >>>>>> >>>>>> Thanks for advice >>>>>> francesco pietra >>>>>> >>>>> --000000000000f1c72a05d1273f5b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
How were you running autopsf, and with what version o= f vmd?

autopsf -mol 0 -top 1009279.rtf
(= after having loaded chcl3.pdb) works fine for me with the files that you pr= ovided, using vmd1.9.4a51

Best,
Pete= r

On Fri, Nov 19, 2021 at 11:56 AM Francesco Pietra <chiendarret@gmail.com> wrote:
U= nfortunately I have no access to that journal. At any event, I never use SH= AKE, so that I parameterized CHCL3 on the MATCH server, getting the attache= d rtf. On that basis, I first tried to generate psf/pdb for a single CHCL3 = molecule. With autopsf the error.log was


ERROR: failed on e= nd of segment
MOLECULE DESTROYED BY FATAL ERROR!=C2=A0 Use resetpsf to s= tart over.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATA= L ERROR!=C2=A0 Use resetpsf to start over.
=C2=A0 =C2=A0 while executing=
"segment $segid {
=C2=A0 =C2=A0 =C2=A0 pdb $segfile

=C2=A0 =C2=A0 = =C2=A0 # We alias the C-terminal OXT atoms to OT2 so that psfgen has to gue= ss one atom less.
=C2=A0 =C2=A0 =C2=A0 # Otherwise psf..."
=C2= =A0 =C2=A0 (procedure "psfsegments" line 37)
=C2=A0 =C2=A0 inv= oked from within
"psfsegments $logfileout"
=C2=A0 =C2=A0 (p= rocedure "::autopsf::afterchains_gui" line 66)
=C2=A0 =C2=A0 i= nvoked from within
"::autopsf::afterchains_gui"
=C2=A0 =C2= =A0 invoked from within
".autopsf.chains.finish invoke"
=C2= =A0 =C2=A0 ("uplevel" body line 1)
=C2=A0 =C2=A0 invoked from = within
"uplevel #0 [list $w invoke]"
=C2=A0 =C2=A0 (procedu= re "tk::ButtonUp" line 22)
=C2=A0 =C2=A0 invoked from within"tk::ButtonUp .autopsf.chains.finish"
=C2=A0 =C2=A0 (command= bound to event)

while the terminal l= ast lines told

segfiles CHCl3_autopsf-temp.pdb_XO1.pdb
CHCl3_autopsf-te= mp.pdb_XO1.pdb
1 4
psfgen) building segment XO1
psfgen) reading re= sidues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb
psfgen) unknown resi= due type CCL3
psfgen) extracted 1 residues from pdb file
psfgen) sett= ing patch for first residue to none
psfgen) setting patch for last resid= ue to none
Info: generating structure...
psfgen) unknown residue type= CCL3

Then, I made recourse to vmd te= xt mode, getting attached chcl3.psf/pdb without any issue.

However, I needed psf/pdb for the solvent box, again from the box = generated with packmol that I reported previously. In this case I was not a= ware of any trick to avoid writing 1000-fold inputs on the .gen file, so th= at I tried with autopsf. The last lines on the terminal were:
psfgen) extra= cted 1000 residues from pdb file
psfgen) setting patch for first residue= to none
psfgen) setting patch for last residue to none
Info: generat= ing structure...
psfgen) unknown residue type CCL3
Segmentation fault=

Obviously CCL3 was and is the residu= e. Probably, without additional information no one will be able to suggest = a remedy for autopsf=C2=A0 (perhaps, however, suggesting how to deal with v= md text mode for the solvent box, i.e. a shortcut for the onethousand block= s)

Thanks for your attention
frances= co


On Fri, Nov 19, 2021 at 2:57 PM Peter Freddolino= <petefred@umich= .edu> wrote:
Based on the comments in that topology file (whic= h I had to google -- it would really help to include such things in the mai= ling list discussion), it looks like those CL-CL and other problematic bond= s are present only for SHAKE. That suggests to me that this is supposed to = be a rigid chloroform model, which might not be possible in NAMD. Did you c= heck the original paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Ch= em 1985, 89, 968) for how this is supposed to be implemented?
Tha= nks,
Peter

On Fri, Nov 19, 2021 at 4:33 AM Francesco= Pietra <chie= ndarret@gmail.com> wrote:
Hi Peter
Bonds between all= couple of atoms, even CL-CL
5000 !NBOND: bonds
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 4 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 5= =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A02 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 = =C2=A0 =C2=A0 =C2=A0 =C2=A010 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 = =C2=A0 =C2=A011
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A07 =C2=A0 =C2=A0 =C2=A0= =C2=A012 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 9 =C2= =A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2= =A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A016
=C2=A0 =C2=A0 =C2=A0 =C2=A0 1= 3 =C2=A0 =C2=A0 =C2=A0 =C2=A017 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0= =C2=A0 =C2=A018 =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 =C2=A0 =C2=A0 =C2=A01= 5 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A020
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 19 =C2=A0 =C2=A0 =C2=A0 =C2=A022 =C2=A0 =C2=A0 =C2=A0 =C2= =A019 =C2=A0 =C2=A0 =C2=A0 =C2=A023 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 = =C2=A0 =C2=A0 =C2=A024 =C2=A0 =C2=A0 =C2=A0 =C2=A020 =C2=A0 =C2=A0 =C2=A0 = =C2=A021
where atom numbering is
5000 !NATOM
=C2=A0 =C2=A0 =C2= =A0 =C2=A01 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 C =C2=A0 =C2=A0CCM =C2=A0 =C2=A00= .179000 =C2=A0 =C2=A0 =C2=A0 12.0110 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0=C2=A0 =C2=A0 =C2=A0 =C2=A02 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL1 =C2=A0CLCM= =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A03 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 CL2 = =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A04 AO1 =C2=A01 =C2=A0 =C2= =A0CCL3 CL3 =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A05 AO1 =C2=A01 = =C2=A0 =C2=A0CCL3 HX =C2=A0 HCM =C2=A0 =C2=A00.082000 =C2=A0 =C2=A0 =C2=A0 = =C2=A01.0080 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0

All such bonding is als= o evident from loading psf/pdb to vmd.

I start= ed from a box prepared with packmol, and I tried also adding TER between re= sidues
HEADER
TITLE =C2=A0 =C2=A0 Built with Packmol =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 <= br>REMARK =C2=A0 Packmol generated pdb file
REMARK =C2=A0 Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
HETAT= M =C2=A0 =C2=A01 CL1 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.522 =C2=A0= 5.429 =C2=A0 3.173 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0CL =C2=A0
HETATM =C2=A0 =C2=A02 CL2 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2= =A0 =C2=A030.670 =C2=A0 3.053 =C2=A0 4.852 =C2=A01.00 =C2=A00.00 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A03 CL3 =C2=A0CCL3A = =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.018 =C2=A0 2.823 =C2=A0 1.969 =C2=A01.00 = =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2= =A04 C =C2=A0 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.285 =C2=A0 3.845 = =C2=A0 3.391 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2= =A0
HETATM =C2=A0 =C2=A05 =C2=A0HX =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 = =C2=A032.361 =C2=A0 3.996 =C2=A0 3.509 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
HETATM =C2=A0 =C2=A06 CL1 =C2=A0CCL= 3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.817 =C2=A017.228 =C2=A0 1.210 =C2=A01.00= =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 = =C2=A07 CL2 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 1.496 =C2=A017.919 = =C2=A0 2.829 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2= =A0
HETATM =C2=A0 =C2=A08 CL3 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 = 3.573 =C2=A016.195 =C2=A0 3.922 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A09 C =C2=A0 =C2=A0CCL3A =C2=A0= 2 =C2=A0 =C2=A0 =C2=A0 3.231 =C2=A017.561 =C2=A0 2.849 =C2=A01.00 =C2=A00.= 00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2=A0
HETATM =C2=A0 10 =C2=A0HX= =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.759 =C2=A018.439 =C2=A0 3.230 = =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
No such probl= ems encountered in making a MEOH box, starting from "RESI MEOH" i= n CGenFF. Clear, not interacting MEOH molecules where obtained,
w= ith psf indicating only the correct bonds.

Wit= h CHARMM36/CGenFF the only source of topology for CHCL3 is toppar_chlorofor= m_dh.str
I can't understand where I am wrong with CHCL3
Thanks for advice
francesco

On Thu, Nov 18, 202= 1 at 3:38 PM Peter Freddolino <petefred@umich.edu> wrote:
Have you looked at t= he bonds in your psf to make sure they are correct? This looks like you'= ;ve hydrogen atoms that have two bonds...
Best,
Pet= er

On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra <chiendarret@gmail.com&= gt; wrote:
It seems thatb the str used is inadequate. Alsdo adjusting= angles in str, namd assks for dihedrals
fp

On Thu, Nov = 18, 2021 at 9:29 AM Francesco Pietra <chiendarret@gmail.com> wrote:
While a= ttempting to minimize a CHCL3 box built from CHARMM36-provided toppar_chlor= oform_dh.str, namd crashes

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR= CCM HCM CLCM (ATOMS 1 5 4)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS= FOR CCM HCM CLCM (ATOMS 1 5 4)

Actua= lly, the prm part of the str (which was read by namd) l correctly furnishes=
ANGLES
= CLCM =C2=A0CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2=A0111.30
HCM =C2= =A0 CCM =C2=A0CLCM =C2=A0 =C2=A00.0 =C2=A0 =C2=A0107.57
<= div>
Why is namd looking for those wrong angles? The central = atom is carbon not hydrogen.

Thanks for advice=
francesco pietra
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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I thank you for your help. Your mode or running autopsf from the Tk console worked also for me with vmd 1.9.4a55, and also for the box. As usual with me, I run autopsf from the gui after having loaded the solvent molecule (or solvent box). Then, in a sequence, Add the .rtf file, Load input files, Guess and split chains, Create chains. Thanks indeed On Fri, Nov 19, 2021 at 6:03 PM Peter Freddolino wrote: > How were you running autopsf, and with what version of vmd? > > autopsf -mol 0 -top 1009279.rtf > (after having loaded chcl3.pdb) works fine for me with the files that you > provided, using vmd1.9.4a51 > > Best, > Peter > > On Fri, Nov 19, 2021 at 11:56 AM Francesco Pietra > wrote: > >> Unfortunately I have no access to that journal. At any event, I never use >> SHAKE, so that I parameterized CHCL3 on the MATCH server, getting the >> attached rtf. On that basis, I first tried to generate psf/pdb for a sin= gle >> CHCL3 molecule. With autopsf the error.log was >> >> >> ERROR: failed on end of segment >>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. >>> ERROR: failed on end of segment >>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. >>> while executing >>> "segment $segid { >>> pdb $segfile >>> >> >> # We alias the C-terminal OXT atoms to OT2 so that psfgen has to >>> guess one atom less. >>> # Otherwise psf..." >>> (procedure "psfsegments" line 37) >>> invoked from within >>> "psfsegments $logfileout" >>> (procedure "::autopsf::afterchains_gui" line 66) >>> invoked from within >>> "::autopsf::afterchains_gui" >>> invoked from within >>> ".autopsf.chains.finish invoke" >>> ("uplevel" body line 1) >>> invoked from within >>> "uplevel #0 [list $w invoke]" >>> (procedure "tk::ButtonUp" line 22) >>> invoked from within >>> "tk::ButtonUp .autopsf.chains.finish" >>> (command bound to event) >> >> >> while the terminal last lines told >> >> segfiles CHCl3_autopsf-temp.pdb_XO1.pdb >>> CHCl3_autopsf-temp.pdb_XO1.pdb >>> 1 4 >>> psfgen) building segment XO1 >>> psfgen) reading residues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb >>> psfgen) unknown residue type CCL3 >>> psfgen) extracted 1 residues from pdb file >>> psfgen) setting patch for first residue to none >>> psfgen) setting patch for last residue to none >>> Info: generating structure... >>> psfgen) unknown residue type CCL3 >>> >> >> Then, I made recourse to vmd text mode, getting attached chcl3.psf/pdb >> without any issue. >> >> However, I needed psf/pdb for the solvent box, again from the box >> generated with packmol that I reported previously. In this case I was not >> aware of any trick to avoid writing 1000-fold inputs on the .gen file, so >> that I tried with autopsf. The last lines on the terminal were: >> >> psfgen) extracted 1000 residues from pdb file >>> psfgen) setting patch for first residue to none >>> psfgen) setting patch for last residue to none >>> Info: generating structure... >>> psfgen) unknown residue type CCL3 >>> Segmentation fault >>> >> >> Obviously CCL3 was and is the residue. Probably, without additional >> information no one will be able to suggest a remedy for autopsf (perhap= s, >> however, suggesting how to deal with vmd text mode for the solvent box, >> i.e. a shortcut for the onethousand blocks) >> >> Thanks for your attention >> francesco >> >> >> On Fri, Nov 19, 2021 at 2:57 PM Peter Freddolino >> wrote: >> >>> Based on the comments in that topology file (which I had to google -- it >>> would really help to include such things in the mailing list discussion= ), >>> it looks like those CL-CL and other problematic bonds are present only = for >>> SHAKE. That suggests to me that this is supposed to be a rigid chlorofo= rm >>> model, which might not be possible in NAMD. Did you check the original >>> paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 9= 68) >>> for how this is supposed to be implemented? >>> Thanks, >>> Peter >>> >>> On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra >>> wrote: >>> >>>> Hi Peter >>>> Bonds between all couple of atoms, even CL-CL >>>> >>>>> 5000 !NBOND: bonds >>>>> 1 2 1 4 1 5 1 >>>>> 6 >>>>> 2 3 7 8 7 10 7 >>>>> 11 >>>>> 7 12 8 9 13 14 13 >>>>> 16 >>>>> 13 17 13 18 14 15 19 >>>>> 20 >>>>> 19 22 19 23 19 24 20 >>>>> 21 >>>>> >>>> where atom numbering is >>>> >>>>> 5000 !NATOM >>>>> 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0 >>>>> 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0 >>>>> 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0 >>>>> 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0 >>>>> 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0 >>>>> >>>> >>>>> All such bonding is also evident from loading psf/pdb to vmd. >>>>> >>>>> I started from a box prepared with packmol, and I tried also adding >>>>> TER between residues >>>>> HEADER >>>>> TITLE Built with Packmol >>>>> >>>>> REMARK Packmol generated pdb file >>>>> REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicam= p.br/packmol__;!!DZ3fjg!oU5LcoEmxeOd9WjCKnc2FF4OCPoJQwOBy-phxMnBFjnGqH92u1C= iKsFx1Sv3YtoLmw$=20 >>>>> REMARK >>>>> HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00 >>>>> CL >>>>> HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00 >>>>> CL >>>>> HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00 >>>>> CL >>>>> HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00 >>>>> C >>>>> HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00 >>>>> H >>>>> TER >>>>> HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00 >>>>> CL >>>>> HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00 >>>>> CL >>>>> HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00 >>>>> CL >>>>> HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00 >>>>> C >>>>> HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00 >>>>> H >>>>> TER >>>>> >>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >>>> No such problems encountered in making a MEOH box, starting from "RESI >>>> MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained, >>>> with psf indicating only the correct bonds. >>>> >>>> With CHARMM36/CGenFF the only source of topology for CHCL3 is >>>> toppar_chloroform_dh.str >>>> I can't understand where I am wrong with CHCL3 >>>> Thanks for advice >>>> francesco >>>> >>>> On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino >>>> wrote: >>>> >>>>> Have you looked at the bonds in your psf to make sure they are >>>>> correct? This looks like you've hydrogen atoms that have two bonds... >>>>> Best, >>>>> Peter >>>>> >>>>> On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra < >>>>> chiendarret@gmail.com> wrote: >>>>> >>>>>> It seems thatb the str used is inadequate. Alsdo adjusting angles in >>>>>> str, namd assks for dihedrals >>>>>> fp >>>>>> >>>>>> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra < >>>>>> chiendarret@gmail.com> wrote: >>>>>> >>>>>>> While attempting to minimize a CHCL3 box built from >>>>>>> CHARMM36-provided toppar_chloroform_dh.str, namd crashes >>>>>>> >>>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS >>>>>>>> 1 5 4) >>>>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM >>>>>>>> (ATOMS 1 5 4) >>>>>>>> >>>>>>> >>>>>>> Actually, the prm part of the str (which was read by namd) l >>>>>>> correctly furnishes >>>>>>> >>>>>>>> ANGLES >>>>>>>> CLCM CCM CLCM 0.0 111.30 >>>>>>>> HCM CCM CLCM 0.0 107.57 >>>>>>>> >>>>>>> >>>>>>> Why is namd looking for those wrong angles? The central atom is >>>>>>> carbon not hydrogen. >>>>>>> >>>>>>> Thanks for advice >>>>>>> francesco pietra >>>>>>> >>>>>> --00000000000065103e05d12acaae Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
I thank you for your help. Your mod= e or running autopsf from the Tk console worked also for me with vmd 1.9.4a= 55, and also for the box.

As usual with me, I run = autopsf from the gui after having loaded the solvent molecule (or solvent b= ox). Then, in a sequence, Add the .rtf file, Load input files, Guess and sp= lit chains, Create chains.


Thanks i= ndeed

On Fri, Nov 19, 2021 at 6:03 PM Peter Freddolino <petefred@umich.edu> wrote:
How were you running au= topsf, and with what version of vmd?

autopsf -mol = 0 -top 1009279.rtf
(after having loaded chcl3.pdb) works fine for= me with the files that you provided, using vmd1.9.4a51

Best,
Peter

On Fri, Nov 19, 2021 at 11:56 AM F= rancesco Pietra <chiendarret@gmail.com> = wrote:
Unfortunately I have no access to that journal. At any event,= I never use SHAKE, so that I parameterized CHCL3 on the MATCH server, gett= ing the attached rtf. On that basis, I first tried to generate psf/pdb for = a single CHCL3 molecule. With autopsf the error.log was


ERR= OR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR!=C2=A0 Us= e resetpsf to start over.
ERROR: failed on end of segment
MOLECULE DE= STROYED BY FATAL ERROR!=C2=A0 Use resetpsf to start over.
=C2=A0 =C2=A0 = while executing
"segment $segid {
=C2=A0 =C2=A0 =C2=A0 pdb $segf= ile

= =C2=A0 =C2=A0 =C2=A0 # We alias the C-terminal OXT atoms to OT2 so that psf= gen has to guess one atom less.
=C2=A0 =C2=A0 =C2=A0 # Otherwise psf...&= quot;
=C2=A0 =C2=A0 (procedure "psfsegments" line 37)
=C2= =A0 =C2=A0 invoked from within
"psfsegments $logfileout"
= =C2=A0 =C2=A0 (procedure "::autopsf::afterchains_gui" line 66)=C2=A0 =C2=A0 invoked from within
"::autopsf::afterchains_gui"= ;
=C2=A0 =C2=A0 invoked from within
".autopsf.chains.finish invo= ke"
=C2=A0 =C2=A0 ("uplevel" body line 1)
=C2=A0 =C2= =A0 invoked from within
"uplevel #0 [list $w invoke]"
=C2= =A0 =C2=A0 (procedure "tk::ButtonUp" line 22)
=C2=A0 =C2=A0 in= voked from within
"tk::ButtonUp .autopsf.chains.finish"
=C2= =A0 =C2=A0 (command bound to event)

w= hile the terminal last lines told

segfiles CHCl3_autopsf-temp.pdb_XO1.pdbCHCl3_autopsf-temp.pdb_XO1.pdb
1 4
psfgen) building segment XO1
= psfgen) reading residues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb
ps= fgen) unknown residue type CCL3
psfgen) extracted 1 residues from pdb fi= le
psfgen) setting patch for first residue to none
psfgen) setting pa= tch for last residue to none
Info: generating structure...
psfgen) un= known residue type CCL3

Then, I made = recourse to vmd text mode, getting attached chcl3.psf/pdb without any issue= .

However, I needed psf/pdb for the solvent box, a= gain from the box generated with packmol that I reported previously. In thi= s case I was not aware of any trick to avoid writing 1000-fold inputs on th= e .gen file, so that I tried with autopsf. The last lines on the terminal w= ere:

=
psfgen) extracted 1000 residues from pdb file
psfgen) setting patch= for first residue to none
psfgen) setting patch for last residue to non= e
Info: generating structure...
psfgen) unknown residue type CCL3
= Segmentation fault

Obviously CCL3 was= and is the residue. Probably, without additional information no one will b= e able to suggest a remedy for autopsf=C2=A0 (perhaps, however, suggesting = how to deal with vmd text mode for the solvent box, i.e. a shortcut for the= onethousand blocks)

Thanks for your attention=
francesco


On Fri, Nov 19, 2021 at 2:57 P= M Peter Freddolino <petefred@umich.edu> wro= te:
Based on the comments in that topology file (which I had to googl= e -- it would really help to include such things in the mailing list discus= sion), it looks like those CL-CL and other problematic bonds are present on= ly for SHAKE. That suggests to me that this is supposed to be a rigid chlor= oform model, which might not be possible in NAMD. Did you check the origina= l paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968= ) for how this is supposed to be implemented?
Thanks,
Peter

On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra <chiendarret@gmail.com> wrote:
Hi Peter
Bonds between all couple of atoms, even CL-CL
5000 !NBOND: bonds
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A0 =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0= =C2=A0 =C2=A0 =C2=A0 5 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 6
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A02 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 3 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A010 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A011
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A07 = =C2=A0 =C2=A0 =C2=A0 =C2=A012 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 9 =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A014= =C2=A0 =C2=A0 =C2=A0 =C2=A013 =C2=A0 =C2=A0 =C2=A0 =C2=A016
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 13 =C2=A0 =C2=A0 =C2=A0 =C2=A017 =C2=A0 =C2=A0 =C2=A0 =C2= =A013 =C2=A0 =C2=A0 =C2=A0 =C2=A018 =C2=A0 =C2=A0 =C2=A0 =C2=A014 =C2=A0 = =C2=A0 =C2=A0 =C2=A015 =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 = =C2=A020
=C2=A0 =C2=A0 =C2=A0 =C2=A0 19 =C2=A0 =C2=A0 =C2=A0 =C2=A022 = =C2=A0 =C2=A0 =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A023 =C2=A0 =C2=A0 = =C2=A0 =C2=A019 =C2=A0 =C2=A0 =C2=A0 =C2=A024 =C2=A0 =C2=A0 =C2=A0 =C2=A020= =C2=A0 =C2=A0 =C2=A0 =C2=A021
where atom numbering = is
5000 !NATOM<= br>=C2=A0 =C2=A0 =C2=A0 =C2=A01 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 C =C2=A0 =C2= =A0CCM =C2=A0 =C2=A00.179000 =C2=A0 =C2=A0 =C2=A0 12.0110 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A02 AO1 =C2=A01 =C2=A0 =C2= =A0CCL3 CL1 =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.4500 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A03 AO1 =C2=A01 = =C2=A0 =C2=A0CCL3 CL2 =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2=A0 35.45= 00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 =C2=A04 AO1= =C2=A01 =C2=A0 =C2=A0CCL3 CL3 =C2=A0CLCM =C2=A0-0.087000 =C2=A0 =C2=A0 =C2= =A0 35.4500 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0
=C2=A0 =C2=A0 =C2=A0 = =C2=A05 AO1 =C2=A01 =C2=A0 =C2=A0CCL3 HX =C2=A0 HCM =C2=A0 =C2=A00.082000 = =C2=A0 =C2=A0 =C2=A0 =C2=A01.0080 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0

Al= l such bonding is also evident from loading psf/pdb to vmd.
<= br>
I started from a box prepared with packmol, and I tried also = adding TER between residues
HEADER
TITLE =C2=A0 =C2=A0 Built = with Packmol =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0
REMARK =C2=A0 Packmol generated pdb file
REMARK = =C2=A0 Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
HETATM =C2=A0 =C2= =A01 CL1 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.522 =C2=A0 5.429 =C2= =A0 3.173 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0=
HETATM =C2=A0 =C2=A02 CL2 =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A030.6= 70 =C2=A0 3.053 =C2=A0 4.852 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A03 CL3 =C2=A0CCL3A =C2=A0 1 =C2= =A0 =C2=A0 =C2=A031.018 =C2=A0 2.823 =C2=A0 1.969 =C2=A01.00 =C2=A00.00 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A04 C =C2=A0 = =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A031.285 =C2=A0 3.845 =C2=A0 3.391 = =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C =C2=A0
HETATM= =C2=A0 =C2=A05 =C2=A0HX =C2=A0CCL3A =C2=A0 1 =C2=A0 =C2=A0 =C2=A032.361 = =C2=A0 3.996 =C2=A0 3.509 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 H =C2=A0
TER
HETATM =C2=A0 =C2=A06 CL1 =C2=A0CCL3A =C2=A0 2 = =C2=A0 =C2=A0 =C2=A0 3.817 =C2=A017.228 =C2=A0 1.210 =C2=A01.00 =C2=A00.00 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM =C2=A0 =C2=A07 CL2 = =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 1.496 =C2=A017.919 =C2=A0 2.829 = =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CL =C2=A0
HETATM= =C2=A0 =C2=A08 CL3 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.573 =C2=A01= 6.195 =C2=A0 3.922 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= CL =C2=A0
HETATM =C2=A0 =C2=A09 C =C2=A0 =C2=A0CCL3A =C2=A0 2 =C2=A0 =C2= =A0 =C2=A0 3.231 =C2=A017.561 =C2=A0 2.849 =C2=A01.00 =C2=A00.00 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 C =C2=A0
HETATM =C2=A0 10 =C2=A0HX =C2=A0CCL3A = =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3.759 =C2=A018.439 =C2=A0 3.230 =C2=A01.00 = =C2=A00.00 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 H =C2=A0
TER
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
No such problems encount= ered in making a MEOH box, starting from "RESI MEOH" in CGenFF. C= lear, not interacting MEOH molecules where obtained,
with psf ind= icating only the correct bonds.

With CHARMM36/= CGenFF the only source of topology for CHCL3 is toppar_chloroform_dh.str
I can't understand where I am wrong with CHCL3
Th= anks for advice
francesco

On Thu, Nov 18, 2021 at 3:38 P= M Peter Freddolino <petefred@umich.edu> wro= te:
Have you looked at the bonds in your psf to make sure they are co= rrect? This looks like you've hydrogen atoms that have two bonds...
Best,
Peter

On Thu, Nov 18, 2021 at 5:42 AM F= rancesco Pietra <chiendarret@gmail.com> = wrote:
It seems thatb the str used is inadequate. Alsdo adjusting an= gles in str, namd assks for dihedrals
fp

On Thu, Nov 18,= 2021 at 9:29 AM Francesco Pietra <chiendarret@= gmail.com> wrote:
While attempting to minimize a CHCL3 box b= uilt from CHARMM36-provided toppar_chloroform_dh.str, namd crashes

FATAL ER= ROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4)
FATA= L ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5 4)

Actually, the prm part of the str (which= was read by namd) l correctly furnishes
ANGLES
CLCM =C2=A0CCM =C2=A0CLCM =C2=A0 = =C2=A00.0 =C2=A0 =C2=A0111.30
HCM =C2=A0 CCM =C2=A0CLCM =C2=A0 =C2=A00.0= =C2=A0 =C2=A0107.57

Why is namd look= ing for those wrong angles? The central atom is carbon not hydrogen.

Thanks for advice
= francesco pietra
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boundary="000000000000f0e20805d131ad7c" X-Proofpoint-ORIG-GUID: WHFGbla6aDLa32ueLLSn8unzcOI3kpz0 X-CLX-Response: 1TFkXGx0SEQpMehcZGBIRCllEF2ZbAUJEbk8cW09oEQpYWBdmHxN7GV8bWkV vWBEKeE4XY1Nja3sTWH4aX14RCnlMF2hGWEhJcEZLQAFBEQpDSBcHEh4RCkNZFwcYHhsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxJxGR0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XfWJsbUhGSxxLbmZLGRhfT2ZmeUQSX0RQSWVjGUFaUBoRClhcFx8EGgQYHhgF GxoEGxsaBB0EGxkZEBseGh8aEQpeWRdzUENSRxEKTVwXGB0cEQpMWhdsaU1NTREKTEYXb2tra2t rEQpCTxduHGcdWXJnZl5IchEKQ1oXGBoTBBIfBBgaEgQeHhEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdsf0FSQ25jE2RQHhEKQk4XY1Nja3sTW H4aX14RCkJMF2YfE3sZXxtaRW9YEQpCbBdjEk5aQV9MbFocGhEKQkAXb1xvbkd6G2tMfmERCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5Qxdhcn9LaElTQEN9ehEKWUsXEx8THBEKcGgXenJ TR2JhemISYxIQGRoRCnBoF2FHUxsSGGFZfklPEBkaEQpwaBdhH0tdGx5gRWZMYhAZGhEKcGgXYl 8TWXoFHlxFUHMQGRoRCnBoF21kW3hQWGYcQ0l5EBkaEQpwbBdtehl7RmxSbU1kZhAZGhEKbX4XG xEKWE0XSxEg X-Proofpoint-GUID: WHFGbla6aDLa32ueLLSn8unzcOI3kpz0 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 clxscore=178 malwarescore=0 mlxscore=0 lowpriorityscore=0 bulkscore=0 spamscore=0 priorityscore=328 suspectscore=0 adultscore=0 mlxlogscore=653 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111200033 domainage_hfrom=9596 X-Spam-Score: 0 X-Spam-OrigSender: dishipsrivastava@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Diship Srivastava --000000000000f0e20805d131ad7c Content-Type: text/plain; charset="UTF-8" Hi, I am currently working on insertion of an antimicrobial peptide (AMP) on bilayer membrane using constant pH MD. I am trying to constrain the center of mass of AMP and membrane, while cphmd is active. Since cphmd doesn't have colvar support and number of atoms during cphmd changes during the run, both colvars and constraints result in fatal error during the job. How can I constrain the com under cphmd conditions? Thanks in advance. -- Diship Srivastava SRF Department of Chemistry IIT(ISM) - Dhanbad India --000000000000f0e20805d131ad7c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,=C2=A0
I am currently working on insertion of an an= timicrobial peptide (AMP) on bilayer membrane using constant pH MD. I am tr= ying to constrain the center of mass of AMP and membrane, while cphmd is ac= tive. Since cphmd doesn't have colvar support and number of atoms durin= g cphmd changes during the run, both colvars and constraints result in fata= l error during the job. How can I constrain the com under cphmd conditions?=

Thanks in advance.

=C2= =A0 =C2=A0 =C2=A0


--
Diship Srivastava=C2=A0
SRF=C2=A0
Department of Chem= istry
IIT(ISM) - Dhanbad
India
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[73.253.124.38]) by smtp.gmail.com with ESMTPSA id l10sm1759339qkp.3.2021.11.20.08.25.31 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sat, 20 Nov 2021 08:25:32 -0800 (PST) Subject: Re: namd-l: applying harmonic constraints in cphmd To: namd-l@ks.uiuc.edu, Diship Srivastava References: From: Brian Radak Message-ID: <94047a4f-3ace-a178-317a-c92606c12ff5@gmail.com> Date: Sat, 20 Nov 2021 11:25:31 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------506D8EB8BB9DDBA5B832B8BA" Content-Language: en-US X-Proofpoint-GUID: smL3sC8qkReTjpdtagwLg2TnXyN17qWy X-Proofpoint-ORIG-GUID: smL3sC8qkReTjpdtagwLg2TnXyN17qWy X-CLX-Response: 1TFkXGBseEQpMehcZGxMRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGxIZEQpDWRcHGBoaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxMecRsdGRAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdZR2YZWWkSW0F4T35AWk5eS01dZk0YfkRyU2QbHVt9UxEKWFwXHwQaBBge GAUbGgQbGxoEHQQbGRgQGx4aHxoRCl5ZF3NQWXNzEQpNXBcbHRMRCkxaF3xpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZWlQZ2FGfWwbBQURCkNaFxgaEwQSHwQYGB gEGx0aEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2sTGmFOX15YGB1lEQpCThdjU2NrexNYfhpfXhEKQkwXaUlIGkt+aUYbeHMRCkJs F2EeGXhabmxnY19iEQpCQBdtSH1DGRIBTk5HZBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxg RCnlDF2NrfHhIaGJyWx5lEQpZSxcTHxMcEQpwZxdmRkRAZVhtQHp9WhAZGhEKcGgXZ0xfHVNwYl xOE0AQGRoRCnBoF2EfS10bHmBFZkxiEB4SEQpwaBdrG2REWG5vUG1QZBAZGhEKcGgXZxNLekF7T 08eEkQQGRoRCnBoF2R8Tnx/Yl0fXW1YEBkaEQpwbBduHWZ7EksaeBJcbRAZGhEKcEMXaXASBX9G HlpzQWIQGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 lowpriorityscore=0 spamscore=0 clxscore=214 mlxscore=0 malwarescore=0 suspectscore=0 phishscore=0 bulkscore=0 impostorscore=0 priorityscore=319 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111200105 domainage_hfrom=9596 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------506D8EB8BB9DDBA5B832B8BA Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit This is unfortunately an unsolved problem. As you point out - the atom indices change during a CpHMD simulation and so the selections would need to be updated at each cycle (probably with a bit of bookkeeping). One thing that can be exploited is that the number of residues does not change, so if it is possible to use residue and name based selections, that should work. In previous work where we used restraints we took advantage of the fact that it was only a single residue that was titrating and so all indices above the atom sidechain are fixed during the simulation (a bit of a hack). To be honest, it might be easier for someone to implement restraints based on a selection syntax rather than solve the indexing problem that is specific to CpHMD. HTH, BKR On 11/20/21 12:29 AM, Diship Srivastava wrote: > Hi, > I am currently working on insertion of an antimicrobial peptide (AMP) > on bilayer membrane using constant pH MD. I am trying to constrain the > center of mass of AMP and membrane, while cphmd is active. Since cphmd > doesn't have colvar support and number of atoms during cphmd changes > during the run, both colvars and constraints result in fatal error > during the job. How can I constrain the com under cphmd conditions? > > Thanks in advance. > > > > -- > Diship Srivastava > SRF > Department of Chemistry > IIT(ISM) - Dhanbad > India --------------506D8EB8BB9DDBA5B832B8BA Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

This is unfortunately an unsolved problem. As you point out - the atom indices change during a CpHMD simulation and so the selections would need to be updated at each cycle (probably with a bit of bookkeeping). One thing that can be exploited is that the number of residues does not change, so if it is possible to use residue and name based selections, that should work.

In previous work where we used restraints we took advantage of the fact that it was only a single residue that was titrating and so all indices above the atom sidechain are fixed during the simulation (a bit of a hack).

To be honest, it might be easier for someone to implement restraints based on a selection syntax rather than solve the indexing problem that is specific to CpHMD.

HTH,

BKR


On 11/20/21 12:29 AM, Diship Srivastava wrote:
Hi, 
I am currently working on insertion of an antimicrobial peptide (AMP) on bilayer membrane using constant pH MD. I am trying to constrain the center of mass of AMP and membrane, while cphmd is active. Since cphmd doesn't have colvar support and number of atoms during cphmd changes during the run, both colvars and constraints result in fatal error during the job. How can I constrain the com under cphmd conditions?

Thanks in advance.

     


--
Diship Srivastava 
SRF 
Department of Chemistry
IIT(ISM) - Dhanbad
India
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Sat, 20 Nov 2021 16:27:08 +0000 Date: Sat, 20 Nov 2021 16:26:31 +0000 (UTC) From: Fateme Ghadirian To: NAMD List Message-ID: <636432175.3841890.1637425591618@mail.yahoo.com> Subject: namd-l: eFieldNormalized MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_3841889_1685167334.1637425591616" References: <636432175.3841890.1637425591618.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19306 YMailNorrin X-Proofpoint-ORIG-GUID: O8F9RERfBEtq6-m3U5fEvAAU5gY7-SjE X-Proofpoint-GUID: O8F9RERfBEtq6-m3U5fEvAAU5gY7-SjE X-CLX-Shades: MLX X-CLX-Response: 1TFkXHh0fEQpMehcZHhgRCllEF2tfQX1nbkdQaUxnEQpYWBd6X1lGGWZTY2M ZbxEKeE4XekQcHW9FbG1EQ2YRCnlMF2wTWF4YfUZtck4cEQpDSBcHGxwSEQpDWRcHEhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXHxpxGQYZGXcGGBoaBh4SQhsaBhoGGxoaBh0ScR8QGncGGgYaBhoGG gYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdlEmwTeG94TGhvXlscB0cZ fx9Mb1xra38fTXMdB3lAbxEKWFwXHwQaBBgeGAUbGgQbGxoEHQQbGRgQGx4aHxoRCl5ZF3NQWXA eEQpNXBcYGBgRCkxaF2hpa2trEQpMRhdva2tva2sRCkJPF2tMbkRTXmlYeUJoEQpDWhccHAQbHB kEGxISBBseHREKQl4XGxEKQlwXGxEKXk4XGxEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtR ENmEQpCRRdlf08SUxxBBWMFbREKQk4XekQcHW9FbG1EQ2YRCkJMF3pfWUYZZlNjYxlvEQpCbBdr QUZAaGR8Ux1uQhEKQkAXZnxdfU9BYEhHc0ERCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp 5QxdmfF19T0FgSEdzQREKWUsXExIaGREKcGgXa11tWlh7b2hYHVoQGRoRCnBoF2VsfEJ8R3p7ZR JLEBkaEQpwaBdoQmRMfHBSY3BPQhAZGhEKcGgXYxNdHHpHGl9QU1kQGRoRCnBoF29pH35+YF1pH 2ZyEBkaEQpwfRdmU29jU2gTX1p9YxAZGhEKcH0Xa2RbX1kBUE1vY0gQGRoRCnB9F29jQEhkWmAc UExyEBkaEQpwfxdgbGZGfHljU3IaaxAbGRoRCnBfF2xiYFhjT0FAXmRMEBkaEQpwfxdlGXlmXkd pG2RPcxAeEhEKcF8XZ05cAWV4QUtnXWYQGRoRCnBfF2keR2lsYEgBZnhMEBkaEQpwbBdpWXgFU3 x/E2liSxAZGhEKcEwXZgVhHEcdRmF5Q38QGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=475 mlxlogscore=928 lowpriorityscore=0 phishscore=0 impostorscore=0 malwarescore=0 suspectscore=0 priorityscore=342 mlxscore=0 spamscore=0 adultscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111200105 domainage_hfrom=9803 X-Spam-Score: 0 X-Spam-OrigSender: fateme.ghadirian@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fateme Ghadirian ------=_Part_3841889_1685167334.1637425591616 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear NAMD users, I have a system which contains afully hydrated bilayer with some particles = in the aqueous part of the system. Thesimulation run is in NPT.=C2=A0I want= to add constant electricfield to this system to investigate its possible e= ffects on the particles andthe bilayer.=C2=A0In the following tutorial http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion-co= nduction It has used=20 eFieldOn yes eField 0.0 0.0 -0.134 In its.conf file to do the constant electric field simulation. But in the following link https://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.html The electric field in the .conf file hasapplied as follows eFieldOn yes eField 0.0 0.0 -0.134 eFieldNormalized yes By searching in namd-l questions, I foundsome opposite explanations about e= FieldNormilized: https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2016-2017/2486.ht= ml 1) The eFieldNormilized statement is intended toavoid excessive pressure in= an NPTsimulation in the presence of a constant electric field. 2) The eFieldNormalized does not protect the simulation from =E2=80=9Cexces= sivepressure=E2=80=9D: it simply defines the electric field with units rela= tive to the unitcell.=20 I do not understand what eFieldNormalizedmeans and what its function in an = NPT simulation is, any help for itsclarification would be appreciated. And also I need to apply constant electricfield to my NPT simulation, shoul= d I use eFieldNormalized yes or not??? What are the consequences of not using theeFieldNormalized in Simulations? =C2=A0 Thanks in advance ------=_Part_3841889_1685167334.1637425591616 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear NAMD users,

I have a system which contains a fully hydrated bilayer with some particles in the aqueous part of the syste= m. The simulation run is in NPT. I want to add constant electric field to this system to investigate its possible effects on the particles a= nd the bilayer. In the following tutorial

http://bionano.physics.illinois.ed= u/tutorials/electrostatic-maps-and-ion-conduction

It has used

eFieldOn yes

eField 0.0 0.0 -0.134

= In its .conf file to do the constant electric field simulation.

But in the= following link

https://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.htm= l

The electr= ic field in the .conf file has applied as follows

eFieldOn yes

eField 0.0 0.0 -0.134

eFieldNormalized yes

By searchi= ng in namd-l questions, I found some opposite explanations about eFieldNormilized:

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2016-2017/248= 6.html

1) The eFieldNormilized statement <= span style=3D"line-height: 107%;">is intended to avoid excessive pressure in an NPT simulation in the presence of a constant electric field.=

2) The eFieldNormalized does not protect the simulation from =E2=80=9Cex= cessive pressure=E2=80=9D: it simply defines the electric field with units relative= to the unit cell.


<= span style=3D"line-height: 107%; background: white; font-style: normal;">
I do not understand what eFieldNormalized means and what its function in an NPT simulation is, any help for its clarification would be appreciated.

And also I= need to apply constant electric field to my NPT simulation, should I use eFieldNormalized yes or not???

What are t= he consequences of not using the eFieldNormalized in Simulations?

 

Thanks in advance

=


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charset="UTF-8" Thanks for the suggestion. Based on your reply I have written an ad hoc tcl script for the same purpose (it harmonically constrains the com of bilayer and first few non titratable residues of protein ) but during run time the script crashes with unknown tcl error. Any help regarding this error will be highly appreciated. script snippet : tclForces on tclForcesScript { set k 0.05 set r0 9.847 # com of bilayer set group1 [addgroup {13 143 266 389 519 649 779 909....}] # com of amp set group2 [addgroup {15367 15369 15381 15382..}] print "starting proc" print "-------------" proc calcforces {} { print "inside proc" print "changing scope of variables" # set change variable global group1 group2 k r0 # load coordinates loadcoords c # get z coords of both groups set r1 [$c(1)] set r2 [$c(2)] foreach {x1 y1 z1} $r1 {} foreach {x2 y2 z2} $r2 {} set r_z [expr {$z2-$z1}] set disp [expr {$r_z-$r0}] # optional add energy - will be displayed in MISC # addenergy [expr {$k*$disp*$disp/2.0}] # calculate force set force [expr {-$k*$disp}] addforce $group1 $force addforce $group2 [expr {-1.0*$force}] } # close proc calcforces # deleting all atomslections clearconfig } In logfile the error encountered was : Info: Startup phase 10 took 6.5302e-05 s, 324.613 MB of memory in use Info: Startup phase 11 took 0.000188028 s, 324.613 MB of memory in use LDB: Central LB being created... Info: Startup phase 12 took 0.000182779 s, 324.613 MB of memory in use Info: CREATING 1104 COMPUTE OBJECTS TCL: starting proc TCL: ------------- TCL: parameter unknown for NAMD config parameter FATAL ERROR: Unknown Tcl error On Sat, 20 Nov 2021 at 21:55, Brian Radak wrote: > This is unfortunately an unsolved problem. As you point out - the atom > indices change during a CpHMD simulation and so the selections would need > to be updated at each cycle (probably with a bit of bookkeeping). One thing > that can be exploited is that the number of residues does not change, so if > it is possible to use residue and name based selections, that should work. > > In previous work where we used restraints we took advantage of the fact > that it was only a single residue that was titrating and so all indices > above the atom sidechain are fixed during the simulation (a bit of a hack). > > To be honest, it might be easier for someone to implement restraints based > on a selection syntax rather than solve the indexing problem that is > specific to CpHMD. > > HTH, > > BKR > > > On 11/20/21 12:29 AM, Diship Srivastava wrote: > > Hi, > I am currently working on insertion of an antimicrobial peptide (AMP) on > bilayer membrane using constant pH MD. I am trying to constrain the center > of mass of AMP and membrane, while cphmd is active. Since cphmd doesn't > have colvar support and number of atoms during cphmd changes during the > run, both colvars and constraints result in fatal error during the job. How > can I constrain the com under cphmd conditions? > > Thanks in advance. > > > > > -- > Diship Srivastava > SRF > Department of Chemistry > IIT(ISM) - Dhanbad > India > > --00000000000033755d05d15daabf Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thanks for the suggestion. Based on your reply I have writ= ten an ad hoc=C2=A0tcl script for the same purpose (it harmonically constra= ins the com of bilayer and first few non titratable residues of protein ) b= ut during run time the script crashes with unknown=C2=A0tcl error. Any help= regarding this error will be highly appreciated.=C2=A0

=
script snippet :=C2=A0
=C2=A0tclForces on
tclFo= rcesScript {
set k 0.05
set r0 9.847

# com of bilayer
set g= roup1 [addgroup {13 143 266 389 519 649 779 909....}]
# com of amp
se= t group2 [addgroup {15367 15369 15381 15382..}]
print "starting pro= c"
print "-------------"
proc calcforces {} {
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 print "inside proc"
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 print "changing scope of variables"
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 # set change variable
=C2=A0 =C2=A0 =C2=A0 =C2=A0 glob= al group1 group2 k r0
=C2=A0 =C2=A0 =C2=A0 =C2=A0 # load coordinates
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 loadcoords c
=C2=A0 =C2=A0 =C2=A0 =C2=A0 # g= et z coords of both groups
=C2=A0 =C2=A0 =C2=A0 =C2=A0 set r1 [$c(1)]=C2=A0 =C2=A0 =C2=A0 =C2=A0 set r2 [$c(2)]
=C2=A0 =C2=A0 =C2=A0 =C2=A0 = foreach {x1 y1 z1} $r1 {}
=C2=A0 =C2=A0 =C2=A0 =C2=A0 foreach {x2 y2 z2}= $r2 {}
=C2=A0 =C2=A0 =C2=A0 =C2=A0 set r_z [expr {$z2-$z1}]

=C2= =A0 =C2=A0 =C2=A0 =C2=A0 set disp [expr {$r_z-$r0}]
=C2=A0 =C2=A0 =C2=A0= =C2=A0 # optional add energy - will be displayed in MISC
# =C2=A0 =C2= =A0 =C2=A0 =C2=A0addenergy [expr {$k*$disp*$disp/2.0}]

=C2=A0 =C2=A0= =C2=A0 =C2=A0 # calculate force
=C2=A0 =C2=A0 =C2=A0 =C2=A0 set force = [expr {-$k*$disp}]

=C2=A0 =C2=A0 =C2=A0 =C2=A0 addforce $group1 $for= ce
=C2=A0 =C2=A0 =C2=A0 =C2=A0 addforce $group2 [expr {-1.0*$force}]
=
}
# close proc calcforces
# deleting all atomslections
clearco= nfig
}

In logfile=C2=A0the error encountere= d was :=C2=A0
Info: Startup phase 10 took 6.5302e-05 s, 324.613 MB of me= mory in use
Info: Startup phase 11 took 0.000188028 s, 324.613 MB of mem= ory in use
LDB: Central LB being created...
Info: Startup phase 12 to= ok 0.000182779 s, 324.613 MB of memory in use
Info: CREATING 1104 COMPUT= E OBJECTS
TCL: starting proc
TCL: -------------
TCL: parameter unk= nown for NAMD config parameter
FATAL ERROR: Unknown Tcl error
<= /div>

On Sat, 20 Nov 2021 at 21:55, Brian Radak <brian.radak@gmail.com> wrote:
=
=20 =20 =20

This is unfortunately an unsolved problem. As you point out - the atom indices change during a CpHMD simulation and so the selections would need to be updated at each cycle (probably with a bit of bookkeeping). One thing that can be exploited is that the number of residues does not change, so if it is possible to use residue and name based selections, that should work.

In previous work where we used restraints we took advantage of the fact that it was only a single residue that was titrating and so all indices above the atom sidechain are fixed during the simulation (a bit of a hack).

To be honest, it might be easier for someone to implement restraints based on a selection syntax rather than solve the indexing problem that is specific to CpHMD.

HTH,

BKR


On 11/20/21 12:29 AM, Diship Srivastava wrote:
=20
Hi,=C2=A0
I am currently working on insertion of an antimicrobial peptide (AMP) on bilayer membrane using constant pH MD. I am trying to constrain the center of mass of AMP and membrane, while cphmd is active. Since cphmd doesn't have colvar suppor= t and number of atoms during cphmd changes during the run, both colvars and constraints result in fatal error during the job. How can I constrain the com under cphmd conditions?

Thanks in advance.

=C2=A0 =C2=A0 =C2=A0


--
Diship Srivastava=C2=A0
SRF=C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
India
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My diameter for restraint is 50 (-25,25) Best, Geo. 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[73.253.124.38]) by smtp.gmail.com with ESMTPSA id t11sm4956209qtx.48.2021.11.22.11.05.41 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Mon, 22 Nov 2021 11:05:41 -0800 (PST) Subject: Re: namd-l: applying harmonic constraints in cphmd To: Diship Srivastava Cc: namd-l References: <94047a4f-3ace-a178-317a-c92606c12ff5@gmail.com> From: Brian Radak Message-ID: Date: Mon, 22 Nov 2021 14:05:40 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------D31DD14DC07F35EE1AC4F670" Content-Language: en-US X-CLX-Response: 1TFkXGxMZEQpMehcZHxsRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGRseEQpDWRcHGxMTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0ZcRsaHBAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdfU3J4Tn1vTl4YUlljSHpEcE54bnhJW3plbUtyY3l6ehEKWFwXHwQaBBge GAUbGgQbGxoEHQQbGRgQGx4aHxoRCl5ZF3MacxxDEQpNXBcYGRwRCkxaF3tpTU1NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHB oEGxIbEQpCXhcbEQpESRcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2sTGmFOX15YGB1lEQpCThdjU2NrexNYfhpfXhEKQkwXaUlIGkt+aUYbeHMRCkJs F2EeGXhabmxnY19iEQpCQBdtSH1DGRIBTk5HZBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxg RCnlDF2NrfHhIaGJyWx5lEQpZSxcTHxMSEQpwZxdgfR9+TVl9BVtkbBAZGhEKcGgXYmdBe1AdTU sSS24QGRoRCnBoF20ZTElcaV9JYhpAEBkaEQpwaBdpWkYcR2NdQF59cxAZGhEKcGgXbWkdTRldG gVyG0cQGRoRCnBoF29Na3pCHnJFXHhkEBkaEQpwbBduHWZ7EksaeBJcbRAZGhEKcEMXaXASBX9G HlpzQWIQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: uyXRdWEdt2xsIbPnZdRDRcqPOGaXISPP X-Proofpoint-GUID: uyXRdWEdt2xsIbPnZdRDRcqPOGaXISPP X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 spamscore=0 clxscore=193 mlxscore=0 adultscore=0 lowpriorityscore=0 phishscore=0 suspectscore=0 bulkscore=0 impostorscore=0 mlxlogscore=999 priorityscore=351 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111220096 domainage_hfrom=9598 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------D31DD14DC07F35EE1AC4F670 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit If I'm not mistaken, this usually means there's a syntax error and NAMD is interpreting a stray character or variable name as a keyword. I couldn't say what the problem is without seeing the entire input script. On 11/22/21 4:58 AM, Diship Srivastava wrote: > Thanks for the suggestion. Based on your reply I have written an ad > hoc tcl script for the same purpose (it harmonically constrains the > com of bilayer and first few non titratable residues of protein ) but > during run time the script crashes with unknown tcl error. Any help > regarding this error will be highly appreciated. > > > script snippet : >  tclForces on > tclForcesScript { > set k 0.05 > set r0 9.847 > > # com of bilayer > set group1 [addgroup {13 143 266 389 519 649 779 909....}] > # com of amp > set group2 [addgroup {15367 15369 15381 15382..}] > print "starting proc" > print "-------------" > proc calcforces {} { >         print "inside proc" >         print "changing scope of variables" >         # set change variable >         global group1 group2 k r0 >         # load coordinates >         loadcoords c >         # get z coords of both groups >         set r1 [$c(1)] >         set r2 [$c(2)] >         foreach {x1 y1 z1} $r1 {} >         foreach {x2 y2 z2} $r2 {} >         set r_z [expr {$z2-$z1}] > >         set disp [expr {$r_z-$r0}] >         # optional add energy - will be displayed in MISC > #        addenergy [expr {$k*$disp*$disp/2.0}] > >         # calculate force >         set force [expr {-$k*$disp}] > >         addforce $group1 $force >         addforce $group2 [expr {-1.0*$force}] > > } > # close proc calcforces > # deleting all atomslections > clearconfig > } > > In logfile the error encountered was : > Info: Startup phase 10 took 6.5302e-05 s, 324.613 MB of memory in use > Info: Startup phase 11 took 0.000188028 s, 324.613 MB of memory in use > LDB: Central LB being created... > Info: Startup phase 12 took 0.000182779 s, 324.613 MB of memory in use > Info: CREATING 1104 COMPUTE OBJECTS > TCL: starting proc > TCL: ------------- > TCL: parameter unknown for NAMD config parameter > FATAL ERROR: Unknown Tcl error > > On Sat, 20 Nov 2021 at 21:55, Brian Radak > wrote: > > This is unfortunately an unsolved problem. As you point out - the > atom indices change during a CpHMD simulation and so the > selections would need to be updated at each cycle (probably with a > bit of bookkeeping). One thing that can be exploited is that the > number of residues does not change, so if it is possible to use > residue and name based selections, that should work. > > In previous work where we used restraints we took advantage of the > fact that it was only a single residue that was titrating and so > all indices above the atom sidechain are fixed during the > simulation (a bit of a hack). > > To be honest, it might be easier for someone to implement > restraints based on a selection syntax rather than solve the > indexing problem that is specific to CpHMD. > > HTH, > > BKR > > > On 11/20/21 12:29 AM, Diship Srivastava wrote: >> Hi, >> I am currently working on insertion of an antimicrobial peptide >> (AMP) on bilayer membrane using constant pH MD. I am trying to >> constrain the center of mass of AMP and membrane, while cphmd is >> active. Since cphmd doesn't have colvar support and number of >> atoms during cphmd changes during the run, both colvars and >> constraints result in fatal error during the job. How can I >> constrain the com under cphmd conditions? >> >> Thanks in advance. >> >> >> >> -- >> Diship Srivastava >> SRF >> Department of Chemistry >> IIT(ISM) - Dhanbad >> India > --------------D31DD14DC07F35EE1AC4F670 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

If I'm not mistaken, this usually means there's a syntax error and NAMD is interpreting a stray character or variable name as a keyword. I couldn't say what the problem is without seeing the entire input script.

On 11/22/21 4:58 AM, Diship Srivastava wrote:
Thanks for the suggestion. Based on your reply I have written an ad hoc tcl script for the same purpose (it harmonically constrains the com of bilayer and first few non titratable residues of protein ) but during run time the script crashes with unknown tcl error. Any help regarding this error will be highly appreciated. 


script snippet : 
 tclForces on
tclForcesScript {
set k 0.05
set r0 9.847

# com of bilayer
set group1 [addgroup {13 143 266 389 519 649 779 909....}]
# com of amp
set group2 [addgroup {15367 15369 15381 15382..}]
print "starting proc"
print "-------------"
proc calcforces {} {
        print "inside proc"
        print "changing scope of variables"
        # set change variable
        global group1 group2 k r0
        # load coordinates
        loadcoords c
        # get z coords of both groups
        set r1 [$c(1)]
        set r2 [$c(2)]
        foreach {x1 y1 z1} $r1 {}
        foreach {x2 y2 z2} $r2 {}
        set r_z [expr {$z2-$z1}]

        set disp [expr {$r_z-$r0}]
        # optional add energy - will be displayed in MISC
#        addenergy [expr {$k*$disp*$disp/2.0}]

        # calculate force
        set force [expr {-$k*$disp}]

        addforce $group1 $force
        addforce $group2 [expr {-1.0*$force}]

}
# close proc calcforces
# deleting all atomslections
clearconfig
}

In logfile the error encountered was : 
Info: Startup phase 10 took 6.5302e-05 s, 324.613 MB of memory in use
Info: Startup phase 11 took 0.000188028 s, 324.613 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 12 took 0.000182779 s, 324.613 MB of memory in use
Info: CREATING 1104 COMPUTE OBJECTS
TCL: starting proc
TCL: -------------
TCL: parameter unknown for NAMD config parameter
FATAL ERROR: Unknown Tcl error

On Sat, 20 Nov 2021 at 21:55, Brian Radak <brian.radak@gmail.com> wrote:

This is unfortunately an unsolved problem. As you point out - the atom indices change during a CpHMD simulation and so the selections would need to be updated at each cycle (probably with a bit of bookkeeping). One thing that can be exploited is that the number of residues does not change, so if it is possible to use residue and name based selections, that should work.

In previous work where we used restraints we took advantage of the fact that it was only a single residue that was titrating and so all indices above the atom sidechain are fixed during the simulation (a bit of a hack).

To be honest, it might be easier for someone to implement restraints based on a selection syntax rather than solve the indexing problem that is specific to CpHMD.

HTH,

BKR


On 11/20/21 12:29 AM, Diship Srivastava wrote:
Hi, 
I am currently working on insertion of an antimicrobial peptide (AMP) on bilayer membrane using constant pH MD. I am trying to constrain the center of mass of AMP and membrane, while cphmd is active. Since cphmd doesn't have colvar support and number of atoms during cphmd changes during the run, both colvars and constraints result in fatal error during the job. How can I constrain the com under cphmd conditions?

Thanks in advance.

     


--
Diship Srivastava 
SRF 
Department of Chemistry
IIT(ISM) - Dhanbad
India
--------------D31DD14DC07F35EE1AC4F670-- From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 23 09:21:33 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANFLXvW002763; Tue, 23 Nov 2021 09:21:33 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANFLXRT002761; Tue, 23 Nov 2021 09:21:33 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANFLWxq002757; Tue, 23 Nov 2021 09:21:32 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANFLWoS002756; Tue, 23 Nov 2021 09:21:32 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANFLPcg002747 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 23 Nov 2021 09:21:25 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1ANFHDwS031661 for ; Tue, 23 Nov 2021 15:21:24 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0a-00007101.pphosted.com with ESMTP id 3cg4qhbjer-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 23 Nov 2021 15:21:24 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 42FF51E43CB9; Tue, 23 Nov 2021 16:21:21 +0100 (CET) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id vOFGhsd1MkQk; Tue, 23 Nov 2021 16:21:20 +0100 (CET) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 3666D1E43CBD; Tue, 23 Nov 2021 16:21:20 +0100 (CET) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id 9e-Eb2X8Ep2t; Tue, 23 Nov 2021 16:21:20 +0100 (CET) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id C15EC1E43CB9; Tue, 23 Nov 2021 16:21:19 +0100 (CET) Date: Tue, 23 Nov 2021 16:21:14 +0100 (CET) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , =?utf-8?Q?Rop=C3=B3n-Palacios?= Message-ID: <1666325184.7997366.1637680874829.JavaMail.zimbra@ibpc.fr> In-Reply-To: <8C2F3E26-6270-4CC4-B946-159C8221ACF4@gmail.com> References: <8C2F3E26-6270-4CC4-B946-159C8221ACF4@gmail.com> Subject: Re: namd-l: HarmonicWall colvar MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_89c08fd3-da8f-490a-a949-65333da6c44a" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: HarmonicWall colvar Thread-Index: svdE2+tDi+bugJeG4eizX6qtJrinSQ== X-Proofpoint-GUID: 0ylyJ9n2N_XNprpZ08Ggi1uNCeUuun6F X-Proofpoint-ORIG-GUID: 0ylyJ9n2N_XNprpZ08Ggi1uNCeUuun6F X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwSEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxIYEQpDWRcHGxsdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ScR8TEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxpTRlNgE0QYZHVyZFpYWnAaEm1NQxtfZGlPf19fRBxsEQpYXBcfBBoEGB4YBRsa BBsaGgQdBBseHhAbHhofGhEKXlkXcxpbX3oRCk1cFxIZEQpMWhd4bWtNTREKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdsa2sRCkJPF2hARUgYGHxrW3oZEQpDWhcbExkEHhMEGBkeBBgYGxEKQl 4XGxEKRF4XGBEKQkUXZFhcXE1+UkkbZUkRCkJOF2VPfhJDaWZZHAFpEQpCTBd6EmdpYFl5RkFPZ REKQmwXYRIST09MTX9PHgURCkJAF2ZDb3JpbBpSS29JEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEK WlgXGBEKeUMXa21zW0dtaR5bXEwRCnBoF2dQX0FsQ3AcTH9AEBkaEQpwaBdtf0gFEkZ+RmRzaBA ZGhEKcGgXaAUfYV59QGZncGkQGRoRCnBoF2Aaa3J6cH9ScGVeEB8dEQpwaBdiGWBZZHprb08eQB AZGhEKcGwXZmATZFxNGmdPelAQGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=464 malwarescore=0 priorityscore=0 suspectscore=0 spamscore=0 clxscore=168 adultscore=0 mlxscore=0 bulkscore=0 impostorscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111230080 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_89c08fd3-da8f-490a-a949-65333da6c44a Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Geo,=20 Once you have defined a distanceXY variable (say it is named "d_xy"), you c= an use this restraint block:=20 harmonicWalls {=20 colvars d_xy=20 upperWalls 25=20 forceConstant =20 }=20 Where is the desired value of the force constant. Note that some keywor= ds are plural because they can take a list of values if the restraint is ac= ting on several colvars at the same time.=20 Best,=20 J=C3=A9r=C3=B4me=20 ----- On 22 Nov 21, at 19:25, Rop=C3=B3n-Palacios w= rote:=20 > Dear Users, > I like applie to colvar distancexy an cylinder restraint, but not know as= define > right harmonicWall, please help me. > My diameter for restraint is 50 (-25,25) > Best, > Geo. > Enviado desde mi iPhone --=_89c08fd3-da8f-490a-a949-65333da6c44a Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Geo,

Once you have defined a distanceXY variable (say it is named "= d_xy"), you can use this restraint block:

harmonic= Walls {
    colvars d_xy
=
    upperWalls 25
    forceConstant <= k>
}

Where <k= > is the desired value of the force constant. Note that some keywords ar= e plural because they can take a list of values if the restraint is acting = on several colvars at the same time.

Best,
J=C3=A9r=C3=B4me


----- On 22 Nov 21, at 19:25, Rop=C3=B3n-Palacios <b= iodano.geo@gmail.com> wrote:
Dear U= sers,

I like applie to colvar distancexy an cylinder restraint, but= not know as define right harmonicWall, please help me.

My diameter= for restraint is 50 (-25,25)

Best,

Geo.

Enviado de= sde mi iPhone
--=_89c08fd3-da8f-490a-a949-65333da6c44a-- From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 23 10:27:10 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANGRAAN005724; Tue, 23 Nov 2021 10:27:10 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANGRAE5005723; Tue, 23 Nov 2021 10:27:10 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANGR9L3005719; Tue, 23 Nov 2021 10:27:09 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANGR9cP005718; Tue, 23 Nov 2021 10:27:09 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANGR3dj005711 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000000bd0ac05d17736e5" X-Proofpoint-ORIG-GUID: ldCmtBl823Ktv76D3Da6sI-R5-raOHpz X-CLX-Response: 1TFkXGxISEQpMehcZGRsRCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHGBsSEQpDWRcHHxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBJxHh0QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XRk5pR15oRhIYGWFeXB0cbhluSxxZYwd4HwdYS2ViWlARClhcFx8EGgQYHhgF GxoEGxsaBB0EGxkYEBseGh8aEQpeWRdzGlhYUhEKTVwXGRMdEQpMWhdoaU1NTREKTEYXb2tra2t rEQpCTxdrQVNMHhJab08SbBEKQ1oXGBoTBBIfBBscGgQbHRgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZmkYXWx4bWNhUB0RCkJOF2NTY2t7E 1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwXZRhFRWJHS2FoS2wRCkJAF2dfaH5rbE9JSGhSEQpC WBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXYHJjXkcYWhJaQB8RCllLFxMfExMRCnBoF2lbXBkabkx DSWwTEBkaEQpwaBdiUEsBcnNifXJdGBAZGhEKcGgXZxtHa01NcH1JU2QQGRoRCnBoF255T0luf2 VaUAFwEBkaEQpwaBdsE2sYHXNCSWdIcxAZGhEKcGwXZHl+ZFlnHlNTaW8QGRoRCm1+FxoRClhNF 0sRIA== X-CLX-Shades: MLX X-Proofpoint-GUID: ldCmtBl823Ktv76D3Da6sI-R5-raOHpz X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=188 suspectscore=0 phishscore=0 mlxscore=0 bulkscore=0 adultscore=0 lowpriorityscore=0 malwarescore=0 priorityscore=331 impostorscore=0 spamscore=0 mlxlogscore=830 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111230084 domainage_hfrom=9599 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000000bd0ac05d17736e5 Content-Type: text/plain; charset="UTF-8" An organic molecule of 28 CHON atoms could be optimized, with all positive frequency analysis, with latest ORCA 5 at level PBE0 RIJCOSX D4 def2-TZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM) With QMMM 100 cycles in CHCl3, starting from an MD quasi equilibrated .pdb in that solvent, at level PBE0 RIJCOSX D4 def2-TZVP defgrid2 enGrad CPCM one of the tree rings of the molecule, and only that, underwent rapidly extreme distortion, even against the sp3 sp3 sp protocols. Adding optimization (is that permitted with QMMM?), i.e., level ## ORCA # qmConfigLine "! MORead" qmConfigLine "! PBE0 RIJCOSX D4 def2-TZVP Opt tightscf defgrid2 CPCM" # qmConfigLine "%%moinp \"........gbw\"" qmConfigLine "%%maxcore 5000" qmConfigLine "%%scf Maxiter 500 end" qmConfigLine "%%geom Maxiter 500 end" qmConfigLine "%%pal nproc 47 end" qmConfigLine "%%output Printlevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end" rapid scf convergence was observed. However, at the ORCA GEOMETRY RELAXATION STEP Warning: the length of the step is outside the trust region - taking restricted step instead The input lambda is .... -862.826127 iter: 1 x= -888.315690 g= 0.656919 f(x)= 16.744573 ...................... ..................... iter: 101 x=-1512.546611 g= 0.000257 f(x)= 0.000000 [file orca_gstep/orca_gstep.cpp, line 790]: Error (ORCA_GSTEP): The lambda equations have not converged Does that suggest any adjustment? After a couple of hours of thinking, I am short of ideas Thanks for advice francesco pietran MD --0000000000000bd0ac05d17736e5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
An organic molecule of 28 CHON atoms could be optimiz= ed, with all positive frequency analysis, with latest ORCA 5 at level
=
PBE0 RIJCOSX D4 def2-TZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM)=

With QMMM 100 cycles in CHCl3, starting from an M= D quasi equilibrated .pdb in that solvent, at level
PBE0 RIJ= COSX D4 def2-TZVP defgrid2 enGrad CPCM
one of the tree rings of t= he molecule, and only that, underwent rapidly extreme distortion, even agai= nst the sp3 sp3 sp protocols.

Adding optimization = (is that permitted with QMMM?), i.e., level
## ORCA
# qmConfig= Line =C2=A0 =C2=A0 "! MORead"
qmConfigLine =C2=A0 =C2=A0 "= ;! PBE0 RIJCOSX D4 def2-TZVP Opt tightscf defgrid2 CPCM"
# qmConfig= Line =C2=A0 =C2=A0 "%%moinp \"........gbw\""
qmConfi= gLine =C2=A0 =C2=A0 "%%maxcore 5000"
qmConfigLine =C2=A0 =C2= =A0 "%%scf Maxiter 500 end"
qmConfigLine =C2=A0 =C2=A0 "%= %geom Maxiter 500 end"
qmConfigLine =C2=A0 =C2=A0 "%%pal nproc= 47 end"
qmConfigLine =C2=A0 =C2=A0"%%output Printlevel Mini P= rint\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"

rapid scf convergence was observed. However, at the ORCA GEOMETRY R= ELAXATION STEP
Warning: the length of the step is outside the tru= st region - taking restricted step instead
The input lambda is =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 .... =C2=A0-= 862.826127
=C2=A0 =C2=A0iter: =C2=A0 1 =C2=A0x=3D -888.315690 =C2=A0g=3D= =C2=A0 =C2=A00.656919 f(x)=3D =C2=A0 =C2=A016.744573
...........= ...........
......................
iter: 101 =C2=A0x= =3D-1512.546611 =C2=A0g=3D =C2=A0 =C2=A00.000257 f(x)=3D =C2=A0 =C2=A0 0.00= 0000
[file orca_gstep/orca_gstep.cpp, line 790]: Error (ORCA_GSTEP): The= lambda equations have not converged

Does that sug= gest any adjustment? After a couple of hours of thinking, I am short of ide= as

Thanks for advice
francesco pietran M= D

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boundary="00000000000071e03405d17771a9" X-CLX-Response: 1TFkXGxITEQpMehcZGx4RCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHh8dEQpDWRcHGxocEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwTcR4SEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFx9JZxpBYHVkTxJbTmJuTGBSYWxPfkZHWVgcGh1IR1xOEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGBAbHhofGhEKXlkXcxpYHX0RCk1cFxkYGhEKTFoXaGlNTU0RCkxGF29ra2x raxEKQk8Xa0FTTB4SWm9PEmwRCkNaFxgaEwQSHwQbHBoEGxIbEQpCXhcbEQpCXBcbEQpeThcbEQ pCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2ZpGF1seG1jYVAdEQpCThdjU2Nre xNYfhpfXhEKQkwXZHtPUn8TSVp6cxwRCkJsF2UYRUViR0thaEtsEQpCQBdobxxDf11BQQFzHREK QlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF2FobEZJGElBG3wfEQpZSxcTHxMTEQpwZxdpQ25QAVl zRwEeUxAaEQpwaBd6cBhLRXkcfmNLYxAaEQpwaBdkeXwSQ3JHflBdThAaEQpwaBdiUEsBcnNifX JdGBAdGhEKcGgXZxtHa01NcH1JU2QQHRoRCnBoF2wTaxgdc0JJZ0hzEB0aEQpwbBdkeX5kWWceU 1NpbxAdGhEKbX4XGhEKWE0XSxEg X-Proofpoint-ORIG-GUID: 5cM0kJ_Ne8qdHDfJxKFeTlmsr607bmvd X-Proofpoint-GUID: 5cM0kJ_Ne8qdHDfJxKFeTlmsr607bmvd X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 spamscore=0 clxscore=189 mlxscore=0 adultscore=0 lowpriorityscore=0 phishscore=0 suspectscore=0 bulkscore=0 impostorscore=0 mlxlogscore=999 priorityscore=314 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111230084 domainage_hfrom=9599 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --00000000000071e03405d17771a9 Content-Type: text/plain; charset="UTF-8" Just to add why I did that QMMM, I expected an 6-exo-trig cyclization reaction forming a fourth cycle. fp ---------- Forwarded message --------- From: Francesco Pietra Date: Tue, Nov 23, 2021 at 5:26 PM Subject: QMMM convergence/optimization issues in CHCL3 solvent To: NAMD An organic molecule of 28 CHON atoms could be optimized, with all positive frequency analysis, with latest ORCA 5 at level PBE0 RIJCOSX D4 def2-TZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM) With QMMM 100 cycles in CHCl3, starting from an MD quasi equilibrated .pdb in that solvent, at level PBE0 RIJCOSX D4 def2-TZVP defgrid2 enGrad CPCM one of the tree rings of the molecule, and only that, underwent rapidly extreme distortion, even against the sp3 sp3 sp protocols. Adding optimization (is that permitted with QMMM?), i.e., level ## ORCA # qmConfigLine "! MORead" qmConfigLine "! PBE0 RIJCOSX D4 def2-TZVP Opt tightscf defgrid2 CPCM" # qmConfigLine "%%moinp \"........gbw\"" qmConfigLine "%%maxcore 5000" qmConfigLine "%%scf Maxiter 500 end" qmConfigLine "%%geom Maxiter 500 end" qmConfigLine "%%pal nproc 47 end" qmConfigLine "%%output Printlevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end" rapid scf convergence was observed. However, at the ORCA GEOMETRY RELAXATION STEP Warning: the length of the step is outside the trust region - taking restricted step instead The input lambda is .... -862.826127 iter: 1 x= -888.315690 g= 0.656919 f(x)= 16.744573 ...................... ..................... iter: 101 x=-1512.546611 g= 0.000257 f(x)= 0.000000 [file orca_gstep/orca_gstep.cpp, line 790]: Error (ORCA_GSTEP): The lambda equations have not converged Does that suggest any adjustment? After a couple of hours of thinking, I am short of ideas Thanks for advice francesco pietran MD --00000000000071e03405d17771a9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Just to add why I did that QMMM, I exp= ected an 6-exo-trig cyclization reaction forming a fourth cycle.
= fp
---------- Forwarded message ---------
From: Francesco Pietra <chiendarret@gmail.com>
D= ate: Tue, Nov 23, 2021 at 5:26 PM
Subject: QMMM convergence/optimization= issues in CHCL3 solvent
To: NAMD <namd-l@ks.uiuc.edu>


An or= ganic molecule of 28 CHON atoms could be optimized, with all positive frequ= ency analysis, with latest ORCA 5 at level
PBE0 RIJCOSX D4 def2-T= ZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM)

W= ith QMMM 100 cycles in CHCl3, starting from an MD quasi equilibrated .pdb i= n that solvent, at level
PBE0 RIJCOSX D4 def2-TZVP defgrid2 = enGrad CPCM
one of the tree rings of the molecule, and only that,= underwent rapidly extreme distortion, even against the sp3 sp3 sp protocol= s.

Adding optimization (is that permitted with QMM= M?), i.e., level
## ORCA
# qmConfigLine =C2=A0 =C2=A0 "! = MORead"
qmConfigLine =C2=A0 =C2=A0 "! PBE0 RIJCOSX D4 def2-TZV= P Opt tightscf defgrid2 CPCM"
# qmConfigLine =C2=A0 =C2=A0 "%%= moinp \"........gbw\""
qmConfigLine =C2=A0 =C2=A0 "%= %maxcore 5000"
qmConfigLine =C2=A0 =C2=A0 "%%scf Maxiter 500 e= nd"
qmConfigLine =C2=A0 =C2=A0 "%%geom Maxiter 500 end"qmConfigLine =C2=A0 =C2=A0 "%%pal nproc 47 end"
qmConfigLine= =C2=A0 =C2=A0"%%output Printlevel Mini Print\[ P_Mulliken \] 1 Print\= [P_AtCharges_M\] 1 end"

rapid scf convergence= was observed. However, at the ORCA GEOMETRY RELAXATION STEP
Warn= ing: the length of the step is outside the trust region - taking restricted= step instead
The input lambda is =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 .... =C2=A0-862.826127
=C2=A0 =C2=A0iter= : =C2=A0 1 =C2=A0x=3D -888.315690 =C2=A0g=3D =C2=A0 =C2=A00.656919 f(x)=3D = =C2=A0 =C2=A016.744573
.......................
........= .............
iter: 101 =C2=A0x=3D-1512.546611 =C2=A0g=3D =C2=A0= =C2=A00.000257 f(x)=3D =C2=A0 =C2=A0 0.000000
[file orca_gstep/orca_gst= ep.cpp, line 790]: Error (ORCA_GSTEP): The lambda equations have not conver= ged

Does that suggest any adjustment? After a coup= le of hours of thinking, I am short of ideas

Thank= s for advice
francesco pietran MD

--00000000000071e03405d17771a9-- From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 23 10:47:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANGlH2Q009371; Tue, 23 Nov 2021 10:47:17 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANGlHwk009370; Tue, 23 Nov 2021 10:47:17 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANGlGPw009366; Tue, 23 Nov 2021 10:47:16 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANGlGBr009365; Tue, 23 Nov 2021 10:47:16 -0600 (CST) Received: from [10.0.0.50] (c-73-246-117-209.hsd1.il.comcast.net [73.246.117.209]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANGlCD6009269 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 23 Nov 2021 10:47:14 -0600 (CST) From: Mariano Spivak Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 (Mac OS X Mail 11.5 \(3445.9.7\)) Subject: Re: namd-l: QMMM convergence/optimization issues in CHCL3 solvent Date: Tue, 23 Nov 2021 10:47:07 -0600 References: To: namd-l@ks.uiuc.edu, Francesco Pietra In-Reply-To: Message-Id: X-Mailer: Apple Mail (2.3445.9.7) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id 1ANGlED5009351 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Mariano Spivak Hi Francesco, >From this email, it is not quite clear what simulation you are trying to run. Is this a QM/MM of your organic molecule (QM) in explicit CHCl3 (MM)? If so, then you should not include implicit solvent in your QM calculation, because you already accounting for solute-solvent interactions through the NAMD interface. Also adding optimization to the QM/MM config line is not recommended to say the least. It defeats the purpose of the method and will give you wrong results. Hope this helps Best > On Nov 23, 2021, at 10:26 AM, Francesco Pietra wrote: > > An organic molecule of 28 CHON atoms could be optimized, with all positive frequency analysis, with latest ORCA 5 at level > PBE0 RIJCOSX D4 def2-TZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM) > > With QMMM 100 cycles in CHCl3, starting from an MD quasi equilibrated .pdb in that solvent, at level > PBE0 RIJCOSX D4 def2-TZVP defgrid2 enGrad CPCM > one of the tree rings of the molecule, and only that, underwent rapidly extreme distortion, even against the sp3 sp3 sp protocols. > > Adding optimization (is that permitted with QMMM?), i.e., level > ## ORCA > # qmConfigLine "! MORead" > qmConfigLine "! PBE0 RIJCOSX D4 def2-TZVP Opt tightscf defgrid2 CPCM" > # qmConfigLine "%%moinp \"........gbw\"" > qmConfigLine "%%maxcore 5000" > qmConfigLine "%%scf Maxiter 500 end" > qmConfigLine "%%geom Maxiter 500 end" > qmConfigLine "%%pal nproc 47 end" > qmConfigLine "%%output Printlevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end" > > rapid scf convergence was observed. However, at the ORCA GEOMETRY RELAXATION STEP > Warning: the length of the step is outside the trust region - taking restricted step instead > The input lambda is .... -862.826127 > iter: 1 x= -888.315690 g= 0.656919 f(x)= 16.744573 > ...................... > ...................... > iter: 101 x=-1512.546611 g= 0.000257 f(x)= 0.000000 > [file orca_gstep/orca_gstep.cpp, line 790]: Error (ORCA_GSTEP): The lambda equations have not converged > > Does that suggest any adjustment? After a couple of hours of thinking, I am short of ideas > > Thanks for advice > francesco pietran MD > From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 23 14:32:30 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANKWTj3013174; Tue, 23 Nov 2021 14:32:29 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANKWTqT013173; Tue, 23 Nov 2021 14:32:29 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANKWTgm013168; Tue, 23 Nov 2021 14:32:29 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ANKWTjc013167; Tue, 23 Nov 2021 14:32:29 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ANKWHkl013159 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT); 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boundary="0000000000001f1c0905d17aa36d" X-CLX-Response: 1TFkXGx0cEQpMehcZHh4RCllEF20fH0NCQWcdQUdAEQpYWBdke09SfxNJWnp zHBEKeE4XY1Nja3sTWH4aX14RCnlMF2l9ExMYfkxeY18bEQpDSBcHHBobEQpDWRcHGxgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxxxGR8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XHUV1YF5cYVppbWxjHmV1c2FkYkVfTWF8H2xtT0tNGXoRClhcFx8EGgQYHhgF GxoEGxsaBB0EGxkbEBseGh8aEQpeWRdzGlx4WREKTVwXHhsfEQpMWhdNaxEKTEYXb2trYmtrEQp CTxdlaVBnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGAQbHBMRCkJeFxsRCkRYFxgRCkRJFxsRCkJcFx sRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZmkYXWx4bWNhUB0RC kJOF2NTY2t7E1h+Gl9eEQpCTBdke09SfxNJWnpzHBEKQmwXZRhFRWJHS2FoS2wRCkJAF2kBc3lb e25iEmxCEQpaWBcYEQp5QxdjSUVPYX1kE1pPUBEKWUsXEx8TExEKcGcXYURzSRhYThtQQ3oQGRo RCnBoF3p5TGMBb2h/X0taEB4SEQpwaBdkeXwSQ3JHflBdThAeEhEKcGgXawFOH0BifVkTGUwQHh IRCnBoF2JQSwFyc2J9cl0YEBwaEQpwaBdsE2sYHXNCSWdIcxAcGhEKcGwXZHl+ZFlnHlNTaW8QH hIRCnBMF2kTUB1rH1wTH2Z+EBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: 7o_JtvKpCGFI4O_YKNHougKV5FGeag3P X-Proofpoint-ORIG-GUID: 7o_JtvKpCGFI4O_YKNHougKV5FGeag3P X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 malwarescore=0 clxscore=176 spamscore=0 impostorscore=0 mlxlogscore=999 lowpriorityscore=0 phishscore=0 priorityscore=344 bulkscore=0 suspectscore=0 adultscore=0 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111230100 domainage_hfrom=9599 X-Spam-Score: 0 X-Spam-OrigSender: chiendarret@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Francesco Pietra --0000000000001f1c0905d17aa36d Content-Type: text/plain; charset="UTF-8" Hi Mariano Thanks for answering. Yes, this is a QM/MM of my organic molecule (QM) in explicit CHCl3 (MM) Now I removed both Opt and CPCM from the qmConfigLine. What happened is like I described before, viewed with VMD from the QMonly dcd. This corresponds to an explosion of the molecule, when the last ORCA Cartesian coordinates are viewed with Jmol. Still not clear to me why the different results from running QM with ORCA in a continuum CPCM or QMMM with NAMD-ORCA in explicit CHCl3 francesco On Tue, Nov 23, 2021 at 5:47 PM Mariano Spivak wrote: > Hi Francesco, > > From this email, it is not quite clear what simulation you are trying to > run. > Is this a QM/MM of your organic molecule (QM) in explicit CHCl3 (MM)? > If so, then you should not include implicit solvent in your QM > calculation, because you already accounting for solute-solvent interactions > through the NAMD interface. > Also adding optimization to the QM/MM config line is not recommended to > say the least. It defeats the purpose of the method and will give you wrong > results. > > Hope this helps > > Best > > > > > On Nov 23, 2021, at 10:26 AM, Francesco Pietra > wrote: > > > > An organic molecule of 28 CHON atoms could be optimized, with all > positive frequency analysis, with latest ORCA 5 at level > > PBE0 RIJCOSX D4 def2-TZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM) > > > > With QMMM 100 cycles in CHCl3, starting from an MD quasi equilibrated > .pdb in that solvent, at level > > PBE0 RIJCOSX D4 def2-TZVP defgrid2 enGrad CPCM > > one of the tree rings of the molecule, and only that, underwent rapidly > extreme distortion, even against the sp3 sp3 sp protocols. > > > > Adding optimization (is that permitted with QMMM?), i.e., level > > ## ORCA > > # qmConfigLine "! MORead" > > qmConfigLine "! PBE0 RIJCOSX D4 def2-TZVP Opt tightscf defgrid2 CPCM" > > # qmConfigLine "%%moinp \"........gbw\"" > > qmConfigLine "%%maxcore 5000" > > qmConfigLine "%%scf Maxiter 500 end" > > qmConfigLine "%%geom Maxiter 500 end" > > qmConfigLine "%%pal nproc 47 end" > > qmConfigLine "%%output Printlevel Mini Print\[ P_Mulliken \] 1 > Print\[P_AtCharges_M\] 1 end" > > > > rapid scf convergence was observed. However, at the ORCA GEOMETRY > RELAXATION STEP > > Warning: the length of the step is outside the trust region - taking > restricted step instead > > The input lambda is .... -862.826127 > > iter: 1 x= -888.315690 g= 0.656919 f(x)= 16.744573 > > ...................... > > ...................... > > iter: 101 x=-1512.546611 g= 0.000257 f(x)= 0.000000 > > [file orca_gstep/orca_gstep.cpp, line 790]: Error (ORCA_GSTEP): The > lambda equations have not converged > > > > Does that suggest any adjustment? After a couple of hours of thinking, I > am short of ideas > > > > Thanks for advice > > francesco pietran MD > > > > --0000000000001f1c0905d17aa36d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Mariano
Thanks for answering. Yes, this = is a QM/MM of my organic molecule (QM) in explicit CHCl3 (MM)
Now I removed both Opt and CPCM from the qmConfigLine.=C2=A0 Wh= at happened is like I described before, viewed with VMD from the QMonly dcd= .

This corresponds to an explosion of the molecule= , when the last ORCA Cartesian coordinates are viewed with Jmol.
=
Still not clear to me why the different results from running= QM with ORCA in a continuum CPCM or QMMM with NAMD-ORCA in explicit CHCl3<= /div>

francesco

On Tue, Nov 23, 2021 at 5:47 PM= Mariano Spivak <mariano@ks.uiuc.= edu> wrote:
Hi Francesco,

>From this email, it is not quite clear what simulation you are trying to ru= n.
Is this a QM/MM of your organic molecule (QM) in explicit CHCl3 (MM)?
If so, then you should not include implicit solvent in your QM calculation,= because you already accounting for solute-solvent interactions through the= NAMD interface.
Also adding optimization to the QM/MM config line is not recommended to say= the least. It defeats the purpose of the method and will give you wrong re= sults.

Hope this helps

Best



> On Nov 23, 2021, at 10:26 AM, Francesco Pietra <chiendarret@gmail.com> wrote= :
>
> An organic molecule of 28 CHON atoms could be optimized, with all posi= tive frequency analysis, with latest ORCA 5 at level
> PBE0 RIJCOSX D4 def2-TZVP Opt Freq tightscf defgrid2 CPCM (CHLOROFORM)=
>
> With QMMM 100 cycles in CHCl3, starting from an MD quasi equilibrated = .pdb in that solvent, at level
> PBE0 RIJCOSX D4 def2-TZVP defgrid2 enGrad CPCM
> one of the tree rings of the molecule, and only that, underwent rapidl= y extreme distortion, even against the sp3 sp3 sp protocols.
>
> Adding optimization (is that permitted with QMMM?), i.e., level
> ## ORCA
> # qmConfigLine=C2=A0 =C2=A0 =C2=A0"! MORead"
> qmConfigLine=C2=A0 =C2=A0 =C2=A0"! PBE0 RIJCOSX D4 def2-TZVP Opt = tightscf defgrid2 CPCM"
> # qmConfigLine=C2=A0 =C2=A0 =C2=A0"%%moinp \"........gbw\&qu= ot;"
> qmConfigLine=C2=A0 =C2=A0 =C2=A0"%%maxcore 5000"
> qmConfigLine=C2=A0 =C2=A0 =C2=A0"%%scf Maxiter 500 end"
> qmConfigLine=C2=A0 =C2=A0 =C2=A0"%%geom Maxiter 500 end"
> qmConfigLine=C2=A0 =C2=A0 =C2=A0"%%pal nproc 47 end"
> qmConfigLine=C2=A0 =C2=A0 "%%output Printlevel Mini Print\[ P_Mul= liken \] 1 Print\[P_AtCharges_M\] 1 end"
>
> rapid scf convergence was observed. However, at the ORCA GEOMETRY RELA= XATION STEP
> Warning: the length of the step is outside the trust region - taking r= estricted step instead
> The input lambda is=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0....=C2=A0 -862.826127
>=C2=A0 =C2=A0 iter:=C2=A0 =C2=A01=C2=A0 x=3D -888.315690=C2=A0 g=3D=C2= =A0 =C2=A0 0.656919 f(x)=3D=C2=A0 =C2=A0 16.744573
> ......................
> ......................
> iter: 101=C2=A0 x=3D-1512.546611=C2=A0 g=3D=C2=A0 =C2=A0 0.000257 f(x)= =3D=C2=A0 =C2=A0 =C2=A00.000000
> [file orca_gstep/orca_gstep.cpp, line 790]: Error (ORCA_GSTEP): The la= mbda equations have not converged
>
> Does that suggest any adjustment? After a couple of hours of thinking,= I am short of ideas
>
> Thanks for advice
> francesco pietran MD
>

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Thu, 25 Nov 2021 08:15:44 +0000 Date: Thu, 25 Nov 2021 08:15:39 +0000 (UTC) From: Alexei Rossokhin To: NAMD List Message-ID: <1044293900.4525095.1637828139769@mail.yahoo.com> Subject: namd-l: residue_rmsd.tcl script MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_Part_4525094_16669099.1637828139769" References: <1044293900.4525095.1637828139769.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19306 YMailNorrin X-CLX-Shades: MLX X-Proofpoint-GUID: odwmG8-R9T91CeyrvbV2lzoo-CdCs_r- X-CLX-Response: 1TFkXExoRCkx6FxkbHhEKWUQXYXBQX3NaQ1oef1sRClhYF2EbYnATT11sfFM ZEQp4Thd6RBwdb0VsbURDZhEKeUwXZWJIGHMcREBwbHoRCkNIFwcZGx4RCkNZFwccHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3Bh0acR4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XRU5dR20SB3gTfhMbaU9TWFxIfBhGUEVFB2lOaVl1WAcRClhcFx8EGgQYHhgFGxoE GxsaBB0EGxkYEBseGh8aEQpeWRdzG2VYZxEKTVwXGBkfEQpMWhdsaWtraxEKTEYXb2trb2trEQp CTxdrTG5EU15pWHlCaBEKQ1oXHBwEGxwZBBsTGgQZGxEKQl4XGxEKQlwXGxEKXk4XGxEKQksXek QcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtRENmEQpCRRdmHAFtc1xTHnpDHREKQk4XekQcHW9FbG1EQ 2YRCkJMF2EbYnATT11sfFMZEQpCbBdrE2JoWGtCXX9fHhEKQkAXb0Zpa1tpR05QQHoRCkJYF2dz ZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdoAUhff2kBbBhcRREKWUsXExIaEhEKcGgXYHtTTQF Sc3N4SBwQGRoRCnBoF2F+Uh1PeGB9ekNzEBkaEQpwaBdkGFIZbxhrQW4ZEhAZGhEKcGgXbEhHaU 0dG39cZWQQGRoRCnBoF2VMHUVoGhxmQ1NGEBkaEQpwaxdkc2Z8WUsda3lFfhAZGhEKcEsXYxgYZ X5LfkJyfQUQEhwRCnBrF2NIeV1+f19oUHlaEBkaEQpwbBdsY0lIeUJ6RGMFZhAZGhEKcEwXZgVh HEcdRmF5Q38QGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: odwmG8-R9T91CeyrvbV2lzoo-CdCs_r- X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 malwarescore=0 phishscore=0 spamscore=0 priorityscore=314 lowpriorityscore=0 suspectscore=0 mlxlogscore=773 impostorscore=0 clxscore=90 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111250044 domainage_hfrom=9808 X-Spam-Score: 0 X-Spam-OrigSender: alrossokhin@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alexei Rossokhin ------=_Part_4525094_16669099.1637828139769 Content-Type: multipart/alternative; boundary="----=_Part_4525093_2088988697.1637828139580" ------=_Part_4525093_2088988697.1637828139580 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear NAMD users, While browsing the NAMD tutorial I found the residue_rmsd.= tcl script to calculate RMSD for individual residues. When I tried to run i= t, the results puzzled me a little.=20 When I used the selection "protein and chain A and resid 174 and name CA an= d noh" for my MD calculations I got the following result RMSD of residue 174 is 1.3978458595465855 =C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.3978458595465855 When I used the selection "protein and chain A and resid 174 and name CA CB= CG CD and noh" I got the following result RMSD of residue 174 is 5.591383438186342 RMSD of residue 174 is 0.022276428040583034 RMSD of residue 174 is 8.875070932503201e-5 RMSD of residue 174 is 3.535884833666614e-7 =C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.4034372426311832 Using "protein and chain A and resid 174 and name CB and noh" I got=20 RMSD of residue 174 is 1.3978458595465855 =C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.3978458595465855 If to run the script separately for CA or CB=C2=A0 result is the same. If t= o run the script with the selection "name CA CB CG CD", the result for indi= vidual atoms is strange, although the average is close in all cases.=20 What does it mean,=C2=A0 any bug in the script?Thank you for help. Alexey PS I attached the residue_rmsd.tcl script. ------=_Part_4525093_2088988697.1637828139580 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear NAMD users,
While browsing the NAMD tutorial I found = the residue_rmsd.tcl script to calculate RMSD for individual residues= . When I tried to run it, the results puzzled me a little.

When I used the selection "protein and cha= in A and resid 174 and name CA and noh" for my MD calculations I got the fo= llowing result

RMSD of residue 174 is 1.39784= 58595465855
 Average rmsd per residue:   1.39784585954658= 55

When I used t= he selection "protein and chain A and resid 174 and name CA CB = CG CD and noh" I got the following result

RMSD of residue 174 is 5.59138343818634= 2
RMSD of residue 174 is 0.022276428040583034
RMSD of residue 174 is = 8.875070932503201e-5
RMSD of residue 174 is 3.535884833666614e-7
&nbs= p;Average rmsd per residue:   1.4034372426311832

Using "= protein and chain A and resid 174 and name CB and noh" I got

RMSD of residue 174 is 1.3978458595465855
 Average rmsd per residu= e:   1.3978458595465855

If to run the script separately for CA or CB=   result is the same. If to run the script with the selection "name CA CB CG CD", the result for ind= ividual atoms is strange, although the average is close in all cases.

What does it mean,  any bug in the scr= ipt?
Thank you for help.

Alexey

PS I attached the residue_rmsd.tcl script.

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Date: Thu, 25 Nov 2021 15:44:03 +0530 Message-ID: Subject: namd-l: =?UTF-8?Q?FEP_calculation_for_Binding_of_a_potassium_ion_to_18?= =?UTF-8?Q?=E2=80=93crown=E2=80=936?= To: namd-l@ks.uiuc.edu Content-Type: multipart/mixed; boundary="00000000000088653305d19a3c48" X-Proofpoint-GUID: 0GYtVdr4-p_XnOea1P7NtIYfXDoyf0w2 X-Proofpoint-ORIG-GUID: 0GYtVdr4-p_XnOea1P7NtIYfXDoyf0w2 X-CLX-Response: 1TFkXGx0cEQpMehcaEQpZRBd6Y28Yfh5LX3lofxEKWFgXYB5vTW5+eRMacEc RCnhOF2xdW2FlQh1wSU0TEQp5TBdsYxhnf1hlYGZ+cxEKQ0gXBxgcHBEKQ1kXBxscHREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfHHEZHxAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThcabXNefE5YHgdadXJEZU9LG3odZF5jc0xybkVTTBpdGBEKWFwXHwQaBBgeGAUb GgQbGxoEHQQbGRkQGx4aHxoRCl5ZF3Mbe0t5EQpNXBcHGR8RCkxaF3hpTU1rEQpFWRdvEQpMXxd 6BQUFBQUFBQUFQxEKTEYXb2tra2trEQpCTxdkflhPZm5zSXBbTxEKQ1oXGBoTBBIfBBgbHAQeGB EKQl4XGxEKQlwXGxEKQksXYF1IWVsTAVgbQVARCkJJF2xdW2FlQh1wSU0TEQpCRRdtZHp5e2Z8Y 11uTREKQk4XbF1bYWVCHXBJTRMRCkJMF2Aeb01ufnkTGnBHEQpCbBdgQFNhb0djWUhOQBEKQkAX YWFpZhlDBWBlYlsRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdkY1tGHWtDfB9NbRE KWUsXHBIeHxEKcGgXYk5lUlpfTGtefGYQGRoRCnBoF2ZOY3IZE0lCWERgEBsbGhEKcGgXbX9eQ2 N5W0VeSX8QGRoRCnBoF2hOe10aHR8TTFBiEBkaEQpwaBdgX0NiXRpHHAFdaBAbGh8RCnBrF21+W nNYQVl8fXBCEBkaEQpwSxdkZh1/El9dTl5tGBAZGhEKcGsXY15zTEBBG354ZEgQGRoRCnBrF3oF HG1aU3weRWdYEBkaEQpwSxdrUmRtGBJ9G2BNYxAZGhEKcGsXb3h8ZR96Xx9mG0QQGRoRCnBrF2l ceXtiTVB8cEFQEBkaEQpwbBdjf2Jhb2dlXEtrTRAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 spamscore=0 phishscore=0 adultscore=0 suspectscore=0 mlxlogscore=716 mlxscore=0 clxscore=176 bulkscore=0 lowpriorityscore=0 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111250056 domainage_hfrom=6845 X-Spam-Score: 0 X-Spam-OrigSender: p20190061@hyderabad.bits-pilani.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "SYEDA SABIHA SULTANA LUBNA ." --00000000000088653305d19a3c48 Content-Type: multipart/alternative; boundary="00000000000088652f05d19a3c46" --00000000000088652f05d19a3c46 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable HI, I am not able to replicate the results for Binding of a potassium ion to 18=E2=80=93crown=E2=80=936, even though i have exactly followed the steps g= iven in protocol. Can someone please help me out to troubleshoot where i am going wrong. I have attached the FEP run files. I am getting a final delta G value of -1.99 kcal/mol whereas, according to tutorials it should be =E2=88= =922.6 kcal/mol. Thank you --=20 The information contained in this electronic communication is intended=20 solely for the individual(s) or entity to which it is addressed. It may=20 contain proprietary, confidential and/or legally privileged information.=20 Any review, retransmission, dissemination, printing, copying or other use= =20 of, or taking any action in reliance on the contents of this information by= =20 person(s) or entities other than the intended recipient is strictly=20 prohibited and may be unlawful. If you have received this communication in= =20 error, please notify us by responding to this email or telephone and=20 immediately and permanently delete all copies of this message and any=20 attachments from your system(s). The contents of this message do not=20 necessarily represent the views or policies of BITS Pilani. --00000000000088652f05d19a3c46 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
HI,

I am not able to replica= te the results for Binding of a potassium ion to 18=E2=80=93crown=E2=80=936= , even though i have exactly followed the steps given in protocol. Can some= one please help me out to troubleshoot where i am going wrong. I have attac= hed the FEP run files. I am getting a final delta G value of -1.99 kcal/mol= whereas, according to tutorials it should be =E2=88=922.6 kcal/mol.
<= div>
Thank you

The information contained in this electronic communication is intended sole= ly for the individual(s) or entity to which it is addressed. It may contain= proprietary, confidential and/or legally privileged information. Any revie= w, retransmission, dissemination, printing, copying or other use of, or tak= ing any action in reliance on the contents of this information by person(s)= or entities other than the intended recipient is strictly prohibited and m= ay be unlawful. If you have received this communication in error, please no= tify us by responding to this email or telephone and immediately and perman= ently delete all copies of this message and any attachments from your syste= m(s). The contents of this message do not necessarily represent the views o= r policies of BITS Pilani.
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boundary="00000000000095db0d05d19fbba9" X-Proofpoint-ORIG-GUID: Z84gCYjjxbXsE9o1WcwAYA26y0DHMfrp X-CLX-Response: 1TFkXGx0cEQpMehcbHhkRCllEF2dMU0cZaBJoR0x7EQpYWBdjWGZBfmxIWGB SexEKeE4XYX5mSUN9fVxYHUARCnlMF29Pf24BGnlLH1NlEQpDSBcHGRsbEQpDWRcHGx8bEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ccR0bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3ASHk1pc0BAUkhyWW8TRRt9SV1rc2sYHFMabmJnTFhaEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXcxt9ZmMRCk1cFxgbHxEKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdkflhPZm5zSXBbTxEKQ1oXGBoTBBIfBBgbHA QeHxEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXYX5mSUN9fVxYHUARCkJJF2F+ZklDfX1cW B1AEQpCRRdmGB59bmBIS2ZFchEKQk4XYX5mSUN9fVxYHUARCkJMF2NYZkF+bEhYYFJ7EQpCbBdt b2YcXG9+X1tjXBEKQkAXaR5ZZV1DaWV4bEIRCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp 5Qxdvem54bGd6EkNYThEKcGgXawF8HFx4Z216TnAQGRoRCnBoF29QWwF+WQV6YmcTEBkaEQpwaB doBXJEWkJSXnNNHBAZGhEKcGgXbUlwEmsYeEhhEnsQGRoRCnBoF2BmH0hfEn9oSW9NEBkaEQpwb BdmTGEaSHhwH3xibxAZGhEKcEwXZgVhHEcdRmF5Q38QGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: Z84gCYjjxbXsE9o1WcwAYA26y0DHMfrp X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 bulkscore=0 impostorscore=0 adultscore=0 mlxlogscore=999 spamscore=0 clxscore=176 phishscore=0 suspectscore=0 malwarescore=0 lowpriorityscore=0 priorityscore=143 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111250091 X-Spam-Score: 0 X-Spam-OrigSender: petefred@umich.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Peter Freddolino --00000000000095db0d05d19fbba9 Content-Type: text/plain; charset="UTF-8" Dear Alexey, I think the problem is that this script was written under the assumption that you're operating at a residue level, and thus, that there aren't repeated residue entries in the second argument to rmsd_residue_over_time (given the function name, one would not expect the user to give multiple atoms from the same residue in the function argument). If such entries do exist, it is going to behave oddly because the loops in that function act over the list of residues passed will then be repeatedly adding to the residue level rmsd, and then dividing by it. Now, that script *should* have been written defensively and passed the residue id list through [lsort -unique ...] prior to acting on it, but as it is, there is a clear deviation in your input from what the function is expecting. Best, Peter On Thu, Nov 25, 2021 at 4:02 AM Alexei Rossokhin < alrossokhin@remove_yahoo.com> wrote: > Dear NAMD users, > While browsing the NAMD tutorial I found the residue_rmsd.tcl script to > calculate RMSD for individual residues. When I tried to run it, the > results puzzled me a little. > > When I used the selection "protein and chain A and resid 174 and name CA > and noh" for my MD calculations I got the following result > > RMSD of residue 174 is 1.3978458595465855 > Average rmsd per residue: 1.3978458595465855 > > When I used the selection "protein and chain A and resid 174 and name CA > CB CG CD and noh" I got the following result > > RMSD of residue 174 is 5.591383438186342 > RMSD of residue 174 is 0.022276428040583034 > RMSD of residue 174 is 8.875070932503201e-5 > RMSD of residue 174 is 3.535884833666614e-7 > Average rmsd per residue: 1.4034372426311832 > > Using "protein and chain A and resid 174 and name CB and noh" I got > > RMSD of residue 174 is 1.3978458595465855 > Average rmsd per residue: 1.3978458595465855 > > If to run the script separately for CA or CB result is the same. If to > run the script with the selection "name CA CB CG CD", the result for > individual atoms is strange, although the average is close in all cases. > > What does it mean, any bug in the script? > Thank you for help. > > Alexey > > PS I attached the residue_rmsd.tcl script. > > --00000000000095db0d05d19fbba9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Alexey,
I think the p= roblem is that this script was written under the assumption that you're= operating at a residue level, and thus, that there aren't repeated res= idue entries in the second argument to rmsd_residue_over_time (given the fu= nction name, one would not expect the user to give multiple atoms from the = same residue in the function argument). If such entries do exist, it is goi= ng to behave oddly because the loops in that function act over the list of = residues passed will then be repeatedly adding to the residue level rmsd, a= nd then dividing by it. Now, that script *should* have been written defensi= vely and passed the residue id list through [lsort -unique ...] prior to ac= ting on it, but as it is, there is a clear deviation in your input from wha= t the function is expecting.
Best,
Peter

On Th= u, Nov 25, 2021 at 4:02 AM Alexei Rossokhin <alrossokhin@remove_yahoo.com> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex">
= Dear NAMD users,
While browsing the NAMD tutor= ial I found the residue_rmsd.tcl script to calculate RMSD for = individual residues. When I tried to run it, the results puzzled me a= little.

When I used the selection "protein and chain A and resid 174 a= nd name CA and noh" for my MD calculations I got the following result<= /span>

RMSD of residu= e 174 is 1.3978458595465855
=C2=A0Average rmsd per residue:=C2=A0=C2=A0 = 1.3978458595465855

When I used the sel= ection "protein and chain A and resid 174 and name CA CB C= G CD and noh" I got the following result

RM= SD of residue 174 is 5.591383438186342
RMSD of residue 174 is 0.02227642= 8040583034
RMSD of residue 174 is 8.875070932503201e-5
RMSD of residu= e 174 is 3.535884833666614e-7
=C2=A0Average rmsd per residue:=C2=A0=C2= =A0 1.4034372426311832

Using "protein and chain A and resid 174 and name CB and noh= " I got

RMSD of residue 174 is 1.39784585954658= 55
=C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.3978458595465855
<= div>
If to run the script separately for CA or CB=C2=A0 result is the same. If to run the script with the selec= tion "name CA CB CG CD", <= span>the result for individual atoms is strange, although the average is cl= ose in all cases.

What does it mean,=C2=A0 any bug in the script?
Thank you for help.

Alexey
<= /div>

PS I attached the residue_rmsd.tcl script.

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Fri, 26 Nov 2021 08:13:49 +0000 Date: Fri, 26 Nov 2021 07:36:07 +0000 (UTC) From: Alexei Rossokhin To: "namd-l@ks.uiuc.edu" Message-ID: <351876258.5591866.1637912167285@mail.yahoo.com> In-Reply-To: References: <1044293900.4525095.1637828139769.ref@mail.yahoo.com> <1044293900.4525095.1637828139769@mail.yahoo.com> Subject: Re: namd-l: residue_rmsd.tcl script MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_5591865_711051806.1637912167281" X-Mailer: WebService/1.1.19306 YMailNorrin X-Proofpoint-GUID: uvRsXcvj275WaqZC6sC9aMZFjGRV7HrF X-Proofpoint-ORIG-GUID: uvRsXcvj275WaqZC6sC9aMZFjGRV7HrF X-CLX-Response: 1TFkXExIRCkx6FxkbGxEKWUQXYXBQX3NaQ1oef1sRClhYF2EbYnATT11sfFM ZEQp4Thd6RBwdb0VsbURDZhEKeUwXZWJIGHMcREBwbHoRCkNIFwcZHh4RCkNZFwcbHxsRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYdEnEfEBp3BhgaBhoRClleF2xseREKSUYXX0NfSXVCR VleT04RCkNOF19ceFlySVxAGB0ffUtbcGkcWWkTS2dwbEBteHwdYlhsEQpYXBcfBBoEGB4YBRsa BBsbGgQdBBsZGBAbHhofGhEKXlkXcxtAXHARCk1cFxkcGREKTFoXeGlNa2sRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdrTG5EU15pWHlCaBEKQ1oXHBwEGxwZBBsTGwQbHh wRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF3pEHB1vRWxtRENmEQpCSRd6RBwdb0VsbURDZ hEKQkUXZhwBbXNcUx56Qx0RCkJOF3pEHB1vRWxtRENmEQpCTBdhG2JwE09dbHxTGREKQmwXaxNi aFhrQl1/Xx4RCkJAF2keWWVdQ2lleGxCEQpCWBdnc2VzQG5hYUxdYhEKWlgXGBEKeUMXb3pueGx nehJDWE4RCllLFxMSGhMRCnBnF2tuZHNYGEIBSx9BEB4SEQpwaBdpeXNtWxtiQ2NdYRAZGhEKcG gXb29kE05cZh8BREgQGRoRCnBoF2FFUlxwYRN7bWhOEBkaEQpwaBdjYkNjYFBmGRpmWRAZGhEKc GgXZWh9S0BtXltkX20QGRoRCnBnF2hJXUUYWFJlaGsTEBkaEQpwbBdsY0lIeUJ6RGMFZhAZGhEK bX4XGhEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=311 spamscore=0 phishscore=0 adultscore=0 suspectscore=0 mlxlogscore=999 mlxscore=0 clxscore=98 bulkscore=0 lowpriorityscore=0 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111260048 domainage_hfrom=9809 X-Spam-Score: 0 X-Spam-OrigSender: alrossokhin@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Alexei Rossokhin ------=_Part_5591865_711051806.1637912167281 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Peter, thanks for your answer. When I first ran this script, I was surprised that when choosing the select= ion as=C2=A0 "protein" (without specifying any atom), the script runs over = all atoms in the residues, and these calculations are wrong, as I showed in= the previous letter. Thus, it seems that some atom should still be specifi= ed in selection, for example, "protein and alpha", and in that case=C2=A0 t= he script works correctly. I have just started to learn the tcl language an= d do not understand all the details. Could you please point me to which ope= rators in the script operate with the name of the atom. Thanks,Alexey =C2=A0 On Thursday, November 25, 2021, 07:49:24 PM GMT+3, Peter Freddolino wrote: =20 =20 Dear Alexey,I think the problem is that this script was written under the = assumption that you're operating at a residue level, and thus, that there a= ren't repeated residue entries in the second argument to rmsd_residue_over_= time (given the function name, one would not expect the user to give multip= le atoms from the same residue in the function argument). If such entries d= o exist, it is going to behave oddly because the loops in that function act= over the list of residues passed will then be repeatedly adding to the res= idue level rmsd, and then dividing by it. Now, that script *should* have be= en written defensively and passed the residue id list through [lsort -uniqu= e ...] prior to acting on it, but as it is, there is a clear deviation in y= our input from what the function is expecting.Best,Peter On Thu, Nov 25, 2021 at 4:02 AM Alexei Rossokhin wrote: Dear NAMD users, While browsing the NAMD tutorial I found the residue_rmsd.= tcl script to calculate RMSD for individual residues. When I tried to run i= t, the results puzzled me a little.=20 When I used the selection "protein and chain A and resid 174 and name CA an= d noh" for my MD calculations I got the following result RMSD of residue 174 is 1.3978458595465855 =C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.3978458595465855 When I used the selection "protein and chain A and resid 174 and name CA CB= CG CD and noh" I got the following result RMSD of residue 174 is 5.591383438186342 RMSD of residue 174 is 0.022276428040583034 RMSD of residue 174 is 8.875070932503201e-5 RMSD of residue 174 is 3.535884833666614e-7 =C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.4034372426311832 Using "protein and chain A and resid 174 and name CB and noh" I got=20 RMSD of residue 174 is 1.3978458595465855 =C2=A0Average rmsd per residue:=C2=A0=C2=A0 1.3978458595465855 If to run the script separately for CA or CB=C2=A0 result is the same. If t= o run the script with the selection "name CA CB CG CD", the result for indi= vidual atoms is strange, although the average is close in all cases.=20 What does it mean,=C2=A0 any bug in the script?Thank you for help. Alexey PS I attached the residue_rmsd.tcl script. =20 ------=_Part_5591865_711051806.1637912167281 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Peter, thanks for your answer.
When I first ran this script, I was surprised that when choo= sing the selection as  "protein" (without specifying any atom), the sc= ript runs over all atoms in the residues, and these calculations are wrong,= as I showed in the previous letter. Thus, it seems that some atom should still be specified in s= election, for example, "protein and alpha", and in that case  the scri= pt works correctly. I = have just started to learn the tcl language and do not understand all the d= etails. Could you plea= se point me to which operators in the script<= /span> operate with the name of the atom.
Thanks, Alexey
 
<= /div>

=20
=20
On Thursday, November 25, 2021, 07:49:24 PM GMT+3, Pete= r Freddolino <petefred@umich.edu> wrote:


Dear Alexey,
I think the problem is th= at this script was written under the assumption that you're operating at a = residue level, and thus, that there aren't repeated residue entries in the = second argument to rmsd_residue_over_time (given the function name, one wou= ld not expect the user to give multiple atoms from the same residue in the = function argument). If such entries do exist, it is going to behave oddly b= ecause the loops in that function act over the list of residues passed will= then be repeatedly adding to the residue level rmsd, and then dividing by = it. Now, that script *should* have been written defensively and passed the = residue id list through [lsort -unique ...] prior to acting on it, but as i= t is, there is a clear deviation in your input from what the function is ex= pecting.
Best,
Peter

On T= hu, Nov 25, 2021 at 4:02 AM Alexei Rossokhin <alr= ossokhin@remove_yahoo.com> wrote:
Dear NAMD users,
While bro= wsing the NAMD tutorial I found the residue_rmsd.tcl script to= calculate RMSD for individual residues. When I tried to run it, the = results puzzled me a little.

When I used the selecti= on "protein and chain A and resid 174 and name CA and noh" for my MD = calculations I got the following result

RMSD of residue 174 is 1.397845859= 5465855
 Average rmsd per residue:   1.397= 8458595465855

When I us= ed the selection "protein and chain A and resid 174 and name CA= CB CG CD and noh" I got the following result

RMSD of residue 174 is 5.591383438186342
RMSD of residue 174 is 0.022276428040583034
RMSD of r= esidue 174 is 8.875070932503201e-5
RMSD of residue 174 is= 3.535884833666614e-7
 Average rmsd per residue:&nbs= p;  1.4034372426311832

Using "protein and chain A and resid 174 and name CB= and noh" I got

RMSD o= f residue 174 is 1.3978458595465855
 Average rmsd pe= r residue:   1.3978458595465855

If to run the script separately for CA or C= B  result is the same. If to run the script with the selection <= span>"name CA CB CG CD", the result for in= dividual atoms is strange, although the average is close in all cases.

What does it mean,  any bug in the script?
Thank you for help.

Alexey

PS I attached the residue_rmsd.tcl script.
=

------=_Part_5591865_711051806.1637912167281-- From owner-namd-l@halifax.ks.uiuc.edu Mon Nov 29 06:31:18 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ATCVIPv000398; Mon, 29 Nov 2021 06:31:18 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ATCVIRW000396; Mon, 29 Nov 2021 06:31:18 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ATCVHJm000392; Mon, 29 Nov 2021 06:31:17 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1ATCVH93000391; Mon, 29 Nov 2021 06:31:17 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1ATCV4Hr000362 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT); Mon, 29 Nov 2021 06:31:04 -0600 (CST) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AT5Q3oo009688; Mon, 29 Nov 2021 12:31:03 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0a-00007101.pphosted.com with ESMTP id 3ckdenwak0-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Mon, 29 Nov 2021 12:31:03 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id B57741E419BB; Mon, 29 Nov 2021 13:31:00 +0100 (CET) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id oBLhPL024p_V; Mon, 29 Nov 2021 13:30:59 +0100 (CET) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 59FBA1E419C2; Mon, 29 Nov 2021 13:30:59 +0100 (CET) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id g_15cm9k2Or8; Mon, 29 Nov 2021 13:30:59 +0100 (CET) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id D32A51E419BB; Mon, 29 Nov 2021 13:30:58 +0100 (CET) Date: Mon, 29 Nov 2021 13:30:58 +0100 (CET) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: Yogesh Sharma Cc: vmd-l , NAMD list Message-ID: <1303753451.9060684.1638189058529.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: namd-l: Re: vmd-l: basic procedure for ABF-PMF calculation MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_92cf137b-9fbb-4e70-b428-43c678c2a511" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: vmd-l: basic procedure for ABF-PMF calculation Thread-Index: ham5pvQ4pSaqsKev54YVAPjpROntEw== X-Proofpoint-GUID: fh-QSaHLKWN4NKqhnGgFWFgDwcxXgnHt X-Proofpoint-ORIG-GUID: fh-QSaHLKWN4NKqhnGgFWFgDwcxXgnHt X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0bEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxscHREKQ1kXBxwdEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8bcRkbEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0xCB3t5S2JmYX1kHmRhW0JEbU1sfWxNbl1JUnJNRGJeEQpYXBcfBBoEGB4YBRsa BBsaGgQdBBseGBAbHhofGhEKXlkXcxhHU0MRCk1cFxsTHxEKTFoXbG1rTU0RCkxGF2xraxEKQk8 XaEBFSBgYfGtbehkRCkNaFxsTGQQeEwQYGR4EGBgbEQpCXhcbEQpEWBcYEQpESRcYEQpCRRdkWF xcTX5SSRtlSREKQk4XZU9+EkNpZlkcAWkRCkJMF3oSZ2lgWXlGQU9lEQpCbBdhEhJPT0xNf08eB REKQkAXbWtdQG1NWhxgZ3wRCk1eFxsRClpYFxgRCnlDF2tgSGcBXH9IQAFkEQpwZxdkTBlCZ0R8 Ekt9ARAZGhEKcGgXeloFSEV7b0JEARIQGRoRCnBoF3pTeGNMYQFsXUYSEBkaEQpwaBdsRk8aGmw aRwFhaBAZGhEKcGgXYEwbZm4fY21EHU4QGRoRCnBoF2x/e25FZXtLfHtIEBkaEQpwbBdmYBNkXE 0aZ096UBAZGhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxsRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 phishscore=0 spamscore=0 mlxscore=0 priorityscore=0 malwarescore=0 lowpriorityscore=0 clxscore=171 bulkscore=0 mlxlogscore=894 adultscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111290063 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_92cf137b-9fbb-4e70-b428-43c678c2a511 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Yogesh,=20 This is a question for the NAMD mailing list, I am cross-posting there.=20 The most important parameter here is probably fullSamples, which controls h= ow soon the biasing force is applied when a free energy gradient is measure= d. If this happens much faster than other degrees of freedom can relax, the= biasing force can be overestimated, and this will take a long time to rela= x, which can be monitored as the time it takes for the reverse transition t= o happen. So setting this parameter too low will increase the time to final= convergence.=20 Best,=20 J=C3=A9r=C3=B4me=20 ----- On 26 Nov 21, at 18:53, Yogesh Sharma wrote:= =20 > Hi users > I am trying to pull a ion through nanotubes. I was building on the NAMD > tutorial. i divided my tube in 3 parts But the PMF in each part is increa= sing > exponentially. considering force optimization i tried setting > lower/upperwallconstants from 1, 5, 10, 100 but still results are similar= --=_92cf137b-9fbb-4e70-b428-43c678c2a511-- From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 30 04:30:56 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUAUu8s013609; Tue, 30 Nov 2021 04:30:56 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AUAUuid013608; Tue, 30 Nov 2021 04:30:56 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUAUtbr013604; Tue, 30 Nov 2021 04:30:55 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AUAUtUZ013603; Tue, 30 Nov 2021 04:30:55 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUAUd87013594 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 30 Nov 2021 04:30:40 -0600 (CST) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AU8rIi4029762 for ; Tue, 30 Nov 2021 10:30:38 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=vlad.cojocaru@mpi-muenster.mpg.de Received: from tmailer.gwdg.de (tmailer.gwdg.de [134.76.10.23]) by mx0a-00007101.pphosted.com with ESMTP id 3cn36ypher-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 30 Nov 2021 10:30:38 +0000 Received: from excmbx-24.um.gwdg.de ([134.76.9.234] helo=email.gwdg.de) by mailer.gwdg.de with esmtp (GWDG Mailer) (envelope-from ) id 1ms0PD-0002AW-Un; Tue, 30 Nov 2021 11:30:35 +0100 Received: from [192.168.178.22] (10.250.9.199) by excmbx-24.um.gwdg.de (134.76.9.234) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P521) id 15.1.2375.17; Tue, 30 Nov 2021 11:30:35 +0100 Message-ID: Date: Tue, 30 Nov 2021 11:30:35 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.0.3 Content-Language: en-US To: NAMD From: Vlad Cojocaru Subject: namd-l: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Organization: MPI Muenster CC: HORIA-LEONARD BANCIU Content-Type: text/plain; charset="UTF-8"; format=flowed X-Originating-IP: [10.250.9.199] X-ClientProxiedBy: EXCMBX-13.um.gwdg.de (134.76.9.222) To excmbx-24.um.gwdg.de (134.76.9.234) X-Virus-Scanned: (clean) by clamav X-CLX-Response: 1TFkXGx0ZEQpMehcaEQpZRBdobGYFR1kZcgVJQxEKWFgXYk1gcnlNSRNPWWU RCnhOF2BfRF14RXlbcGZrEQp5TBdncHlGcFplZUVdTxEKQ0gXBx4fHBEKQ1kXBxgbGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGXEcHBAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdLYWUda1p1H31za0RiWGUHZWZGE3V5fnATSBJFZm5MaREKWFwXHwQaBBgeGAUb GgQbGhoEHQQbHhkQGx4aHxoRCl5ZF3MYHGJaEQpNXBcZGhIRCkxaF2hpTU1NEQpCTxdtSGBsXGB SHUd4ehEKQ1oXGxkeBB0cBBsaBBgZEQpCXhcbEQpESRcbEQpCRRdnR2JAYGNnTVBwaREKQk4XYF 9EXXhFeVtwZmsRCkJMF2JNYHJ5TUkTT1llEQpCbBdpS3obZB5fZ01BfhEKQkAXZG56BXhhQVofe loRCkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5Qxd6cE98YVIee39tbBEKcGgXY2lYGVxtSEEdeAEQ GRoRCnBoF2Zlbl9hSG9ARmBOEBkaEQpwaBdmYgF7bRMdHV5pXBAZGhEKcGgXemlOf0RpTRlzRFM QGRoRCnBoF2RmeH9jQExuWBJwEBkaEQpwfRdgGlJ7Y2BPXU9PZBAZGhEKcH8XZFAFWEltfklNTG wQGx4bEQpwXxd6QB5FXU9+SFpteBAZGhEKcGwXZFl8eh8SeH5IQW0QGRoRCm1+FxoRClhNF0sRI A== X-Proofpoint-ORIG-GUID: aKO7Ap_5WYAnHrO-OLl9_STZ9b8oLDfC X-CLX-Shades: MLX X-Proofpoint-GUID: aKO7Ap_5WYAnHrO-OLl9_STZ9b8oLDfC MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 malwarescore=0 adultscore=0 spamscore=0 bulkscore=0 suspectscore=0 mlxscore=0 clxscore=173 mlxlogscore=926 priorityscore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300059 X-Spam-Score: 0 X-Spam-OrigSender: vlad.cojocaru@mpi-muenster.mpg.de X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 1AUAUe86013595 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vlad Cojocaru Dear all, We submitted a proposal to run some extensive atomistic simulations with NAMD of systems ranging between 500 K to 2M atoms on a supercomputer with  Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path Full-Fat Tree interconnection. Apparently, our project may fail the technical evaluation because during our tests we did not achieve a 75 % parallel efficiency between 2 to 48 nodes (each node has 2 CPUs - 24 cores/CPU).  We have tested the NAMD 2.14 provided by default at the site and we do not know how this was built. Looking at the NAMD benchmarks available for the Frontera supercomputer (quite similar architecture if I understand it correctly but for larger systems), it seems we should definitely achieve with NAMD 2.15 (maybe even 2.14) much better performance and parallel efficiency up to 48/64 nodes on this architecture than we actually achieved in our tests. So, my reasoning is that probably the NAMD built by default was not really carefully optimized. I would appreciate if anyone who has experience with building and optimizing NAMD on such an architecture could recommend any compiler/MPI/configuration/options for building an NAMD with a better performance and parallel efficiency. If I have some clear ideas about how to optimize NAMD, maybe I could make the case for our project to not fail the technical evaluation. Thank you very much for any advice Best wishes Vlad -- Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Paw$ From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 30 05:15:01 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUBF11B015652; Tue, 30 Nov 2021 05:15:01 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AUBF1Sk015651; Tue, 30 Nov 2021 05:15:01 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUBF0A7015647; 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Tue, 30 Nov 2021 03:14:43 -0800 (PST) References: In-Reply-To: From: Axel Kohlmeyer Date: Tue, 30 Nov 2021 06:14:31 -0500 Message-ID: Subject: Re: namd-l: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree To: NAMD list , Vlad Cojocaru Cc: HORIA-LEONARD BANCIU Content-Type: multipart/alternative; boundary="0000000000000b3b2a05d1ffaad1" X-Proofpoint-ORIG-GUID: lijKzij6ozJ4BMar7bJlBfxPtkcaCkI4 X-Proofpoint-GUID: lijKzij6ozJ4BMar7bJlBfxPtkcaCkI4 X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIaEQpMehcZHhsRCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHHxscEQpDWRcHGxkfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwacRkTEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0ZDQGFQQ0AcRVBgHmhnS1gdSGBGaExSel5BSUtpQWMeEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGxAbHhofGhEKXlkXcxgcUmsRCk1cFxgTGREKTFoXfGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGw QeEhEKQl4XGxEKRF4XGBEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY 2t7E1h+Gl9eEQpCRRdgYEsZZkRjXl5QeBEKQk4XY1Nja3sTWH4aX14RCkJMF3pYa0xjZV1bBURw EQpCbBdmeG5+GGRlQRJYfxEKQkAXbmFOQ1pdQ2daQn8RCkJYF2dzZXNAbmFhTF1iEQpNXhcbEQp aWBcSEQp5QxdvAWZdBVIeelAZaBEKWUsXExwaHBEKcGcXZ1N+UkNjTkgZHVgQGRoRCnBoF3ppTn 9EaU0Zc0RTEB4SEQpwaBdkZnh/Y0BMblgScBAeEhEKcGgXbXISAVNtGXJOSFwQGRoRCnBoF2Zde kBcem9PcHxuEBkaEQpwaBdiZhJ6H01ie1NtXxAZGhEKcH0XYBhFGwFIGhMaeVIQGRoRCnB9F2FL RGYZYUZHSwV6EB4SEQpwfRdjX31ceEh/eWRFXxAZGhEKcH0XZXJ8cGtQUx1pe3IQGRoRCnB/F2h 6X2IeflsFZFIbEBMaEQpwXxdgExlmS05sTkVTexAeEhEKcH8XbURfRkVtfUh5GW4QGxgYEQpwXx drRksTeWhpbnwTeBATHhEKcH8XZFAFWEltfklNTGwQGxkaEQpwXxdjX31ceEh/eWRFXxAZGhEKc H8XYWZvWxpnZEJIHVsQGxsZEQpwXxdjYhJQSGN4H3xCfRASHREKcGwXYGlHZ2lSX39feEwQHBoR CnBMF21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 bulkscore=0 clxscore=180 phishscore=0 spamscore=0 mlxscore=0 adultscore=0 mlxlogscore=999 priorityscore=341 lowpriorityscore=0 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300065 domainage_hfrom=9606 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --0000000000000b3b2a05d1ffaad1 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Actually, if you optimize how NAMD is compiled better than the system provided executable, your parallel efficiency will go down. Please recall Amdahl's law: the parallel efficiency is determined by the relation of time spent on parallel execution and serial execution. A better optimized executable will spend even less time computing and thus have more parallel overhead. To get better parallel efficiency, you have to avoid or reduce all non parallel operations like output or use of features like Tcl scripting or make your computations more expensive by increasing the cutoff or the system size or make the executable slower by compiling a less optimized version. -- Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://go= o.gl/1wk0__;!!DZ3fjg!vTfAy2yEX2CbE-RC_oXIbJCP-TYotczi7lvqSPqNSBEGEfUDyM103t= 2gWOCxycm24A$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste, Italy On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru wrote: > Dear all, > > We submitted a proposal to run some extensive atomistic simulations with > NAMD of systems ranging between 500 K to 2M atoms on a supercomputer > with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path > Full-Fat Tree interconnection. > > Apparently, our project may fail the technical evaluation because during > our tests we did not achieve a 75 % parallel efficiency between 2 to 48 > nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD > 2.14 provided by default at the site and we do not know how this was > built. Looking at the NAMD benchmarks available for the Frontera > supercomputer (quite similar architecture if I understand it correctly > but for larger systems), it seems we should definitely achieve with NAMD > 2.15 (maybe even 2.14) much better performance and parallel efficiency > up to 48/64 nodes on this architecture than we actually achieved in our > tests. > > So, my reasoning is that probably the NAMD built by default was not > really carefully optimized. > > I would appreciate if anyone who has experience with building and > optimizing NAMD on such an architecture could recommend any > compiler/MPI/configuration/options for building an NAMD with a better > performance and parallel efficiency. If I have some clear ideas about > how to optimize NAMD, maybe I could make the case for our project to not > fail the technical evaluation. > > Thank you very much for any advice > > Best wishes > Vlad > > > > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru= __;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8= Paw$ > > > --0000000000000b3b2a05d1ffaad1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Actually, if you optimize how NAMD is compiled better tha= n the system provided executable, your parallel efficiency will go down. Pl= ease recall Amdahl's law: the parallel efficiency is determined by the = relation of time spent on parallel execution and serial execution.=C2=A0

=C2=A0A better= optimized executable will spend even less time computing and thus have mor= e parallel overhead.=C2=A0

To get better parallel efficiency, you have to avoid or reduce all non p= arallel operations like output or use of features like Tcl scripting or mak= e your computations more expensive by increasing the cutoff or the system s= ize or make the executable slower by compiling a less optimized version.=C2= =A0

--
Dr. A= xel Kohlmeyer akohlmey@gmail.com = http://goo.g= l/1wk0
College of Science & Technology, Temple University, Phila= delphia PA, USA
International Centre for Theoretical Physics, Trieste, I= taly

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mp= g.de> wrote:
Dear all,

We submitted a proposal to run some extensive atomistic simulations with NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD =
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD 2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-mue= nster.mpg.de
https://urld= efense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!ou= au8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Paw$


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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Something in addition to what Axel says (all of which is absolutely true, even the counter-intuitive part about making the single-node performance artificially slower to get through the bottom-most tier of technical review). One possible issue to look at is how the cluster's network is utilized by other users/applications. In a local cluster that I use, the InfiniBand network is also used by the nodes to access data storage and there are many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by design). So the InfiniBand network is constantly busy and does not necessarily offer very low latency for NAMD or other message-passing applications. Something that helped in that case was building Charm++ on top of the UCX library instead of IBverbs directly. I am wholly unfamiliar with the details of how UCX works, but in essence it provides better utilization of the network when the ratio of compute cores vs. network links is high. If the cluster's staff has a copy of UCX, try that. It wasn't easy to build, but it paid off specifically for those runs that were communication-bound. The main significant addition in 2.15 is the AVX-512 tiles algorithm, which would help with the most expensive Intel CPUs like those, but would also make the computation part faster with the caveat that Axel mentioned. Giacomo On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer wrote: > Actually, if you optimize how NAMD is compiled better than the system > provided executable, your parallel efficiency will go down. Please recall > Amdahl's law: the parallel efficiency is determined by the relation of ti= me > spent on parallel execution and serial execution. > > A better optimized executable will spend even less time computing and > thus have more parallel overhead. > > To get better parallel efficiency, you have to avoid or reduce all non > parallel operations like output or use of features like Tcl scripting or > make your computations more expensive by increasing the cutoff or the > system size or make the executable slower by compiling a less optimized > version. > > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!pwzY0TGjPpkoWGMl1spgzEGTqZiiPI6q5hqp2_Z40c3KK2cxBOkr= YzqiONt88a7OEw$=20 > > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste, Italy > > On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru < > vlad.cojocaru@mpi-muenster.mpg.de> wrote: > >> Dear all, >> >> We submitted a proposal to run some extensive atomistic simulations with >> NAMD of systems ranging between 500 K to 2M atoms on a supercomputer >> with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path >> Full-Fat Tree interconnection. >> >> Apparently, our project may fail the technical evaluation because during >> our tests we did not achieve a 75 % parallel efficiency between 2 to 48 >> nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD >> 2.14 provided by default at the site and we do not know how this was >> built. Looking at the NAMD benchmarks available for the Frontera >> supercomputer (quite similar architecture if I understand it correctly >> but for larger systems), it seems we should definitely achieve with NAMD >> 2.15 (maybe even 2.14) much better performance and parallel efficiency >> up to 48/64 nodes on this architecture than we actually achieved in our >> tests. >> >> So, my reasoning is that probably the NAMD built by default was not >> really carefully optimized. >> >> I would appreciate if anyone who has experience with building and >> optimizing NAMD on such an architecture could recommend any >> compiler/MPI/configuration/options for building an NAMD with a better >> performance and parallel efficiency. If I have some clear ideas about >> how to optimize NAMD, maybe I could make the case for our project to not >> fail the technical evaluation. >> >> Thank you very much for any advice >> >> Best wishes >> Vlad >> >> >> >> -- >> Vlad Cojocaru, PD (Habil.), Ph.D. >> ----------------------------------------------- >> Project Group Leader >> Department of Cell and Developmental Biology >> Max Planck Institute for Molecular Biomedicine >> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >> ----------------------------------------------- >> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >> >> >> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocar= u__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx= 8Paw$ >> >> >> --0000000000006e6a7505d202720e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Something in addition to what Axel says (= all of which is absolutely true, even the counter-intuitive part about maki= ng the single-node performance artificially slower to get through the botto= m-most tier of technical review).

One possible iss= ue to look at is=C2=A0how the cluster's network is utilized by other us= ers/applications.=C2=A0 In a local cluster that I use, the InfiniBand netwo= rk is also used by the nodes to access data storage and there are many othe= r users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-= parallel by design).=C2=A0 So the InfiniBand network is constantly busy and= does not necessarily offer very low latency for NAMD or other message-pass= ing applications.

Something that helped in that ca= se was building Charm++ on top of the UCX library instead of IBverbs direct= ly.=C2=A0 I am wholly unfamiliar with the details of how UCX works, but in = essence it provides better utilization of the network when the ratio of com= pute cores vs. network links is high.=C2=A0 If the cluster's staff has = a copy of UCX, try that.=C2=A0 It wasn't easy to build, but it paid off= specifically for those runs that were communication-bound.

<= /div>
The main significant addition in 2.15 is the AVX-512 tiles algori= thm, which would help with the most expensive Intel CPUs like those, but wo= uld also make the computation part faster with the caveat that Axel mention= ed.

Giacomo

On Tue, Nov 30, 2021 at 6:16 AM Axel Ko= hlmeyer <akohlmey@gmail.com>= ; wrote:
Actually, if you optimize how NAMD is compiled better than the s= ystem provided executable, your parallel efficiency will go down. Please re= call Amdahl's law: the parallel efficiency is determined by the relatio= n of time spent on parallel execution and serial execution.=C2=A0

=C2=A0A better opti= mized executable will spend even less time computing and thus have more par= allel overhead.=C2=A0

To= get better parallel efficiency, you have to avoid or reduce all non parall= el operations like output or use of features like Tcl scripting or make you= r computations more expensive by increasing the cutoff or the system size o= r make the executable slower by compiling a less optimized version.=C2=A0
--
Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo.gl/1w= k0
College of Science & Technology, Temple University, Philadelp= hia PA, USA
International Centre for Theoretical Physics, Trieste, Italy=

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojocaru@m= pi-muenster.mpg.de> wrote:
Dear all,

We submitted a proposal to run some extensive atomistic simulations with NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during our tests we did not achieve a 75 % parallel efficiency between 2 to 48 nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD =
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD 2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-mue= nster.mpg.de
https://urld= efense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!ou= au8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Paw$


--0000000000006e6a7505d202720e-- From owner-namd-l@halifax.ks.uiuc.edu Tue Nov 30 09:14:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUFEKPO021175; Tue, 30 Nov 2021 09:14:20 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AUFEKYR021174; Tue, 30 Nov 2021 09:14:20 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUFEJsU021170; Tue, 30 Nov 2021 09:14:19 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1AUFEJ6H021169; Tue, 30 Nov 2021 09:14:19 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1AUFE8oe021162 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 30 Nov 2021 09:14:09 -0600 (CST) Received: from pps.filterd (m0166257.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1AUD92s4028791 for ; Tue, 30 Nov 2021 15:14:08 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=vlad.cojocaru@mpi-muenster.mpg.de Received: from tmailer.gwdg.de (tmailer.gwdg.de [134.76.10.23]) by mx0a-00007101.pphosted.com with ESMTP id 3cn36yrj21-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 30 Nov 2021 15:14:08 +0000 Received: from excmbx-24.um.gwdg.de ([134.76.9.234] helo=email.gwdg.de) by mailer.gwdg.de with esmtp (GWDG Mailer) (envelope-from ) id 1ms4pZ-0005oA-SE; Tue, 30 Nov 2021 16:14:05 +0100 Received: from [192.168.178.22] (10.250.9.199) by excmbx-24.um.gwdg.de (134.76.9.234) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P521) id 15.1.2375.17; Tue, 30 Nov 2021 16:14:05 +0100 Content-Type: multipart/alternative; boundary="------------XNf3Vb50gExU39j0loyg0g6Z" Message-ID: <2919008c-ce4e-3fda-8a5b-6ef37e9d6af2@mpi-muenster.mpg.de> Date: Tue, 30 Nov 2021 16:14:04 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.0.3 Subject: Re: namd-l: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Content-Language: en-US To: Giacomo Fiorin , NAMD list , Axel Kohlmeyer References: From: Vlad Cojocaru Organization: MPI Muenster CC: HORIA-LEONARD BANCIU In-Reply-To: X-Originating-IP: [10.250.9.199] X-ClientProxiedBy: EXCMBX-04.um.gwdg.de (134.76.9.219) To excmbx-24.um.gwdg.de (134.76.9.234) X-Virus-Scanned: (clean) by clamav X-CLX-Response: 1TFkXGx0YEQpMehcaEQpZRBdobGYFR1kZcgVJQxEKWFgXYk1gcnlNSRNPWWU RCnhOF2BfRF14RXlbcGZrEQp5TBdncHlGcFplZUVdTxEKQ0gXBx8dExEKQ1kXBxsZHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsfGHEcHxAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdDW29ZQHltQWVLBxt6GmlOE2hMH059B2xnaRxuW2YHSxEKWFwXHwQaBBgeGAUb GgQbGhoEHQQbHhgQGx4aHxoRCl5ZF3MYAXhIEQpNXBceGRkRCkxaF3hpa01NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF2xraxEKQk8XbUhgbFxgUh1HeHoRCkNaFxsZHgQdHAQbGgQYGREKQl 4XGxEKRF4XGREKREkXGxEKQkUXZ0diQGBjZ01QcGkRCkJOF2BfRF14RXlbcGZrEQpCTBdiTWBye U1JE09ZZREKQmwXaUt6G2QeX2dNQX4RCkJAF25hTkNaXUNnWkJ/EQpCWBdnc2VzQG5hYUxdYhEK WlgXEhEKeUMXbwFmXQVSHnpQGWgRCnBnF2dTflJDY05IGR1YEB4SEQpwaBdtU2VwHXhtWgV6cxA ZGhEKcGgXYGdGTEtNH1J8YlwQGRoRCnBoF3pFRWEZWlxfRUBGEBkaEQpwaBdrZ19pUHlZR2VSfx AZGhEKcGgXa2BrBWwbZnxSTkAQGRoRCnB9F2AYRRsBSBoTGnlSEB4SEQpwfRdnS0xoTF97b1hFZ BAeEhEKcH0XYUxpThxLQ05ZXB0QHhIRCnB9F2FLRGYZYUZHSwV6EB4SEQpwfRdgGlJ7Y2BPXU9P ZBAZGhEKcGcXaENBbRJuXGdDTXkQGRoRCnB9F2NPfGtCf0t+fR1jEB4SEQpwfRdoY0dOWW5tQGR /fRAeEhEKcH0XZXJ8cGtQUx1pe3IQHhIRCnB/F2h6X2IeflsFZFIbEBsaHREKcF8XYBMZZktObE 5FU3sQHhIRCnB/F21EX0ZFbX1IeRluEBseGREKcF8Xa0ZLE3loaW58E3gQGxodEQpwfxdkUAVYS W1+SU1MbBAbGxsRCnBfF3pAHkVdT35IWm14EBkaEQpwfxdhZm9bGmdkQkgdWxAbGRkRCnBfF2Ni ElBIY3gffEJ9EBsaGxEKcGwXZFl8eh8SeH5IQW0QGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhc aEQpYTRdLESA= X-Proofpoint-ORIG-GUID: iqEsjSGkOa-1P0Cd9Bf5dW-FMC6DqL-a X-CLX-Shades: MLX X-Proofpoint-GUID: iqEsjSGkOa-1P0Cd9Bf5dW-FMC6DqL-a MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 malwarescore=0 adultscore=0 spamscore=0 bulkscore=0 suspectscore=0 mlxscore=0 clxscore=172 mlxlogscore=999 priorityscore=0 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300082 X-Spam-Score: 0 X-Spam-OrigSender: vlad.cojocaru@mpi-muenster.mpg.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Vlad Cojocaru --------------XNf3Vb50gExU39j0loyg0g6Z Content-Type: text/plain; charset="UTF-8"; format=flowed Content-Transfer-Encoding: Quoted-printable Thanks for your thoughts ! One thing that seemed weird during our tests on this site was that the=20 performance and parallel scaling rapidly degraded when using all 48=20 cores available per node (2 CPUs with 24 cores each) . We actually saw=20 negative scaling after as few as 16 nodes. Then, when using 47, 32, and=20 24 cores/node, we got better parallel efficiency to higher node count,=20 with the best efficiency obtained using just half of the core available=20 on each node (24). At the end, when running on 48 nodes, we achieved the=20 most ns/day when using 24 cores/node. However, the resources requested=20 in the project we needed to calculate using all 48 cores/node regardless=20 of how many we are actually using. I haven't experienced anything like this on other sites (similar=20 systems, same configuration files). Normally using all cores available=20 per node has always given the best performance. So, I am wondering=20 whether there is anything obvious that could explain such a behavior ? Best Vlad On 11/30/21 15:33, Giacomo Fiorin wrote: > Something in addition to what Axel says (all of which is absolutely=20 > true, even the counter-intuitive part about making the single-node=20 > performance artificially slower to get through the bottom-most tier of=20 > technical review). > > One possible issue to look at is=C2=A0how the cluster's network is utiliz= ed=20 > by other users/applications.=C2=A0 In a local cluster that I use, the=20 > InfiniBand network is also used by the nodes to access data storage=20 > and there are many other users processing MRI, cryo-EM or=20 > bioinformatics data (all embarrassingly-parallel by design).=C2=A0 So the= =20 > InfiniBand network is constantly busy and does not necessarily offer=20 > very low latency for NAMD or other message-passing applications. > > Something that helped in that case was building Charm++ on top of the=20 > UCX library instead of IBverbs directly.=C2=A0 I am wholly unfamiliar wit= h=20 > the details of how UCX works, but in essence it provides better=20 > utilization of the network when the ratio of compute cores vs. network=20 > links is high.=C2=A0 If the cluster's staff has a copy of UCX, try that.= =C2=A0=20 > It wasn't easy to build, but it paid off specifically for those runs=20 > that were communication-bound. > > The main significant addition in 2.15 is the AVX-512 tiles algorithm,=20 > which would help with the most expensive Intel CPUs like those, but=20 > would also make the computation part faster with the caveat that Axel=20 > mentioned. > > Giacomo > > On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer wrote: > > Actually, if you optimize how NAMD is compiled better than the > system provided executable, your parallel efficiency will go down. > Please recall Amdahl's law: the parallel efficiency is determined > by the relation of time spent on parallel execution and serial > execution. > > =C2=A0A better optimized executable will spend even less time computi= ng > and thus have more parallel overhead. > > To get better parallel efficiency, you have to avoid or reduce all > non parallel operations like output or use of features like Tcl > scripting or make your computations more expensive by increasing > the cutoff or the system size or make the executable slower by > compiling a less optimized version. > > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__htt= p://goo.gl/1wk0__;!!DZ3fjg!vqb8Aw2vjDMitJSEPbF74htFKf2mY9JVQk1mwfueoHqSLJz3= 6Td3erIQ1SNH2zl4Jw$=20 > > College of Science & Technology, Temple University, Philadelphia > PA, USA > International Centre for Theoretical Physics, Trieste, Italy > > On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru > wrote: > > Dear all, > > We submitted a proposal to run some extensive atomistic > simulations with > NAMD of systems ranging between 500 K to 2M atoms on a > supercomputer > with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel > Omni-path > Full-Fat Tree interconnection. > > Apparently, our project may fail the technical evaluation > because during > our tests we did not achieve a 75 % parallel efficiency > between 2 to 48 > nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested > the NAMD > 2.14 provided by default at the site and we do not know how > this was > built. Looking at the NAMD benchmarks available for the Frontera > supercomputer (quite similar architecture if I understand it > correctly > but for larger systems), it seems we should definitely achieve > with NAMD > 2.15 (maybe even 2.14) much better performance and parallel > efficiency > up to 48/64 nodes on this architecture than we actually > achieved in our > tests. > > So, my reasoning is that probably the NAMD built by default > was not > really carefully optimized. > > I would appreciate if anyone who has experience with building and > optimizing NAMD on such an architecture could recommend any > compiler/MPI/configuration/options for building an NAMD with a > better > performance and parallel efficiency. If I have some clear > ideas about > how to optimize NAMD, maybe I could make the case for our > project to not > fail the technical evaluation. > > Thank you very much for any advice > > Best wishes > Vlad > > > > --=20 > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/= cojocaru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5= uCvq0Gx8Paw$ > > > --=20 Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__= ;!!DZ3fjg!vqb8Aw2vjDMitJSEPbF74htFKf2mY9JVQk1mwfueoHqSLJz36Td3erIQ1SMxxRzYI= A$=20 --------------XNf3Vb50gExU39j0loyg0g6Z Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks for your thoughts !

One thing that seemed weird during our tests on this site was that the performance and parallel scaling rapidly degraded when using all 48 cores available per node (2 CPUs with 24 cores each) . We actually saw negative scaling after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we got better parallel efficiency to higher node count, with the best efficiency obtained using just half of the core available on each node (24). At the end, when running on 48 nodes, we achieved the most ns/day when using 24 cores/node. However, the resources requested in the project we needed to calculate using all 48 cores/node regardless of how many we are actually using.

I haven't experienced anything like this on other sites (similar systems, same configuration files). Normally using all cores available per node has always given the best performance. So, I am wondering whether there is anything obvious that could explain such a behavior ?

Best
Vlad

On 11/30/21 15:33, Giacomo Fiorin wrote:
Something in addition to what Axel says (all of which is absolutely true, even the counter-intuitive part about making the single-node performance artificially slower to get through the bottom-most tier of technical review).

One possible issue to look at is=C2=A0how the cluster's network is utilized by other users/applications.=C2=A0 In a local cluster that I use, the InfiniBand network is also used by the nodes to access data storage and there are many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by design).=C2=A0 So the InfiniBand netwo= rk is constantly busy and does not necessarily offer very low latency for NAMD or other message-passing applications.

Something that helped in that case was building Charm++ on top of the UCX library instead of IBverbs directly.=C2=A0 I am wholly unfamiliar with the details of how UCX works, but in essence it provides better utilization of the network when the ratio of compute cores vs. network links is high.=C2=A0 If the cluster's staff has a copy of UCX, try that.=C2=A0 It wasn't easy to build, but it paid off specifically for those runs that were communication-bound.

The main significant addition in 2.15 is the AVX-512 tiles algorithm, which would help with the most expensive Intel CPUs like those, but would also make the computation part faster with the caveat that Axel mentioned.

Giacomo

On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer <akoh= lmey@gmail.com> wrote:
Actually, if you optimize how NAMD is compiled better than the system provided executable, your parallel efficiency will go down. Please recall Amdahl's law: the parallel efficiency is determined by the relation of time spent on parallel execution and serial execution.=C2= =A0

=C2=A0A better optimized executable will spend even less time computing and thus have more parallel overhead.=C2=A0

To get better parallel efficiency, you have to avoid or reduce all non parallel operations like output or use of features like Tcl scripting or make your computations more expensive by increasing the cutoff or the system size or make the executable slower by compiling a less optimized version.=C2=A0

--
Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo= .gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojocaru@mpi-muenste= r.mpg.de> wrote:
Dear all,

We submitted a proposal to run some extensive atomistic simulations with
NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path
Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during
our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD
2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not
fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
= https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__= ;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Pa= w$



--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.=
de/43241/cojocaru
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boundary="000000000000f8d35c05d2033bf0" X-Proofpoint-ORIG-GUID: aip_BhW6CvbXwS-cCASi4RZow5pDwJtV X-Proofpoint-GUID: aip_BhW6CvbXwS-cCASi4RZow5pDwJtV X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBgSEQpMehcZGRwRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHhIcEQpDWRcHGxkfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGBoScRsYGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdLQ1p1aEJ9HGlcSHJdeQdJaWt5Qx54cEVdH1puXWBefBEKWFwXHwQaBBge GAUbGgQbGxoEHQQbGRsQGx4aHxoRCl5ZF3MYAU1BEQpNXBcYHRoRCkxaF3tpa01NEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XYVkceRhIBRIbQngRCkNaFxgaEwQSHwQYGx MEGx0cEQpCXhcbEQpESRcZEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2xlQFJLG3JleU5NEQpCThdjU2NrexNYfhpfXhEKQkwXZ11bch1ubE9YeGARCkJs F2FfelMZQ0Qaeht+EQpCQBduYU5DWl1DZ1pCfxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxI RCnlDF28BZl0FUh56UBloEQpZSxcTHBocEQpwZxdnU35SQ2NOSBkdWBAdGhEKcGgXemgeWHhJb2 lpZVAQGhEKcGgXZkVnG0dbHhlGfwEQGRoRCnBoF2VjRWN6GUZpG3NJEBoRCnBoF3pFRWEZWlxfR UBGEBoRCnBoF2RmbHtPQ1gdWFN7EBkaEQpwfRdgGEUbAUgaExp5UhAeEhEKcH0XZ0tMaExfe29Y RWQQHhIRCnB9F2FMaU4cS0NOWVwdEBkaEQpwfRdhS0RmGWFGR0sFehAdEhEKcH0XYBpSe2NgT11 PT2QQGhEKcH0XY098a0J/S359HWMQHhIRCnB9F2hjR05Zbm1AZH99EB4SEQpwfRdlcnxwa1BTHW l7chAcGhEKcH0XY199XHhIf3lkRV8QGRoRCnB/F2h6X2IeflsFZFIbEBMYEQpwXxdgExlmS05sT kVTexAcGhEKcH8XbURfRkVtfUh5GW4QGx4ZEQpwXxdrRksTeWhpbnwTeBAbGhMRCnB/F2RQBVhJ bX5JTUxsEBsZHBEKcF8XekAeRV1PfkhabXgQGhEKcH8XYWZvWxpnZEJIHVsQGxkcEQpwXxdjYhJ QSGN4H3xCfRAbGhkRCnBfF2NffVx4SH95ZEVfEBkaEQpwbBdmH3tYXGIFS1hkHxAZGhEKcEwXbW hlGUFSfXsYRVIQHhIRCm1+FxsRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 bulkscore=0 clxscore=228 phishscore=0 spamscore=0 mlxscore=0 adultscore=0 mlxlogscore=999 priorityscore=336 lowpriorityscore=0 impostorscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300082 domainage_hfrom=9606 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000f8d35c05d2033bf0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Check that the build is not an "SMP" one, for which Charm++ would require dedicated communication threads, so you'd need fewer than all the cores. Other than that, you're dealing with a cluster where probably more money was spent on the CPUs than on the networking hardware. This translates into additional work for you and the staff to try and figure out ways for the network to keep up with the CPUs, and minimize latency. Giacomo On Tue, Nov 30, 2021 at 10:14 AM Vlad Cojocaru < vlad.cojocaru@mpi-muenster.mpg.de> wrote: > Thanks for your thoughts ! > > One thing that seemed weird during our tests on this site was that the > performance and parallel scaling rapidly degraded when using all 48 cores > available per node (2 CPUs with 24 cores each) . We actually saw negative > scaling after as few as 16 nodes. Then, when using 47, 32, and 24 > cores/node, we got better parallel efficiency to higher node count, with > the best efficiency obtained using just half of the core available on each > node (24). At the end, when running on 48 nodes, we achieved the most > ns/day when using 24 cores/node. However, the resources requested in the > project we needed to calculate using all 48 cores/node regardless of how > many we are actually using. > > I haven't experienced anything like this on other sites (similar systems, > same configuration files). Normally using all cores available per node has > always given the best performance. So, I am wondering whether there is > anything obvious that could explain such a behavior ? > > Best > Vlad > > On 11/30/21 15:33, Giacomo Fiorin wrote: > > Something in addition to what Axel says (all of which is absolutely true, > even the counter-intuitive part about making the single-node performance > artificially slower to get through the bottom-most tier of technical > review). > > One possible issue to look at is how the cluster's network is utilized by > other users/applications. In a local cluster that I use, the InfiniBand > network is also used by the nodes to access data storage and there are ma= ny > other users processing MRI, cryo-EM or bioinformatics data (all > embarrassingly-parallel by design). So the InfiniBand network is > constantly busy and does not necessarily offer very low latency for NAMD = or > other message-passing applications. > > Something that helped in that case was building Charm++ on top of the UCX > library instead of IBverbs directly. I am wholly unfamiliar with the > details of how UCX works, but in essence it provides better utilization of > the network when the ratio of compute cores vs. network links is high. If > the cluster's staff has a copy of UCX, try that. It wasn't easy to build, > but it paid off specifically for those runs that were communication-bound. > > The main significant addition in 2.15 is the AVX-512 tiles algorithm, > which would help with the most expensive Intel CPUs like those, but would > also make the computation part faster with the caveat that Axel mentioned. > > Giacomo > > On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer wrote: > >> Actually, if you optimize how NAMD is compiled better than the system >> provided executable, your parallel efficiency will go down. Please recall >> Amdahl's law: the parallel efficiency is determined by the relation of t= ime >> spent on parallel execution and serial execution. >> >> A better optimized executable will spend even less time computing and >> thus have more parallel overhead. >> >> To get better parallel efficiency, you have to avoid or reduce all non >> parallel operations like output or use of features like Tcl scripting or >> make your computations more expensive by increasing the cutoff or the >> system size or make the executable slower by compiling a less optimized >> version. >> >> -- >> Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http:/= /goo.gl/1wk0__;!!DZ3fjg!oreWcmssSlgO61lkAjMQkPaGX2SRSyT7ZWuzlehZ_QveMPKQeLx= R0obUOeEzNDQk6g$=20 >> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste, Italy >> >> On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru < >> vlad.cojocaru@mpi-muenster.mpg.de> wrote: >> >>> Dear all, >>> >>> We submitted a proposal to run some extensive atomistic simulations with >>> NAMD of systems ranging between 500 K to 2M atoms on a supercomputer >>> with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path >>> Full-Fat Tree interconnection. >>> >>> Apparently, our project may fail the technical evaluation because during >>> our tests we did not achieve a 75 % parallel efficiency between 2 to 48 >>> nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD >>> 2.14 provided by default at the site and we do not know how this was >>> built. Looking at the NAMD benchmarks available for the Frontera >>> supercomputer (quite similar architecture if I understand it correctly >>> but for larger systems), it seems we should definitely achieve with NAMD >>> 2.15 (maybe even 2.14) much better performance and parallel efficiency >>> up to 48/64 nodes on this architecture than we actually achieved in our >>> tests. >>> >>> So, my reasoning is that probably the NAMD built by default was not >>> really carefully optimized. >>> >>> I would appreciate if anyone who has experience with building and >>> optimizing NAMD on such an architecture could recommend any >>> compiler/MPI/configuration/options for building an NAMD with a better >>> performance and parallel efficiency. If I have some clear ideas about >>> how to optimize NAMD, maybe I could make the case for our project to not >>> fail the technical evaluation. >>> >>> Thank you very much for any advice >>> >>> Best wishes >>> Vlad >>> >>> >>> >>> -- >>> Vlad Cojocaru, PD (Habil.), Ph.D. >>> ----------------------------------------------- >>> Project Group Leader >>> Department of Cell and Developmental Biology >>> Max Planck Institute for Molecular Biomedicine >>> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >>> ----------------------------------------------- >>> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >>> >>> >>> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojoca= ru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0G= x8Paw$ >>> >>> >>> > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de= /43241/cojocaru > > --000000000000f8d35c05d2033bf0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Check that the build is not an "SMP" one, for wh= ich Charm++ would require dedicated communication threads, so you'd nee= d fewer than all the cores.

Other than that, you're = dealing with a cluster where probably more money was spent on the CPUs than= on the networking hardware.=C2=A0 This translates into additional work for= you and the staff to try and figure out ways for the network to keep up wi= th the CPUs, and minimize latency.

Giacomo

On= Tue, Nov 30, 2021 at 10:14 AM Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de> wrote:=
=20=20 =20=20=20=20 =20=20
Thanks for your thoughts !

One thing that seemed weird during our tests on this site was that the performance and parallel scaling rapidly degraded when using all 48 cores available per node (2 CPUs with 24 cores each) . We actually saw negative scaling after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we got better parallel efficiency to higher node count, with the best efficiency obtained using just half of the core available on each node (24). At the end, when running on 48 nodes, we achieved the most ns/day when using 24 cores/node. However, the resources requested in the project we needed to calculate using all 48 cores/node regardless of how many we are actually using.

I haven't experienced anything like this on other sites (similar systems, same configuration files). Normally using all cores available per node has always given the best performance. So, I am wondering whether there is anything obvious that could explain such a behavior ?

Best
Vlad

On 11/30/21 15:33, Giacomo Fiorin wrote:
=20=20=20=20=20=20
Something in addition to what Axel says (all of which is absolutely true, even the counter-intuitive part about making the single-node performance artificially slower to get through the bottom-most tier of technical review).

One possible issue to look at is=C2=A0how the cluster's ne= twork is utilized by other users/applications.=C2=A0 In a local cluster that I use, the InfiniBand network is also used by the nodes to access data storage and there are many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by design).=C2=A0 So the InfiniBand netwo= rk is constantly busy and does not necessarily offer very low latency for NAMD or other message-passing applications.

Something that helped in that case was building Charm++ on top of the UCX library instead of IBverbs directly.=C2=A0 I am wholly unfamiliar with the details of how UCX works, but in essence it provides better utilization of the network when the ratio of compute cores vs. network links is high.=C2=A0 If the cluster's staff has a copy of UCX, try that.=C2=A0 It wasn= 9;t easy to build, but it paid off specifically for those runs that were communication-bound.

The main significant addition in 2.15 is the AVX-512 tiles algorithm, which would help with the most expensive Intel CPUs like those, but would also make the computation part faster with the caveat that Axel mentioned.

Giacomo

On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer <akohlmey@gmail.com> wrote:
Actually, if you optimize how NAMD is compiled better than the system provided executable, your parallel efficiency will go down. Please recall Amdahl's law: the parallel efficiency is determined by the relation of time spent on parallel execution and serial execution.=C2= =A0

=C2=A0A better optimized executable will spend even less time computing and thus have more parallel overhead.=C2=A0

To get better parallel efficiency, you have to avoid or reduce all non parallel operations like output or use of features like Tcl scripting or make your computations more expensive by increasing the cutoff or the system size or make the executable slower by compiling a less optimized version.=C2=A0

--
Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de&g= t; wrote:
Dear all,
We submitted a proposal to run some extensive atomistic simulations with
NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path
Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during
our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD
2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not
fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojoca= ru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0G= x8Paw$



--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojoc=
aru
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boundary="000000000000dd4edb05d203844c" X-Proofpoint-GUID: _06-E2T_0Ix6alchbgXD6U1VXgmwbB9l X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: _06-E2T_0Ix6alchbgXD6U1VXgmwbB9l X-CLX-Response: 1TFkXGxIfEQpMehcZHxsRCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGBMbEQpDWRcHGxkfEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwfcR4eEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3UaHAdvGH51GmNSHEtGSUJITXJuHH8bfHJNR11IaBNGEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXcxgBUFkRCk1cFxkcGREKTFoXe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGw QeExEKQl4XGxEKREkXGREKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdgYEsZZkRjXl5QeBEKQk4XY1Nja3sTWH4aX14RCkJMF3pYa0xjZV1bBURwEQpCbBdm eG5+GGRlQRJYfxEKQkAXbmFOQ1pdQ2daQn8RCkJYF2dzZXNAbmFhTF1iEQpaWBccEQp5QxdvAWZ dBVIeelAZaBEKWUsXExwaHBEKcGcXZ1N+UkNjTkgZHVgQHRoRCnBoF2RaeXNofGUSBRlzEBkaEQ pwaBdnRnxcZk0BRx1LGRAZGhEKcGgXbUkbbHlCRmBfbF0QGRoRCnBoF2RAHhhPc2xkQ0N6EBkaE QpwaBdsUl5QQk1tQEhEbxAZGhEKcH0XYBhFGwFIGhMaeVIQHBoRCnB9F2dLTGhMX3tvWEVkEB0a EQpwfRdhTGlOHEtDTllcHRAdGhEKcH0XYUtEZhlhRkdLBXoQHRoRCnB9F2AaUntjYE9dT09kEBw aEQpwfxdoel9iHn5bBWRSGxAbGh0RCnBfF2ATGWZLTmxORVN7EBwaEQpwfxdtRF9GRW19SHkZbh AbHh0RCnBfF2tGSxN5aGlufBN4EBsaHhEKcH8XZFAFWEltfklNTGwQGxsfEQpwXxd6QB5FXU9+S FpteBAcGhEKcGwXYGlHZ2lSX39feEwQHhIRCnBMF21oZRlBUn17GEVSEB4SEQptfhcaEQpYTRdL ESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 impostorscore=0 bulkscore=0 spamscore=0 clxscore=185 priorityscore=351 lowpriorityscore=0 phishscore=0 malwarescore=0 mlxlogscore=999 suspectscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300083 domainage_hfrom=9606 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --000000000000dd4edb05d203844c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Vlad, a few more comments and a possible explanation for your observations. First off, it is **very** important to understand the parallelization approach used in NAMD. Unlike most parallel scientific applications, NAMD uses a more abstract parallelization scheme by running on top of the charm++ library (which may be using different modes of communication for exchanging messages between CPU cores). With plain MPI and MPI+OpenMP parallelization, an MD system is decomposed into subdomains matching the number of MPI ranks (with threads optionally on top of that) and the number of MPI ranks and threads per rank determining how this is done. The MD loop then progresses mostly as if this was a serial execution and then inserts communication where necessary. This allows for rather low communication overhead but introduces synchronization points which can interfere with strong parallel scaling. With charm++, however, you parallelize into a "virtual parallel machine" with an (essentially arbitrarily) chosen number of "parallel compute units". This is also referred to as over-parallelization. While this adds some overhead, it facilitates the superior ability of NAMD to do load balancing and hiding of communication overhead by overlapping communication of completed work units while working on others. This works very well when the number of physical nodes remains small to moderate, but becomes a problem when you have many tasks. In that case the ability to hide communication overhead is diminished since there is little work left to hide behind. This is where the "twoaway" options can help because they make the subdomains smaller and thus create more work units. That will increase the overhead somewhat, but that is usually overcompensated by the gains in load balance and communication hiding. That is until you reach the limit of parallel scaling. Unlike with MPI based MD codes, which using too many nodes will only introduce a moderate overhead, NAMD's performance will drop dramatically when using too many CPU cores for a given system and its decomposition. Now about the lack of performance when using all CPU cores per node. This is not uncommon for regular Linux clusters. There are multiple possible explanations: - The fact that using 47 cores per node instead of 48 cores is almost always due to what is called "OS Jitter" or "OS Overhead". This means, there are other processes running on the compute nodes and they also need to occupy the CPU occasionally. The scheduler in the kernel will try to balance those to give all a "fair chance" to doing their job, but that can often lead to bouncing process between CPU cores (and thus requiring invalidating/refreshing CPU caches). This can be alleviated by using processor and memory affinity, but if one CPU core is **not** used by the application, that can significantly improve the situation since al OS and kernel processes will be bounced by the scheduler to run on that one CPU core while the remaining can be dedicated to the attached compute processes - With a large number of CPU cores per node, the available memory bandwidth is shared and caches are also shared. That can be rather severe for applications requiring a lot of reading and writing to memory like quantum chemical calculations. For MD the consideration of the cache size is more relevant. If you reduce the number of tasks per node to half, each has effectively double the CPU cache available and if your compute kernel has memory requirements that are under/over that threshold for the problem at hand, you may see a significant in per CPU core performance. - With a large number of CPU cores per node, the communication bandwidth becomes a scarce resource that can be performance limiting, especially when there are other users of the communication like a parallel file system and when the communication bandwidth is limited due to the technology used. The considerations are similar to those for memory bandwidth. In this case careful benchmarking of the different communication options that NAMD offers (either within the same binary or due to different compilation settings where you could have a dedicated communication process/thread). What also can make a difference is how individual nodes are placed/allocated by the job scheduler and what the so-called bisection bandwidth of the high-speed network of the cluster is. This latter option requires working with the cluster system managers to figure out the optimal settings for the hardware in question. On Tue, Nov 30, 2021 at 10:14 AM Vlad Cojocaru < vlad.cojocaru@mpi-muenster.mpg.de> wrote: > Thanks for your thoughts ! > > One thing that seemed weird during our tests on this site was that the > performance and parallel scaling rapidly degraded when using all 48 cores > available per node (2 CPUs with 24 cores each) . We actually saw negative > scaling after as few as 16 nodes. Then, when using 47, 32, and 24 > cores/node, we got better parallel efficiency to higher node count, with > the best efficiency obtained using just half of the core available on each > node (24). At the end, when running on 48 nodes, we achieved the most > ns/day when using 24 cores/node. However, the resources requested in the > project we needed to calculate using all 48 cores/node regardless of how > many we are actually using. > > I haven't experienced anything like this on other sites (similar systems, > same configuration files). Normally using all cores available per node has > always given the best performance. So, I am wondering whether there is > anything obvious that could explain such a behavior ? > > Best > Vlad > > On 11/30/21 15:33, Giacomo Fiorin wrote: > > Something in addition to what Axel says (all of which is absolutely true, > even the counter-intuitive part about making the single-node performance > artificially slower to get through the bottom-most tier of technical > review). > > One possible issue to look at is how the cluster's network is utilized by > other users/applications. In a local cluster that I use, the InfiniBand > network is also used by the nodes to access data storage and there are ma= ny > other users processing MRI, cryo-EM or bioinformatics data (all > embarrassingly-parallel by design). So the InfiniBand network is > constantly busy and does not necessarily offer very low latency for NAMD = or > other message-passing applications. > > Something that helped in that case was building Charm++ on top of the UCX > library instead of IBverbs directly. I am wholly unfamiliar with the > details of how UCX works, but in essence it provides better utilization of > the network when the ratio of compute cores vs. network links is high. If > the cluster's staff has a copy of UCX, try that. It wasn't easy to build, > but it paid off specifically for those runs that were communication-bound. > > The main significant addition in 2.15 is the AVX-512 tiles algorithm, > which would help with the most expensive Intel CPUs like those, but would > also make the computation part faster with the caveat that Axel mentioned. > > Giacomo > > On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer wrote: > >> Actually, if you optimize how NAMD is compiled better than the system >> provided executable, your parallel efficiency will go down. Please recall >> Amdahl's law: the parallel efficiency is determined by the relation of t= ime >> spent on parallel execution and serial execution. >> >> A better optimized executable will spend even less time computing and >> thus have more parallel overhead. >> >> To get better parallel efficiency, you have to avoid or reduce all non >> parallel operations like output or use of features like Tcl scripting or >> make your computations more expensive by increasing the cutoff or the >> system size or make the executable slower by compiling a less optimized >> version. >> >> -- >> Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http:/= /goo.gl/1wk0__;!!DZ3fjg!sBsOUMUE8RdbXjZzrvM8sQK3Kfkf-4m6P9MyTEAFTej2RoK3Fdc= h2D_AbLc__nB4xw$=20 >> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste, Italy >> >> On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru < >> vlad.cojocaru@mpi-muenster.mpg.de> wrote: >> >>> Dear all, >>> >>> We submitted a proposal to run some extensive atomistic simulations with >>> NAMD of systems ranging between 500 K to 2M atoms on a supercomputer >>> with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path >>> Full-Fat Tree interconnection. >>> >>> Apparently, our project may fail the technical evaluation because during >>> our tests we did not achieve a 75 % parallel efficiency between 2 to 48 >>> nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD >>> 2.14 provided by default at the site and we do not know how this was >>> built. Looking at the NAMD benchmarks available for the Frontera >>> supercomputer (quite similar architecture if I understand it correctly >>> but for larger systems), it seems we should definitely achieve with NAMD >>> 2.15 (maybe even 2.14) much better performance and parallel efficiency >>> up to 48/64 nodes on this architecture than we actually achieved in our >>> tests. >>> >>> So, my reasoning is that probably the NAMD built by default was not >>> really carefully optimized. >>> >>> I would appreciate if anyone who has experience with building and >>> optimizing NAMD on such an architecture could recommend any >>> compiler/MPI/configuration/options for building an NAMD with a better >>> performance and parallel efficiency. If I have some clear ideas about >>> how to optimize NAMD, maybe I could make the case for our project to not >>> fail the technical evaluation. >>> >>> Thank you very much for any advice >>> >>> Best wishes >>> Vlad >>> >>> >>> >>> -- >>> Vlad Cojocaru, PD (Habil.), Ph.D. >>> ----------------------------------------------- >>> Project Group Leader >>> Department of Cell and Developmental Biology >>> Max Planck Institute for Molecular Biomedicine >>> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >>> ----------------------------------------------- >>> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >>> >>> >>> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojoca= ru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0G= x8Paw$ >>> >>> >>> > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de= /43241/cojocaru > > --=20 Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!sBsOUMUE8RdbXjZzrvM8sQK3Kfkf-4m6P9MyTEAFTej2RoK3Fdch= 2D_AbLc__nB4xw$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. --000000000000dd4edb05d203844c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Vlad,

a few more comments and a possible explanation for your ob= servations.

First off, it is **very** important to understand the parallel= ization approach used in NAMD. Unlike most parallel scientific applications= , NAMD uses a more abstract parallelization scheme by running on top of the= charm++ library (which may be using different modes of communication for e= xchanging messages between CPU cores). With plain MPI and MPI+OpenMP parall= elization, an MD system is decomposed into subdomains matching the number o= f MPI ranks (with threads optionally on top of that) and the number of MPI = ranks and threads per rank determining how this is done. The MD loop then p= rogresses mostly as if this was a serial execution and then inserts communi= cation where necessary. This allows for rather low communication overhead b= ut introduces synchronization points which can interfere with strong parall= el scaling.
With charm++, however, you parallelize into a "virtual paral= lel machine" with an (essentially arbitrarily) chosen number of "= parallel compute units". This is also referred to as over-parallelizat= ion. While this adds some overhead, it facilitates the superior=C2=A0abilit= y of NAMD to do load balancing and hiding of communication overhead by over= lapping communication of completed work units while working on others. This= works very well when the number of physical nodes remains small to moderat= e, but becomes a problem when you have many tasks. In that case the ability= to hide communication overhead is diminished since there is little work le= ft to hide behind. This is where the "twoaway" options can help b= ecause they make the subdomains smaller and thus create more work units. Th= at will increase the overhead somewhat, but that is usually overcompensated= by the gains in load balance and communication hiding. That is until you r= each the limit of parallel scaling. Unlike with MPI based MD codes, which u= sing too many nodes will only introduce a moderate overhead, NAMD's per= formance will drop dramatically when using too many CPU cores for a given s= ystem and its decomposition.

Now about the lack of performance when using = all CPU cores per node. This is not uncommon for regular Linux clusters. Th= ere are multiple possible explanations:
- The fact that using 47 cores per no= de instead of 48 cores is almost always due to what is called "OS Jitt= er" or "OS Overhead". This means, there are other processes = running on the compute nodes and they also need to occupy the CPU occasiona= lly. The scheduler in the kernel will try to balance those to give all a &q= uot;fair chance" to doing their job, but that can often lead to bounci= ng process between CPU cores (and thus requiring invalidating/refreshing CP= U caches). This can be alleviated by using processor and memory affinity, b= ut if one CPU core is **not** used by the application, that can significant= ly improve the situation since al OS and kernel processes will be bounced b= y the scheduler to run on that one CPU core while the remaining can be dedi= cated to the attached compute processes
- With a large number of CPU cores pe= r node, the available memory bandwidth is shared and caches are also shared= . That can be rather severe for applications requiring a lot of reading and= writing to memory like quantum chemical calculations. For MD the considera= tion of the cache size is more relevant. If you reduce the number of tasks = per node to half, each has effectively double the CPU cache available and i= f your compute kernel has memory requirements that are under/over that thre= shold for the problem at hand, you may see a significant in per CPU core pe= rformance.
- With a large number of CPU cores per node, the communication ban= dwidth becomes a scarce resource that can be performance limiting, especial= ly when there are other users of the communication like a parallel file sys= tem and when the communication bandwidth is limited due to the technology u= sed. The considerations are similar to those for memory bandwidth. In this = case careful benchmarking of the different communication options that NAMD = offers (either within the same binary or due to different compilation setti= ngs where you could have a dedicated communication process/thread). What al= so can make a difference is how individual nodes are placed/allocated by th= e job scheduler and what the so-called bisection bandwidth of the high-spee= d network of the cluster is. This latter option requires working with the c= luster system managers to figure out the optimal settings for the hardware = in question.




On Tue, Nov 30, 2021 at 10:14 AM Vlad Cojocaru &= lt;vlad.cojocaru@mpi-m= uenster.mpg.de> wrote:
=20=20 =20=20=20=20 =20=20
Thanks for your thoughts !

One thing that seemed weird during our tests on this site was that the performance and parallel scaling rapidly degraded when using all 48 cores available per node (2 CPUs with 24 cores each) . We actually saw negative scaling after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we got better parallel efficiency to higher node count, with the best efficiency obtained using just half of the core available on each node (24). At the end, when running on 48 nodes, we achieved the most ns/day when using 24 cores/node. However, the resources requested in the project we needed to calculate using all 48 cores/node regardless of how many we are actually using.

I haven't experienced anything like this on other sites (similar systems, same configuration files). Normally using all cores available per node has always given the best performance. So, I am wondering whether there is anything obvious that could explain such a behavior ?

Best
Vlad

On 11/30/21 15:33, Giacomo Fiorin wrote:
=20=20=20=20=20=20
Something in addition to what Axel says (all of which is absolutely true, even the counter-intuitive part about making the single-node performance artificially slower to get through the bottom-most tier of technical review).

One possible issue to look at is=C2=A0how the cluster's ne= twork is utilized by other users/applications.=C2=A0 In a local cluster that I use, the InfiniBand network is also used by the nodes to access data storage and there are many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by design).=C2=A0 So the InfiniBand netwo= rk is constantly busy and does not necessarily offer very low latency for NAMD or other message-passing applications.

Something that helped in that case was building Charm++ on top of the UCX library instead of IBverbs directly.=C2=A0 I am wholly unfamiliar with the details of how UCX works, but in essence it provides better utilization of the network when the ratio of compute cores vs. network links is high.=C2=A0 If the cluster's staff has a copy of UCX, try that.=C2=A0 It wasn= 9;t easy to build, but it paid off specifically for those runs that were communication-bound.

The main significant addition in 2.15 is the AVX-512 tiles algorithm, which would help with the most expensive Intel CPUs like those, but would also make the computation part faster with the caveat that Axel mentioned.

Giacomo

On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer <akohlmey@gmail.com> wrote:
Actually, if you optimize how NAMD is compiled better than the system provided executable, your parallel efficiency will go down. Please recall Amdahl's law: the parallel efficiency is determined by the relation of time spent on parallel execution and serial execution.=C2= =A0

=C2=A0A better optimized executable will spend even less time computing and thus have more parallel overhead.=C2=A0

To get better parallel efficiency, you have to avoid or reduce all non parallel operations like output or use of features like Tcl scripting or make your computations more expensive by increasing the cutoff or the system size or make the executable slower by compiling a less optimized version.=C2=A0

--
Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de&g= t; wrote:
Dear all,
We submitted a proposal to run some extensive atomistic simulations with
NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path
Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during
our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD
2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not
fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
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Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojoca= ru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0G= x8Paw$



--=20
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojoc=
aru


--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://= goo.gl/1wk0
College of Science & Technology, Temple University, = Philadelphia PA, USA
International Centre for Theoretical Physics, Tries= te. Italy.
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boundary="_000_5082A382FE164F37B56B3B83A26A010Dmsuedu_" X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 2cb96bce-1bf2-41a1-9315-08d9b4243fd8 X-MS-Exchange-CrossTenant-originalarrivaltime: 30 Nov 2021 17:10:03.0893 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: Nldbpn9qryMEyF7CWNcbDMWqYXPPLafzfq4sw9AUOA3X2zQomlLG6MqrwE3Gn9Yy18A0Tst1RENWZqbzFYlI+g== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB4085 X-Proofpoint-ORIG-GUID: fhVtkQqmzfUk7RjCDY74YOtAtVfV1kzJ X-CLX-Response: 1TFkXGBkYEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxscGREKQ1kXBxsZGhEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhgbGHEbGRoQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04XTEJ8XkF7W0dQTH9BHXhAaW5zHR5zZV5rXnxMfBtBUGARClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4eEBseGh8aEQpeWRdzGAUBYxEKTVwXHxMdEQpMWhdpeGlNTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2tra2xraxEKQk8Xeh5/Zm9CH1Nya30RCkNaFx4aBBsaHQQTGQ QSGREKQl4XGxEKRF4XHxEKREkXGxEKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCT BdvYVgTGktdG0NBZREKQmwXYXkcHxJce09aaUIRCkJAF2VlYRNwHX9fW3xSEQpCWBdnc2VzQG5h YUxdYhEKWlgXHBEKeUMXb2ZsRGVbfxwFGVwRCllLFxsYHBgdEQpwZxdtR2FrTWMZTFNpbhAaEQp waBduaXBhRVIYHmtCXBAaEQpwaBdtBW9sThxFGF5oQhAaEQpwaBdtcmRmWmxYRUNMcxAaEQpwaB d6YmRZG11Pbm5iRRAaEQpwaBdjaXlOBVhwYm98eBAaEQpwZxdnU35SQ2NOSBkdWBAdGhEKcGcXa UNuUAFZc0cBHlMQGhEKcH0XZgVtZWdpf2UbUhwQGhEKcH0Xel5rYl9ibXxBH1gQGhEKcH0XZGxj U15NQn1DUHkQGhEKcH0XZmJbGBtgfXJmEloQGhEKcH8XaHpfYh5+WwVkUhsQGxoaEQpwXxdvWXB 8f2gcUlpGARAaEQpwfxdtRF9GRW19SHkZbhAbHh4RCnBfF25NZWVPb1tAE2lPEBoRCnBfF2tGSx N5aGlufBN4EBsaEhEKcH8XZFAFWEltfklNTGwQGxsTEQpwXxdtXXhoYR5ARk1oWxAaEQpwbBdne BpAYhhJGn55TRAZGhEKbX4XGhEKWE0XSxEg X-Proofpoint-GUID: fhVtkQqmzfUk7RjCDY74YOtAtVfV1kzJ X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 impostorscore=0 malwarescore=0 spamscore=0 mlxlogscore=999 clxscore=232 phishscore=0 adultscore=0 mlxscore=0 suspectscore=0 priorityscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300087 domainage_hfrom=12627 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" --_000_5082A382FE164F37B56B3B83A26A010Dmsuedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: Quoted-printable Hi Vlad, In addition to the great points Axel and Giacomo have made, I=E2=80=99d lik= e to point out that the 8160 is a 24 core processor, and that there are lik= ely 2 of them on a given node. In these two socket configurations, where th= ere are two physical CPU dies, I=E2=80=99ve often found that the best perfo= rmance is achieved when you treat each socket as its own node, and allocate= 2x the number of =E2=80=9Ctasks=E2=80=9D as you have nodes. That way, each= SMP task gets placed on its own socket. If you don=E2=80=99t, each node is= trying to get all 48 cores across both sockets to work together, which end= s up saturating the UPI links between the sockets, and can be detrimental t= o performance. This is usually a bigger problem for SMP-based builds. In my experience, CP= U-only systems benefit from MPI based builds, where the number of tasks is = equal to the number of CPUs. Usually this is a performance win for modestly= sized systems at the expense of scalability for really big systems. -Josh From: on behalf of Vlad Cojocaru Organization: MPI Muenster Reply-To: "namd-l@ks.uiuc.edu" , Vlad Cojocaru Date: Tuesday, November 30, 2021 at 10:18 AM To: Giacomo Fiorin , NAMD list , Axel Kohlmeyer Cc: HORIA-LEONARD BANCIU Subject: Re: namd-l: NAMD performance on a supercomputer with Intel Xeon Pl= atinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Thanks for your thoughts ! One thing that seemed weird during our tests on this site was that the perf= ormance and parallel scaling rapidly degraded when using all 48 cores avail= able per node (2 CPUs with 24 cores each) . We actually saw negative scalin= g after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we = got better parallel efficiency to higher node count, with the best efficien= cy obtained using just half of the core available on each node (24). At the= end, when running on 48 nodes, we achieved the most ns/day when using 24 c= ores/node. However, the resources requested in the project we needed to cal= culate using all 48 cores/node regardless of how many we are actually using. I haven't experienced anything like this on other sites (similar systems, s= ame configuration files). Normally using all cores available per node has a= lways given the best performance. So, I am wondering whether there is anyth= ing obvious that could explain such a behavior ? Best Vlad On 11/30/21 15:33, Giacomo Fiorin wrote: Something in addition to what Axel says (all of which is absolutely true, e= ven the counter-intuitive part about making the single-node performance art= ificially slower to get through the bottom-most tier of technical review). One possible issue to look at is how the cluster's network is utilized by o= ther users/applications. In a local cluster that I use, the InfiniBand net= work is also used by the nodes to access data storage and there are many ot= her users processing MRI, cryo-EM or bioinformatics data (all embarrassingl= y-parallel by design). So the InfiniBand network is constantly busy and do= es not necessarily offer very low latency for NAMD or other message-passing= applications. Something that helped in that case was building Charm++ on top of the UCX l= ibrary instead of IBverbs directly. I am wholly unfamiliar with the detail= s of how UCX works, but in essence it provides better utilization of the ne= twork when the ratio of compute cores vs. network links is high. If the cl= uster's staff has a copy of UCX, try that. It wasn't easy to build, but it= paid off specifically for those runs that were communication-bound. The main significant addition in 2.15 is the AVX-512 tiles algorithm, which= would help with the most expensive Intel CPUs like those, but would also m= ake the computation part faster with the caveat that Axel mentioned. Giacomo On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer > wrote: Actually, if you optimize how NAMD is compiled better than the system provi= ded executable, your parallel efficiency will go down. Please recall Amdahl= 's law: the parallel efficiency is determined by the relation of time spent= on parallel execution and serial execution. A better optimized executable will spend even less time computing and thus= have more parallel overhead. To get better parallel efficiency, you have to avoid or reduce all non para= llel operations like output or use of features like Tcl scripting or make y= our computations more expensive by increasing the cutoff or the system size= or make the executable slower by compiling a less optimized version. -- Dr. Axel Kohlmeyer akohlmey@gmail.com https://ur= ldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!oDB0IIjP0rhwjt-PwoJbwOzMX_6= Ty5PWfCDLVNBl5Nib9PeKQgiY_-I2TN-aFWhnEA$ College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste, Italy On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru > wrote: Dear all, We submitted a proposal to run some extensive atomistic simulations with NAMD of systems ranging between 500 K to 2M atoms on a supercomputer with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path Full-Fat Tree interconnection. Apparently, our project may fail the technical evaluation because during our tests we did not achieve a 75 % parallel efficiency between 2 to 48 nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD 2.14 provided by default at the site and we do not know how this was built. Looking at the NAMD benchmarks available for the Frontera supercomputer (quite similar architecture if I understand it correctly but for larger systems), it seems we should definitely achieve with NAMD 2.15 (maybe even 2.14) much better performance and parallel efficiency up to 48/64 nodes on this architecture than we actually achieved in our tests. So, my reasoning is that probably the NAMD built by default was not really carefully optimized. I would appreciate if anyone who has experience with building and optimizing NAMD on such an architecture could recommend any compiler/MPI/configuration/options for building an NAMD with a better performance and parallel efficiency. If I have some clear ideas about how to optimize NAMD, maybe I could make the case for our project to not fail the technical evaluation. Thank you very much for any advice Best wishes Vlad -- Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru__= ;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Pa= w$ -- Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de 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<5082A382-FE16-4F37-B56B-3B83A26A010D@msu.edu> In-Reply-To: <5082A382-FE16-4F37-B56B-3B83A26A010D@msu.edu> From: James M Davis Date: Tue, 30 Nov 2021 13:07:32 -0500 Message-ID: Subject: Re: namd-l: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Cc: Vlad Cojocaru , Giacomo Fiorin , Axel Kohlmeyer , HORIA-LEONARD BANCIU Content-Type: multipart/alternative; boundary="0000000000000e733605d2056f4a" X-CLX-Response: 1TFkXGx0dEQpMehcbGR4RCllEF2dwbkl/fBMeQHkaEQpYWBdlfkJwWlhtRHB +GhEKeE4XaBJuT2ViQllAWxwRCnlMF24Se0BDXGZ/XWdsEQpDSBcHGR8eEQpDWRcHGxgTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8dcRkcEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxkaY1xHQ29+GxNeRmxSE2JSSR5oSGhwHkJcblJuBxxwEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGRAbHhofGhEKXlkXcxlrGngRCk1cFxseGBEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw 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release notes. I think you will need to build from scratch for Omnipath. Intel Omni-Path networks are incompatible with the pre-built verbs NAMD > binaries. Charm++ for verbs can be built with --with-qlogic to support > Omni-Path, but the Charm++ MPI network layer performs better than the ver= bs > layer. Hangs have been observed with Intel MPI but not with OpenMPI, so > OpenMPI is preferred. See "Compiling NAMD" below for MPI build > instructions. NAMD MPI binaries may be launched directly with mpiexec > rather than via the provided charmrun script." https://www.ks.uiuc.edu/Research/namd/cvs/notes.html ---- Mike Davis Technical Director: High Performance Research Computing Virginia Commonwealth University (804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c) https://urldefense.com/v3/__https://chipc.vcu.edu__;!!DZ3fjg!tBqcYe25cf24sZ= 9_e4pE4S0MfI7TUwx4UR9D0O_0i4e4sXoGWogadgTbIibB33t_1A$=20 On Tue, Nov 30, 2021 at 1:00 PM Vermaas, Josh wrote: > Hi Vlad, > > > > In addition to the great points Axel and Giacomo have made, I=E2=80=99d l= ike to > point out that the 8160 is a 24 core processor, and that there are likely= 2 > of them on a given node. In these two socket configurations, where there > are two physical CPU dies, I=E2=80=99ve often found that the best perform= ance is > achieved when you treat each socket as its own node, and allocate 2x the > number of =E2=80=9Ctasks=E2=80=9D as you have nodes. That way, each SMP t= ask gets placed on > its own socket. If you don=E2=80=99t, each node is trying to get all 48 c= ores > across both sockets to work together, which ends up saturating the UPI > links between the sockets, and can be detrimental to performance. > > > > This is usually a bigger problem for SMP-based builds. In my experience, > CPU-only systems benefit from MPI based builds, where the number of tasks > is equal to the number of CPUs. Usually this is a performance win for > modestly sized systems at the expense of scalability for really big syste= ms. > > > > -Josh > > > > *From: * on behalf of Vlad Cojocaru < > vlad.cojocaru@mpi-muenster.mpg.de> > *Organization: *MPI Muenster > *Reply-To: *"namd-l@ks.uiuc.edu" , Vlad Cojocaru < > vlad.cojocaru@mpi-muenster.mpg.de> > *Date: *Tuesday, November 30, 2021 at 10:18 AM > *To: *Giacomo Fiorin , NAMD list < > namd-l@ks.uiuc.edu>, Axel Kohlmeyer > *Cc: *HORIA-LEONARD BANCIU > *Subject: *Re: namd-l: NAMD performance on a supercomputer with Intel > Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree > > > > Thanks for your thoughts ! > > One thing that seemed weird during our tests on this site was that the > performance and parallel scaling rapidly degraded when using all 48 cores > available per node (2 CPUs with 24 cores each) . We actually saw negative > scaling after as few as 16 nodes. Then, when using 47, 32, and 24 > cores/node, we got better parallel efficiency to higher node count, with > the best efficiency obtained using just half of the core available on each > node (24). At the end, when running on 48 nodes, we achieved the most > ns/day when using 24 cores/node. However, the resources requested in the > project we needed to calculate using all 48 cores/node regardless of how > many we are actually using. > > I haven't experienced anything like this on other sites (similar systems, > same configuration files). Normally using all cores available per node has > always given the best performance. So, I am wondering whether there is > anything obvious that could explain such a behavior ? > > Best > Vlad > > On 11/30/21 15:33, Giacomo Fiorin wrote: > > Something in addition to what Axel says (all of which is absolutely true, > even the counter-intuitive part about making the single-node performance > artificially slower to get through the bottom-most tier of technical > review). > > > > One possible issue to look at is how the cluster's network is utilized by > other users/applications. In a local cluster that I use, the InfiniBand > network is also used by the nodes to access data storage and there are ma= ny > other users processing MRI, cryo-EM or bioinformatics data (all > embarrassingly-parallel by design). So the InfiniBand network is > constantly busy and does not necessarily offer very low latency for NAMD = or > other message-passing applications. > > > > Something that helped in that case was building Charm++ on top of the UCX > library instead of IBverbs directly. I am wholly unfamiliar with the > details of how UCX works, but in essence it provides better utilization of > the network when the ratio of compute cores vs. network links is high. If > the cluster's staff has a copy of UCX, try that. It wasn't easy to build, > but it paid off specifically for those runs that were communication-bound. > > > > The main significant addition in 2.15 is the AVX-512 tiles algorithm, > which would help with the most expensive Intel CPUs like those, but would > also make the computation part faster with the caveat that Axel mentioned. > > > > Giacomo > > > > On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer wrote: > > Actually, if you optimize how NAMD is compiled better than the system > provided executable, your parallel efficiency will go down. Please recall > Amdahl's law: the parallel efficiency is determined by the relation of ti= me > spent on parallel execution and serial execution. > > > > A better optimized executable will spend even less time computing and > thus have more parallel overhead. > > > > To get better parallel efficiency, you have to avoid or reduce all non > parallel operations like output or use of features like Tcl scripting or > make your computations more expensive by increasing the cutoff or the > system size or make the executable slower by compiling a less optimized > version. > > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!tBqcYe25cf24sZ9_e4pE4S0MfI7TUwx4UR9D0O_0i4e4sXoGWoga= dgTbIib9XSAtIQ$=20 > > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste, Italy > > > > On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru < > vlad.cojocaru@mpi-muenster.mpg.de> wrote: > > Dear all, > > We submitted a proposal to run some extensive atomistic simulations with > NAMD of systems ranging between 500 K to 2M atoms on a supercomputer > with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path > Full-Fat Tree interconnection. > > Apparently, our project may fail the technical evaluation because during > our tests we did not achieve a 75 % parallel efficiency between 2 to 48 > nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD > 2.14 provided by default at the site and we do not know how this was > built. Looking at the NAMD benchmarks available for the Frontera > supercomputer (quite similar architecture if I understand it correctly > but for larger systems), it seems we should definitely achieve with NAMD > 2.15 (maybe even 2.14) much better performance and parallel efficiency > up to 48/64 nodes on this architecture than we actually achieved in our > tests. > > So, my reasoning is that probably the NAMD built by default was not > really carefully optimized. > > I would appreciate if anyone who has experience with building and > optimizing NAMD on such an architecture could recommend any > compiler/MPI/configuration/options for building an NAMD with a better > performance and parallel efficiency. If I have some clear ideas about > how to optimize NAMD, maybe I could make the case for our project to not > fail the technical evaluation. > > Thank you very much for any advice > > Best wishes > Vlad > > > > -- > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > > > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru= __;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8= Paw$ > > > > > -- > > Vlad Cojocaru, PD (Habil.), Ph.D. > > ----------------------------------------------- > > Project Group Leader > > Department of Cell and Developmental Biology > > Max Planck Institute for Molecular Biomedicine > > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > > ----------------------------------------------- > > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > > https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru= __;!!DZ3fjg!tBqcYe25cf24sZ9_e4pE4S0MfI7TUwx4UR9D0O_0i4e4sXoGWogadgTbIiamghz= cLQ$ > > --0000000000000e733605d2056f4a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
A few notes from the 2.15 release notes. I think you will = need to build from scratch for Omnipath.=C2=A0

Intel Omni-Path networks are incompatible= with the pre-built verbs NAMD binaries. Charm++ for verbs can be built wit= h --with-qlogic to support Omni-Path, but the Charm++ MPI network layer per= forms better than the verbs layer.=C2=A0 Hangs have been observed with Inte= l MPI but not with OpenMPI, so OpenMPI is preferred.=C2=A0 See "Compil= ing NAMD" below for MPI build instructions.=C2=A0 NAMD MPI binaries ma= y be launched directly with mpiexec rather than via the provided charmrun s= cript."
https://www.=
ks.uiuc.edu/Research/namd/cvs/notes.html
----
Mike Davis
Technical Director: High Performance Resea= rch Computing=C2=A0
Virginia Commonwealth University<= br>
(804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c)




On Tue, Nov 30, 2021 at 1:00 PM Ve= rmaas, Josh <vermaasj@msu.edu>= ; wrote:

Hi Vlad,

=C2=A0

In addition to the great points Axel and Giacomo hav= e made, I=E2=80=99d like to point out that the 8160 is a 24 core processor,= and that there are likely 2 of them on a given node. In these two socket c= onfigurations, where there are two physical CPU dies, I=E2=80=99ve often found that the best performance is achieved w= hen you treat each socket as its own node, and allocate 2x the number of = =E2=80=9Ctasks=E2=80=9D as you have nodes. That way, each SMP task gets pla= ced on its own socket. If you don=E2=80=99t, each node is trying to get all 48 cores across both sockets to work together, which ends up satur= ating the UPI links between the sockets, and can be detrimental to performa= nce.

=C2=A0

This is usually a bigger problem for SMP-based build= s. In my experience, CPU-only systems benefit from MPI based builds, where = the number of tasks is equal to the number of CPUs. Usually this is a perfo= rmance win for modestly sized systems at the expense of scalability for really big systems.

=C2=A0

-Josh

=C2=A0

From: = <owner-namd-l@ks.uiuc.edu&g= t; on behalf of Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de>
Organization: MPI Muenster
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, Vlad Cojocaru <vlad.cojocaru@m= pi-muenster.mpg.de>
Date: Tuesday, November 30, 2021 at 10:18 AM
To: Giacomo Fiorin <giacomo.fiorin@gmail.com>, NAMD list <namd-l@ks.uiuc.edu>, A= xel Kohlmeyer <a= kohlmey@gmail.com>
Cc: HORIA-LEONARD BANCIU <horia.banciu@ubbcluj.ro>
Subject: Re: namd-l: NAMD performance on a supercomputer with Intel = Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree

=C2=A0

Thanks for your thought= s !

One thing that seemed weird during our tests on this site was that the perf= ormance and parallel scaling rapidly degraded when using all 48 cores avail= able per node (2 CPUs with 24 cores each) . We actually saw negative scalin= g after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we got better parallel efficiency to= higher node count, with the best efficiency obtained using just half of th= e core available on each node (24). At the end, when running on 48 nodes, w= e achieved the most ns/day when using 24 cores/node. However, the resources requested in the project we ne= eded to calculate using all 48 cores/node regardless of how many we are act= ually using.

I haven't experienced anything like this on other sites (similar system= s, same configuration files). Normally using all cores available per node h= as always given the best performance. So, I am wondering whether there is a= nything obvious that could explain such a behavior ?

Best
Vlad

On 11/30/21 15:33, Giacomo Fiorin wrote:

Something in addition to what Axel says (all of whic= h is absolutely true, even the counter-intuitive part about making the sing= le-node performance artificially slower to get through the bottom-most tier= of technical review).

=C2=A0

One possible issue to look at is=C2=A0how the cluste= r's network is utilized by other users/applications.=C2=A0 In a local c= luster that I use, the InfiniBand network is also used by the nodes to acce= ss data storage and there are many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by design= ).=C2=A0 So the InfiniBand network is constantly busy and does not necessar= ily offer very low latency for NAMD or other message-passing applications.<= u>

=C2=A0

Something that helped in that case was building Char= m++ on top of the UCX library instead of IBverbs directly.=C2=A0 I am wholl= y unfamiliar with the details of how UCX works, but in essence it provides = better utilization of the network when the ratio of compute cores vs. network links is high.=C2=A0 If the cluster= 's staff has a copy of UCX, try that.=C2=A0 It wasn't easy to build= , but it paid off specifically for those runs that were communication-bound= .

=C2=A0

The main significant addition in 2.15 is the AVX-512= tiles algorithm, which would help with the most expensive Intel CPUs like = those, but would also make the computation part faster with the caveat that= Axel mentioned.

=C2=A0

Giacomo

=C2=A0

On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer <<= a href=3D"mailto:akohlmey@gmail.com" target=3D"_blank">akohlmey@gmail.com> wrote:

Actually, if you optimize how NAMD is compiled bette= r than the system provided executable, your parallel efficiency will go dow= n. Please recall Amdahl's law: the parallel efficiency is determined by= the relation of time spent on parallel execution and serial execution.=C2=A0

=C2=A0

=C2=A0A better optimized executable will spend even = less time computing and thus have more parallel overhead.=C2=A0

=C2=A0

To get better parallel = efficiency, you have to avoid or reduce all non parallel operations like ou= tput or use of features like Tcl scripting or make your computations more e= xpensive by increasing the cutoff or the system size or make the executable slower by compiling a less optim= ized version.=C2=A0

--
Dr. Axel Kohlmeyer = akohlmey@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, US= A
International Centre for Theoretical Physics, Trieste, Italy<= /p>

=C2=A0

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojoc= aru@mpi-muenster.mpg.de> wrote:

Dear all,

We submitted a proposal to run some extensive atomistic simulations with NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD =
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD 2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
https://urldefense.com/v3/__http://www.mpi-= muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7t= QfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Paw$



-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/c=
ojocaru
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boundary="000000000000463b0205d205b03b" X-CLX-Response: 1TFkXGx0dEQpMehcbHRsRCllEF2dwbkl/fBMeQHkaEQpYWBdlfkJwWlhtRHB +GhEKeE4XaBJuT2ViQllAWxwRCnlMF24Se0BDXGZ/XWdsEQpDSBcHGRkbEQpDWRcHGxkaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8dcRkcEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOFxp5TEgSHEtTHUkdG2dwSAdFb11dcFsfU0QfQmx5GEdTEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXcxlobHkRCk1cFxkcGxEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRgRCkJeFxsRCkReFxgRCkRJFx4RCkJcFxsRCl5OFxsRCkJLF2gSbk9lYkJZQFscEQpCSRdoE m5PZWJCWUBbHBEKQkUXZhttbUsBWWV5HF4RCkJOF2gSbk9lYkJZQFscEQpCTBdlfkJwWlhtRHB+ GhEKQmwXb11TBWJ4eXNrQlsRCkJAF2VlYRNwHX9fW3xSEQpCWBdnc2VzQG5hYUxdYhEKWlgXGxg RCnlDF29mbERlW38cBRlcEQpwZxdtR2FrTWMZTFNpbhAbEhEKcGgXYU0fThgZSGlwZ1oQGRoRCn BoF25pcGFFUhgea0JcEBsSEQpwaBduGE1yTF8baxxgWRAbEhEKcGgXY1J6HF5bXBxERmAQGxIRC nBoF21Zc3lPS21oHkZ8EBsSEQpwfRdvX0t9YE5+HmBbQBAZGhEKcH0XYhJMclNkblljEnMQGRoR CnB9F2JYHU5CcFtsaX8fEBsSEQpwZxdnU35SQ2NOSBkdWBAeEhEKcGcXaUNuUAFZc0cBHlMQGxI RCnB9F2AYRRsBSBoTGnlSEB0SEQpwfRdlTx8fU2kTTF5TaxAbEhEKcH0Xel5rYl9ibXxBH1gQGx IRCnB9F2FLRGYZYUZHSwV6EB4ZEQpwfRd6UGBabHBDf30TQhAbEhEKcH0XYBpSe2NgT11PT2QQH hIRCnB9F2cda19FeHJwYwEZEBsSEQpwfxdvcGBrTEt8TR1DXRAbHhkRCnBfF29fS31gTn4eYFtA EBkaEQpwfxdlGXlmXkdpG2RPcxAdGhEKcF8XYU5LQkd5ZxpvRWMQGxIRCnB/F2h6X2IeflsFZFI bEBsaHBEKcF8XYBMZZktObE5FU3sQHRIRCnB/F21EX0ZFbX1IeRluEBsZEhEKcF8XY2FNU3ISGF xoGEQQGxgfEQpwXxduTWVlT29bQBNpTxAZGhEKcF8Xa0ZLE3loaW58E3gQGxoZEQpwXxdgHHBMb 2d9RGF4XhAbHxsRCnB/F2RQBVhJbX5JTUxsEBsbGxEKcF8XekAeRV1PfkhabXgQHhIRCnBsF25H UllpHEVaXX1lEBsSEQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: 0Sfb86ay7c71MZb-oEwwZq5yn5hFS2my X-CLX-Shades: MLX X-Proofpoint-GUID: 0Sfb86ay7c71MZb-oEwwZq5yn5hFS2my MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 malwarescore=0 adultscore=0 spamscore=0 bulkscore=0 suspectscore=0 mlxscore=0 clxscore=177 mlxlogscore=999 priorityscore=171 phishscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2111300095 X-Spam-Score: 0 X-Spam-OrigSender: jmdavis1@vcu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, James M Davis --000000000000463b0205d205b03b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable I should have said build from scratch to support Omnipath or use the Charrm++ mpi with open-mpi. There will still be testing involved to tweak the system and the performance. It still might not support 48*48. But you should be able to get to something higher than 48*24. ---- Mike Davis Technical Director: High Performance Research Computing Virginia Commonwealth University (804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c) https://urldefense.com/v3/__https://chipc.vcu.edu__;!!DZ3fjg!tdYi7N1NVr8KtU= 5IVzoCwBS8jTMzgmjY0Kb-WyaRtZgNVLJ-IVL91DFQum10OvRJ0w$=20 On Tue, Nov 30, 2021 at 1:07 PM James M Davis wrote: > A few notes from the 2.15 release notes. I think you will need to build > from scratch for Omnipath. > > Intel Omni-Path networks are incompatible with the pre-built verbs NAMD >> binaries. Charm++ for verbs can be built with --with-qlogic to support >> Omni-Path, but the Charm++ MPI network layer performs better than the ve= rbs >> layer. Hangs have been observed with Intel MPI but not with OpenMPI, so >> OpenMPI is preferred. See "Compiling NAMD" below for MPI build >> instructions. NAMD MPI binaries may be launched directly with mpiexec >> rather than via the provided charmrun script." > > https://www.ks.uiuc.edu/Research/namd/cvs/notes.html > > ---- > Mike Davis > Technical Director: High Performance Research Computing > Virginia Commonwealth University > (804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c) > https://urldefense.com/v3/__https://chipc.vcu.edu__;!!DZ3fjg!tdYi7N1NVr8K= tU5IVzoCwBS8jTMzgmjY0Kb-WyaRtZgNVLJ-IVL91DFQum10OvRJ0w$=20 > > > > > On Tue, Nov 30, 2021 at 1:00 PM Vermaas, Josh wrote: > >> Hi Vlad, >> >> >> >> In addition to the great points Axel and Giacomo have made, I=E2=80=99d = like to >> point out that the 8160 is a 24 core processor, and that there are likel= y 2 >> of them on a given node. In these two socket configurations, where there >> are two physical CPU dies, I=E2=80=99ve often found that the best perfor= mance is >> achieved when you treat each socket as its own node, and allocate 2x the >> number of =E2=80=9Ctasks=E2=80=9D as you have nodes. That way, each SMP = task gets placed on >> its own socket. If you don=E2=80=99t, each node is trying to get all 48 = cores >> across both sockets to work together, which ends up saturating the UPI >> links between the sockets, and can be detrimental to performance. >> >> >> >> This is usually a bigger problem for SMP-based builds. In my experience, >> CPU-only systems benefit from MPI based builds, where the number of tasks >> is equal to the number of CPUs. Usually this is a performance win for >> modestly sized systems at the expense of scalability for really big syst= ems. >> >> >> >> -Josh >> >> >> >> *From: * on behalf of Vlad Cojocaru < >> vlad.cojocaru@mpi-muenster.mpg.de> >> *Organization: *MPI Muenster >> *Reply-To: *"namd-l@ks.uiuc.edu" , Vlad Cojocaru < >> vlad.cojocaru@mpi-muenster.mpg.de> >> *Date: *Tuesday, November 30, 2021 at 10:18 AM >> *To: *Giacomo Fiorin , NAMD list < >> namd-l@ks.uiuc.edu>, Axel Kohlmeyer >> *Cc: *HORIA-LEONARD BANCIU >> *Subject: *Re: namd-l: NAMD performance on a supercomputer with Intel >> Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree >> >> >> >> Thanks for your thoughts ! >> >> One thing that seemed weird during our tests on this site was that the >> performance and parallel scaling rapidly degraded when using all 48 cores >> available per node (2 CPUs with 24 cores each) . We actually saw negative >> scaling after as few as 16 nodes. Then, when using 47, 32, and 24 >> cores/node, we got better parallel efficiency to higher node count, with >> the best efficiency obtained using just half of the core available on ea= ch >> node (24). At the end, when running on 48 nodes, we achieved the most >> ns/day when using 24 cores/node. However, the resources requested in the >> project we needed to calculate using all 48 cores/node regardless of how >> many we are actually using. >> >> I haven't experienced anything like this on other sites (similar systems, >> same configuration files). Normally using all cores available per node h= as >> always given the best performance. So, I am wondering whether there is >> anything obvious that could explain such a behavior ? >> >> Best >> Vlad >> >> On 11/30/21 15:33, Giacomo Fiorin wrote: >> >> Something in addition to what Axel says (all of which is absolutely true, >> even the counter-intuitive part about making the single-node performance >> artificially slower to get through the bottom-most tier of technical >> review). >> >> >> >> One possible issue to look at is how the cluster's network is utilized by >> other users/applications. In a local cluster that I use, the InfiniBand >> network is also used by the nodes to access data storage and there are m= any >> other users processing MRI, cryo-EM or bioinformatics data (all >> embarrassingly-parallel by design). So the InfiniBand network is >> constantly busy and does not necessarily offer very low latency for NAMD= or >> other message-passing applications. >> >> >> >> Something that helped in that case was building Charm++ on top of the UCX >> library instead of IBverbs directly. I am wholly unfamiliar with the >> details of how UCX works, but in essence it provides better utilization = of >> the network when the ratio of compute cores vs. network links is high. = If >> the cluster's staff has a copy of UCX, try that. It wasn't easy to buil= d, >> but it paid off specifically for those runs that were communication-boun= d. >> >> >> >> The main significant addition in 2.15 is the AVX-512 tiles algorithm, >> which would help with the most expensive Intel CPUs like those, but would >> also make the computation part faster with the caveat that Axel mentione= d. >> >> >> >> Giacomo >> >> >> >> On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer >> wrote: >> >> Actually, if you optimize how NAMD is compiled better than the system >> provided executable, your parallel efficiency will go down. Please recall >> Amdahl's law: the parallel efficiency is determined by the relation of t= ime >> spent on parallel execution and serial execution. >> >> >> >> A better optimized executable will spend even less time computing and >> thus have more parallel overhead. >> >> >> >> To get better parallel efficiency, you have to avoid or reduce all non >> parallel operations like output or use of features like Tcl scripting or >> make your computations more expensive by increasing the cutoff or the >> system size or make the executable slower by compiling a less optimized >> version. >> >> -- >> Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http:/= /goo.gl/1wk0__;!!DZ3fjg!tdYi7N1NVr8KtU5IVzoCwBS8jTMzgmjY0Kb-WyaRtZgNVLJ-IVL= 91DFQum0bMcA6Ag$=20 >> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste, Italy >> >> >> >> On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru < >> vlad.cojocaru@mpi-muenster.mpg.de> wrote: >> >> Dear all, >> >> We submitted a proposal to run some extensive atomistic simulations with >> NAMD of systems ranging between 500 K to 2M atoms on a supercomputer >> with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path >> Full-Fat Tree interconnection. >> >> Apparently, our project may fail the technical evaluation because during >> our tests we did not achieve a 75 % parallel efficiency between 2 to 48 >> nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD >> 2.14 provided by default at the site and we do not know how this was >> built. Looking at the NAMD benchmarks available for the Frontera >> supercomputer (quite similar architecture if I understand it correctly >> but for larger systems), it seems we should definitely achieve with NAMD >> 2.15 (maybe even 2.14) much better performance and parallel efficiency >> up to 48/64 nodes on this architecture than we actually achieved in our >> tests. >> >> So, my reasoning is that probably the NAMD built by default was not >> really carefully optimized. >> >> I would appreciate if anyone who has experience with building and >> optimizing NAMD on such an architecture could recommend any >> compiler/MPI/configuration/options for building an NAMD with a better >> performance and parallel efficiency. If I have some clear ideas about >> how to optimize NAMD, maybe I could make the case for our project to not >> fail the technical evaluation. >> >> Thank you very much for any advice >> >> Best wishes >> Vlad >> >> >> >> -- >> Vlad Cojocaru, PD (Habil.), Ph.D. >> ----------------------------------------------- >> Project Group Leader >> Department of Cell and Developmental Biology >> Max Planck Institute for Molecular Biomedicine >> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >> ----------------------------------------------- >> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >> >> >> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocar= u__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx= 8Paw$ >> >> >> >> >> -- >> >> Vlad Cojocaru, PD (Habil.), Ph.D. >> >> ----------------------------------------------- >> >> Project Group Leader >> >> Department of Cell and Developmental Biology >> >> Max Planck Institute for Molecular Biomedicine >> >> R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany >> >> ----------------------------------------------- >> >> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >> >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >> >> https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocar= u__;!!DZ3fjg!tdYi7N1NVr8KtU5IVzoCwBS8jTMzgmjY0Kb-WyaRtZgNVLJ-IVL91DFQum3g_J= SMjQ$ >> >> --000000000000463b0205d205b03b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
I should have said build from scratch to support Omnipath= =C2=A0or use the Charrm++=C2=A0mpi with open-mpi. There will still be testi= ng involved to tweak the system and the performance. It still might not sup= port 48*48. But you should be able to get to something higher than 48*24.
----
Mike Davis
Technical Dir= ector: High Performance Research Computing=C2=A0
Virg= inia Commonwealth University
(804) 828-3885 (o) =E2=80=A2 (804) 307= -3428(c)

On Tue, Nov 30, 2021 at 1:07 PM James M Davis <jmdavis1@vcu.edu> wrote:
A few notes from the 2.15 rele= ase notes. I think you will need to build from scratch for Omnipath.=C2=A0<= br>
Intel Omni-Pa= th networks are incompatible with the pre-built verbs NAMD binaries. Charm+= + for verbs can be built with --with-qlogic to support Omni-Path, but the C= harm++ MPI network layer performs better than the verbs layer.=C2=A0 Hangs = have been observed with Intel MPI but not with OpenMPI, so OpenMPI is prefe= rred.=C2=A0 See "Compiling NAMD" below for MPI build instructions= .=C2=A0 NAMD MPI binaries may be launched directly with mpiexec rather than= via the provided charmrun script."
https://www.ks.uiuc.edu/Research/namd/cvs=
/notes.html
----
Mike Davis
Technical Director: High Performance Research Computing= =C2=A0
Virginia Commonwealth University
(804)= 828-3885 (o) =E2=80=A2 (804) 307-3428(c)


=


On Tue, Nov 30, 2021 at 1:00 PM Vermaas, Josh= <vermaasj@msu.edu= > wrote:

Hi Vlad,

=C2=A0

In addition to the great points Axel and Giacomo hav= e made, I=E2=80=99d like to point out that the 8160 is a 24 core processor,= and that there are likely 2 of them on a given node. In these two socket c= onfigurations, where there are two physical CPU dies, I=E2=80=99ve often found that the best performance is achieved w= hen you treat each socket as its own node, and allocate 2x the number of = =E2=80=9Ctasks=E2=80=9D as you have nodes. That way, each SMP task gets pla= ced on its own socket. If you don=E2=80=99t, each node is trying to get all 48 cores across both sockets to work together, which ends up satur= ating the UPI links between the sockets, and can be detrimental to performa= nce.

=C2=A0

This is usually a bigger problem for SMP-based build= s. In my experience, CPU-only systems benefit from MPI based builds, where = the number of tasks is equal to the number of CPUs. Usually this is a perfo= rmance win for modestly sized systems at the expense of scalability for really big systems.

=C2=A0

-Josh

=C2=A0

From: = <owner-namd-l@ks.uiuc.edu&g= t; on behalf of Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de>
Organization: MPI Muenster
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, Vlad Cojocaru <vlad.cojocaru@m= pi-muenster.mpg.de>
Date: Tuesday, November 30, 2021 at 10:18 AM
To: Giacomo Fiorin <giacomo.fiorin@gmail.com>, NAMD list <namd-l@ks.uiuc.edu>, A= xel Kohlmeyer <a= kohlmey@gmail.com>
Cc: HORIA-LEONARD BANCIU <horia.banciu@ubbcluj.ro>
Subject: Re: namd-l: NAMD performance on a supercomputer with Intel = Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree

=C2=A0

Thanks for your thought= s !

One thing that seemed weird during our tests on this site was that the perf= ormance and parallel scaling rapidly degraded when using all 48 cores avail= able per node (2 CPUs with 24 cores each) . We actually saw negative scalin= g after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we got better parallel efficiency to= higher node count, with the best efficiency obtained using just half of th= e core available on each node (24). At the end, when running on 48 nodes, w= e achieved the most ns/day when using 24 cores/node. However, the resources requested in the project we ne= eded to calculate using all 48 cores/node regardless of how many we are act= ually using.

I haven't experienced anything like this on other sites (similar system= s, same configuration files). Normally using all cores available per node h= as always given the best performance. So, I am wondering whether there is a= nything obvious that could explain such a behavior ?

Best
Vlad

On 11/30/21 15:33, Giacomo Fiorin wrote:

Something in addition to what Axel says (all of whic= h is absolutely true, even the counter-intuitive part about making the sing= le-node performance artificially slower to get through the bottom-most tier= of technical review).

=C2=A0

One possible issue to look at is=C2=A0how the cluste= r's network is utilized by other users/applications.=C2=A0 In a local c= luster that I use, the InfiniBand network is also used by the nodes to acce= ss data storage and there are many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by design= ).=C2=A0 So the InfiniBand network is constantly busy and does not necessar= ily offer very low latency for NAMD or other message-passing applications.<= u>

=C2=A0

Something that helped in that case was building Char= m++ on top of the UCX library instead of IBverbs directly.=C2=A0 I am wholl= y unfamiliar with the details of how UCX works, but in essence it provides = better utilization of the network when the ratio of compute cores vs. network links is high.=C2=A0 If the cluster= 's staff has a copy of UCX, try that.=C2=A0 It wasn't easy to build= , but it paid off specifically for those runs that were communication-bound= .

=C2=A0

The main significant addition in 2.15 is the AVX-512= tiles algorithm, which would help with the most expensive Intel CPUs like = those, but would also make the computation part faster with the caveat that= Axel mentioned.

=C2=A0

Giacomo

=C2=A0

On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer <<= a href=3D"mailto:akohlmey@gmail.com" target=3D"_blank">akohlmey@gmail.com> wrote:

Actually, if you optimize how NAMD is compiled bette= r than the system provided executable, your parallel efficiency will go dow= n. Please recall Amdahl's law: the parallel efficiency is determined by= the relation of time spent on parallel execution and serial execution.=C2=A0

=C2=A0

=C2=A0A better optimized executable will spend even = less time computing and thus have more parallel overhead.=C2=A0

=C2=A0

To get better parallel = efficiency, you have to avoid or reduce all non parallel operations like ou= tput or use of features like Tcl scripting or make your computations more e= xpensive by increasing the cutoff or the system size or make the executable slower by compiling a less optim= ized version.=C2=A0

--
Dr. Axel Kohlmeyer = akohlmey@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, US= A
International Centre for Theoretical Physics, Trieste, Italy<= /p>

=C2=A0

On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru <vlad.cojoc= aru@mpi-muenster.mpg.de> wrote:

Dear all,

We submitted a proposal to run some extensive atomistic simulations with NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with=C2=A0 Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).=C2=A0 We have tested the NAMD =
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD 2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
https://urldefense.com/v3/__http://www.mpi-= muenster.mpg.de/43241/cojocaru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7t= QfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Paw$



-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/c=
ojocaru
--000000000000463b0205d205b03b-- From owner-namd-l@halifax.ks.uiuc.edu Thu Dec 2 03:23:52 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B29Nqll025917; Thu, 2 Dec 2021 03:23:52 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B29Nqkt025916; Thu, 2 Dec 2021 03:23:52 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B29Npnl025912; Thu, 2 Dec 2021 03:23:51 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B29NpsQ025911; Thu, 2 Dec 2021 03:23:51 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B29NcKl025890 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000482e3005d22658fa" X-Proofpoint-ORIG-GUID: xwD_ItkVQZvtPLDvjaZzuOwhzktFJ-D8 X-CLX-Shades: MLX X-Proofpoint-GUID: xwD_ItkVQZvtPLDvjaZzuOwhzktFJ-D8 X-CLX-Response: 1TFkXGxIeEQpMehcZGBoRCllEF2ltSV5uekVpZBhAEQpYWBd6ell9RkVfGx1 dHBEKeE4XY1Nja3sTWH4aX14RCnlMF2NfHU5/Z04ebmdvEQpDSBcHGRwRCkNZFwcZGxoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB5xHhkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XUl1udWNeQXx7cFxeemZuXEBLcFBfZV1CUEFebGAHbhIRClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4ZEBseGh8aEQpeWRdzGUB/GhEKTVwXGBocEQpMWhdsaU1NTREKTEYXb2tra2t rEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGwQeGxEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRduYHJkaFtMem9gBREKQk4XY1Nja3sTW H4aX14RCkJMF3p6WX1GRV8bHV0cEQpCbBdpXGNYT25hZ0lQExEKQkAXaW9ucBNpaxpjXhIRCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcZEQp5QxdnRhNzeH8aa15+cBEKWUsXExwaEhEKcGgXbhx Fc3JJZWFde14QGRoRCnBoF2BPc21sT2RIXE8ZEBkaEQpwaBdkEhNgEhJ+ZEJSHxAZGhEKcGgXaG 19E2BrGB8YE08QGRoRCnBoF2V6GUkcZElkUhkZEBkaEQpwfRdmUG5SG2xJWlpnexAZGhEKcH8XZ Rl5Zl5HaRtkT3MQHRoRCnBfF2taWHJYYmNCaUVCEBkaEQpwbBdoGRtoH2JlRkhOQBAeEhEKbX4X GxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 malwarescore=0 spamscore=0 clxscore=184 priorityscore=320 mlxscore=0 suspectscore=0 mlxlogscore=412 bulkscore=0 lowpriorityscore=0 adultscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112020057 domainage_hfrom=9608 X-Spam-Score: 0 X-Spam-OrigSender: jingliang2015@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, jing liang --000000000000482e3005d22658fa Content-Type: text/plain; charset="UTF-8" Hi, I don't understand well the description of the parameter qmLinkElement from the documentation page: https://www.ks.uiuc.edu/Research/namd/2.14/ug/node90.html#47512 It looks to me that when there are two or more bonds I need to pass the atom numbers of the MM atoms involved. Are these atom numbers obtained from the *psf file? I used QwikMD for setting the simulation and when I look at the value that this parameter got it says: #QMLinkElement "18 38 Cl" but the numbers 18 and 38 don't correspond to the atom numbers in the psf file of the atoms involved in the bond. I wonder how the numbers 18 and 38 are obtained? What they are? thank you --000000000000482e3005d22658fa Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I don't understand w= ell the description of the parameter qmLinkElement from the documentation p= age: https://www.ks.uiuc.edu/Research/namd/2.14/ug/node90.html#47512

It looks to me that when there are two or more bond= s I need to pass the atom numbers of the MM atoms involved. Are these atom = numbers obtained from the *psf file?

I used Q= wikMD for setting the simulation and when I look at the value that this par= ameter got it says:

#QMLinkElement "18 3= 8 Cl"

but the numbers 18 and 38 don't cor= respond to the atom numbers in the psf file of the atoms involved in the bo= nd.

I wonder how the numbers 18 and 38 are ob= tained? What they are?

thank you


--000000000000482e3005d22658fa-- From owner-namd-l@halifax.ks.uiuc.edu Thu Dec 2 11:06:03 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B2H63VP001921; Thu, 2 Dec 2021 11:06:03 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B2H62mc001920; Thu, 2 Dec 2021 11:06:02 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B2H62W2001916; Thu, 2 Dec 2021 11:06:02 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B2H62HP001915; Thu, 2 Dec 2021 11:06:02 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B2H5r6g001899 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Thu, 2 Dec 2021 11:05:54 -0600 (CST) Received: from pps.filterd (m0166260.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with SMTP id 1B2H4s7V009293 for ; Thu, 2 Dec 2021 17:05:53 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=melomcr@gmail.com; dkim=pass header.d=gmail.com header.s=20210112; dmarc=pass header.from=gmail.com Received: from mail-lj1-f176.google.com (mail-lj1-f176.google.com [209.85.208.176]) by mx0b-00007101.pphosted.com with ESMTP id 3cq220r48m-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Thu, 02 Dec 2021 17:05:53 +0000 Received: by mail-lj1-f176.google.com with SMTP id 207so923477ljf.10 for ; Thu, 02 Dec 2021 09:05:53 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=9OiXXoX2mu3c8sgjMKVWywHUIvUfDtL+uBE18QN+z64=; b=MIPYieiWDKETHVESjK0xMFHigElpASPyjPTG0I4jqIEcbHg9rovRdgfyXSfE9OYT86 9yRfnS78R+2GHv7OzFhpmFkZgn/pdffCgkQaWbxxV961J0cI2LnJIa+kxeyqlX0adiJC Zp1rVvVkS8uKVNXaJNg7eyMbgiTpqFsZYZzYq263L64I7ikgiDQCQ1ZactqtoUjnIFy8 gY3dfuMajfqteV5oNx1wBrKtQVr3nAt2qEy/awXEadgPcom+Ka0V7Ajs1ZPQ8oCbD31X ME5iYcUwXKPix9lI+hrpqyN9X1Ays8G4h7MFteU2smgt/evg7pedI28XbX1tTeD9cWoJ Bs6g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=9OiXXoX2mu3c8sgjMKVWywHUIvUfDtL+uBE18QN+z64=; b=DzfnpyyfL5MGBJ6KQ58kLyEOj2gyc5p2ALEz2ig7ccrOHrE6hOmHwibOEy+hsy0tbM QZhWD/QVnPY9cu3ZskgqryigKRcO49I1wT/DgpzIKN4izquq7lNrNjZaPLJPwSv0zH66 yAlfnDiaT1oCWlIyWEdM1dLJhvRrWCCcu53DlLSyPcjskBY+CDLs4JgMdHFget/BmV3V w080lS05lo1riE3PqnTIOve9QU/ks3xS6Bezkse6obMIz2mUOySWBztvgY8Z6MdLUSWu 9XPPX0cc2494r/QqmE12W47E+2Ps0uJIJk1u/9qeyPI6TIAF12wibJve1qnG0XooP/lg +qCA== X-Gm-Message-State: AOAM530xzxxa9ND82usZKC9GRaXPmb+UIlOr9utg3s1AyRc5fchCjmFS Z4FSA9MQ0q9ghCySOmjvtQP2oK/oAqp6zjkAoh7fSrPwd3M= X-Google-Smtp-Source: ABdhPJxvXimu4hUv9ud0DV+89GWxa68dQ+LQETqfqhF35o99eXzBndLOH3NxyBSjN6DzQXRivfsY+3QbN41MDHFV320= X-Received: by 2002:a2e:144a:: with SMTP id 10mr12368449lju.75.1638464751206; Thu, 02 Dec 2021 09:05:51 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: "Marcelo C. R. Melo" Date: Thu, 2 Dec 2021 12:05:25 -0500 Message-ID: Subject: Re: namd-l: setting the value of qmLinkElement in NAMD/QMMM script To: NAMD , jing liang Content-Type: multipart/alternative; boundary="00000000000079070105d22ccdd4" X-Proofpoint-GUID: tXQfgHoYljGk-s1R6rHjkCaykmU25Vue X-Proofpoint-ORIG-GUID: tXQfgHoYljGk-s1R6rHjkCaykmU25Vue X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBobEQpMehcZHx8RCllEF21ta2xYEn9bT2ZFEQpYWBdsekNpUlJ7QlN lTBEKeE4XY1Nja3sTWH4aX14RCnlMF28bTHN9E0ZMW0FFEQpDSBcHGBsZEQpDWRcHGB8cEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxIbcRsYExAadwYYGgYaEQpZXhdsbHkRCklGF19DX 0l1QkVZXk9OEQpDThdecntMTWJFc0ZAbUEHWRt4HFhiQEFpS1NBR38YH3xfTxEKWFwXHwQaBBge GAUbGgQbGxoEHQQbGRsQGx4aHxoRCl5ZF3MZW21nEQpNXBcYGhoRCkxaF3xpTU1rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8Xa3xZUFgZaV4YZloRCkNaFxgaEwQSHwQYGh IEGx0cEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTW H4aX14RCkJFF2RrWlhuXgFzRU9/EQpCThdjU2NrexNYfhpfXhEKQkwXbHpDaVJSe0JTZUwRCkJs F2ZzaEYYTRNaEh5bEQpCQBdpTE9tEkZAE1pQZxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxg RCnlDF2BAHE5ZZEdcY2ZFEQpZSxcTHBoSEQpwZxdsGlJsYl4Ff0x7GxAZGhEKcGgXbmx6bURCUB psS1MQGRoRCnBoF2RfU1tzfm1uQklZEBkaEQpwaBdvX3tyTBJbXFBeHhAZGhEKcGgXbG1mQHB5e WZtZxkQGRoRCnBoF2ZzRh8eGAVcZVsfEBkaEQpwfRdmUG5SG2xJWlpnexAeEhEKcH8XZRl5Zl5H aRtkT3MQGxsbEQpwXxdrWlhyWGJjQmlFQhAZGhEKcGwXaFt4TnpnWkBTUGYQGRoRCm1+FxsRClh NF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 suspectscore=0 clxscore=201 mlxscore=0 bulkscore=0 spamscore=0 mlxlogscore=816 impostorscore=0 adultscore=0 phishscore=0 priorityscore=355 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112020111 domainage_hfrom=9608 X-Spam-Score: 0 X-Spam-OrigSender: melomcr@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Marcelo C. R. Melo" --00000000000079070105d22ccdd4 Content-Type: text/plain; charset="UTF-8" Hi Jing Liang, This may be related to a difference in atom numbering between VMD and NAMD, one being one-based and the other zero-based, so the atom numbers would be shifted by 1. However, it is hard to say without knowing more about your system. Do you mind sharing a minimal example and the steps you are taking with QwikMD? Regarding the description for the qmLinkElement parameter, it should get the two indices for the QM and MM atoms involved in the QM-MM bond, as well as the element string. If there is only one QM-MM bond in your simulation, you will not need to pass the atom numbers, just the element. Best, Marcelo On Thu, 2 Dec 2021 at 04:25, jing liang wrote: > Hi, > > I don't understand well the description of the parameter qmLinkElement > from the documentation page: > https://www.ks.uiuc.edu/Research/namd/2.14/ug/node90.html#47512 > > It looks to me that when there are two or more bonds I need to pass the > atom numbers of the MM atoms involved. Are these atom numbers obtained from > the *psf file? > > I used QwikMD for setting the simulation and when I look at the value that > this parameter got it says: > > #QMLinkElement "18 38 Cl" > > but the numbers 18 and 38 don't correspond to the atom numbers in the psf > file of the atoms involved in the bond. > > I wonder how the numbers 18 and 38 are obtained? What they are? > > thank you > > > > --00000000000079070105d22ccdd4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Jing Liang,

This may be related to a= difference=C2=A0in atom numbering between VMD and NAMD, one being one-base= d and the other zero-based, so the atom numbers would be shifted by 1. Howe= ver, it is hard to say without knowing more about your system.=C2=A0
<= div>Do you mind sharing a minimal example=C2=A0and the steps you are taking= with QwikMD?

Regarding the=C2=A0description for t= he qmLinkElement parameter, it should get the two=C2=A0indices for the QM a= nd MM atoms involved in the QM-MM bond, as well as the element string. If t= here is only one QM-MM bond in your simulation, you will not need to pass t= he atom numbers, just the element.

Best,
Marcelo

On Thu, 2 Dec 2021 at 04:25, jing liang <jingliang2015@gmail.com> wrote:
Hi= ,

I don't understand well the description of t= he parameter qmLinkElement from the documentation page: = https://www.ks.uiuc.edu/Research/namd/2.14/ug/node90.html#47512

It looks to me that when there are two or more bonds I ne= ed to pass the atom numbers of the MM atoms involved. Are these atom number= s obtained from the *psf file?

I used QwikMD = for setting the simulation and when I look at the value that this parameter= got it says:

#QMLinkElement "18 38 Cl&q= uot;

but the numbers 18 and 38 don't correspon= d to the atom numbers in the psf file of the atoms involved in the bond.

I wonder how the numbers 18 and 38 are obtained= ? What they are?

thank you



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Sat, 4 Dec 2021 13:57:23 +0000 Date: Sat, 4 Dec 2021 13:56:47 +0000 (UTC) From: Fateme Ghadirian To: NAMD List Message-ID: <1106941959.1215584.1638626207144@mail.yahoo.com> Subject: namd-l: eFieldNormalized MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1215583_61403780.1638626207140" References: <1106941959.1215584.1638626207144.ref@mail.yahoo.com> X-Mailer: WebService/1.1.19306 YMailNorrin X-Proofpoint-ORIG-GUID: iYVJZpUaBet26nNPO2AmIPHpFqrKo_Rn X-CLX-Shades: MLX X-CLX-Response: 1TFkXGR0TEQpMehcZHhoRCllEF2tfQX1nbkdQaUxnEQpYWBd6X1lGGWZTY2M ZbxEKeE4XekQcHW9FbG1EQ2YRCnlMF2wTWF4YfUZtck4cEQpDSBcHGx4SEQpDWRcHGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXHhtxGwYSG3cGGx4dBhIbQhsaBhoGGxoaBhpxGhAadwYaBhsaBhoGG gYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdDc3xgcFp/S2hPXhgcRGR6 ZRhrR2N6YlpsW1hhRXV4RBEKWFwXHwQaBBgeGAUbGgQbGhoEHQQbHh4QGx4aHxoRCl5ZF3MeeEJ MEQpNXBcYHhgRCkxaF2hpa2trEQpMRhdva2tva2sRCkJPF2tMbkRTXmlYeUJoEQpDWhccHAQbHB kEGxIeBBseHBEKQl4XGxEKQlwXGxEKXk4XGxEKQksXekQcHW9FbG1EQ2YRCkJJF3pEHB1vRWxtR ENmEQpCRRdlf08SUxxBBWMFbREKQk4XekQcHW9FbG1EQ2YRCkJMF3pfWUYZZlNjYxlvEQpCbBdr QUZAaGR8Ux1uQhEKQkAXZnxdfU9BYEhHc0ERCkJYF2dzZXNAbmFhTF1iEQpNXhcHGxEKWlgXGRE KeUMXZnxdfU9BYEhHc0ERCllLFxMSGx0RCnBoF2EfBRocTQETcEt+EAcZGhEKcGgXbkRLWm9wSR huQBwQBxkaEQpwaBdpUBkBc0N7fx9nQRAHGRoRCnBoF2xQRl56S0heaFxEEAcZGhEKcGgXbF5pb U9ZX19/G2IQBxkaEQpwfRdmU29jU2gTX1p9YxAHGRoRCnB9F2tkW19ZAVBNb2NIEAcZGhEKcH0X b2NASGRaYBxQTHIQBxkaEQpwfxdgbGZGfHljU3IaaxAbHhsRCnBfF2xiYFhjT0FAXmRMEAcZGhE KcH8XZRl5Zl5HaRtkT3MQHB4RCnBfF2dOXAFleEFLZ11mEAcZGhEKcF8XaR5HaWxgSAFmeEwQBx kaEQpwbBdpWXgFU3x/E2liSxAHGRoRCnBMF2YFYRxHHUZheUN/EAcZGhEKbX4XBxsRClhNF0sRI A== X-Proofpoint-GUID: iYVJZpUaBet26nNPO2AmIPHpFqrKo_Rn X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 malwarescore=0 bulkscore=0 adultscore=0 clxscore=379 spamscore=0 suspectscore=0 mlxlogscore=809 impostorscore=0 priorityscore=340 mlxscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112040086 domainage_hfrom=9817 X-Spam-Score: 0 X-Spam-OrigSender: fateme.ghadirian@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fateme Ghadirian ------=_Part_1215583_61403780.1638626207140 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear NAMD users, I have a system which contains a fully hydrated bilayer with some particles= in the aqueous part of the system.=C2=A0I did not use any free ions in the= aqueous part of the system, so I justhave water +Bilayer + water+ some neu= tral particles in water.=C2=A0 The simulation run is in NPT to represent at= mospheric pressure of a natural cell.=C2=A0I want to addconstant electric f= ield in the z direction (bilayer's normal vector)=C2=A0to this system to in= vestigate its possible effects on theparticles and the bilayer.=C2=A0In the= following tutorial: http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion-co= nduction It has used eFieldOn yes eField 0.0 0.0 -0.134 In its .conf file to run the constant electric field simulation. But in the following link https://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.html The electric field in the .conf file has been applied as follows eFieldOn yes eField 0.0 0.0 -0.134 eFieldNormalized yes By searching in namd-l threads, I have found some opposite explanations abo= ut eFieldNormilized,=C2=A0which are given below: namd-l: Re: Electric field simulation: eFieldNormalized |=20 |=20 | |=20 namd-l: Re: Electric field simulation: eFieldNormalized | | | 1) The eFieldNormilized statement=C2=A0is=C2=A0intended to avoid excessive = pressure=C2=A0in an NPT simulation in the presence of a constant electric f= ield. 2) The eFieldNormalized does not protect the simulation from =E2=80=9Cexces= sive pressure=E2=80=9D: it simply defines the electric field with units rel= ative to the unit cell. I do not understand what eFieldNormalized means and what its function in an= electric field simulation is, any help for its clarification would be appr= eciated. And also I need to apply constant electric field to my NPT simulation, shou= ld I use eFieldNormalized yes or not???=C2=A0I do not have free ions in my = system. What are the consequences of not using the eFieldNormalized in Simulations? =C2=A0 Thanks in advance ------=_Part_1215583_61403780.1638626207140 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear NAMD users,

I have a system which contains a fully hydrated bi= layer with some particles in the aqueous part of the system. I did not use any free ion= s in the aqueous part of the system, so I just have water +Bilayer + water+ some neutral particles in water. <= /span> The simulation run is in NPT to represent atmospheric pressure of a natural cell.&nbs= p;I want to add constant electric field in the z direction (bilayer's normal vector) <= /span>to this system to investigate its possible ef= fects on the particles and the bilayer. In the following tutorial:

http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion= -conduction

It has used

eFieldOn yes

eField 0.0 0.0 -0.134=

In its .c= onf file to run the constant electric field simulation.

But in the following link

https://www.ks.uiuc.edu/Research/namd/= 2.10b1/ug/node42.html

The electric field in the .conf file has been appli= ed as follows

eFieldOn yes

eField 0.0 0.0 -0.134

=

eFieldNormalize= d yes

By searching in namd= -l threads, I have found some opposite explanations about eFieldNormilized,=  which are given below:

= namd-l: Re: Elec= tric field simulation: eFieldNormalized

=

=

1) The eFieldNormili= zed statement is=  intended to avoid excessive pressure = in an NPT simulation in the presence of a constant electric fie= ld.

2) The eFieldNormalized does not protect th= e simulation from =E2=80=9Cexcessive pressure=E2=80=9D: it simply defines t= he electric field with units relative to the unit cell.



I do not understand what eFieldNormalized means and= what its function in an electric field simulation is, any help for its clarification would be appreciated.

And also I need to apply = constant electric field to my NPT simulation, should I use eFieldNormalized= yes or not??? I do not have free ions in my system.

What are the consequences of not using the eFieldNormaliz= ed in Simulations?

 

Thank= s in advance



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boundary="00000000000091797505d2579cbf" X-Proofpoint-ORIG-GUID: NUGD08uUOmZB9u5SP7BA1ngk-wSM1XlQ X-CLX-Response: 1TFkXGBgTEQpMehcYHR8RCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGBITEQpDWRcHGB8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYYGhNxGB4cEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF2R/bW4aEl9/ZUdwaBNfH3l6HWhrG0RNQQddeWcbckZ7EQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXcx59BWkRCk1cFxgSEhEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRkRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF29BHk0FTHhBSB1nEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXYUVsS3lLTB56QhgRCllLFxMcGxoRCnBoF2xaek5QZht9E19mEBkaEQpwaBdsZFwcbE19em BYWBAZGhEKcGgXYBNoc3pTQGZQfEUQGRoRCnBoF2NFWkN7eE55eR9NEBkaEQpwaBd6Z3x5SW9lZ mNgbRAZGhEKcH0XYBlkUFgBfl1gen4QGRoRCnB/F2UZeWZeR2kbZE9zEB8cEQpwXxdrWlhyWGJj QmlFQhAZGhEKcGwXZh97WFxiBUtYZB8QGRoRCnBMF2YFYRxHHUZheUN/EBkaEQptfhcbEQpYTRd LESA= X-Proofpoint-GUID: NUGD08uUOmZB9u5SP7BA1ngk-wSM1XlQ X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 spamscore=0 lowpriorityscore=0 clxscore=229 adultscore=0 mlxlogscore=999 suspectscore=0 malwarescore=0 mlxscore=0 bulkscore=0 priorityscore=275 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112040131 domainage_hfrom=9610 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000091797505d2579cbf Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Part of the info that you're asking to clarify is not correct. The second of the two links that you shared is the *documentation* of the electric keywords, i.e. it is not a tutorial with a pre-cooked input that you may copy and paste for your pruse. Here's the updated one for 2.14: https://www.ks.uiuc.edu/Research/namd/2.14/ug/node42.html Just because the eFieldNormalized keyword is listed in the manual, it doesn't mean that you must necessarily add it to your input. It is there for you to read what that keyword does, and then decide whether it's needed based on the specifics of your scientific question. Do you want to specify a constant field, or a constant potential drop between the edges of the unit cell? That's essentially what that keyword is asking. That decision is up to you. Giacomo On Sat, Dec 4, 2021 at 9:00 AM Fateme Ghadirian < fateme.ghadirian@remove_yahoo.com> wrote: > Dear NAMD users, > I have a system which contains a fully hydrated bilayer with some > particles in the aqueous part of the system. I did not use any free ions > in the aqueous part of the system, so I just have water +Bilayer + water+ > some neutral particles in water. The simulation run is in NPT to > represent atmospheric pressure of a natural cell. I want to add constant > electric field in the z direction (bilayer's normal vector) to this > system to investigate its possible effects on the particles and the > bilayer. In the following tutorial: > > > http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion-= conduction > > It has used > > eFieldOn yes > > eField 0.0 0.0 -0.134 > *In its .conf file to run the constant electric field simulation**.* > > *But in the following link* > > https://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.html > > *The electric field in the .conf file has been applied as follows* > > eFieldOn yes > > eField 0.0 0.0 -0.134 > > eFieldNormalized yes > > *By searching in namd-l threads, I have found some opposite explanations > about eFieldNormilized, which are given below:* > > *namd-l: Re: Electric field simulation: eFieldNormalized > * > > *namd-l: Re: Electric field simulation: eFieldNormalized > * > > > *1) The eFieldNormilized statement *is* intended to avoid excessive > pressure* *in an NPT simulation in the presence of a constant electric > field.* > > 2) The eFieldNormalized does not protect the simulation from =E2=80=9Cexc= essive > pressure=E2=80=9D: it simply defines the electric field with units relati= ve to the > unit cell. > > > *I do not understand what eFieldNormalized means and what its function in > an electric field simulation is, any help for its clarification would be > appreciated.* > > *And also I need to apply constant electric field to my NPT simulation, > should I use eFieldNormalized yes or not??? I do not have free ions in my > system.* > > *What are the consequences of not using the eFieldNormalized in > Simulations?* > > > > > > *Thanks in advance* > > > --00000000000091797505d2579cbf Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Part of the info that you're asking to clarify is not = correct.

The second of the two links that you shared is = the documentation of the electric keywords, i.e. it is not a tutoria= l with a pre-cooked input that you may copy and paste for your pruse.=C2=A0= Here's the updated one for 2.14:
https://www.ks.uiuc.e= du/Research/namd/2.14/ug/node42.html
Just because the eFieldNormaliz= ed keyword is listed in the manual, it doesn't mean that you must neces= sarily add it to your input.=C2=A0 It is there for you to read what that ke= yword does, and then decide whether it's needed based on the specifics = of your scientific question.

Do you want to specify a constant field= , or a constant potential drop between the edges of the unit cell?=C2=A0 Th= at's essentially what that keyword is asking.=C2=A0 That decision is up= to you.

Giacomo

On Sat, Dec 4, 2021 at 9:00 AM Fateme Ghad= irian <fateme.ghadirian@remove_yahoo.com> wrote:

Dear NAMD users,

I have a system which contains a fully hydrated bilayer with some parti= cles in the aqueous part of the system.=C2=A0I did not use any free ions in the aqueous part of = the system, so I just have water +Bilayer + water+ some neutral particles in water.=C2=A0<= /span> The simulation run is in NPT to represent atmospheric pressure of a natural cell.=C2=A0I = want to add constant electric field in the z direction (bilayer's normal vector)=C2= =A0to this system to investigate its possible effect= s on the particles and the bilayer.=C2=A0In the following tutorial:

http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion= -conduction

It has used

eFieldOn yes

= eField 0.0 0.= 0 -0.134

In its .conf file to run the constant electric field si= mulation= .

But in the following link

https:= //www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.html

=

The electric field in the .conf file has been applied as fo= llows

eFieldOn yes

eField 0.0 0.0 -0.134

eFieldNo= rmalized yes

By = searching in namd-l threads, I have found some opposite explanations about = eFieldNormilized,=C2=A0which are given below:

namd-l: Re: Ele= ctric field simulation: eFieldNormalized


=

namd-l: Re= : Electric field simulation: eFieldNormalized


1) The eFieldNormilized statement=C2=A0is=C2=A0i= ntended to avoid excessive pressure=C2=A0in an NPT simulation in the presence of a constan= t electric field.

2) The eFieldNormalized does not protect the = simulation from =E2=80=9Cexcessive pressure=E2=80=9D: it simply defines the= electric field with units relative to the unit cell.



I do not understand what eFieldNo= rmalized means and what its function in an ele= ctric field simulation is, any help for its clarification wou= ld be appreciated.

And also I need to apply constant electric f= ield to my NPT simulation, should I use eFieldNormalized yes or not???=C2= =A0I do not have free ions in my system.=

What are the consequences of= not using the eFieldNormalized in Simulations?

=C2=A0

Thanks in advance



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Sat, 04 Dec 2021 19:24:37 -0800 (PST) MIME-Version: 1.0 References: <1106941959.1215584.1638626207144.ref@mail.yahoo.com> <1106941959.1215584.1638626207144@mail.yahoo.com> In-Reply-To: From: Hemanth Haridas Date: Sun, 5 Dec 2021 08:54:25 +0530 Message-ID: Subject: Re: namd-l: eFieldNormalized To: namd-l@ks.uiuc.edu, fateme.ghadirian@yahoo.com Content-Type: multipart/alternative; boundary="0000000000000a430405d25dae39" X-CLOUD-SEC-AV-Sent: true X-CLOUD-SEC-AV-Info: iitgn,google_mail,monitor X-Gm-Spam: 0 X-Gm-Phishy: 0 X-CLX-Response: 1TFkXGxwZEQpMehcaEQpZRBd6TGFZQlJpY2BGHxEKWFgXaUVcWHhmZhsYXxk RCnhOF2dpW2ZtYl9AGwFjEQp5TBdkbEseZX4TYmxkfhEKQ0gXBxsZHREKQ1kXBxgfEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4ZcR8YEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxtzRV9ZUkxleXJEW2YZYH5yR1lBfWBcGGRIUn9uf2IcEQpYXBcfBBoEGB4YBRsa BBsbGgQdBBsZGBAbHhofGhEKXlkXcx5OfXgRCk1cFxsZGBEKTFoXfGlNTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxd6TENJc2l5AVtAexEKQ1oXGBoTBBIfBBgbGgQeExEKQl 4XGxEKRF4XGBEKQkUXYkdgb3IBXFpcHW0RCkJOF2dpW2ZtYl9AGwFjEQpCTBdpRVxYeGZmGxhfG REKQmwXZkdpBWV4Uh9sek4RCkJAF29BHk0FTHhBSB1nEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEK WlgXGBEKeUMXYUVsS3lLTB56QhgRCllLFx4dHxgRCnBoF2lsZhN9XU5+fklhEBkaEQpwaBdkQk5 pTxsFTX9wZhAZGhEKcGgXbl9kYk9JWkhdZVMQGRoRCnBoF3peeVNtbWBFXExdEBkaEQpwaBdsXG R5SU1LfmNiRhAZGhEKcGwXZ2QFZ3gcSEtvU3AQGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: 1YousxfOSXnqL3JTXmskWJv2NbxUDUH6 X-Proofpoint-GUID: 1YousxfOSXnqL3JTXmskWJv2NbxUDUH6 X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=6 clxscore=163 malwarescore=0 mlxscore=6 suspectscore=0 lowpriorityscore=0 mlxlogscore=118 bulkscore=0 spamscore=6 adultscore=0 phishscore=0 priorityscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112050019 domainage_hfrom=4752 X-Spam-Score: 6 X-Spam-OrigSender: hemanth.h@iitgn.ac.in X-Spam-Bar: * Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hemanth Haridas --0000000000000a430405d25dae39 Content-Type: text/plain; charset="UTF-8" I would like to add a few points to the discussion. I was in a similar situation some 8 months ago where I had to apply a constant potential bias accross the system. I tried both efieldNormalized and efield keywords, and found that if you are interested in applying a constant potential bias accross the system, you must not use efieldNormalized. Best, Hemanth --0000000000000a430405d25dae39 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I would like to add a few points to the discussion. I was= in a similar situation some 8 months ago where I had to apply a constant p= otential bias accross the system. I tried both efieldNormalized and efield = keywords, and found that if you are interested in applying a constant poten= tial bias accross the system, you must not use efieldNormalized.

Best,
Hemanth
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Sun, 5 Dec 2021 15:29:41 +0000 Date: Sun, 5 Dec 2021 15:29:36 +0000 (UTC) From: Fateme Ghadirian To: "namd-l@ks.uiuc.edu" , Giacomo Fiorin Message-ID: <133477374.8463213.1638718176459@mail.yahoo.com> In-Reply-To: References: <1106941959.1215584.1638626207144.ref@mail.yahoo.com> <1106941959.1215584.1638626207144@mail.yahoo.com> Subject: Re: namd-l: eFieldNormalized MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_8463212_1659378242.1638718176455" X-Mailer: WebService/1.1.19306 YMailNorrin X-Proofpoint-GUID: EyXpDUJze9PABfQ_VTkjqeqhIh44u5ov X-CLX-Shades: MLX X-CLX-Response: 1TFkXGR0fEQpMehcZGRkRCllEF2tfQX1nbkdQaUxnEQpYWBd6X1lGGWZTY2M ZbxEKeE4XekQcHW9FbG1EQ2YRCnlMF2wTWF4YfUZtck4cEQpDSBcHGRIaEQpDWRcHGB8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxsTcRsGGRJ3BhsSHAYbGhpCHQYaBhsaGgYZGnEbEBp3BhoGGgYaB gccGgYaBhpxGhAadwYaEQpZXhdsbHkRCklGF19DX0l1QkVZXk9OEQpDThdvU3Jabn9gUE8Temto THt1fH5BQFtPW0JjQh4eXx9FXBEKWFwXHwQaBBgeGAUbGgQbGxoEHQQbGRsQGx4aHxoRCl5ZF3M eRAFoEQpNXBcYEx0RCkxaF3hpTWtrEQpFWRdvaxEKTF8XegUFBQUFBQUFBW8RCkxGF29ra2xrax EKQk8Xa0xuRFNeaVh5QmgRCkNaFxwcBBscGQQbEhIEGx4dEQpCXhcbEQpEXhcZEQpCXBcbEQpeT hcbEQpCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRCkJFF2V/TxJTHEEFYwVtEQpCThd6 RBwdb0VsbURDZhEKQkwXel9ZRhlmU2NjGW8RCkJsF2tBRkBoZHxTHW5CEQpCQBdvQR5NBUx4QUg dZxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2FFbEt5S0weekIYEQpZSxcTEhsSEQ pwZxduXFhfS1hveUxjGBAZGhEKcGgXYV9DUBxrWWd5E1kQGRoRCnBoF3pieFobQRxfZ1BEEBkaE QpwaBdvcB9uRX0deXtaGxAZGhEKcGgXYR5cQnocX35CZX4QGRoRCnBoF2cYfnxmZUUabFxeEBka EQpwfRdgGWRQWAF+XWB6fhAZGhEKcH8XZRl5Zl5HaRtkT3MQGxoeEQpwXxdrWlhyWGJjQmlFQhA ZGhEKcGwXaVl4BVN8fxNpYksQHhIRCm1+FxsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: EyXpDUJze9PABfQ_VTkjqeqhIh44u5ov X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=333 bulkscore=0 clxscore=375 impostorscore=0 mlxscore=0 adultscore=0 malwarescore=0 phishscore=0 spamscore=0 mlxlogscore=999 suspectscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112050089 domainage_hfrom=9818 X-Spam-Score: 0 X-Spam-OrigSender: fateme.ghadirian@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fateme Ghadirian ------=_Part_8463212_1659378242.1638718176455 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable =20 May be I did not properly describemy problem. This is the issue=E2=80=99s details: Iwanted to add a constant electric field (not constant potential drop betwe= enthe edges of the system) on my fully hydrated bilayer in NPT ensemble sim= ulation.I saw there was =E2=80=98eFieldNormalized=E2=80=99 keyword and I di= d not get what exactly itdoes, even by searching and studying some related = links (even though it seemed to me that it maybe somehow affects system=E2= =80=99s pressure, but in the second link of previous email,it has mentioned= that when eFieldNormalized is true the eField forces do notcontribute to t= he pressure calculation). So Ihave ran 2 identical fully hydrated bilayer systems, with and without e= FieldNormalizedkeyword.=20 For bothof them the electric fields has been applied in z direction (bilaye= r=E2=80=99s normal)and its value was chosen a big one ( Ez (kcal/mol.A.e)*L= z(A)*0.0434(Volts/A)=3D10Volts,Box_Lz~100 Ang ) to see the visual differenc= es. Periodic boundary conditionswere applied in all directions. WitheFieldNormalized set to on, I could not see any pore formation in the l= ipidbilayer, or even any water fingers in the hydrophobic part of bilayer. = It seemsif I want to see pore formation, eFieldNormalized musb be off?! And bychecking Total energy and volume of the system (when eFieldNormalized= set to on),there were not any changes before and after exerting the electr= ic field! Butfor the case without eFieldNormalized (efield on, eFieldNormal= ized off), therewas a great drop in Total energy and Volume of the system r= ight after exertingthe e field and then with time passing, they stood stead= y. And also there waspore formation and even lipid distortion. Whythere is no change in total energy and volume of the system wheneFieldNo= rmalized set to on? and why there is no pore formation, even with sucha big= electric field value?! Is it because when eFieldNormalized is true the eFi= eld forces do not contribute to thepressure calculation? Byprevious email, I meant eFieldNormalized exact function, which I am tryin= g toget by different simulations. Alsothe contents of link that you have mentioned, seems the same as the lin= k that Isent before, to me. I did not see any differences or updates. There= was thesame description of eFieldNormalized in both of them.=20 =C2=A0 Fateme On Sunday, December 5, 2021, 12:12:34 AM GMT+3:30, Giacomo Fiorin wrote: =20 =20 Part of the info that you're asking to clarify is not correct. The second of the two links that you shared is the documentation of the ele= ctric keywords, i.e. it is not a tutorial with a pre-cooked input that you = may copy and paste for your pruse.=C2=A0 Here's the updated one for 2.14: https://www.ks.uiuc.edu/Research/namd/2.14/ug/node42.html Just because the eFieldNormalized keyword is listed in the manual, it doesn= 't mean that you must necessarily add it to your input.=C2=A0 It is there f= or you to read what that keyword does, and then decide whether it's needed = based on the specifics of your scientific question. Do you want to specify a constant field, or a constant potential drop betwe= en the edges of the unit cell?=C2=A0 That's essentially what that keyword i= s asking.=C2=A0 That decision is up to you. Giacomo On Sat, Dec 4, 2021 at 9:00 AM Fateme Ghadirian wrote: Dear NAMD users, I have a system which contains a fully hydrated bilayer with some particles= in the aqueous part of the system.=C2=A0I did not use any free ions in the= aqueous part of the system, so I justhave water +Bilayer + water+ some neu= tral particles in water.=C2=A0 The simulation run is in NPT to represent at= mospheric pressure of a natural cell.=C2=A0I want to addconstant electric f= ield in the z direction (bilayer's normal vector)=C2=A0to this system to in= vestigate its possible effects on theparticles and the bilayer.=C2=A0In the= following tutorial: http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion-co= nduction It has used eFieldOn yes eField 0.0 0.0 -0.134 In its .conf file to run the constant electric field simulation. But in the following link https://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.html The electric field in the .conf file has been applied as follows eFieldOn yes eField 0.0 0.0 -0.134 eFieldNormalized yes By searching in namd-l threads, I have found some opposite explanations abo= ut eFieldNormilized,=C2=A0which are given below: namd-l: Re: Electric field simulation: eFieldNormalized |=20 |=20 | |=20 namd-l: Re: Electric field simulation: eFieldNormalized | | | 1) The eFieldNormilized statement=C2=A0is=C2=A0intended to avoid excessive = pressure=C2=A0in an NPT simulation in the presence of a constant electric f= ield. 2) The eFieldNormalized does not protect the simulation from =E2=80=9Cexces= sive pressure=E2=80=9D: it simply defines the electric field with units rel= ative to the unit cell. I do not understand what eFieldNormalized means and what its function in an= electric field simulation is, any help for its clarification would be appr= eciated. And also I need to apply constant electric field to my NPT simulation, shou= ld I use eFieldNormalized yes or not???=C2=A0I do not have free ions in my = system. What are the consequences of not using the eFieldNormalized in Simulations? =C2=A0 Thanks in advance =20 ------=_Part_8463212_1659378242.1638718176455 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

May be I did not pro= perly describe my problem.

This is the = issue=E2=80=99s details:

I wanted to add a constant electric field (not constant potential drop bet= ween the edges of the system) on my fully hydrated bilayer in NPT ensemble s= imulation. I saw there was =E2=80=98eFieldNormalized=E2=80=99 keyword and I did not ge= t what exactly it does, even by searching and studying some related links (even though it seemed to me that it may be somehow affects system=E2=80=99s pressure, but in the second link of pre= vious email, it has mentioned that when eFieldNormalized is true the eField forces do no= t contribute to the pressure calculation).

So I have ran 2 identical fully hydrated bilayer systems, with and without eFiel= dNormalized keyword.

For both of them the electric fields has been applied in z direction (bilayer=E2=80= =99s normal) and its value was chosen a big one ( Ez (kcal/mol.A.e)*Lz(A)*0.0434(Volts/A= )=3D10Volts, Box_Lz~100 Ang ) to see the visual differences. Periodic boundary condition= s were applied in all directions.

With eFieldNormalized set to on, I could not see any pore formation in the lipid bilayer, or even any water fingers in the hydrophobic part of bilayer. It s= eems if I want to see pore formation, eFieldNormalized musb be off?!

And by checking Total energy and volume of the system (when eFieldNormalized set t= o on), there were not any changes before and after exerting the electric field! Bu= t for the case without eFieldNormalized (efield on, eFieldNormalized off), th= ere was a great drop in Total energy and Volume of the system right after exert= ing the e field and then with time passing, they stood steady. And also there w= as pore formation and even lipid distortion.

Why there is no change in total energy and volume of the system when eFieldNormalized set to on? and why there is no pore formation, even with s= uch a big electric field value?! Is it because when eFieldNormalized is true the eField forces do not con= tribute to the pressure calculation?

By previous email, I meant eFieldNormalized exact function, which I am trying = to get by different simulations.

Also the contents of link that you have mentioned, seems the same as the link th= at I sent before, to me. I did not see any differences or updates. There was the same description of eFieldNormalized in both of them.

 

Fateme


=20
=20
On Sunday, December 5, 2021, 12:12:34 AM GMT+3:30, Giac= omo Fiorin <giacomo.fiorin@gmail.com> wrote:


Part o= f the info that you're asking to clarify is not correct.

The second of the two links that you shared is the docum= entation of the electric keywords, i.e. it is not a tutorial with a pre= -cooked input that you may copy and paste for your pruse.  Here's the = updated one for 2.14:
https://www.ks.uiuc.edu/Research/namd/2.14/ug= /node42.html
Just because the eFieldNormalized keywor= d is listed in the manual, it doesn't mean that you must necessarily add it= to your input.  It is there for you to read what that keyword does, a= nd then decide whether it's needed based on the specifics of your scientifi= c question.

Do you want to specify a c= onstant field, or a constant potential drop between the edges of the unit c= ell?  That's essentially what that keyword is asking.  That decis= ion is up to you.

Giacomo

On Sat, Dec 4, 2021 at 9:0= 0 AM Fateme Ghadirian <fateme.ghadirian@remove= _yahoo.com> wrote:

Dear NAMD users,

<= div dir=3D"ltr">I have a system which contains a fully hydrated bilayer with som= e particles in the aqueous part of the system. I did not use any free ions in the aqueous = part of the system, so I just have water +Bilayer + water+ some neutral particles in water. <= /span> The simulation run is in NPT to represent atmospheric pressure of a natural cell. I= want to add constant electric field in the z direction (bilayer's normal vector) <= /span>to this system to investigate its possible effects o= n the particles and the bilayer. In the following tutorial:

http://bionano.physics.illinois.edu/= tutorials/electrostatic-maps-and-ion-conduction

It has used

eFieldOn yes

eField 0.0 0.0 -0.134

= In its .conf file to run the constant electric field simulat= ion.

=

But in the foll= owing link

https://www.ks.uiuc.edu/Resear= ch/namd/2.10b1/ug/node42.html

The electric field in the .conf file has been applied as = follows

eFieldOn yes

eField 0.0 0.0 -0.134

= eFieldNormalized yes

By searchin= g in namd-l threads, I have found some opposite explanations about eFieldNo= rmilized, which are given below:

namd-l: Re: Electric field simulat= ion: eFieldNormalized


<= div id=3D"yiv4185429921gmail-m_1527480271221803811gmail-m_-2709254559694564= 011ydpa71256eaenhancr_card_9280831531" style=3D"max-width:400px;">

namd-l: Re: = Electric field simulation: eFieldNormalized



1) The = eFieldNormilized statement is=  intended to avoid excessive pressure in an NPT simula= tion in the presence of a constant electric field.

2) The eFie= ldNormalized does not protect the simulation from =E2=80=9Cexcessive pressu= re=E2=80=9D: it simply defines the electric field with units relative to th= e unit cell.

<= br clear=3D"none">

I do not understand what eFieldNormali= zed means and what its function in an electr= ic field simulation is, any help for its clarification would = be appreciated.

And also I need to apply constant electric field to= my NPT simulation, should I use eFieldNormalized yes or not??? = I do not have free ions in my system.=

What are= the consequences of not using the eFieldNormalized in Simulations?<= /span>

 

Thanks in advance

<= /span>



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Sun, 5 Dec 2021 15:32:27 +0000 Date: Sun, 5 Dec 2021 15:32:22 +0000 (UTC) From: Fateme Ghadirian To: "namd-l@ks.uiuc.edu" , Hemanth Haridas Message-ID: <1992215342.8438455.1638718342843@mail.yahoo.com> In-Reply-To: References: <1106941959.1215584.1638626207144.ref@mail.yahoo.com> <1106941959.1215584.1638626207144@mail.yahoo.com> Subject: Re: namd-l: eFieldNormalized MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_8438454_2077669500.1638718342841" X-Mailer: WebService/1.1.19306 YMailNorrin X-Proofpoint-ORIG-GUID: LHOlgMDZOooMj0bgEnWrMD7xCJXtf13_ X-CLX-Response: 1TFkXHBIRCkx6FxkYGREKWUQXa19BfWduR1BpTGcRClhYF3pfWUYZZlNjYxl vEQp4Thd6RBwdb0VsbURDZhEKeUwXbBNYXhh9Rm1yThwRCkNIFwcYGxIRCkNZFwcYHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3Bh4ScRgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19JdUJFW V5PThEKQ04XZmJlRk1nbnBlRUVnQBpITW9EfVhnbh1SaWByXkwbGXURClhcFx8EGgQYHhgFGxoE GxoaBB0EGx4ZEBseGh8aEQpeWRdzHkVrRBEKTVwXGx8SEQpMWhd4aU1raxEKRVkXb2sRCkxfF3o FBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2tMbkRTXmlYeUJoEQpDWhccHAQbHBkEGxIfBBkbEQ pCXhcbEQpEXhcZEQpCXBcbEQpeThcbEQpCSxd6RBwdb0VsbURDZhEKQkkXekQcHW9FbG1EQ2YRC kJFF2V/TxJTHEEFYwVtEQpCThd6RBwdb0VsbURDZhEKQkwXel9ZRhlmU2NjGW8RCkJsF2tBRkBo ZHxTHW5CEQpCQBdvQR5NBUx4QUgdZxEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2F FbEt5S0weekIYEQpZSxcTEhsSEQpwZxdlZG0FfkhHfxJdHxAZGhEKcGgXbXoYXXxmGFxdY3sQGR oRCnBoF2huQlhHWElrSVt5EBkaEQpwaBdlGkcfaExHEm8dHRAZGhEKcGgXZ2VNfklJXhIYaH4QG RoRCnBoF2BBAXleaXBCGFpGEBkaEQpwbBdpWXgFU3x/E2liSxAeEhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: LHOlgMDZOooMj0bgEnWrMD7xCJXtf13_ X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 impostorscore=0 spamscore=0 lowpriorityscore=0 clxscore=68 adultscore=0 mlxlogscore=412 suspectscore=0 malwarescore=0 mlxscore=0 bulkscore=0 priorityscore=323 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112050089 domainage_hfrom=9818 X-Spam-Score: 0 X-Spam-OrigSender: fateme.ghadirian@yahoo.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fateme Ghadirian ------=_Part_8438454_2077669500.1638718342841 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable =20 Dear Hemanth,=20 Thanks for yourkind reply, appreciate for sharing your experience. Soyou mean by setting this keyword to off, we get constant potential drop f= oredges of the system. And if I want to add just constant electric field (n= otconstant potential drop), I need to set this keyword to on=E2=80=A6 Iwill check it, thank you. On Sunday, December 5, 2021, 06:58:02 AM GMT+3:30, Hemanth Haridas wrote: =20 =20 I would like to add a few points to the discussion. I was in a similar sit= uation some 8 months ago where I had to apply a constant potential bias acc= ross the system. I tried both efieldNormalized and efield keywords, and fou= nd that if you are interested in applying a constant potential bias accross= the system, you must not use efieldNormalized. Best,Hemanth =20 ------=_Part_8438454_2077669500.1638718342841 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Hemanth,

Thanks for your kind reply, appreciate for sharing your experience.

So you mean by setting this keyword to off, we get constant potential drop for edges of the system. And if I want to add just constant electric field (not constant potential drop), I need to set this keyword to on=E2=80=A6<= /p>

I will check it, thank you.

=


=20
=20
On Sunday, December 5, 2021, 06:58:02 AM GMT+3:30, Hema= nth Haridas <hemanth.h@iitgn.ac.in> wrote:


I would like to ad= d a few points to the discussion. I was in a similar situation some 8 month= s ago where I had to apply a constant potential bias accross the system. I = tried both efieldNormalized and efield keywords, and found that if you are = interested in applying a constant potential bias accross the system, you mu= st not use efieldNormalized.

Best,
<= div>Hemanth
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boundary="0000000000005302ce05d26aa93c" X-CLX-Response: 1TFkXGRkZEQpMehcbGhIRCllEF2IbckZ/TkZ/QhNMEQpYWBdtE0J6WBNzSEN DQREKeE4XZGUaYHJwbltyWh0RCnlMF2ltXmJpfk5ackRIEQpDSBcHGRkfEQpDWRcHGBsaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcbHHEbBhkYdwYbGx0GGxoaQhsbBhoGGxoaBhkacRsQGncGGgYaB hoGBxkaBhoGGnEaEBp3BhoRClleF2hjeREKSUYXX0NfSXVCRVleT04RCkNOF2tAaF0aQQdiWl1n fG1EWG9eU0NTGV9wR29fR2xJcEx9EQpYXBcfBBoEGB4YBRsaBBsbGgQdBBsZGRAbHhofGhEKXlk Xcx5bE04RCk1cFxgdHxEKTFoXeGlNa2sRCkVZF28RCkxfF3oFBQUFBQUFBQVDEQpCTxdofUFgQ1 p9c0dBExEKQ1oXGBoTBBIfBBsYEgQeHhEKQl4XGxEKQkUXaxlaEmxEWnl7RV8RCkJOF2RlGmByc G5bclodEQpCTBdtE0J6WBNzSENDQREKQmwXYXxmXG9PX39zWmARCkJAF2xFH0l5fGZyQ01wEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXaU4fWXxickxmbBwRCnBoF2NSXUxgSVgbeEh vEBkaEQpwaBdpWEBERk8aYntIUhAZGhEKcGgXbRJmG1xfHVpjXB8QGRoRCnBoF2VSE3lzfmtpBU leEBkaEQpwaBdpZktmZHMSaHwcGxAZGhEKcH0Xb2t4bmNleGxlQWwQGRoRCnB9F2d6HUlER31oe 2leEBkaEQpwfRdvYlxPZ31sc0Z6UhAZGhEKcH0XZwFfeVpcb15SGQEQGRoRCnB/F3occH4SaXxa f0VEEBsdEhEKcF8XbU1HXFJjEwVBZR4QGRoRCnB/F2VmRAEeSEZkfFobEBsYGBEKcF8Xb3tQE29 YRERFf0cQGRoRCnBfF2JEWB1rbQUdZ1wdEBkaEQpwbBdiHmVnExx6E2lsRxAZGhEKbX4XGxEKWE 0XSxEg X-Proofpoint-ORIG-GUID: AjBw0k-HpwMVGnrEtyiy3uZmEumFcZfW X-Proofpoint-GUID: AjBw0k-HpwMVGnrEtyiy3uZmEumFcZfW X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=333 malwarescore=0 mlxscore=0 suspectscore=0 lowpriorityscore=0 mlxlogscore=999 bulkscore=0 spamscore=0 adultscore=0 phishscore=0 priorityscore=108 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112050112 X-Spam-Score: 0 X-Spam-OrigSender: denilson@ufla.br X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, DENILSON FERREIRA DE OLIVEIRA --0000000000005302ce05d26aa93c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear all, 1) The C3_WIN-1-COR.str file was generated for an organic substance, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://urldefense.com/v3/__https://cgenff.umaryland.edu= /__;!!DZ3fjg!r7TXiOBr_-a2sDPPFdaSlwVkONXiVoumQ25REM534_RqlbdCV3b9vi9PM9pbFg= 7WUg$ ) 2) Using the topology files contained in toppar_c36_jul21.tgz, which is available through the MacKerell Lab Homepage ( https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*= charmm__;Iw!!DZ3fjg!r7TXiOBr_-a2sDPPFdaSlwVkONXiVoumQ25REM534_RqlbdCV3b9vi9= PM9pbBsvQnw$ ), as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55. 3) In the configuration file to carry out calculations with Namd 2.14 I have provided all the parameter files in the order that seems correct to me. The following is observed in the output from Namd: "... Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ./par_all36m_prot.prm Info: PARAMETERS ./par_all36_lipid.prm Info: PARAMETERS ./par_all36_carb.prm Info: PARAMETERS ./par_all36_na.prm Info: PARAMETERS ./par_all36_cgenff.prm Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str Info: PARAMETERS ./toppar_water_ions_namd.str Info: PARAMETERS ./C3_WIN-1-COR.str Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE " 4) However, Namd 2.14 did not perform the calculations because it encountered an error: "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1 CG1T2 (ATOMS 53401 53404 53407 53408)" 5) It is clear to me that this error is due to the fact that there is no parameter for dihedral angles of atoms of the terminal alkyne function anywhere: CG1T2 : C(sp1) terminal CG1T1 : C(sp1) non-terminal CG3C50 : C(sp3) linked to CG1T1 CG3RC1 : C(sp3) linked to CG3C50 6) To be clearer, I could not find data for the dihedral angle CG3RC1 CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in item "3" of this message. 7) In fact, it seems to me that there is no point in working with a dihedral angle for such atoms. 8) Consequently, I will be grateful if anyone can be kind enough to make a suggestion to solve the problem. Thanks. Denilson. --=20 O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de=20 responsabilidade do remetente. O uso do e-mail deve estar de acordo com os= =20 regulamentos institucionais vigentes. --0000000000005302ce05d26aa93c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dea= r all,

1) The C3_WIN-1-COR.str file was generated for an=20 organic substance, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://cgenf= f.umaryland.edu/)

2) Using the topology files contained in toppa= r_c36_jul21.tgz, which is available through the MacKerell Lab Homepage (http://mackerell.umaryland.edu/char= mm_ff.shtml#charmm), as well as the C3_WIN-1-COR.str file generated in = Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55.

3) In the configuration file to carry out calculations with Namd 2.14 I=20 have provided all the parameter files in the order that seems correct to me. The following is observed in the output from = Namd:

"...
Info: COORDINATE PDB ./6vxx_C3_WIN-1_autop= sf.pdb
Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf
Info: PARAMET= ER file: CHARMM format!
Info: PARAMETERS ./par_all36m_prot.prm
Info: = PARAMETERS ./par_all36_lipid.prm
Info: PARAMETERS ./par_all36_carb.prmInfo: PARAMETERS ./par_all36_na.prm
Info: PARAMETERS ./par_all36_cgenf= f.prm
Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str
Info: PAR= AMETERS ./toppar_water_ions_namd.str
Info: PARAMETERS ./C3_WIN-1-COR.str=
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: = SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM= FILE
"

4) However, Namd 2.1= 4 did not perform the calculations because it encountered an error:

= "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1= T1 CG1T2 (ATOMS 53401 53404 53407 53408)"

5) It is clear to me that this error is due to the fact that there is no=20 parameter for dihedral angles of atoms of the terminal alkyne function=20 anywhere:

=C2=A0 =C2=A0CG1T2 : C(sp1) terminal
=C2=A0 =C2=A0CG1T1= : C(sp1) non-terminal
=C2=A0 =C2=A0CG3C50 : C(sp3) linked to CG1T1
= =C2=A0 =C2=A0CG3RC1 : C(sp3) linked to CG3C50

6) To be clearer, I could not find data for the dihedral angle CG3RC1=20 CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed=20 in item "3" of this message.

7) In fact, it seems to me t= hat there is no point in working with a dihedral angle for such atoms.
<= br>8) Consequently, I will be grateful if anyone can be kind enough to make= a suggestion to solve the problem.

Thanks.<= font color=3D"#888888">

Denilson.

O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.
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[195.220.151.96]) by smtp.gmail.com with ESMTPSA id w22sm7517768edd.49.2021.12.05.21.32.21 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Sun, 05 Dec 2021 21:32:22 -0800 (PST) From: Fabrice Gardebien X-Google-Original-From: Fabrice Gardebien Subject: Re: namd-l: Dihedral parameters for terminal alkyne To: namd-l@ks.uiuc.edu, DENILSON FERREIRA DE OLIVEIRA References: Message-ID: Date: Mon, 6 Dec 2021 09:35:07 +0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Thunderbird/45.8.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------539BDA3C447F51450EF939B0" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBIcEQpMehcbGBIRCllEF2BLTRpnQx9bR3tkEQpYWBdoW0tEYkMYb0J /ZBEKeE4XZBwZYRlTbhhmTHMRCnlMF2lwTBNJHxNCQ1lAEQpDSBcHGRkeEQpDWRcHHB8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFx4ZcRsGEhx3BhsbEgYSH0IbHwYaBhsaGgYacRoQGncGGgYaBhoGB xwaBhoGGnEaEBp3BhoRClleF2hjeREKSUYXX0NfSXVCRVleT04RCkNOF1tGaG4fYG0SckJ6TF5t aR1Gc2dtaURkYBtpWEtuS3hdEQpYXBcfBBoEGB4YBRsaBBsaGgQdBBseGRAbHhofGhEKXlkXcx4 af2wRCk1cFxgdGREKTFoXeGlNa2sRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTx duHGcdWXJnZl5IchEKQ1oXGBoTBBIfBBgaEgQeGBEKQl4XGxEKRF4XGBEKQkUXaUhnARtFXR9sH G4RCkJOF2QcGWEZU24YZkxzEQpCTBdoW0tEYkMYb0J/ZBEKQmwXZVNSbhwYX0cBS0ERCkJAF2Zc HGx4cGhQeVJmEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxIRCnlDF2RZGUlIGF1PHENbEQp wZxdrWUBTQxJoaWtHThAHGRoRCnBoF2wcHwFyfBgaZmtcEAcZGhEKcGgXYRJgcEQBYAFhf38QBx kaEQpwaBdrbE5rYGVNbGhpRhAHGRoRCnBoF2RoeF5QTkVeX3liEAcZGhEKcGgXek0dRE9Zch5MH mwQBxkaEQpwfRdvYlxPZ31sc0Z6UhAHGRoRCnB9F2Qac09HcFMBbmBhEAcZGhEKcH0XZwFfeVpc b15SGQEQBxkaEQpwfRdiQFpHUBhzG0xMQBAHGRoRCnB9F21ER3JpE15CXWBQEAcZGhEKcH8Xehx wfhJpfFp/RUQQEx8RCnBfF2JEWB1rbQUdZ1wdEAcZGhEKcH8XYWZvWxpnZEJIHVsQGxsZEQpwXx djYhJQSGN4H3xCfRATGREKcH8XZWZEAR5IRmR8WhsQHB0RCnBfF297UBNvWERERX9HEAcZGhEKc H8XbURfRkVtfUh5GW4QGxgeEQpwXxdrRksTeWhpbnwTeBAbGhoRCnBsF2FefkcbQxxoQUgTEAcZ GhEKcEMXbWlyGWdkUx9CXF0QBxkaEQptfhcHGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: qlBD5JG8XhPftGC7lYMGCnNJ1CraDaRw X-Proofpoint-GUID: qlBD5JG8XhPftGC7lYMGCnNJ1CraDaRw MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=286 malwarescore=0 priorityscore=128 bulkscore=0 impostorscore=0 phishscore=0 suspectscore=0 mlxscore=0 spamscore=0 mlxlogscore=999 adultscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112060033 X-Spam-Score: 0 X-Spam-OrigSender: fabrice.gardebien@univ-reunion.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Fabrice Gardebien This is a multi-part message in MIME format. --------------539BDA3C447F51450EF939B0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable Dear Dennilson, I am not sure whether this could solve your problem but have you tried=20 to tick the option " Include parameters that are already in CGenFF" in=20 generating your STR file? Best wishes. On 05/12/2021 22:53, DENILSON FERREIRA DE OLIVEIRA wrote: > Dear all, > > 1) The C3_WIN-1-COR.str file was generated for an organic substance,=20 > using the CHARMM General Force Field (CGenFF) program version 2.5,=20 > through the Paramchem website (https://urldefense.com/v3/__https://cgenff= .umaryland.edu/__;!!DZ3fjg!urjR7jusgMSv5fCA8YPkDTta5__Z_ca10t9ZR-e9wkv071o2= 7Hv2sSAfi2tw1muEVQ$=20=20 > ) > > 2) Using the topology files contained in toppar_c36_jul21.tgz, which=20 > is available through the MacKerell Lab Homepage=20 > (https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.sht= ml*charmm__;Iw!!DZ3fjg!urjR7jusgMSv5fCA8YPkDTta5__Z_ca10t9ZR-e9wkv071o27Hv2= sSAfi2tNRxZRpw$=20=20 > ),=20 > as well as the C3_WIN-1-COR.str file generated in Paramchem, I=20 > prepared the pdb and psf files using VMD 1.9.4a55. > > 3) In the configuration file to carry out calculations with Namd 2.14=20 > I have provided all the parameter files in the order that seems=20 > correct to me. The following is observed in the output from Namd: > > "... > Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb > Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf > Info: PARAMETER file: CHARMM format! > Info: PARAMETERS ./par_all36m_prot.prm > Info: PARAMETERS ./par_all36_lipid.prm > Info: PARAMETERS ./par_all36_carb.prm > Info: PARAMETERS ./par_all36_na.prm > Info: PARAMETERS ./par_all36_cgenff.prm > Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str > Info: PARAMETERS ./toppar_water_ions_namd.str > Info: PARAMETERS ./C3_WIN-1-COR.str > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SKIPPING rtf SECTION IN STREAM FILE > " > > 4) However, Namd 2.14 did not perform the calculations because it=20 > encountered an error: > > "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50=20 > CG1T1 CG1T2 (ATOMS 53401 53404 53407 53408)" > > 5) It is clear to me that this error is due to the fact that there is=20 > no parameter for dihedral angles of atoms of the terminal alkyne=20 > function anywhere: > > CG1T2 : C(sp1) terminal > CG1T1 : C(sp1) non-terminal > CG3C50 : C(sp3) linked to CG1T1 > CG3RC1 : C(sp3) linked to CG3C50 > > 6) To be clearer, I could not find data for the dihedral angle CG3RC1=20 > CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed=20 > in item "3" of this message. > > 7) In fact, it seems to me that there is no point in working with a=20 > dihedral angle for such atoms. > > 8) Consequently, I will be grateful if anyone can be kind enough to=20 > make a suggestion to solve the problem. > > Thanks. > > Denilson. > > O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destina= t=C3=A1rios=20 > e de responsabilidade do remetente. O uso do e-mail deve estar de=20 > acordo com os regulamentos institucionais vigentes. --------------539BDA3C447F51450EF939B0 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit
Dear Dennilson,

I am not sure whether this could solve your problem but have you tried to tick the option " On 05/12/2021 22:53, DENILSON FERREIRA DE OLIVEIRA wrote:
Dear all,

1) The C3_WIN-1-COR.str file was generated for an organic substance, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://cgenff.umaryland.edu/)

2) Using the topology files contained in toppar_c36_jul21.tgz, which is available through the MacKerell Lab Homepage (http://mackerell.umaryland.edu/charmm_ff.shtml#charmm), as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55.

3) In the configuration file to carry out calculations with Namd 2.14 I have provided all the parameter files in the order that seems correct to me. The following is observed in the output from Namd:

"...
Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb
Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ./par_all36m_prot.prm
Info: PARAMETERS ./par_all36_lipid.prm
Info: PARAMETERS ./par_all36_carb.prm
Info: PARAMETERS ./par_all36_na.prm
Info: PARAMETERS ./par_all36_cgenff.prm
Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str
Info: PARAMETERS ./toppar_water_ions_namd.str
Info: PARAMETERS ./C3_WIN-1-COR.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
"

4) However, Namd 2.14 did not perform the calculations because it encountered an error:

"FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1 CG1T2 (ATOMS 53401 53404 53407 53408)"

5) It is clear to me that this error is due to the fact that there is no parameter for dihedral angles of atoms of the terminal alkyne function anywhere:

   CG1T2 : C(sp1) terminal
   CG1T1 : C(sp1) non-terminal
   CG3C50 : C(sp3) linked to CG1T1
   CG3RC1 : C(sp3) linked to CG3C50

6) To be clearer, I could not find data for the dihedral angle CG3RC1 CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in item "3" of this message.

7) In fact, it seems to me that there is no point in working with a dihedral angle for such atoms.

8) Consequently, I will be grateful if anyone can be kind enough to make a suggestion to solve the problem.

Thanks.

Denilson.

O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de responsabilidade do remetente. O uso do e-mail deve estar de acordo com os regulamentos institucionais vigentes.


--------------539BDA3C447F51450EF939B0-- From owner-namd-l@halifax.ks.uiuc.edu Mon Dec 6 05:46:04 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B6Bk4IL004621; Mon, 6 Dec 2021 05:46:04 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B6Bk3Ue004620; Mon, 6 Dec 2021 05:46:03 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B6Bk3YW004616; Mon, 6 Dec 2021 05:46:03 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B6Bk3Dd004615; Mon, 6 Dec 2021 05:46:03 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B6Bju5J004608 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="00000000000097705b05d278ccc9" X-CLX-Response: 1TFkXGxMaEQpMehcdGhEKWUQXZGZbXRoBQkMbfV8RClhYF2ZFS3xkTVsecFh vEQp4ThdvGBIbTAVFQWdoehEKeUwXbx9uTEZHRB9wbxIRCkNIFwcZHxgRCkNZFwccHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsdGnEeExAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThdDUmQbEmNFaF9YWFxlRXodTnllX15fHGRNY0J6YBpCGxEKWFwXHwQaBBgeGAUb GgQbGxoEHQQbGRgQGx4aHxoRCl5ZF3MeH1N6EQpNXBcYHxwRCkxaF3hpTU1NEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XZkwfTWltQUAfE3MRCkNaFxgaEwQSHwQbHB0EGx 0dEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdvGBIbTAVFQWdoehEKQkkXbxgSG0wFRUFna HoRCkJFF2Z/AUFAf2NZYVJaEQpCThdvGBIbTAVFQWdoehEKQkwXZkVLfGRNWx5wWG8RCkJsF3oa ZgFpblt6EklwEQpCQBdmXBxseHBoUHlSZhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFxIRCnl DF2RZGUlIGF1PHENbEQpZSxcdEx0fEQpwaBdpYFlOGkkcG0lIHRAeEhEKcGgXYBhbTWlbTh9Sb0 EQGRoRCnBoF2gZHm5TRkFPBWBuEBkaEQpwaBdtEmYbXF8dWmNcHxAeEhEKcGgXZVITeXN+a2kFS V4QGRoRCnB9F29iXE9nfWxzRnpSEBkaEQpwfRdhXl4fRkNPcG1hexAZGhEKcH0XZwFfeVpcb15S GQEQGRoRCnB9F21wHVlBZUdYQhp/EBkaEQpwfRdsTH9FR0VubBJrQRAZGhEKcH8XehxwfhJpfFp /RUQQGxkfEQpwXxdiRFgda20FHWdcHRAZGhEKcH8XYWZvWxpnZEJIHVsQGxseEQpwXxdjYhJQSG N4H3xCfRASEhEKcH8XZWZEAR5IRmR8WhsQGxkeEQpwXxdve1ATb1hEREV/RxAZGhEKcH8XbURfR kVtfUh5GW4QGxgYEQpwXxdrRksTeWhpbnwTeBATGREKcGwXZV1nRGVYeVBLQEQQHRwRCm1+FxsR ClhNF0sRIA== X-Proofpoint-GUID: ixN18IoBurrvOoP7dSOutu6NgIhPJ0h1 X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: ixN18IoBurrvOoP7dSOutu6NgIhPJ0h1 MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=70 impostorscore=0 malwarescore=0 mlxlogscore=999 suspectscore=0 mlxscore=0 adultscore=0 phishscore=0 bulkscore=0 lowpriorityscore=0 clxscore=190 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112060071 domainage_hfrom=7975 X-Spam-Score: 0 X-Spam-OrigSender: michael.robinson1@monash.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Robinson --00000000000097705b05d278ccc9 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Denilson, If the dihedral for a specific interaction is undefined, such as around the linear atoms of your triple bond, some MD packages will require a dihedral value with a strength of 0, and others won't require a dihedral at all. CHARMM does not require a dihedral value for these instances, but NAMD does; CGenFF is set up for CHARMM, and so will not output a dihedral in these cases. In the case of an undefined dihedral in NAMD, you can simply add a parameter with an equilibrium angle of 0 and a strength of 0 - it won't affect the results in any way, but is required to run NAMD in these cases. Regards, Michael Robinson On Mon, 6 Dec 2021 at 05:58, DENILSON FERREIRA DE OLIVEIRA wrote: > Dear all, > > 1) The C3_WIN-1-COR.str file was generated for an organic substance, using > the CHARMM General Force Field (CGenFF) program version 2.5, through the > Paramchem website (https://urldefense.com/v3/__https://cgenff.umaryland.e= du/__;!!DZ3fjg!vpC3LLjbPFGJ9Czo7ZfxGkt-FQ16kH2b7BFx46m7ETQJcP7QGprivIjJWry1= lucaow$=20 > > ) > > 2) Using the topology files contained in toppar_c36_jul21.tgz, which is > available through the MacKerell Lab Homepage ( > https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtm= l*charmm__;Iw!!DZ3fjg!vpC3LLjbPFGJ9Czo7ZfxGkt-FQ16kH2b7BFx46m7ETQJcP7QGpriv= IjJWrxH4xW3pQ$=20 > ), > as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared t= he > pdb and psf files using VMD 1.9.4a55. > > 3) In the configuration file to carry out calculations with Namd 2.14 I > have provided all the parameter files in the order that seems correct to > me. The following is observed in the output from Namd: > > "... > Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb > Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf > Info: PARAMETER file: CHARMM format! > Info: PARAMETERS ./par_all36m_prot.prm > Info: PARAMETERS ./par_all36_lipid.prm > Info: PARAMETERS ./par_all36_carb.prm > Info: PARAMETERS ./par_all36_na.prm > Info: PARAMETERS ./par_all36_cgenff.prm > Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str > Info: PARAMETERS ./toppar_water_ions_namd.str > Info: PARAMETERS ./C3_WIN-1-COR.str > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SKIPPING rtf SECTION IN STREAM FILE > " > > 4) However, Namd 2.14 did not perform the calculations because it > encountered an error: > > "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1 > CG1T2 (ATOMS 53401 53404 53407 53408)" > > 5) It is clear to me that this error is due to the fact that there is no > parameter for dihedral angles of atoms of the terminal alkyne function > anywhere: > > CG1T2 : C(sp1) terminal > CG1T1 : C(sp1) non-terminal > CG3C50 : C(sp3) linked to CG1T1 > CG3RC1 : C(sp3) linked to CG3C50 > > 6) To be clearer, I could not find data for the dihedral angle CG3RC1 > CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in > item "3" of this message. > > 7) In fact, it seems to me that there is no point in working with a > dihedral angle for such atoms. > > 8) Consequently, I will be grateful if anyone can be kind enough to make a > suggestion to solve the problem. > > Thanks. > > Denilson. > > O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destina= t=C3=A1rios e de > responsabilidade do remetente. O uso do e-mail deve estar de acordo com os > regulamentos institucionais vigentes. > --00000000000097705b05d278ccc9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Denilson,

If the dihedral for a spec= ific interaction is undefined, such as around the linear atoms of your trip= le bond, some MD packages will require a dihedral value with a strength of = 0, and others won't require a dihedral at all. CHARMM does not require = a dihedral value for these instances, but NAMD does; CGenFF is set up for C= HARMM, and so will not output a dihedral in these cases. In the case of an = undefined dihedral in NAMD, you can simply add a parameter with an equilibr= ium=C2=A0angle of 0 and a strength of 0 - it won't affect the results i= n any way, but is required to run NAMD in these cases.

=
Regards,
Michael Robinson

On Mon, 6 Dec 2021 at 05:58, = DENILSON FERREIRA DE OLIVEIRA <denil= son@ufla.br> wrote:
Dear all,

1) The C3_WIN-1-COR.str file was generated for an= =20 organic substance, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://cgenf= f.umaryland.edu/)

2) Using the topology files contained in toppa= r_c36_jul21.tgz, which is available through the MacKerell Lab Homepage (http://mackerell.umaryland.edu/char= mm_ff.shtml#charmm), as well as the C3_WIN-1-COR.str file generated in = Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55.

3) In the configuration file to carry out calculations with Namd= 2.14 I=20 have provided all the parameter files in the order that seems correct to me. The following is observed in the output from Namd:
"...
Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb
Info: STR= UCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf
Info: PARAMETER file: CHARMM for= mat!
Info: PARAMETERS ./par_all36m_prot.prm
Info: PARAMETERS ./par_al= l36_lipid.prm
Info: PARAMETERS ./par_all36_carb.prm
Info: PARAMETERS = ./par_all36_na.prm
Info: PARAMETERS ./par_all36_cgenff.prm
Info: PARA= METERS ./toppar_all36_carb_glycopeptide.str
Info: PARAMETERS ./toppar_wa= ter_ions_namd.str
Info: PARAMETERS ./C3_WIN-1-COR.str
Info: USING ARI= THMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING= rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILEInfo: SKIPPING rtf SECTION IN STREAM FILE
"

4) However, Namd 2.14 did not perform the calculations because it encountered= an error:

"FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR= CG3RC1 CG3C50 CG1T1 CG1T2 (ATOMS 53401 53404 53407 53408)"

5) It is clear to me that this error is due to the fact that there is no=20 parameter for dihedral angles of atoms of the terminal alkyne function=20 anywhere:

=C2=A0 =C2=A0CG1T2 : C(sp1) terminal
=C2=A0 =C2=A0CG1T1= : C(sp1) non-terminal
=C2=A0 =C2=A0CG3C50 : C(sp3) linked to CG1T1
= =C2=A0 =C2=A0CG3RC1 : C(sp3) linked to CG3C50

6) To be clearer, I could not find data for the dihedral angle CG3RC1=20 CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed=20 in item "3" of this message.

7) In fact, it seems to me t= hat there is no point in working with a dihedral angle for such atoms.
<= br>8) Consequently, I will be grateful if anyone can be kind enough to make= a suggestion to solve the problem.

Thanks.<= font color=3D"#888888">

Denilson.

O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.
--00000000000097705b05d278ccc9-- From owner-namd-l@halifax.ks.uiuc.edu Mon Dec 6 16:52:00 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B6Mq0sD013034; Mon, 6 Dec 2021 16:52:00 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B6Mq0YI013033; Mon, 6 Dec 2021 16:52:00 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B6MpxMC013029; Mon, 6 Dec 2021 16:51:59 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B6MpxgZ013028; Mon, 6 Dec 2021 16:51:59 -0600 (CST) Received: from admins-mbp.hsd1.il.comcast.net (c-98-212-87-177.hsd1.il.comcast.net [98.212.87.177]) (authenticated bits=0) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B6MpfSA013019 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 6 Dec 2021 16:51:42 -0600 (CST) From: David Hardy Message-Id: Content-Type: multipart/alternative; boundary="Apple-Mail=_53C161FD-4030-44E3-8F46-368039EF352C" Mime-Version: 1.0 (Mac OS X Mail 13.4 \(3608.120.23.2.4\)) Subject: Re: namd-l: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Date: Mon, 6 Dec 2021 16:51:36 -0600 In-Reply-To: Cc: "Vermaas, Josh" , Vlad Cojocaru , Giacomo Fiorin , Axel Kohlmeyer , HORIA-LEONARD BANCIU To: NAMD list , James M Davis References: <2919008c-ce4e-3fda-8a5b-6ef37e9d6af2@mpi-muenster.mpg.de> <5082A382-FE16-4F37-B56B-3B83A26A010D@msu.edu> X-Mailer: Apple Mail (2.3608.120.23.2.4) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, David Hardy --Apple-Mail=_53C161FD-4030-44E3-8F46-368039EF352C Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Sorry to have come to this thread late. I see that no one has suggested any pemap/commap settings. For Frontera = (Intel Xeon Platinum 8280, so 28 cores per socket, 56 per node), we see = best results running 4 ranks (processes) per node: +ppn 13 +pemap 4-55:2,5-55:2 +commap 0,2,1,3 For Intel Xeon Platinum 8160, I would similarly try 4 ranks per node for = the 48 cores: +ppn 11 +pemap 4-47:2,5-47:2 +commap 0,2,1,3 Also, in NAMD 2.15, we have additional optimizations for Intel CPUs, = including an AVX512 build that introduces special kernels based on a = porting of the CUDA tile list kernels to AVX-512, offering up to 2x = performance over the traditional CPU kernels. Also, there is an SKX = (Skylake) build that improves the traditional CPU kernel performance = using OpenMP directives. I mention them both because the AVX512 is not = compatible with all features, and attempts to use it for unsupported = features might find it either not working or falling back to a slower = implementation, whereas the SKX build should be compatible with all = features. You can build these version of NAMD as follows: ./config Linux-AVX512-icc ... ./config Linux-SKX-icc ... and you have to use Intel's compiler to build (we have been using = version 19.0.0.117 20180804 in house and 19.1.1.217 20200306 on = Frontera). Here are the results from a 2-node test I recently ran with STMV (~1M = atoms) on Frontera to illustrate the difference in performance you might = see between these versions: BUILD ns/day speedup x86_64 1.89547 1.0 SKX 3.17095 1.6729 AVX512 4.17481 2.2025 Hope this helps, Dave -- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy@ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Nov 30, 2021, at 12:25 PM, James M Davis wrote: >=20 > I should have said build from scratch to support Omnipath or use the = Charrm++ mpi with open-mpi. There will still be testing involved to = tweak the system and the performance. It still might not support 48*48. = But you should be able to get to something higher than 48*24. > ---- > Mike Davis > Technical Director: High Performance Research Computing=20 > Virginia Commonwealth University > (804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c) > https://chipc.vcu.edu = >=20 > = >=20 >=20 > On Tue, Nov 30, 2021 at 1:07 PM James M Davis > wrote: > A few notes from the 2.15 release notes. I think you will need to = build from scratch for Omnipath.=20 >=20 > Intel Omni-Path networks are incompatible with the pre-built verbs = NAMD binaries. Charm++ for verbs can be built with --with-qlogic to = support Omni-Path, but the Charm++ MPI network layer performs better = than the verbs layer. Hangs have been observed with Intel MPI but not = with OpenMPI, so OpenMPI is preferred. See "Compiling NAMD" below for = MPI build instructions. NAMD MPI binaries may be launched directly with = mpiexec rather than via the provided charmrun script." > https://www.ks.uiuc.edu/Research/namd/cvs/notes.html = > ---- > Mike Davis > Technical Director: High Performance Research Computing=20 > Virginia Commonwealth University > (804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c) > https://chipc.vcu.edu = >=20 > = >=20 >=20 > On Tue, Nov 30, 2021 at 1:00 PM Vermaas, Josh > wrote: > Hi Vlad, >=20 > =20 >=20 > In addition to the great points Axel and Giacomo have made, I=E2=80=99d = like to point out that the 8160 is a 24 core processor, and that there = are likely 2 of them on a given node. In these two socket = configurations, where there are two physical CPU dies, I=E2=80=99ve = often found that the best performance is achieved when you treat each = socket as its own node, and allocate 2x the number of =E2=80=9Ctasks=E2=80= =9D as you have nodes. That way, each SMP task gets placed on its own = socket. If you don=E2=80=99t, each node is trying to get all 48 cores = across both sockets to work together, which ends up saturating the UPI = links between the sockets, and can be detrimental to performance. >=20 > =20 >=20 > This is usually a bigger problem for SMP-based builds. In my = experience, CPU-only systems benefit from MPI based builds, where the = number of tasks is equal to the number of CPUs. Usually this is a = performance win for modestly sized systems at the expense of scalability = for really big systems. >=20 > =20 >=20 > -Josh >=20 > =20 >=20 > From: > on = behalf of Vlad Cojocaru > > Organization: MPI Muenster > Reply-To: "namd-l@ks.uiuc.edu " = >, Vlad Cojocaru = > > Date: Tuesday, November 30, 2021 at 10:18 AM > To: Giacomo Fiorin >, NAMD list >, Axel Kohlmeyer > > Cc: HORIA-LEONARD BANCIU > > Subject: Re: namd-l: NAMD performance on a supercomputer with Intel = Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree >=20 > =20 >=20 > Thanks for your thoughts ! >=20 > One thing that seemed weird during our tests on this site was that the = performance and parallel scaling rapidly degraded when using all 48 = cores available per node (2 CPUs with 24 cores each) . We actually saw = negative scaling after as few as 16 nodes. Then, when using 47, 32, and = 24 cores/node, we got better parallel efficiency to higher node count, = with the best efficiency obtained using just half of the core available = on each node (24). At the end, when running on 48 nodes, we achieved the = most ns/day when using 24 cores/node. However, the resources requested = in the project we needed to calculate using all 48 cores/node regardless = of how many we are actually using. >=20 > I haven't experienced anything like this on other sites (similar = systems, same configuration files). Normally using all cores available = per node has always given the best performance. So, I am wondering = whether there is anything obvious that could explain such a behavior ? >=20 > Best > Vlad >=20 > On 11/30/21 15:33, Giacomo Fiorin wrote: >=20 > Something in addition to what Axel says (all of which is absolutely = true, even the counter-intuitive part about making the single-node = performance artificially slower to get through the bottom-most tier of = technical review). >=20 > =20 >=20 > One possible issue to look at is how the cluster's network is utilized = by other users/applications. In a local cluster that I use, the = InfiniBand network is also used by the nodes to access data storage and = there are many other users processing MRI, cryo-EM or bioinformatics = data (all embarrassingly-parallel by design). So the InfiniBand network = is constantly busy and does not necessarily offer very low latency for = NAMD or other message-passing applications. >=20 > =20 >=20 > Something that helped in that case was building Charm++ on top of the = UCX library instead of IBverbs directly. I am wholly unfamiliar with = the details of how UCX works, but in essence it provides better = utilization of the network when the ratio of compute cores vs. network = links is high. If the cluster's staff has a copy of UCX, try that. It = wasn't easy to build, but it paid off specifically for those runs that = were communication-bound. >=20 > =20 >=20 > The main significant addition in 2.15 is the AVX-512 tiles algorithm, = which would help with the most expensive Intel CPUs like those, but = would also make the computation part faster with the caveat that Axel = mentioned. >=20 > =20 >=20 > Giacomo >=20 > =20 >=20 > On Tue, Nov 30, 2021 at 6:16 AM Axel Kohlmeyer > wrote: >=20 > Actually, if you optimize how NAMD is compiled better than the system = provided executable, your parallel efficiency will go down. Please = recall Amdahl's law: the parallel efficiency is determined by the = relation of time spent on parallel execution and serial execution.=20 >=20 > =20 >=20 > A better optimized executable will spend even less time computing and = thus have more parallel overhead.=20 >=20 > =20 >=20 > To get better parallel efficiency, you have to avoid or reduce all non = parallel operations like output or use of features like Tcl scripting or = make your computations more expensive by increasing the cutoff or the = system size or make the executable slower by compiling a less optimized = version.=20 >=20 > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com = http://goo.gl/1wk0 = > College of Science & Technology, Temple University, Philadelphia PA, = USA > International Centre for Theoretical Physics, Trieste, Italy >=20 > =20 >=20 > On Tue, Nov 30, 2021, 05:32 Vlad Cojocaru = > wrote: >=20 > Dear all, >=20 > We submitted a proposal to run some extensive atomistic simulations = with=20 > NAMD of systems ranging between 500 K to 2M atoms on a supercomputer=20= > with Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path=20 > Full-Fat Tree interconnection. >=20 > Apparently, our project may fail the technical evaluation because = during=20 > our tests we did not achieve a 75 % parallel efficiency between 2 to = 48=20 > nodes (each node has 2 CPUs - 24 cores/CPU). We have tested the NAMD=20= > 2.14 provided by default at the site and we do not know how this was=20= > built. Looking at the NAMD benchmarks available for the Frontera=20 > supercomputer (quite similar architecture if I understand it correctly=20= > but for larger systems), it seems we should definitely achieve with = NAMD=20 > 2.15 (maybe even 2.14) much better performance and parallel efficiency=20= > up to 48/64 nodes on this architecture than we actually achieved in = our=20 > tests. >=20 > So, my reasoning is that probably the NAMD built by default was not=20 > really carefully optimized. >=20 > I would appreciate if anyone who has experience with building and=20 > optimizing NAMD on such an architecture could recommend any=20 > compiler/MPI/configuration/options for building an NAMD with a better=20= > performance and parallel efficiency. If I have some clear ideas about=20= > how to optimize NAMD, maybe I could make the case for our project to = not=20 > fail the technical evaluation. >=20 > Thank you very much for any advice >=20 > Best wishes > Vlad >=20 >=20 >=20 > --=20 > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de = > = https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/43241/cojocaru_= _;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8= Paw$ = =20 >=20 >=20 >=20 >=20 >=20 > --=20 > Vlad Cojocaru, PD (Habil.), Ph.D. > ----------------------------------------------- > Project Group Leader > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany > ----------------------------------------------- > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de = > http://www.mpi-muenster.mpg.de/43241/cojocaru = --Apple-Mail=_53C161FD-4030-44E3-8F46-368039EF352C Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Sorry= to have come to this thread late.

I see that no one has suggested any = pemap/commap settings. For Frontera (Intel Xeon Platinum 8280, so 28 = cores per socket, 56 per node), we see best results running 4 ranks = (processes) per node:

     +ppn 13 +pemap = 4-55:2,5-55:2 +commap 0,2,1,3

For Intel Xeon = Platinum 8160, I would similarly try 4 ranks per node for the 48 = cores:

    =  +ppn 11 +pemap 4-47:2,5-47:2 +commap 0,2,1,3

Also, in NAMD 2.15, we have additional = optimizations for Intel CPUs, including an AVX512 build that introduces = special kernels based on a porting of the CUDA tile list kernels to = AVX-512, offering up to 2x performance over the traditional CPU kernels. = Also, there is an SKX (Skylake) build that improves the traditional CPU = kernel performance using OpenMP directives. I mention them both because = the AVX512 is not compatible with all features, and attempts to use it = for unsupported features might find it either not working or falling = back to a slower implementation, whereas the SKX build should be = compatible with all features.

You = can build these version of NAMD as follows:

     ./config Linux-AVX512-icc = ..

     ./config = Linux-SKX-icc ...

and you have to = use Intel's compiler to build (we have been using = version 19.0.0.117 20180804 in house and 19.1.1.217 20200306 = on Frontera).

Here are the results = from a 2-node test I recently ran with STMV (~1M atoms) on Frontera to = illustrate the difference in performance you might see between these = versions:

  =    BUILD         ns/day     =      speedup
    =  x86_64       1.89547     = 1.0
     SKX     =        3.17095     1.6729
     AVX512      4.17481   =   2.2025

Hope this helps,
Dave

--
David J. Hardy, = Ph.D.
Beckman Institute
University of Illinois at = Urbana-Champaign
405 N. Mathews Ave., Urbana, IL = 61801


On = Nov 30, 2021, at 12:25 PM, James M Davis <jmdavis1@vcu.edu> = wrote:

I should have said build from scratch to support = Omnipath or use the Charrm++ mpi with open-mpi. There will = still be testing involved to tweak the system and the performance. It = still might not support 48*48. But you should be able to get to = something higher than 48*24.
----
Mike = Davis
Technical Director: High Performance Research = Computing 
Virginia Commonwealth = University
(804) 828-3885 (o) =E2=80=A2 = (804) 307-3428(c)



On Tue, Nov 30, 2021 at 1:07 PM James M = Davis <jmdavis1@vcu.edu> wrote:
A = few notes from the 2.15 release notes. I think you will need to build = from scratch for Omnipath. 

Intel = Omni-Path networks are incompatible with the pre-built verbs NAMD = binaries. Charm++ for verbs can be built with --with-qlogic to support = Omni-Path, but the Charm++ MPI network layer performs better than the = verbs layer.  Hangs have been observed with Intel MPI but not with = OpenMPI, so OpenMPI is preferred.  See "Compiling NAMD" below for = MPI build instructions.  NAMD MPI binaries may be launched directly = with mpiexec rather than via the provided charmrun = script."
https://www.ks.uiuc.edu/Research/namd/cvs/notes.html
----
Mike Davis
Technical Director: = High Performance Research Computing 
Virginia Commonwealth University
(804) 828-3885 (o) =E2=80=A2 (804) 307-3428(c)




On Tue, Nov 30, 2021 at 1:00 PM = Vermaas, Josh <vermaasj@msu.edu> wrote:

Hi Vlad,

 

In addition to the great = points Axel and Giacomo have made, I=E2=80=99d like to point out that = the 8160 is a 24 core processor, and that there are likely 2 of them on = a given node. In these two socket configurations, where there are two = physical CPU dies, I=E2=80=99ve often found that the best performance is = achieved when you treat each socket as its own node, and allocate 2x the = number of =E2=80=9Ctasks=E2=80=9D as you have nodes. That way, each SMP = task gets placed on its own socket. If you don=E2=80=99t, each node is = trying to get all 48 cores across both sockets to work together, which ends up = saturating the UPI links between the sockets, and can be detrimental to = performance.

 

This is usually a bigger problem for SMP-based = builds. In my experience, CPU-only systems benefit from MPI based = builds, where the number of tasks is equal to the number of CPUs. = Usually this is a performance win for modestly sized systems at the expense of scalability for really big systems.

 

-Josh

 

From: <owner-namd-l@ks.uiuc.edu> on behalf = of Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de>
Organization: MPI Muenster
Reply-To: "namd-l@ks.uiuc.edu" <namd-l@ks.uiuc.edu>, Vlad Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de>
Date: Tuesday, November 30, 2021 at 10:18 AM
To: Giacomo Fiorin <giacomo.fiorin@gmail.com>, NAMD list <namd-l@ks.uiuc.edu>, Axel Kohlmeyer <akohlmey@gmail.com>
Cc: HORIA-LEONARD BANCIU <horia.banciu@ubbcluj.ro>
Subject: Re: namd-l: NAMD performance on a = supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path = Full-Fat Tree

 

Thanks for = your thoughts !

One thing that seemed weird during our tests on this site was that the = performance and parallel scaling rapidly degraded when using all 48 = cores available per node (2 CPUs with 24 cores each) . We actually saw = negative scaling after as few as 16 nodes. Then, when using 47, 32, and 24 cores/node, we got better parallel efficiency = to higher node count, with the best efficiency obtained using just half = of the core available on each node (24). At the end, when running on 48 = nodes, we achieved the most ns/day when using 24 cores/node. However, the resources requested in the project we = needed to calculate using all 48 cores/node regardless of how many we = are actually using.

I haven't experienced anything like this on other sites (similar = systems, same configuration files). Normally using all cores available = per node has always given the best performance. So, I am wondering = whether there is anything obvious that could explain such a behavior ?

Best
Vlad

On 11/30/21 15:33, Giacomo Fiorin = wrote:

Something in addition to what = Axel says (all of which is absolutely true, even the counter-intuitive = part about making the single-node performance artificially slower to get = through the bottom-most tier of technical review).

 

One possible issue to look at = is how the cluster's network is utilized by other = users/applications.  In a local cluster that I use, the InfiniBand = network is also used by the nodes to access data storage and there are = many other users processing MRI, cryo-EM or bioinformatics data (all embarrassingly-parallel by = design).  So the InfiniBand network is constantly busy and does not = necessarily offer very low latency for NAMD or other message-passing = applications.

 

Something that helped in that = case was building Charm++ on top of the UCX library instead of IBverbs = directly.  I am wholly unfamiliar with the details of how UCX = works, but in essence it provides better utilization of the network when the ratio of compute cores vs. network links is high.  If the = cluster's staff has a copy of UCX, try that.  It wasn't easy to = build, but it paid off specifically for those runs that were = communication-bound.

 

The main significant addition in = 2.15 is the AVX-512 tiles algorithm, which would help with the most = expensive Intel CPUs like those, but would also make the computation = part faster with the caveat that Axel mentioned.

 

Giacomo

 

On Tue, Nov 30, 2021 at 6:16 AM = Axel Kohlmeyer <akohlmey@gmail.com> wrote:

Actually, if you optimize how = NAMD is compiled better than the system provided executable, your = parallel efficiency will go down. Please recall Amdahl's law: the = parallel efficiency is determined by the relation of time spent on = parallel execution and serial execution. 

 

 A better optimized = executable will spend even less time computing and thus have more = parallel overhead. 

 

To = get better parallel efficiency, you have to avoid or reduce all non = parallel operations like output or use of features like Tcl scripting or = make your computations more expensive by increasing the cutoff or the system size or make the executable slower by compiling a less = optimized version. 

--
Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, = USA
International Centre for Theoretical Physics, Trieste, Italy

 

On Tue, Nov 30, 2021, 05:32 Vlad = Cojocaru <vlad.cojocaru@mpi-muenster.mpg.de> = wrote:

Dear all,

We submitted a proposal to run some extensive atomistic simulations with =
NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with  Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path =
Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during =
our tests we did not achieve a 75 % parallel efficiency between 2 to 48 =
nodes (each node has 2 CPUs - 24 cores/CPU).  We have tested the = NAMD
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly =
but for larger systems), it seems we should definitely achieve with NAMD =
2.15 (maybe even 2.14) much better performance and parallel efficiency =
up to 48/64 nodes on this architecture than we actually achieved in our =
tests.

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better =
performance and parallel efficiency. If I have some clear ideas about =
how to optimize NAMD, maybe I could make the case for our project to not =
fail the technical evaluation.

Thank you very much for any advice

Best wishes
Vlad



--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
https://urldefense.com/v3/__http://www.mpi-muenster.mpg.de/4324= 1/cojocaru__;!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3C= Qj5uCvq0Gx8Paw$



-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
R=C3=B6ntgenstrasse 20, 48149 M=C3=BCnster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru

= --Apple-Mail=_53C161FD-4030-44E3-8F46-368039EF352C-- From owner-namd-l@halifax.ks.uiuc.edu Tue Dec 7 04:07:45 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B7A7jRH020625; Tue, 7 Dec 2021 04:07:45 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B7A7j1G020624; Tue, 7 Dec 2021 04:07:45 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B7A7ib9020619; Tue, 7 Dec 2021 04:07:44 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B7A7if0020617; Tue, 7 Dec 2021 04:07:44 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B7A7SOF020603 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="00000000000059bb0205d28b8a7a" X-Proofpoint-ORIG-GUID: xh5mmDuXf8nr2QuUBTc1wCTnGtimgqVL X-CLX-Shades: MLX X-Proofpoint-GUID: xh5mmDuXf8nr2QuUBTc1wCTnGtimgqVL X-CLX-Response: 1TFkXGxIaEQpMehcZGRgRCllEF2BiTU1Cb0ZjUktbEQpYWBdpXHl7f15je0Z HAREKeE4XY1Nja3sTWH4aX14RCnlMF2hpHxhaf3xcZVJTEQpDSBcHGRgcEQpDWRcHGRgTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRceHXEYBh4ddwYfGQYaBhoGGxoaBhkacRsQGncGGgYHHxoGGgYaB hoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF1JCH0dHbl9yTBJEWBh7X39o fkkbXWl+RG1eQ0dNW3xmEQpYXBcfBBoEGB4YBRsaBBsaGgQdBBseHhAbHhofGhEKXlkXcx9kSB0 RCk1cFxgfGREKTFoXaWxpTWtrEQpMRhdva2tra2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh 8EGxwcBB4ZEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2RPe1NkUBpuH1JfEQpCThdjU2NrexNYfhpfXhEKQkwXaVx5e39eY3tGRwERCkJsF2x9 HxNOch9hGFpFEQpCQBdsH1weQUFYSB4fYBEKQlgXZ3Nlc0BuYWFMXWIRClpYFxgRCnlDF29/HGt FG35aGhhDEQpZSxcTHBsZEQpwaBdvbxpLc3x9b0YbRRAaEQpwaBdgGVAaeWRBQ10deBAaEQpwaB dnbHBEUnhBU11EehAaEQpwaBdseB9OX18FSHx8RRAaEQpwaBdseXBlXlB4UnNSRxAaEQpwbBdlW G0YS0MbflBveRAHGRoRCm1+FxoRClhNF0sRIA== X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 adultscore=0 malwarescore=0 spamscore=0 clxscore=180 phishscore=0 mlxscore=0 suspectscore=0 bulkscore=0 impostorscore=0 priorityscore=332 mlxlogscore=490 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112070060 domainage_hfrom=9613 X-Spam-Score: 0 X-Spam-OrigSender: walkinsnate@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Nate Walkins --00000000000059bb0205d28b8a7a Content-Type: text/plain; charset="UTF-8" Hello, I recently ran a long trajectory for an all-atom system and now wish to compute the force acting only on a subset of the atoms. I set about doing this with tclForces by reading in a dcd files and then calling a custom calcforces script. I read that the force can only be used computed after a step of MD has been run as it computes the forces on the "stale" coordinates so I thought to get around this by running each step twice (inefficient, but I care about the forces and not speed in this case) and passing a flag variable the second time. Eventually this is just going to be a loop, but for now I just copied and pasted it twice to see if it was possible to continue in this manner. The relevant part of the namd configuration files are below. I am getting the error message that "FATAL ERROR: can't read "p": no such variable" and if commenting out that line then "FATAL ERROR: can't read "f": no such variable", however both seem to be defined above. --------------------- tclForces on tclForcesScript forces.tcl coorfile open dcd short.dcd coorfile read set flag 0 set ts 0 firstTimestep $ts run 0 set flag 1 run 0 coorfile read set flag 0 set ts [expr $ts+1] firstTimestep $ts run 0 set flag 1 run 0 ------------------------------------- The accompanying tclForces script is: ------------------------------------- set inStream [open cg-beads.ind r] set atoms {} foreach line [split [read $inStream] \n] { set ind [string trim [string range $line 0 3]] lappend atoms $ind } close $inStream enabletotalforces puts $atoms proc calcforces {} { global atoms flag set coord_step [getstep] print $flag $coord_step if {$flag > 0} { loadforces f loadcoords p print $p print $f } } ------------------------------------- cg-beads.ind is just a text file of the atom indices that I wish to get the forces from. --00000000000059bb0205d28b8a7a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,
I recently ran a long trajectory for= an all-atom system and now wish to compute the force acting only on a subs= et of the atoms. I set about doing this with tclForces by reading in a dcd = files and then calling a custom calcforces script. I read that the force ca= n only be used computed after a step of MD has been run as it computes the = forces on the "stale" coordinates so I thought to get around this= by running each step twice (inefficient, but I care about the forces and n= ot speed in this case) and passing a flag variable the second time. Eventua= lly this is just going to be a loop, but for now I just copied and pasted i= t twice to see if it was possible to continue in this manner.

The relevant part of the namd configuration files are below= . I am getting the error message that=C2=A0 "FATAL ERROR: can't re= ad "p": no such variable" and if commenting out that line th= en=20 "FATAL ERROR: can't read "f": no such variable", ho= wever both seem to be defined above.

---------= ------------
tclForces =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 on<= br>tclForcesScript =C2=A0 =C2=A0 forces.tcl

coorfile open dcd short.= dcd
coorfile read
set flag 0
set ts 0
firstTimestep $ts
run = 0
set flag 1
run 0

coorfile read
set flag 0
set ts [expr= $ts+1]
firstTimestep $ts
run 0
set flag 1
run 0
----= ---------------------------------
The accompanying tclForces = script is:
-------------------------------------
set inStream [open cg-beads.ind r]
set atoms {}
foreach line [split= [read $inStream] \n] {
=C2=A0 =C2=A0 set ind [string trim [string range= $line 0 3]]
=C2=A0 =C2=A0 lappend atoms $ind
}
close $inStreamenabletotalforces
puts $atoms

proc calcforces {} {
=C2=A0 =C2= =A0 global atoms flag
=C2=A0 =C2=A0 set coord_step [getstep]
=C2=A0 = =C2=A0 print $flag $coord_step
=C2=A0 =C2=A0 if {$flag > 0} {
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 loadforces f
=C2=A0 =C2=A0 =C2=A0 =C2=A0 loadco= ords p
=C2=A0 =C2=A0 =C2=A0 =C2=A0 print $p
=C2=A0 =C2=A0 =C2=A0 =C2= =A0 print $f
=C2=A0 =C2=A0 }
}
----------------------------= ---------
cg-beads.ind is just a text file of the atom indice= s that I wish to get the forces from.

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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Michael Robinson, Thank you very much. Denilson Em seg., 6 de dez. de 2021 =C3=A0s 08:45, Michael Robinson < michael.robinson1@monash.edu> escreveu: > Hi Denilson, > > If the dihedral for a specific interaction is undefined, such as around > the linear atoms of your triple bond, some MD packages will require a > dihedral value with a strength of 0, and others won't require a dihedral = at > all. CHARMM does not require a dihedral value for these instances, but NA= MD > does; CGenFF is set up for CHARMM, and so will not output a dihedral in > these cases. In the case of an undefined dihedral in NAMD, you can simply > add a parameter with an equilibrium angle of 0 and a strength of 0 - it > won't affect the results in any way, but is required to run NAMD in these > cases. > > Regards, > Michael Robinson > > On Mon, 6 Dec 2021 at 05:58, DENILSON FERREIRA DE OLIVEIRA < > denilson@ufla.br> wrote: > >> Dear all, >> >> 1) The C3_WIN-1-COR.str file was generated for an organic substance, >> using the CHARMM General Force Field (CGenFF) program version 2.5, throu= gh >> the Paramchem website (https://urldefense.com/v3/__https://cgenff.umaryl= and.edu/__;!!DZ3fjg!qbO3aULYRNRrBmpdN2QzX8LoKemjQmLy7R6IR6os1Vbl8zQ2gjsH3vq= 8Mh75MHwm0A$=20 >> >> ) >> >> 2) Using the topology files contained in toppar_c36_jul21.tgz, which is >> available through the MacKerell Lab Homepage ( >> https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.sht= ml*charmm__;Iw!!DZ3fjg!qbO3aULYRNRrBmpdN2QzX8LoKemjQmLy7R6IR6os1Vbl8zQ2gjsH= 3vq8Mh5elGMALw$=20 >> ), >> as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared = the >> pdb and psf files using VMD 1.9.4a55. >> >> 3) In the configuration file to carry out calculations with Namd 2.14 I >> have provided all the parameter files in the order that seems correct to >> me. The following is observed in the output from Namd: >> >> "... >> Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb >> Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf >> Info: PARAMETER file: CHARMM format! >> Info: PARAMETERS ./par_all36m_prot.prm >> Info: PARAMETERS ./par_all36_lipid.prm >> Info: PARAMETERS ./par_all36_carb.prm >> Info: PARAMETERS ./par_all36_na.prm >> Info: PARAMETERS ./par_all36_cgenff.prm >> Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str >> Info: PARAMETERS ./toppar_water_ions_namd.str >> Info: PARAMETERS ./C3_WIN-1-COR.str >> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS >> Info: SKIPPING rtf SECTION IN STREAM FILE >> Info: SKIPPING rtf SECTION IN STREAM FILE >> Info: SKIPPING rtf SECTION IN STREAM FILE >> " >> >> 4) However, Namd 2.14 did not perform the calculations because it >> encountered an error: >> >> "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1 >> CG1T2 (ATOMS 53401 53404 53407 53408)" >> >> 5) It is clear to me that this error is due to the fact that there is no >> parameter for dihedral angles of atoms of the terminal alkyne function >> anywhere: >> >> CG1T2 : C(sp1) terminal >> CG1T1 : C(sp1) non-terminal >> CG3C50 : C(sp3) linked to CG1T1 >> CG3RC1 : C(sp3) linked to CG3C50 >> >> 6) To be clearer, I could not find data for the dihedral angle CG3RC1 >> CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in >> item "3" of this message. >> >> 7) In fact, it seems to me that there is no point in working with a >> dihedral angle for such atoms. >> >> 8) Consequently, I will be grateful if anyone can be kind enough to make >> a suggestion to solve the problem. >> >> Thanks. >> >> Denilson. >> >> O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destin= at=C3=A1rios e >> de responsabilidade do remetente. O uso do e-mail deve estar de acordo c= om >> os regulamentos institucionais vigentes. >> > --=20 O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de=20 responsabilidade do remetente. O uso do e-mail deve estar de acordo com os= =20 regulamentos institucionais vigentes. --00000000000085e4b905d2a228c4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Michael Robinson,

Thank you very much.

Denilson


Em seg., 6 de dez. de 2021 =C3= =A0s 08:45, Michael Robinson <michael.robinson1@monash.edu> escreveu:
Hi Denilson,

=
If the dihedral for a specific interaction is undefined, such as= around the linear atoms of your triple bond, some MD packages will require= a dihedral value with a strength of 0, and others won't require a dihe= dral at all. CHARMM does not require a dihedral value for these instances, = but NAMD does; CGenFF is set up for CHARMM, and so will not output a dihedr= al in these cases. In the case of an undefined dihedral in NAMD, you can si= mply add a parameter with an equilibrium=C2=A0angle of 0 and a strength of = 0 - it won't affect the results in any way, but is required to run NAMD= in these cases.

Regards,
Michael Robins= on

On Mon, 6 Dec 2021 at 05:58, DENILSON FERREIRA DE OLIVEIRA <denilson@ufla.br> = wrote:
Dear all,

1) The C3_WIN-1-CO= R.str file was generated for an=20 organic substance, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://cgenf= f.umaryland.edu/)

2) Using the topology files contained in toppa= r_c36_jul21.tgz, which is available through the MacKerell Lab Homepage (http://mackerell.umaryland.edu/char= mm_ff.shtml#charmm), as well as the C3_WIN-1-COR.str file generated in = Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55.

3) In the configuration file to carry out calculations with Namd= 2.14 I=20 have provided all the parameter files in the order that seems correct to me. The following is observed in the output from Namd:
"...
Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb
Info: STR= UCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf
Info: PARAMETER file: CHARMM for= mat!
Info: PARAMETERS ./par_all36m_prot.prm
Info: PARAMETERS ./par_al= l36_lipid.prm
Info: PARAMETERS ./par_all36_carb.prm
Info: PARAMETERS = ./par_all36_na.prm
Info: PARAMETERS ./par_all36_cgenff.prm
Info: PARA= METERS ./toppar_all36_carb_glycopeptide.str
Info: PARAMETERS ./toppar_wa= ter_ions_namd.str
Info: PARAMETERS ./C3_WIN-1-COR.str
Info: USING ARI= THMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING= rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILEInfo: SKIPPING rtf SECTION IN STREAM FILE
"

4) However, Namd 2.14 did not perform the calculations because it encountered= an error:

"FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR= CG3RC1 CG3C50 CG1T1 CG1T2 (ATOMS 53401 53404 53407 53408)"

5) It is clear to me that this error is due to the fact that there is no=20 parameter for dihedral angles of atoms of the terminal alkyne function=20 anywhere:

=C2=A0 =C2=A0CG1T2 : C(sp1) terminal
=C2=A0 =C2=A0CG1T1= : C(sp1) non-terminal
=C2=A0 =C2=A0CG3C50 : C(sp3) linked to CG1T1
= =C2=A0 =C2=A0CG3RC1 : C(sp3) linked to CG3C50

6) To be clearer, I could not find data for the dihedral angle CG3RC1=20 CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed=20 in item "3" of this message.

7) In fact, it seems to me t= hat there is no point in working with a dihedral angle for such atoms.
<= br>8) Consequently, I will be grateful if anyone can be kind enough to make= a suggestion to solve the problem.

Thanks.<= font color=3D"#888888">

Denilson.

O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.

O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.
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boundary="00000000000050edf105d2a29b94" X-Proofpoint-ORIG-GUID: cYHaY6noJuBQ0zsqUrBnVwMAT4W_wZiu X-Proofpoint-GUID: cYHaY6noJuBQ0zsqUrBnVwMAT4W_wZiu X-CLX-Response: 1TFkXGx4ZEQpMehcbHhIRCllEF2IbckZ/TkZ/QhNMEQpYWBdtE0J6WBNzSEN DQREKeE4XZGUaYHJwbltyWh0RCnlMF2ltXmJpfk5ackRIEQpDSBcHGBIbEQpDWRcHGBkZEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxgZcRscEBp3BhgaBhoRClleF2hjeREKSUYXX0NfS XVCRVleT04RCkNOF0lzYktzHERFYF9oexpQWVt/WGhEfF1na34efXVdcENfEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGRAbHhofGhEKXlkXcx9GRB4RCk1cFxsbHBEKTFoXfGlNa00RCkVZF28RCkx fF3oFBQUFBQUFBQVDEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGwQeHhEKQl4XGxEKQk UXaxlaEmxEWnl7RV8RCkJOF2RlGmBycG5bclodEQpCTBdtE0J6WBNzSENDQREKQmwXYXxmXG9PX 39zWmARCkJAF25YbkdceV4FRB5iEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGREKeUMXbHBa SUwTE2Jlf30RCnBoF2ZDW2RBWEhMYW59EBoRCnBoF2tbXBtIfBgZZkN9EBoRCnBoF3oBRwF4Ght yfH9fEBoRCnBoF2dOY38ebx9OQVNuEBoRCnBoF29SX0lPUHIBWV5mEBoRCnB9F29reG5jZXhsZU FsEBoRCnB9F2d6HUlER31oe2leEBoRCnB9F29iXE9nfWxzRnpSEBoRCnB9F2cBX3laXG9eUhkBE BoRCnB/F3occH4SaXxaf0VEEBseHhEKcF8XbU1HXFJjEwVBZR4QGhEKcH8XZWZEAR5IRmR8WhsQ GxoSEQpwXxdve1ATb1hEREV/RxAaEQpwXxdiRFgda20FHWdcHRAaEQpwbBdiHmVnExx6E2lsRxA aEQptfhcbEQpYTRdLESA= X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 priorityscore=148 impostorscore=0 phishscore=0 adultscore=0 clxscore=143 malwarescore=0 suspectscore=0 spamscore=0 bulkscore=0 mlxlogscore=999 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112080086 X-Spam-Score: 0 X-Spam-OrigSender: denilson@ufla.br X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, DENILSON FERREIRA DE OLIVEIRA --00000000000050edf105d2a29b94 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear all, 1) The str file was generated for an organic substance containing a chlorine atom, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://urldefense.com/v3/__htt= ps://cgenff.umaryland.edu/__;!!DZ3fjg!ocLi3tymD9reCRvyyWWIJnBKcbtuFXTWOkcD7= neGAJZgYrT8GisQJisI3T7Vhik8LA$ ) 2) In such str file I can find the following: .. ATOM LP1 LPH 0.050 ! lonepair on chlorine .. LONEPAIR COLI LP1 Cl1 C19 DIST 1.6400 SCAL 0.0 ! lonepair on chlorine 2) Using the topology files contained in toppar_c36_jul21.tgz, which is available through the MacKerell Lab Homepage ( https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*= charmm__;Iw!!DZ3fjg!ocLi3tymD9reCRvyyWWIJnBKcbtuFXTWOkcD7neGAJZgYrT8GisQJis= I3T7shi9Q0w$ ), as well as the str file generated in Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55. In the pdb file the lone pair of the chlorine atom is treated as an atom: ... ATOM 53428 LP1 UNK Z 1 226.355 227.015 173.583 1.00 0.00 ZO1 X ... 3) In the configuration file to carry out calculations with Namd 2.14 I have provided all the parameter files. The following is observed in the output from Namd: "... Info: PARAMETERS ./par_all36m_prot.prm Info: PARAMETERS ./par_all36_lipid.prm Info: PARAMETERS ./par_all36_carb.prm Info: PARAMETERS ./par_all36_na.prm Info: PARAMETERS ./par_all36_cgenff.prm Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str Info: PARAMETERS ./toppar_water_ions_namd.str Info: PARAMETERS ./E2_ZINC000006181820_1-19_1-COR.str ! this is the str file generated in Paramchem " 4) However, Namd 2.14 did not perform the calculations because it encountered an error: "FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 53428 53397)" 5) It means that Namd can not find parameters for the "bond" between the chlorine atom and its lonepair of electrons. I would appreciate it if somebody could be kind enough to help me to solve this problem. Best regards. Denilson. --=20 O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de=20 responsabilidade do remetente. O uso do e-mail deve estar de acordo com os= =20 regulamentos institucionais vigentes. --00000000000050edf105d2a29b94 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dea= r all,

1) The str file was generated for an organic substance contai= ning a chlorine atom, using the CHARMM General Force Field (CGenFF) program= version 2.5, through the Paramchem website (https://cgenff.umaryland.edu/)

2) In such str file I can find the following:
...
ATOM LP1 =C2= =A0 =C2=A0LPH =C2=A0 =C2=A0 0.050 ! lonepair on chlorine
...
LONEPAI= R COLI LP1 =C2=A0 =C2=A0Cl1 =C2=A0 =C2=A0C19 =C2=A0 =C2=A0DIST 1.6400 SCAL = 0.0 ! lonepair on chlorine

2) Using the topology files contain= ed in toppar_c36_jul21.tgz, which is available through the MacKerell Lab Ho= mepage (
http://mackerell.umaryland.edu/charmm_ff.s= html#charmm), as well as the str file generated in Paramchem, I prepare= d the pdb and psf files using VMD 1.9.4a55. In the pdb file the lone pair o= f the chlorine atom is treated as an atom:
....
ATOM =C2=A053428 =C2=A0LP1= UNK Z =C2=A0 1 =C2=A0 =C2=A0 226.355 227.015 173.583 =C2=A01.00 =C2=A00.00= =C2=A0 =C2=A0 =C2=A0ZO1 =C2=A0X
.= ..

3) In the configuration file to carry out calculations wit= h Namd 2.14 I have provided all the parameter files. The following is obser= ved in the output from Namd:

".= .
Info: PARAMETERS =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36m_prot.prm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = ./par_all36_lipid.prm
Info: PARAME= TERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_carb.prm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 ./par_all36_na.prm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_c= genff.prm
Info: PARAMETERS =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./toppar_all36_carb_glycopeptide.str
=
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 ./toppar_water_ions_namd.str
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= ./E2_ZINC000006181820_1-19_1-COR.str ! this is the str file generated in P= aramchem
"

4) Ho= wever, Namd 2.14 did not perform the calculations because it encountered an= error:

"FATAL ERROR: UNABLE TO= FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 53428 53397)"

= 5) It means that Namd can not find parameters for the "bond" betw= een the chlorine atom and its lonepair of electrons.

I would appreci= ate it if somebody could be kind enough to help me to solve this problem.
Best regards.

Denilson.


O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.
= --00000000000050edf105d2a29b94-- From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 8 16:50:28 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8MoS5d025914; Wed, 8 Dec 2021 16:50:28 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B8MoRqY025913; Wed, 8 Dec 2021 16:50:27 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8MoReO025909; Wed, 8 Dec 2021 16:50:27 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B8MoRT4025908; Wed, 8 Dec 2021 16:50:27 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8MoHHZ025900 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="0000000000002a46dd05d2aa50f8" X-Proofpoint-GUID: Pj6A-WzJnn1NzfgMVJSUNgkqffyKBMmF X-Proofpoint-ORIG-GUID: Pj6A-WzJnn1NzfgMVJSUNgkqffyKBMmF X-CLX-Response: 1TFkXGx0YEQpMehcZGRoRCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHHBIRCkNZFwcYGBIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxhxGRgQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XekAcawd9UGBERBtkUExNZ3xgeX9kTUFbTExTYWhnR2wRClhcFx8EGgQYHhgF GxoEGxsaBB0EGxkZEBseGh8aEQpeWRdzH15ebhEKTVwXHx0RCkxaF2xpa01NEQpMRhdva2tra2s RCkJPF2h9QWBDWn1zR0ETEQpDWhcYGhMEEh8EGxgSBB4ZEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2ZYfVhrQBoFckRoEQpCThdjU2NrexNYf hpfXhEKQkwXYx9ZeXlpHU98WloRCkJsF29SZxxyQ0lPWn5dEQpCQBduGgV+eGhLGnh/fREKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF2kbRWlPZ2xzWRpIEQpZSxcTHBseEQpwaBdiZX5 eeEFoTX1lehAZGhEKcGgXYW5Je11JaBoaG0kQGRoRCnBoF20BH34SHUN7UnpFEBkaEQpwaBd6T3 Maf2x+eh1tGBAZGhEKcGgXa2cBbB16ZV1rRwEQGRoRCnBsF2hzUllyZ3sfe3lJEB4SEQpwTBdta GUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=537 suspectscore=0 bulkscore=0 phishscore=0 adultscore=0 impostorscore=0 clxscore=172 spamscore=0 lowpriorityscore=0 priorityscore=330 mlxscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112080125 domainage_hfrom=9614 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --0000000000002a46dd05d2aa50f8 Content-Type: text/plain; charset="UTF-8" Dear Users, To restart eABF job do we need to use xx.colvars.state file generated after each run or like normal restart format bincoordinates ./${runold}-restart.coor binvelocities ./${runold}-restart.vel extendedSystem ./${runold}-restart.xsc As I was looking online we have to use colvars.state file, so where shall I put in the input file. Many thanks, Ashutosh --0000000000002a46dd05d2aa50f8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Users,

To restart eABF job do we n= eed to use xx.colvars.state file generated after each run or like normal re= start format

bincoordinates =C2=A0 =C2=A0 ./${runold}-restart.coor


binvelocities=C2=A0 =C2=A0 =C2=A0 ./${runold}-restart.v= el


extendedSystem =C2=A0 =C2=A0 ./${runold}-restart.xsc


As I was looking online we have to use = colvars.state file, so where shall I put in the input file.



Many thanks,=

Ashutosh

--0000000000002a46dd05d2aa50f8-- From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 8 16:57:17 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8MvHU9027715; Wed, 8 Dec 2021 16:57:17 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B8MvHpq027714; Wed, 8 Dec 2021 16:57:17 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8MvGgm027710; Wed, 8 Dec 2021 16:57:17 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B8MvGOt027709; Wed, 8 Dec 2021 16:57:16 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8Mv7hE027701 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!tfQXC1WGCGdTOV7HKdJ3= MvivxxxPwjSpbhclqeL0eefQ2EPXTwft5FLlHjGnyEu2Kg$=20 On Wed, Dec 8, 2021 at 5:52 PM Ashutosh Shandilya wrote: > Dear Users, > > To restart eABF job do we need to use xx.colvars.state file generated > after each run or like normal restart format > > bincoordinates ./${runold}-restart.coor > > > binvelocities ./${runold}-restart.vel > > > extendedSystem ./${runold}-restart.xsc > > > As I was looking online we have to use colvars.state file, so where shall > I put in the input file. > > > > > Many thanks, > > Ashutosh > --000000000000a1e3dc05d2aa6854 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
On Wed, Dec 8, 2021 at 5:52 PM Ashutosh Shandilya &l= t;scfbioiitd@gmai= l.com> wrote:
Dear Users,

To restart eABF job do= we need to use xx.colvars.state file generated after each run or like norm= al restart format

bincoordinates =C2=A0 =C2=A0 ./${runold}-restart.coor


binvelocities=C2=A0 =C2=A0 =C2=A0 ./${runold}-restart.ve= l


extendedSystem =C2=A0 =C2=A0 ./${runold}-restart.xsc


As I was looking online we have to use co= lvars.state file, so where shall I put in the input file.

<= br>



Ma= ny thanks,

Ashutosh

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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Thanks for your reply, just one quick question, so I don't need any of the three files required for restarting the job. So where shall I use (write in the config file) this colvars.state file to restart the job and what would be the command for that. The link provided says writing *cv save* Kindly help, Many thanks, Ashutosh On Wed, Dec 8, 2021 at 5:57 PM Giacomo Fiorin wrote: > > https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd= /colvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!uZ3i667Huer_zkkFl5= 0EQKN08y1ELB8rkElFxKW6ZwVyTMNOtXsOLziOMeMUY4eSfQ$=20 > > On Wed, Dec 8, 2021 at 5:52 PM Ashutosh Shandilya > wrote: > >> Dear Users, >> >> To restart eABF job do we need to use xx.colvars.state file generated >> after each run or like normal restart format >> >> bincoordinates ./${runold}-restart.coor >> >> >> binvelocities ./${runold}-restart.vel >> >> >> extendedSystem ./${runold}-restart.xsc >> >> >> As I was looking online we have to use colvars.state file, so where shall >> I put in the input file. >> >> >> >> >> Many thanks, >> >> Ashutosh >> > --000000000000ff646905d2aaaeef Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Thanks for your reply, just one quick question, so I don&#= 39;t need any of the three files required for restarting the job. So where = shall I use (write in the config file) this colvars.state file to restart t= he job and what would be the command for that. The link provided says writi= ng=C2=A0
cv save

Kindly help,

Many thanks,
Ashutosh=C2=A0

On= Wed, Dec 8, 2021 at 5:57 PM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:

Dear Users,

To restart eABF job do we need to use = xx.colvars.state file generated after each run or like normal restart forma= t

bincoordinates =C2=A0 =C2=A0 ./${runold}-restart.coor


binvelocities=C2=A0 =C2=A0 =C2=A0 ./${runold}-restart.ve= l


extendedSystem =C2=A0 =C2=A0 ./${runold}-restart.xsc


As I was looking online we have to use co= lvars.state file, so where shall I put in the input file.

<= br>



Ma= ny thanks,

Ashutosh

--000000000000ff646905d2aaaeef-- From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 8 17:19:36 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8NJanw001351; Wed, 8 Dec 2021 17:19:36 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B8NJavC001349; Wed, 8 Dec 2021 17:19:36 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8NJZkK001339; Wed, 8 Dec 2021 17:19:35 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B8NJZNJ001338; Wed, 8 Dec 2021 17:19:35 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B8NJSti001306 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000925b2105d2aab844" X-CLX-Response: 1TFkXGx8eEQpMehcZHh0RCllEF2RbSUFZSG58eG9sEQpYWBdjH1l5eWkdT3x aWhEKeE4XY1Nja3sTWH4aX14RCnlMF2dfT0IfAUVMbhljEQpDSBcHGBIfEQpDWRcHGBMdEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxkecRgbEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0VAH2ETYk5Pb01LaxsdaEROeWxyQV9+aGcaWF9gaU5SEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGBAbHhofGhEKXlkXcx9fY0gRCk1cFxkaGxEKTFoXf2lrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGw QeGBEKQl4XGxEKREkXGxEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmWH1Ya0AaBXJEaBEKQk4XY1Nja3sTWH4aX14RCkJMF2MfWXl5aR1PfFpaEQpCbBdv UmccckNJT1p+XREKQkAXYhNPell7fRlySWQRCkJYF2dzZXNAbmFhTF1iEQpaWBcZEQp5QxdnY2J SG1hfHVhCZBEKWUsXExwbHhEKcGgXa01GU15uZEFHYkQQGhEKcGgXZnJSEll6XlpvcEcQGRoRCn BoF2BfWBxGS3pAbVAcEBoRCnBoF2t7R3BGeGZdfn9cEBoRCnBoF2xFHFBEBXNabgVoEBkaEQpwf RdrZn9PHn55b2BdHhAZGhEKcH8XYk4FAXBEXmlEe2UQGxgbEQpwXxdiGl9QTEYBRhwaUhAZGhEK cGwXaHNSWXJnex97eUkQHBoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= X-Proofpoint-GUID: oj5K9HdeEgaA17BndSFXkuTBM0ruJCdx X-Proofpoint-ORIG-GUID: oj5K9HdeEgaA17BndSFXkuTBM0ruJCdx X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 priorityscore=347 suspectscore=0 bulkscore=0 mlxscore=0 lowpriorityscore=0 malwarescore=0 impostorscore=0 spamscore=0 clxscore=154 mlxlogscore=848 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112080127 domainage_hfrom=9614 X-Spam-Score: 0 X-Spam-OrigSender: scfbioiitd@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ashutosh Shandilya --000000000000925b2105d2aab844 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable or *cv load oldjob.colvars.state* in the eABF input file. Thanks, Ashutosh On Wed, Dec 8, 2021 at 6:16 PM Ashutosh Shandilya wrote: > Thanks for your reply, just one quick question, so I don't need any of the > three files required for restarting the job. So where shall I use (write = in > the config file) this colvars.state file to restart the job and what would > be the command for that. The link provided says writing > *cv save* > > Kindly help, > > Many thanks, > Ashutosh > > On Wed, Dec 8, 2021 at 5:57 PM Giacomo Fiorin > wrote: > >> >> https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-nam= d/colvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!u7UQzCdwyUYECYqbb= ZeuPoEy7KnX-I-WqcpmGThbsIhikH6_ocED2Uru038miyTcdg$=20 >> >> On Wed, Dec 8, 2021 at 5:52 PM Ashutosh Shandilya >> wrote: >> >>> Dear Users, >>> >>> To restart eABF job do we need to use xx.colvars.state file generated >>> after each run or like normal restart format >>> >>> bincoordinates ./${runold}-restart.coor >>> >>> >>> binvelocities ./${runold}-restart.vel >>> >>> >>> extendedSystem ./${runold}-restart.xsc >>> >>> >>> As I was looking online we have to use colvars.state file, so where >>> shall I put in the input file. >>> >>> >>> >>> >>> Many thanks, >>> >>> Ashutosh >>> >> --000000000000925b2105d2aab844 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable

or cv load oldjob.colvars.state in t= he eABF input file.

Thanks,
Ashutosh

On W= ed, Dec 8, 2021 at 6:16 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
Thanks for your reply, = just one quick question, so I don't need any of the three files require= d for restarting the job. So where shall I use (write in the config file) t= his colvars.state file to restart the job and what would be the command for= that. The link provided says writing=C2=A0
cv save

Kindly help,

Many thanks,
Ashutosh=C2=A0

On Wed, Dec 8, 2021 at 5:57 PM Giacomo Fio= rin <giaco= mo.fiorin@gmail.com> wrote:

On Wed, Dec 8, = 2021 at 5:52 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
Dear Users,
=
To restart eABF job do we need to use xx.colvars.state file = generated after each run or like normal restart format

=

bincoordinates =C2=A0 =C2=A0 ./${runold}-restart.coor


binvelocities=C2=A0 =C2=A0 =C2=A0 ./${runold}-restart.ve= l


extendedSystem =C2=A0 =C2=A0 ./${runold}-restart.xsc


As I was looking online we have to use co= lvars.state file, so where shall I put in the input file.

<= br>



Ma= ny thanks,

Ashutosh

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boundary="000000000000e615e705d2aba83f" X-Proofpoint-GUID: p5AoGtMjXwpbC6NW756UWT0IGXojOe8J X-CLX-Response: 1TFkXGxIcEQpMehceEhEKWUQXZGZbXRoBQkMbfV8RClhYF2ZFS3xkTVsecFh vEQp4ThdvGBIbTAVFQWdoehEKeUwXbx9uTEZHRB9wbxIRCkNIFwceHhsRCkNZFwcbEx8RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHBxxHh8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWh9rRW1eZ0ByXVpIaRxkfR0fHH99fhpjbXJFQGVPEmARClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4eEBseGh8aEQpeWRdzH1xiSBEKTVwXGRIbEQpMWhd8aU1NTREKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pMQ0lzaXkBW0B7EQpDWhcYGhMEEh8EGBsaBB 8bEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdvGBIbTAVFQWdoehEKQkkXbxgSG0wFRUFna HoRCkJFF2Z/AUFAf2NZYVJaEQpCThdvGBIbTAVFQWdoehEKQkwXZkVLfGRNWx5wWG8RCkJsF3oa ZgFpblt6EklwEQpCQBdiY2dMZmdvQV9IHxEKQlgXZ3Nlc0BuYWFMXWIRClpYFxMRCnlDF2VmHEt +QRlFZxhBEQpZSxcdEx0SEQpwaBdmQ1tkQVhITGFufRAZGhEKcGgXZmJcU3B7YBx5SF8QGRoRCn BoF2FgGHAeXl5lXXoeEBkaEQpwaBdvUxxtRR5jWxtyYRAZGhEKcGgXegFHAXgaG3J8f18QGRoRC nB9F2tYRB1PGXlkbWdnEBkaEQpwfRdvYlxPZ31sc0Z6UhAZGhEKcH0XaW5GcmUSfgEBU0wQGRoR CnB9F2cBX3laXG9eUhkBEBkaEQpwfRduWGIZZQFCRGBmUhAZGhEKcH0XbRlvSUlfGWBoQlwQGRo RCnB9F21/QGFwfGNdQV1HEBkaEQpwfxdlGXlmXkdpG2RPcxAdGhEKcF8XaR5HaWxgSAFmeEwQGR oRCnB/F3occH4SaXxaf0VEEBsfHBEKcF8XYkRYHWttBR1nXB0QGRoRCnB/F2Fmb1saZ2RCSB1bE BsZGxEKcF8XY2ISUEhjeB98Qn0QGxsZEQpwfxdlZkQBHkhGZHxaGxAbHBIRCnBfF297UBNvWERE RX9HEBkaEQpwfxdtRF9GRW19SHkZbhAbHhkRCnBfF2tGSxN5aGlufBN4EBsbHxEKcGwXZV1nRGV YeVBLQEQQGxoZEQptfhcaEQpYTRdLESA= X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: p5AoGtMjXwpbC6NW756UWT0IGXojOe8J MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 lowpriorityscore=0 malwarescore=0 phishscore=0 impostorscore=0 mlxscore=0 suspectscore=0 mlxlogscore=999 priorityscore=48 clxscore=186 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112080132 domainage_hfrom=7978 X-Spam-Score: 0 X-Spam-OrigSender: michael.robinson1@monash.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Michael Robinson --000000000000e615e705d2aba83f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear Denilson, Dummy bonds between lonepair 'atoms' and real atoms were dropped early in development, so there shouldn't be a bond present - see a relatively recent discussion here: https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/1020.ht= ml. It's been a little while since I've dealt with this, but if I recall correctly, older versions of NAMD don't handle these lone pairs appropriately - try your simulation with the latest version of NAMD available. If you're running this via HPC and it doesn't have NAMD 2.14, you can test it locally to see if it gets past this error. Otherwise, you might be able to try the 'lonepairs on' command mentioned in that mailing list post I've linked to. Hopefully that's helpful! Regards, Michael Robinson On Thu, 9 Dec 2021 at 00:42, DENILSON FERREIRA DE OLIVEIRA wrote: > Dear all, > > 1) The str file was generated for an organic substance containing a > chlorine atom, using the CHARMM General Force Field (CGenFF) program > version 2.5, through the Paramchem website (https://urldefense.com/v3/__h= ttps://cgenff.umaryland.edu/__;!!DZ3fjg!uwDckfP_YOefcgj9XsBWR63OEznQu2jSMAU= BsZkqU5KjBxZJRMHjt0S-210JOGWeRg$=20 > > ) > > 2) In such str file I can find the following: > ... > ATOM LP1 LPH 0.050 ! lonepair on chlorine > ... > LONEPAIR COLI LP1 Cl1 C19 DIST 1.6400 SCAL 0.0 ! lonepair on > chlorine > > 2) Using the topology files contained in toppar_c36_jul21.tgz, which is > available through the MacKerell Lab Homepage ( > https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtm= l*charmm__;Iw!!DZ3fjg!uwDckfP_YOefcgj9XsBWR63OEznQu2jSMAUBsZkqU5KjBxZJRMHjt= 0S-212g7m9RmA$=20 > ), > as well as the str file generated in Paramchem, I prepared the pdb and psf > files using VMD 1.9.4a55. In the pdb file the lone pair of the chlorine > atom is treated as an atom: > .... > ATOM 53428 LP1 UNK Z 1 226.355 227.015 173.583 1.00 0.00 > ZO1 X > ... > > 3) In the configuration file to carry out calculations with Namd 2.14 I > have provided all the parameter files. The following is observed in the > output from Namd: > > ".. > Info: PARAMETERS ./par_all36m_prot.prm > Info: PARAMETERS ./par_all36_lipid.prm > Info: PARAMETERS ./par_all36_carb.prm > Info: PARAMETERS ./par_all36_na.prm > Info: PARAMETERS ./par_all36_cgenff.prm > Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str > Info: PARAMETERS ./toppar_water_ions_namd.str > Info: PARAMETERS ./E2_ZINC000006181820_1-19_1-COR.str ! this > is the str file generated in Paramchem > " > > 4) However, Namd 2.14 did not perform the calculations because it > encountered an error: > > "FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 53428 > 53397)" > > 5) It means that Namd can not find parameters for the "bond" between the > chlorine atom and its lonepair of electrons. > > I would appreciate it if somebody could be kind enough to help me to solve > this problem. > > Best regards. > > Denilson. > > > O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destina= t=C3=A1rios e de > responsabilidade do remetente. O uso do e-mail deve estar de acordo com os > regulamentos institucionais vigentes. > --000000000000e615e705d2aba83f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Denilson,

Dummy bonds b= etween lonepair 'atoms' and real atoms were dropped early in develo= pment, so there shouldn't be a bond present - see a relatively recent d= iscussion here: https://www.ks.uiuc.edu/Research/namd/mailin= g_list/namd-l.2020-2021/1020.html. It's been a little while since I= 've dealt with this, but if I recall correctly, older versions of NAMD = don't handle these lone pairs appropriately - try your simulation with = the latest version of NAMD available. If you're running this via HPC an= d it doesn't have NAMD 2.14, you can test it locally to see if it gets = past this error. Otherwise, you might be able to try the 'lonepairs on&= #39; command mentioned in that mailing list post I've linked to.
<= div>
Hopefully that's helpful!
Regards,
Michael Robinson

On Thu, 9 Dec 2021 at 00:42, DENILSON FERREIR= A DE OLIVEIRA <denilson@ufla.br&= gt; wrote:
Dear all= ,

1) The str file was generated for an organic substance containing = a chlorine atom, using the CHARMM General Force Field (CGenFF) program vers= ion 2.5, through the Paramchem website (https://cgenff.uma= ryland.edu/)

2) In such str file I can find the following:
...
= ATOM LP1 =C2=A0 =C2=A0LPH =C2=A0 =C2=A0 0.050 ! lonepair on chlorine
...
LONEPAIR COLI LP1 =C2=A0 =C2=A0Cl1 =C2=A0 =C2=A0C19 =C2=A0 =C2=A0DIST = 1.6400 SCAL 0.0 ! lonepair on chlorine

2) Using the topology f= iles contained in toppar_c36_jul21.tgz, which is available through the MacK= erell Lab Homepage (http://macke= rell.umaryland.edu/charmm_ff.shtml#charmm), as well as the str file gen= erated in Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55. I= n the pdb file the lone pair of the chlorine atom is treated as an atom:
....
ATOM =C2=A053428 =C2=A0LP1 UNK Z =C2=A0 1 =C2=A0 =C2=A0 226.355 227.015= 173.583 =C2=A01.00 =C2=A00.00 =C2=A0 =C2=A0 =C2=A0ZO1 =C2=A0X
...

3) In the configuration file = to carry out calculations with Namd 2.14 I have provided all the parameter = files. The following is observed in the output from Namd:

"..
Inf= o: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36m_prot.p= rm
Info: PARAMETERS =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_lipid.prm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = ./par_all36_carb.prm
Info: PARAMET= ERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./par_all36_na.prm
<= div style=3D"margin-left:80px">Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 ./par_all36_cgenff.prm
Info: PARAMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./toppar_all= 36_carb_glycopeptide.str
Info: PAR= AMETERS =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./toppar_water_ions_namd.= str
Info: PARAMETERS =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 ./E2_ZINC000006181820_1-19_1-COR.str ! this is= the str file generated in Paramchem
"

4) However, Namd 2.14 did not perform the calculatio= ns because it encountered an error:

= "FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 5342= 8 53397)"

5) It means that Namd can not find parameters f= or the "bond" between the chlorine atom and its lonepair of elect= rons.

I would appreciate it if somebody could be kind enough to help= me to solve this problem.

Best regards.

Denilson.

<= /div>
O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.
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Thu, 9 Dec 2021 00:29:27 +0000 From: "Chen, Charles" To: "namd-l@ks.uiuc.edu" Subject: namd-l: Error in running multiple-walkers metadynamics at Bluewaters Thread-Topic: Error in running multiple-walkers metadynamics at Bluewaters Thread-Index: AQHX7JPTdmys1C3afEKNvq5Hn2L9Ww== Date: Thu, 9 Dec 2021 00:29:27 +0000 Message-ID: <3827A399-E734-4EC1-BD99-468FB45C9289@illinois.edu> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: 637f1d36-4a61-44df-af12-08d9baaaf5ab x-ms-traffictypediagnostic: DM6PR11MB4473:EE_ x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:2201; x-ms-exchange-senderadcheck: 1 x-ms-exchange-antispam-relay: 0 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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Ashutosh Shandilya Cc: NAMD list Content-Type: multipart/alternative; boundary="000000000000ba014005d2ac37e8" X-Proofpoint-ORIG-GUID: Yx19A-csQfTJClgLMWiBcGpMxwN_euTo X-Proofpoint-GUID: Yx19A-csQfTJClgLMWiBcGpMxwN_euTo X-CLX-Response: 1TFkXGx0ZEQpMehcZGRwRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGR4YEQpDWRcHGBMdEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ZcRkZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF3NSGxNrB0lZe0x+YGlGTWZnfUNoSW1aZ1JdZHVPX35FEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGRAbHhofGhEKXlkXcx9cWRgRCk1cFxgeHxEKTFoXfGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRMRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2ITT3pZe30ZcklkEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGRE KeUMXZ2NiUhtYXx1YQmQRCllLFxMcGx8RCnBoF2thSEVeHxtZWUdCEBkaEQpwaBdgfmhJUklkGE RTWBAZGhEKcGgXZnJSEll6XlpvcEcQGRoRCnBoF2t7R3BGeGZdfn9cEB4SEQpwaBdlb0tHfUBzQ WRhfBAZGhEKcH0Xa2Z/Tx5+eW9gXR4QGRoRCnB/F2JOBQFwRF5pRHtlEBsbHREKcF8XYhpfUExG AUYcGlIQGRoRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0 XSxEg X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 priorityscore=336 impostorscore=0 phishscore=0 adultscore=0 clxscore=173 malwarescore=0 suspectscore=0 spamscore=0 bulkscore=0 mlxlogscore=988 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112090004 domainage_hfrom=9615 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000ba014005d2ac37e8 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Quoting from the link I sent: When the Colvars module is initialized in NAMD, the *colvarsInput* keyword can be used to give the name of the state file. After initialization, a state file may be loaded at any time with the Tcl command *cv load*. So it's up to your preference which one to use based on how your script is organized. Skipping coor, vel and xsc files will not restart the system: you will need those as well. Giacomo On Wed, Dec 8, 2021 at 6:19 PM Ashutosh Shandilya wrote: > > or *cv load oldjob.colvars.state* in the eABF input file. > > Thanks, > Ashutosh > > On Wed, Dec 8, 2021 at 6:16 PM Ashutosh Shandilya > wrote: > >> Thanks for your reply, just one quick question, so I don't need any of >> the three files required for restarting the job. So where shall I use >> (write in the config file) this colvars.state file to restart the job and >> what would be the command for that. The link provided says writing >> *cv save* >> >> Kindly help, >> >> Many thanks, >> Ashutosh >> >> On Wed, Dec 8, 2021 at 5:57 PM Giacomo Fiorin >> wrote: >> >>> >>> https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-na= md/colvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!o5F2MtV-gzhNMjeW= 5R6U4o2GhGvlbsOOVcGs8TrUIz4Y3LaZZlNrKn9rCTRATaY75A$=20 >>> >>> On Wed, Dec 8, 2021 at 5:52 PM Ashutosh Shandilya >>> wrote: >>> >>>> Dear Users, >>>> >>>> To restart eABF job do we need to use xx.colvars.state file generated >>>> after each run or like normal restart format >>>> >>>> bincoordinates ./${runold}-restart.coor >>>> >>>> >>>> binvelocities ./${runold}-restart.vel >>>> >>>> >>>> extendedSystem ./${runold}-restart.xsc >>>> >>>> >>>> As I was looking online we have to use colvars.state file, so where >>>> shall I put in the input file. >>>> >>>> >>>> >>>> >>>> Many thanks, >>>> >>>> Ashutosh >>>> >>> --000000000000ba014005d2ac37e8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Quoting from the link I sent:=C2=A0

When the Colvars module is initialized i= n NAMD, the=C2=A0colvarsInput=C2=A0keyword can be used to give the name of the state file. Afte= r initialization, a state file may be loaded at any time with the Tcl comma= nd=C2=A0cv=C2=A0load.

So it's up to your= preference which one to use based on how your script is organized.

Skipping coor, vel and xsc files will not restart the sys= tem: you will need those as well.

Giacomo


On Wed, Dec 8, 2021 at 6:19 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
=
or cv load oldjob.colvars.state in the eABF input file.
Thanks,
Ashutosh

On Wed, Dec 8, 2021 at 6:1= 6 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
Thanks for your reply, ju= st one quick question, so I don't need any of the three files required = for restarting the job. So where shall I use (write in the config file) thi= s colvars.state file to restart the job and what would be the command for t= hat. The link provided says writing=C2=A0
cv save
<= br>
Kindly help,

Many thanks,
<= div>Ashutosh=C2=A0

On Wed, Dec 8, 2021 at 5:57 PM Giacomo Fiori= n <giacomo= .fiorin@gmail.com> wrote:

On Wed, Dec 8, 20= 21 at 5:52 PM Ashutosh Shandilya <scfbioiitd@gmail.com> wrote:
Dear Users,
To restart eABF job do we need to use xx.colvars.state file ge= nerated after each run or like normal restart format

bincoordinates =C2=A0 =C2=A0 ./${runold}-restart.coor


binvelocities=C2=A0 =C2=A0 =C2=A0 ./${runold}-restart.ve= l


extendedSystem =C2=A0 =C2=A0 ./${runold}-restart.xsc


As I was looking online we have to use co= lvars.state file, so where shall I put in the input file.

<= br>



Ma= ny thanks,

Ashutosh

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charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi, which version of NAMD are you using? The "Cannot allocate memory" message could be misleading, and may have come from an error field that wasn't properly initialized until the Colvars version included in NAMD 2.14= --000000000000d1564505d2ac4d6f-- From owner-namd-l@halifax.ks.uiuc.edu Thu Dec 9 07:00:48 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B9D0mRb019097; Thu, 9 Dec 2021 07:00:48 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B9D0ma1019096; Thu, 9 Dec 2021 07:00:48 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B9D0lpY019092; Thu, 9 Dec 2021 07:00:47 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B9D0lfQ019091; Thu, 9 Dec 2021 07:00:47 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B9D0XBI019080 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Dear all, I have some Constant pH Molecular Dynamics to analyze. I tried to use the available cphanalyze script by Radak (https://urldefense.com/v3/__https://g= ithub.com/radakb/pynamd__;!!DZ3fjg!owu71G1X9PfyKHaK4gx743wfZ0hYOiQAFtYUdvvp= 0C0usvbyaSDhFFjgVPx7DkWMsg$ ) as described in the tutorial. It works really well when you have only HIS, ASP and GLU as titratable residues on the system (the occupancy vector of these residues is described with two numbers). When you have CYS (1 number) or LYS (3 numbers) it gives you a python error: RuntimeError: dictionary keys changed during iteration Does someone that has more python knowledge than me knows how this could be fixed? Thanks, ingrid --000000000000d82dfd05d2b63008 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Dear all,

I have some Consta= nt pH Molecular Dynamics to analyze. I tried to use the available cphanalyz= e script by Radak (https://github.com/radakb/pynamd) as described in = the tutorial.
It works really well when you have only HIS, ASP an= d GLU as titratable residues on the system (the occupancy vector of these r= esidues is described with two numbers). When you have CYS (1 number) or LYS= (3 numbers) it gives you a python error:
RuntimeError: dictionary keys changed during iteration=
Does someone that has more python knowledge than me knows how th= is could be fixed?

Thanks,
ingrid

--000000000000d82dfd05d2b63008-- From owner-namd-l@halifax.ks.uiuc.edu Thu Dec 9 14:40:00 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B9Ke0XW026642; Thu, 9 Dec 2021 14:40:00 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B9Ke0WD026641; Thu, 9 Dec 2021 14:40:00 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B9KdxDl026636; Thu, 9 Dec 2021 14:39:59 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1B9KdxVW026635; Thu, 9 Dec 2021 14:39:59 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1B9KdqXd026628 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000a33a1505d2bc9bdb" X-Proofpoint-ORIG-GUID: nEEVl-2ZL-b1r_Ux5Qgv-LZfdKAElliL X-Proofpoint-GUID: nEEVl-2ZL-b1r_Ux5Qgv-LZfdKAElliL X-CLX-Response: 1TFkXHhocEQpMehcaEQpZRBdkS0JpTUJQQUBNGhEKWFgXbR9jbnNcXGtsS28 RCnhOF2x6UFlsfEJsRkgcEQp5TBducm9jY31wGGRcYREKQ0gXBxsdHxEKQ1kXBxsYExEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGBpxGwYZE3cGGBoaBhIdQh8GGgYbGhoGGnEaEBp3BhoGGgYaBhoGG gYacRoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XRG9vfEYHGHBmB0gbWHV/Uh97 TVwHZnBMTmFrb0ZGQ2YRClhcFx8EGgQYHhgFGxoEGxsaBB0EGxkbEBseGh8aEQpeWRdzHGseUBE KTVwXGR0eEQpMWhdoaU1raxEKTEYXb2tra2trEQpCTxdiZ1sfUBlTYHscExEKQ1oXGBoTBBIfBB gbGgQbEhgRCkJeFxsRCkJcFxsRCkJLF2h4Q2NAE0hgeVoeEQpCSRdselBZbHxCbEZIHBEKQkUXe kNDXmVnX19SYnwRCkJOF2x6UFlsfEJsRkgcEQpCTBdtH2Nuc1xca2xLbxEKQmwXYwV5TGdSZH1O bxkRCkJAF2YbRx1mH2MaeHxlEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxkRCnlDF2l6eGB fAUtsQ3x+EQpwaBdhHh14BRMZS1p9SRAHGRoRCnBoF2hzWkxla2xtZ2BTEAcZGhEKcGgXYWRaH1 8ZbVNeckIQBxkaEQpwaBdnWRN4WUwFTGxcGRAHGRoRCnBoF25iEmZHeU9lQllLEAcZGhEKcGwXb hJaS0MbWl9iGGQQHR4RCm1+FwcbEQpYTRdLESA= X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxscore=0 lowpriorityscore=0 priorityscore=0 impostorscore=0 phishscore=0 adultscore=0 clxscore=406 malwarescore=0 suspectscore=0 spamscore=0 bulkscore=0 mlxlogscore=969 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112090106 X-Spam-Score: 0 X-Spam-OrigSender: hrs00003@mix.wvu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hannah Scott --000000000000a33a1505d2bc9bdb Content-Type: text/plain; charset="UTF-8" I am seeing an unusually high force being applied in the wrong direction when applying constant velocity steered MD to my system. For this simulation I am applying SMD to a single alpha-carbon in a helical peptide and pulling along the -z axis in an attempt to simulate insertion into a membrane bilayer with a 1 fs timestep. When visualizing my system, I see that the peptide is being pulled in the +z direction instead. The SMD output shows that the initial force applied is very large. What could be causing this and what do you recommend I try? The following are the parameters I have set for the SMD simulation as well as the output: SMD on SMDFile ../current-parameters/rev-smd.ref ;# this is the pbd file with b-column needs remade with different systems SMDk 10 ;#adjusted to pull on termius of phlip SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs SMDDir 0 0 -1 SMDOutputFreq 100 SMD 0 5.801 -4.258 27.644 0 -0 27336.5 SMD 100 6.09131 -4.67441 31.9466 0 -0 24346.4 SMD 200 6.91383 -3.83161 34.0325 0 -0 22896.4 SMD 300 7.37256 -3.92352 36.4932 0 -0 21186.1 SMD 400 7.21118 -4.2608 39.8742 0 -0 18836.3 SMD 500 6.8234 -3.46171 43.0824 0 -0 16606.6 SMD 600 6.92947 -2.77978 46.19 0 -0 14446.8 SMD 700 7.27499 -2.5372 48.6056 0 -0 12767.7 SMD 800 8.21247 -2.39816 50.8552 0 -0 11204 SMD 900 8.02797 -1.72661 53.5881 0 -0 9304.52 SMD 1000 7.32698 -1.27389 55.6482 0 -0 7872.5 Thank you in advance, Hannah --000000000000a33a1505d2bc9bdb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I am seeing an unusually high force being applie= d in the wrong direction when applying constant velocity steered MD to my s= ystem. For this simulation I am applying SMD to a single alpha-carbon in a = helical peptide and pulling along the -z axis in an attempt to simulate ins= ertion into a membrane bilayer with a 1 fs timestep.=C2=A0

When visualizing my system, I see that the peptide is being pulled= in the=C2=A0+z direction instead. The SMD output shows that the initial fo= rce applied is very large. What could be causing this and what do you recom= mend=C2=A0I try?

The following are the param= eters I have set for the SMD simulation as well as the output:
SMD on
SMDFile ../current-parameters/rev-smd.ref =C2=A0 =C2=A0 = =C2=A0;# this is the pbd file with b-column =C2=A0 needs remade with differ= ent systems
SMDk 10 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0;#adjuste= d to pull on termius of phlip
SMDVel .00001 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ;# 10 A/ns = =3D .01 A/ps =3D .00001 A/fs
SMDDir 0 0 -1
SMDOutputFreq 100

=

SMD =C2=A00 5.801 -4.258 27.644 0 -0 27336.5
S= MD =C2=A0100 6.09131 -4.67441 31.9466 0 -0 24346.4
SMD =C2=A0200 6.91383= -3.83161 34.0325 0 -0 22896.4
SMD =C2=A0300 7.37256 -3.92352 36.4932 0 = -0 21186.1
SMD =C2=A0400 7.21118 -4.2608 39.8742 0 -0 18836.3
SMD =C2= =A0500 6.8234 -3.46171 43.0824 0 -0 16606.6
SMD =C2=A0600 6.92947 -2.779= 78 46.19 0 -0 14446.8
SMD =C2=A0700 7.27499 -2.5372 48.6056 0 -0 12767.7=
SMD =C2=A0800 8.21247 -2.39816 50.8552 0 -0 11204
SMD =C2=A0900 8.02= 797 -1.72661 53.5881 0 -0 9304.52
SMD =C2=A01000 7.32698 -1.27389 55.648= 2 0 -0 7872.5



Th= ank you in advance,
Hannah
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Thu, 09 Dec 2021 16:43:40 -0800 (PST) Content-Type: multipart/alternative; boundary=Apple-Mail-D8220E4E-F2DE-480A-A68E-CDB1A64307B2 Content-Transfer-Encoding: 7bit From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: Initial force for steered MD simulations Date: Thu, 9 Dec 2021 19:43:38 -0500 Message-Id: References: In-Reply-To: To: namd-l@ks.uiuc.edu, Hannah Scott X-Mailer: iPhone Mail (18B92) X-Proofpoint-GUID: ay2ryeOzzFAjh_8DmbFt3bBDSiMY6QNb X-CLX-Response: 1TFkXGx0eEQpMehcZGBwRCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHGRsfEQpDWRcHGxgaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ecRkeEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0tTGFhTT2VQUGxrQEJ1Em5HSGxeGUhobnlDZ3Mce2RIEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseHhAbHhofGhEKXlkXcxxvTksRCk1cFxsSEhEKTFoXeGlNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxd6QFp/WlhLcB9wXREKQ1oXGBoTBBIfBBgYGw QbEhoRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXZkttWEYYT2NFQ0ARCkJOF2NTY2t7E1h+Gl9eEQpCTBd6HmNBHl5cHB9ySxEKQmwX b09kQVpCUG1ma1kRCkJAF2NHTFtmW0IaXWVeEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBE KeUMXZE8SXkB/GUtacH8RCllLFxMcGxwRCnBnF2wfT3pNc1xhbU5fEBkaEQpwaBdrXBJSZ3xHU2 NcUxAZGhEKcGgXaV4ZQhlhHx15GVkQGRoRCnBoF2l7SU5/HnJAAWceEBkaEQpwaBdlQGNGS1hNR Ux8HRAZGhEKcGgXZkZ7YxljeXJMY08QGRoRCnB9F2dda0JbemVYZ2RJEBkaEQpwfxdlGXlmXkdp G2RPcxAdGhEKcF8XbkUfaxpMfHkaHV4QGRoRCnBsF2doQ2tzEnkYTWJcEBkaEQpwQxdoeAFZZn1 jTAVoQxAZGhEKbX4XGxEKWE0XSxEg X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: ay2ryeOzzFAjh_8DmbFt3bBDSiMY6QNb X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 lowpriorityscore=0 malwarescore=0 phishscore=0 impostorscore=0 mlxscore=0 suspectscore=0 mlxlogscore=999 priorityscore=326 clxscore=174 spamscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112100002 domainage_hfrom=9616 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= --Apple-Mail-D8220E4E-F2DE-480A-A68E-CDB1A64307B2 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Try use Occupancy column and not beta=20 In contrast with guide only atoms tagged Eith no-zero values into beta colum= n are used as pulling atoms. https://www.ks.uiuc.edu/Research/namd/2.9/ug/node48.html Enviado desde mi iPhone > El 9 dic. 2021, a la(s) 3:41 p. m., Hannah Scott es= cribi=C3=B3: >=20 > =EF=BB=BF > I am seeing an unusually high force being applied in the wrong direction w= hen applying constant velocity steered MD to my system. For this simulation I= am applying SMD to a single alpha-carbon in a helical peptide and pulling a= long the -z axis in an attempt to simulate insertion into a membrane bilayer= with a 1 fs timestep.=20 >=20 > When visualizing my system, I see that the peptide is being pulled in the += z direction instead. The SMD output shows that the initial force applied is v= ery large. What could be causing this and what do you recommend I try? >=20 > The following are the parameters I have set for the SMD simulation as well= as the output: >=20 > SMD on > SMDFile ../current-parameters/rev-smd.ref ;# this is the pbd file wit= h b-column needs remade with different systems > SMDk 10 ;#adjusted to pull on termius of p= hlip > SMDVel .00001 ;# 10 A/ns =3D .01 A/ps =3D .00001= A/fs > SMDDir 0 0 -1 > SMDOutputFreq 100 >=20 >=20 > SMD 0 5.801 -4.258 27.644 0 -0 27336.5 > SMD 100 6.09131 -4.67441 31.9466 0 -0 24346.4 > SMD 200 6.91383 -3.83161 34.0325 0 -0 22896.4 > SMD 300 7.37256 -3.92352 36.4932 0 -0 21186.1 > SMD 400 7.21118 -4.2608 39.8742 0 -0 18836.3 > SMD 500 6.8234 -3.46171 43.0824 0 -0 16606.6 > SMD 600 6.92947 -2.77978 46.19 0 -0 14446.8 > SMD 700 7.27499 -2.5372 48.6056 0 -0 12767.7 > SMD 800 8.21247 -2.39816 50.8552 0 -0 11204 > SMD 900 8.02797 -1.72661 53.5881 0 -0 9304.52 > SMD 1000 7.32698 -1.27389 55.6482 0 -0 7872.5 >=20 >=20 >=20 > Thank you in advance, > Hannah --Apple-Mail-D8220E4E-F2DE-480A-A68E-CDB1A64307B2 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Try use Occupancy column and not beta =

In contrast with guide only atoms tagged Eith no-zero va= lues into beta column are used as pulling atoms.

https://w= ww.ks.uiuc.edu/Research/namd/2.9/ug/node48.html

= Enviado desde mi iPhone

= El 9 dic. 2021, a la(s) 3:41 p. m., Hannah Scott <hrs00003@mix.wvu.e= du> escribi=C3=B3:

=EF=BB=BF
I am seeing an unusually h= igh force being applied in the wrong direction when applying constant veloci= ty steered MD to my system. For this simulation I am applying SMD to a singl= e alpha-carbon in a helical peptide and pulling along the -z axis in an atte= mpt to simulate insertion into a membrane bilayer with a 1 fs timestep. = ;

When visualizing my system, I see that the peptid= e is being pulled in the +z direction instead. The SMD output shows tha= t the initial force applied is very large. What could be causing this and wh= at do you recommend I try?

The following= are the parameters I have set for the SMD simulation as well as the output:=

SMD on
SMDFile ../current-parameters/rev-smd.ref &nb= sp;    ;# this is the pbd file with b-column   needs remade w= ith different systems
SMDk 10             &= nbsp;                    ;= #adjusted to pull on termius of phlip
SMDVel .00001       &= nbsp;                   ;# 10 A= /ns =3D .01 A/ps =3D .00001 A/fs
SMDDir 0 0 -1
SMDOutputFreq 100
<= br>

SMD  0 5.801 -4.258 27.644 0 -0 27336.5SMD  100 6.09131 -4.67441 31.9466 0 -0 24346.4
SMD  200 6.9138= 3 -3.83161 34.0325 0 -0 22896.4
SMD  300 7.37256 -3.92352 36.4932 0 -= 0 21186.1
SMD  400 7.21118 -4.2608 39.8742 0 -0 18836.3
SMD  = ;500 6.8234 -3.46171 43.0824 0 -0 16606.6
SMD  600 6.92947 -2.77978 4= 6.19 0 -0 14446.8
SMD  700 7.27499 -2.5372 48.6056 0 -0 12767.7
S= MD  800 8.21247 -2.39816 50.8552 0 -0 11204
SMD  900 8.02797 -1= .72661 53.5881 0 -0 9304.52
SMD  1000 7.32698 -1.27389 55.6482 0 -0 7= 872.5



Thank you i= n advance,
Hannah
= --Apple-Mail-D8220E4E-F2DE-480A-A68E-CDB1A64307B2-- From owner-namd-l@halifax.ks.uiuc.edu Fri Dec 10 12:28:58 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BAISw6w012242; Fri, 10 Dec 2021 12:28:58 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BAISw6k012241; Fri, 10 Dec 2021 12:28:58 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BAISvs2012237; Fri, 10 Dec 2021 12:28:57 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BAISvER012236; Fri, 10 Dec 2021 12:28:57 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BAISmq6012229 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000c8eb9405d2cee429" X-CLX-Response: 1TFkXGx0ZEQpMehcZGBMRCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGxkdEQpDWRcHGRwRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxlxGRkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWxhcTEZJcEBTdURsXmNaRn1vbVIaa1IZQh9iektcT0YRClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4ZEBseGh8aEQpeWRdzHH9uHREKTVwXGxsaEQpMWhd8aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF3pQeGRrWlJyWkZGEQpDWhcYGhMEEh8EGxwcBB 4SEQpCXhcbEQpEXhcYEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX 14RCkJFF2sTGmFOX15YGB1lEQpCThdjU2NrexNYfhpfXhEKQkwXaUlIGkt+aUYbeHMRCkJsF2Ee GXhabmxnY19iEQpCQBdvaU9yQAVjcG1BfBEKQlgXZ3Nlc0BuYWFMXWIRCk1eFxsRClpYFx8RCnl DF2EdX05EcGNBHB4cEQpZSxcTHBscEQpwaBdnc2NHR34TQ2tkXhAZGhEKcGgXZRtnckhhextMXl oQGRoRCnBoF2BdZ3Nlen9cQVt7EBkaEQpwaBdtfHtobkRLf0lHGxAZGhEKcGgXbkhiWU8eThhte kIQGRoRCnB9F2lCTH5PG3pGT0BiEBkaEQpwfRdmSRpiWhJLZHocYBAZGhEKcH8Xax1rHlN7Z2NL bXoQEx4RCnBfF2h+GE4ZHBhDZmhuEBkaEQpwfxdhZm9bGmdkQkgdWxAbGRsRCnBfF2NiElBIY3g ffEJ9EBMTEQpwbBduHWZ7EksaeBJcbRAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-ORIG-GUID: q2vflcZjy_nFtIplWEGx0Ax3h5HPavel X-Proofpoint-GUID: q2vflcZjy_nFtIplWEGx0Ax3h5HPavel X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=329 impostorscore=0 bulkscore=0 phishscore=0 mlxscore=0 spamscore=0 malwarescore=0 adultscore=0 suspectscore=0 lowpriorityscore=0 mlxlogscore=832 clxscore=173 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112100103 domainage_hfrom=9616 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak --000000000000c8eb9405d2cee429 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Ingrid, This error is new to me - I'm guessing it has to do with the new dict behavior in python 3 - - could you check which subversion you are using by typing "python - - version"? I did not test anything after 3.7 If you could also send me the files that raise error offline, I can hopefully have a chance to track this down. Cheers, Brian On Thu, Dec 9, 2021, 8:02 AM Ingrid Bernardes Santana Martins < ingrid.martins@unesp.br> wrote: > Dear all, > > I have some Constant pH Molecular Dynamics to analyze. I tried to use the > available cphanalyze script by Radak (https://urldefense.com/v3/__https:/= /github.com/radakb/pynamd__;!!DZ3fjg!up-iYBFXcnnspe3bKDuy9mlqNBUN1xBjevNbUz= 0to4X1AG4hIWnUj1LU1F7cp8sKjA$=20 > ) > as described in the tutorial. > It works really well when you have only HIS, ASP and GLU as titratable > residues on the system (the occupancy vector of these residues is describ= ed > with two numbers). When you have CYS (1 number) or LYS (3 numbers) it giv= es > you a python error: > RuntimeError: dictionary keys changed during iteration > Does someone that has more python knowledge than me knows how this could > be fixed? > > Thanks, > ingrid > > --000000000000c8eb9405d2cee429 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Ingrid,=C2=A0

This error is new to me - I'm guessing it has to do wit= h the new dict behavior in python 3 - - could you check which subversion yo= u are using by typing "python - - version"? I did not test anythi= ng after 3.7

If you coul= d also send me the files that raise error offline, I can hopefully have a c= hance to track this down.

Cheers,=C2=A0
Brian=C2=A0
<= br>
On Thu, Dec 9, 2021, 8:02 AM Ingrid Bernardes Santana Martins <= ;ingrid.martins@unesp.br>= wrote:
Dear = all,

I have some Constant pH Molecular Dynamics to= analyze. I tried to use the available cphanalyze script by Radak (https://github.com/radakb/pynamd) as de= scribed in the tutorial.
It works really well when you have only = HIS, ASP and GLU as titratable residues on the system (the occupancy vector= of these residues is described with two numbers). When you have CYS (1 num= ber) or LYS (3 numbers) it gives you a python error:
RuntimeError: dictionary keys changed during iteration
Does someone that has more python knowledge than me = knows how this could be fixed?

Thanks,
i= ngrid

=
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[73.253.124.38]) by smtp.gmail.com with ESMTPSA id m4sm2496317qtu.87.2021.12.10.14.01.11 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 10 Dec 2021 14:01:11 -0800 (PST) Subject: Re: namd-l: Problem with titration curve with cphanalyze script CYS and LYS (Constant pH Molecular Dynamics ) From: Brian Radak To: namd-l , Ingrid Bernardes Santana Martins References: Message-ID: <80a7b427-8239-ef83-1811-b4fd1cee1c51@gmail.com> Date: Fri, 10 Dec 2021 17:01:10 -0500 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------9EB16BC44DE694A65913504D" Content-Language: en-US X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: Pljw9pTajHcMknFT69GLv5gENjxy3vHP X-CLX-Response: 1TFkXGxIdEQpMehcZGR4RCllEF2NCUEUSHl1DextHEQpYWBdpSUgaS35pRht 4cxEKeE4XY1Nja3sTWH4aX14RCnlMF2lPZ0BIfUlFe0lvEQpDSBcHGBgTEQpDWRcHHh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB1xHhwQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XekZAXRNafktAYklnQURsfhwTbWZcH01vZEBSUxlcYnoRClhcFx8EGgQYHhgF GxoEGxsaBB0EGxkZEBseGh8aEQpeWRdzHHJmbhEKTVwXGRsdEQpMWhd4YU1BaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2VpUGdhRn1sGwUFEQpDWhcYGhMEEh8EGBgYBB sdGBEKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdrExphTl9eWBgdZREKQk4XY1Nja3sTWH4aX14RCkJMF2lJSBpLfmlGG3hzEQpCbBdh Hhl4Wm5sZ2NfYhEKQkAXb2lPckAFY3BtQXwRCkJYF2dzZXNAbmFhTF1iEQpaWBcfEQp5QxdhHV9 ORHBjQRweHBEKWUsXExwbHBEKcGcXY0J6Z0VtR11IGnIQGRoRCnBoF2UbZ3JIYXsbTF5aEBkaEQ pwaBdlTB5ieGJ8ZR4aYBAZGhEKcGgXa2tbBUFYREVLSXAQGRoRCnBoF2ZPfmhveEcSTGIfEBkaE QpwaBduSGJZTx5OGG16QhAeEhEKcH0XaUJMfk8bekZPQGIQGRoRCnB9F2ZJGmJaEktkehxgEB4S EQpwfxdrHWseU3tnY0ttehAbGhkRCnBfF2h+GE4ZHBhDZmhuEBkaEQpwfxdhZm9bGmdkQkgdWxA bGBIRCnBfF2NiElBIY3gffEJ9EBMcEQpwbBduHWZ7EksaeBJcbRAeEhEKcEMXaXASBX9GHlpzQW IQGRoRCm1+FxoRClhNF0sRIA== X-Proofpoint-GUID: Pljw9pTajHcMknFT69GLv5gENjxy3vHP MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 priorityscore=334 impostorscore=0 spamscore=0 clxscore=187 mlxlogscore=999 phishscore=0 suspectscore=0 mlxscore=0 adultscore=0 bulkscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112100120 domainage_hfrom=9616 X-Spam-Score: 0 X-Spam-OrigSender: brian.radak@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Brian Radak This is a multi-part message in MIME format. --------------9EB16BC44DE694A65913504D Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable I do not know the exact issue, but this is almost definitely due to the=20 hasty and outdated conversion to python 3 from several years back. The=20 only solution I can recommend right now is to use conda (or some such)=20 to go back to an older version of python (as far back as 3.6 might be=20 necessary). I will see if I can clean things up for the 3.6+ modern age,=20 but I can't promise a quick timeline for that (this is entirely a side=20 project for me these days). Regards, Brian On 12/10/21 1:28 PM, Brian Radak wrote: > Hi Ingrid, > > This error is new to me - I'm guessing it has to do with the new dict=20 > behavior in python 3 - - could you check which subversion you are=20 > using by typing "python - - version"? I did not test anything after 3.7 > > If you could also send me the files that raise error offline, I can=20 > hopefully have a chance to track this down. > > Cheers, > Brian > > > On Thu, Dec 9, 2021, 8:02 AM Ingrid Bernardes Santana Martins=20 > > wrote: > > Dear all, > > I have some Constant pH Molecular Dynamics to analyze. I tried to > use the available cphanalyze script by Radak > (https://urldefense.com/v3/__https://github.com/radakb/pynamd__;!!DZ3= fjg!qDnHjHsAWog1gTK9_km1uxmjVtFA0q-J6glu5aPJkBR209zcVQ79Bc64PdD_7DbrrQ$=20 > ) > as described in the tutorial. > It works really well when you have only HIS, ASP and GLU as > titratable residues on the system (the occupancy vector of these > residues is described with two numbers). When you have CYS (1 > number) or LYS (3 numbers) it gives you a python error: > RuntimeError: dictionary keys changed during iteration > Does someone that has more python knowledge than me knows how this > could be fixed? > > Thanks, > ingrid > --------------9EB16BC44DE694A65913504D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

I do not know the exact issue, but this is almost definitely due to the hasty and outdated conversion to python 3 from several years back. The only solution I can recommend right now is to use conda (or some such) to go back to an older version of python (as far back as 3.6 might be necessary). I will see if I can clean things up for the 3.6+ modern age, but I can't promise a quick timeline for that (this is entirely a side project for me these days).

Regards,

Brian

On 12/10/21 1:28 PM, Brian Radak wrote:
Hi Ingrid, 

This error is new to me - I'm guessing it has to do with the new dict behavior in python 3 - - could you check which subversion you are using by typing "python - - version"? I did not test anything after 3.7

If you could also send me the files that raise error offline, I can hopefully have a chance to track this down.

Cheers, 
Brian 


On Thu, Dec 9, 2021, 8:02 AM Ingrid Bernardes Santana Martins <ingrid.martins@unesp.br> wrote:
Dear all,

I have some Constant pH Molecular Dynamics to analyze. I tried to use the available cphanalyze script by Radak (https://github.com/radakb/pynamd) as described in the tutorial.
It works really well when you have only HIS, ASP and GLU as titratable residues on the system (the occupancy vector of these residues is described with two numbers). When you have CYS (1 number) or LYS (3 numbers) it gives you a python error:
RuntimeError: dictionary keys changed during iteration
Does someone that has more python knowledge than me knows how this could be fixed?

Thanks,
ingrid

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boundary="000000000000bf7bdb05d2f85029" X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIbEQpMehcTHxEKWUQXYhtyRn9ORn9CE0wRClhYF20TQnpYE3NIQ0N BEQp4ThdkZRpgcnBuW3JaHREKeUwXaW1eYml+TlpyREgRCkNIFwcZHBIRCkNZFwcdHBEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscG3EeGhAadwYYGgYaEQpZXhdoY3kRCklGF19DX0l1Q kVZXk9OEQpDThdYEmhvE3sYc2JCb24aTmVYeXVPU1J5S0kdfV5peGdwaREKWFwXHwQaBBgeGAUb GgQbGxoEHQQbGRkQGx4aHxoRCl5ZF3McBUxeEQpNXBcZHhIRCkxaF3hpTU1NEQpFWRdvbxEKTF8 XegUFBQUFBQUFAUcRCkxGF2xraxEKQk8XaH1BYENafXNHQRMRCkNaFxgaEwQSHwQbGBIEHhIRCk JeFxsRCkJFF2sZWhJsRFp5e0VfEQpCThdkZRpgcnBuW3JaHREKQkwXbRNCelgTc0hDQ0ERCkJsF 2F8ZlxvT19/c1pgEQpCQBdmXBxseHBoUHlSZhEKQlgXZ3Nlc0BuYWFMXWIRClpYFx0RCnlDF2RZ GUlIGF1PHENbEQpwZxdoemVHbBtwTVMZbRAZGhEKcGgXYBhbTWlbTh9Sb0EQGRoRCnBoF2gFRnk ST39OZgV4EBkaEQpwaBdtEmYbXF8dWmNcHxAZGhEKcGgXb2tvfFodQWNMen4QGRoRCnBoF2VSE3 lzfmtpBUleEBkaEQpwfRdvYlxPZ31sc0Z6UhAZGhEKcH0XZBpzT0dwUwFuYGEQGRoRCnB9F2cBX 3laXG9eUhkBEBkaEQpwfRdiQFpHUBhzG0xMQBAZGhEKcH0XbURHcmkTXkJdYFAQGRoRCnB/F3oc cH4SaXxaf0VEEBsZHxEKcF8XYkRYHWttBR1nXB0QGRoRCnB/F2Fmb1saZ2RCSB1bEBMTEQpwXxd jYhJQSGN4H3xCfRATGBEKcH8XZWZEAR5IRmR8WhsQGx4fEQpwXxdve1ATb1hEREV/RxAZGhEKcH 8XbURfRkVtfUh5GW4QGxoeEQpwXxdrRksTeWhpbnwTeBATHxEKcGwXYh5lZxMcehNpbEcQGRoRC m1+FxoRClhNF0sRIA== X-Proofpoint-GUID: r8BE9Q2YHhED0dOrS_eyxSac7WtCRMZC X-Proofpoint-ORIG-GUID: r8BE9Q2YHhED0dOrS_eyxSac7WtCRMZC MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 adultscore=0 spamscore=0 phishscore=0 suspectscore=0 impostorscore=0 mlxlogscore=999 mlxscore=0 malwarescore=0 lowpriorityscore=0 clxscore=181 priorityscore=95 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112120121 X-Spam-Score: 0 X-Spam-OrigSender: denilson@ufla.br X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, DENILSON FERREIRA DE OLIVEIRA --000000000000bf7bdb05d2f85029 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Fabrice. Thanks for the suggestion. I don't think this would solve the problem as the data requested by Namd 2.14 is not included in the CGenFF parameters/topology files. Also, following Michael Robinson's suggestion, I inserted dihedral parameters with an equilibrium angle of 0 and a strength of 0, which solved the problem. Anyway, thanks for the help. Best wishes. Denilson. Em seg., 6 de dez. de 2021 =C3=A0s 02:32, Fabrice Gardebien < fabrice.gardebien@univ-reunion.fr> escreveu: > Dear Dennilson, > > I am not sure whether this could solve your problem but have you tried to > tick the option " Include parameters that are already in CGenFF" in > generating your STR file? > > Best wishes. > On 05/12/2021 22:53, DENILSON FERREIRA DE OLIVEIRA wrote: > > Dear all, > > 1) The C3_WIN-1-COR.str file was generated for an organic substance, using > the CHARMM General Force Field (CGenFF) program version 2.5, through the > Paramchem website (https://urldefense.com/v3/__https://cgenff.umaryland.e= du/__;!!DZ3fjg!ugrRDAgoCMT0aUbi6k1ylKk_tih9cjoOeKLQWD87o-WMMwhdJUMxvfqxBEIU= 8UqY6Q$=20 > > ) > > 2) Using the topology files contained in toppar_c36_jul21.tgz, which is > available through the MacKerell Lab Homepage ( > https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtm= l*charmm__;Iw!!DZ3fjg!ugrRDAgoCMT0aUbi6k1ylKk_tih9cjoOeKLQWD87o-WMMwhdJUMxv= fqxBEKYKRBOKA$=20 > ), > as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared t= he > pdb and psf files using VMD 1.9.4a55. > > 3) In the configuration file to carry out calculations with Namd 2.14 I > have provided all the parameter files in the order that seems correct to > me. The following is observed in the output from Namd: > > "... > Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb > Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf > Info: PARAMETER file: CHARMM format! > Info: PARAMETERS ./par_all36m_prot.prm > Info: PARAMETERS ./par_all36_lipid.prm > Info: PARAMETERS ./par_all36_carb.prm > Info: PARAMETERS ./par_all36_na.prm > Info: PARAMETERS ./par_all36_cgenff.prm > Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str > Info: PARAMETERS ./toppar_water_ions_namd.str > Info: PARAMETERS ./C3_WIN-1-COR.str > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SKIPPING rtf SECTION IN STREAM FILE > Info: SKIPPING rtf SECTION IN STREAM FILE > " > > 4) However, Namd 2.14 did not perform the calculations because it > encountered an error: > > "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1 > CG1T2 (ATOMS 53401 53404 53407 53408)" > > 5) It is clear to me that this error is due to the fact that there is no > parameter for dihedral angles of atoms of the terminal alkyne function > anywhere: > > CG1T2 : C(sp1) terminal > CG1T1 : C(sp1) non-terminal > CG3C50 : C(sp3) linked to CG1T1 > CG3RC1 : C(sp3) linked to CG3C50 > > 6) To be clearer, I could not find data for the dihedral angle CG3RC1 > CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in > item "3" of this message. > > 7) In fact, it seems to me that there is no point in working with a > dihedral angle for such atoms. > > 8) Consequently, I will be grateful if anyone can be kind enough to make a > suggestion to solve the problem. > > Thanks. > > Denilson. > > O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destina= t=C3=A1rios e de > responsabilidade do remetente. O uso do e-mail deve estar de acordo com os > regulamentos institucionais vigentes. > > > --=20 O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de=20 responsabilidade do remetente. O uso do e-mail deve estar de acordo com os= =20 regulamentos institucionais vigentes. --000000000000bf7bdb05d2f85029 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Fabrice.

Thanks for the suggestion.

I don't think this would solve the problem as t= he data requested by Namd 2.14 is not included in the CGenFF parameters/top= ology files.

Also, following Michael Robinson's= suggestion, I inserted dihedral parameters with an equilibrium angle of 0 = and a strength of 0, which solved the problem.
Anyway, thanks for the help.
Best wishes.

Denilson.


Em seg., 6 de dez. = de 2021 =C3=A0s 02:32, Fabrice Gardebien <fabrice.gardebien@univ-reunion.fr> escreveu:<= br>
=20 =20 =20
Dear Dennilson,

I am not sure whether this could solve your problem but have you tried to tick the option " On 05/12/2021 22:53, DENILSON FERREIRA DE OLIVEIRA wrote:
Dear all,
1) The C3_WIN-1-COR.str file was generated for an organic substance, using the CHARMM General Force Field (CGenFF) program version 2.5, through the Paramchem website (https://cgenff.umaryland.edu/)

2) Using the topology files contained in toppar_c36_jul21.tgz, which is available through the MacKerell Lab Homepage (http://mackerell.umaryland.edu/charm= m_ff.shtml#charmm), as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared the pdb and psf files using VMD 1.9.4a55.

3) In the configuration file to carry out calculations with Namd 2.14 I have provided all the parameter files in the order that seems correct to me. The following is observed in the output from Namd:

"...
Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb
Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ./par_all36m_prot.prm
Info: PARAMETERS ./par_all36_lipid.prm
Info: PARAMETERS ./par_all36_carb.prm
Info: PARAMETERS ./par_all36_na.prm
Info: PARAMETERS ./par_all36_cgenff.prm
Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str
Info: PARAMETERS ./toppar_water_ions_namd.str
Info: PARAMETERS ./C3_WIN-1-COR.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
"

4) However, Namd 2.14 did not perform the calculations because it encountered an error:

"FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1 CG1T2 (ATOMS 53401 53404 53407 53408)"

5) It is clear to me that this error is due to the fact that there is no parameter for dihedral angles of atoms of the terminal alkyne function anywhere:

=C2=A0 =C2=A0CG1T2 : C(sp1) terminal
=C2=A0 =C2=A0CG1T1 : C(sp1) non-terminal
=C2=A0 =C2=A0CG3C50 : C(sp3) linked to CG1T1
=C2=A0 =C2=A0CG3RC1 : C(sp3) linked to CG3C50

6) To be clearer, I could not find data for the dihedral angle CG3RC1 CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in item "3" of this message.
7) In fact, it seems to me that there is no point in working with a dihedral angle for such atoms.

8) Consequently, I will be grateful if anyone can be kind enough to make a suggestion to solve the problem.

Thanks.

Denilson.

O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat=C3=A1rios e de responsabilidade do remetente. O uso do e-mai= l deve estar de acordo com os regulamentos institucionais vigentes.



O conte=C3=BAdo deste e-mail e anexos s=C3=A3o restritos aos seus destinat= =C3=A1rios e de responsabilidade do remetente. O uso do e-mail deve estar d= e acordo com os regulamentos institucionais vigentes.
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boundary="0000000000003fbf8205d306ec63" X-Proofpoint-GUID: fXbdVfpudpsskDs4-dDHSkYL4Fig0_ii X-Proofpoint-ORIG-GUID: fXbdVfpudpsskDs4-dDHSkYL4Fig0_ii X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxgZEQpMehcdGxgRCllEF2F/RkBpZUlAZ2ZdEQpYWBdubV1SRmN/Rkh lfhEKeE4XY1Nja3sTWH4aX14RCnlMF2Z6TRhiaX0FXHhdEQpDSBcHGx4fEQpDWRcHGx4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxgecRsGHh13Bh0YBhoGBxgfQAYcEgYacRoQGncGGgYaBhoGBxsfB hoGGnEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF0xySE58TFpfTlpZWUFuWR4H Tm5ieUFzZh5sQ00adUNDEQpYXBcfBBoEGB4YBRsaBBsaGgQdBBseGBAbHhofGhEKXlkXcx1lUAU RCk1cFxsZHBEKTFoXe2lNeGsRCkVZF2gRCkxfF3oFBQUFBQUFBQVSEQpNThdpaxEKTEYXb2tra2 trEQpCTxdiZE9dHmR8TV9SXBEKQ1oXGBoTBBIfBBscHQQeHhEKQl4XGxEKQlwXGxEKXk4XGxEKQ ksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdoUG5vGEUba0thZREKQk4XY1Nja3sT WH4aX14RCkJMF25tXVJGY39GSGV+EQpCbBdnaUVjcnpuQRxjGxEKQlgXZ3Nlc0BuYWFMXWIRCk1 eFwcbEQpaWBcZEQpZSxcTHBsTEQpwaBdsfx1LXQFTYxhBUBAHGRoRCnBoF2V/eAV6RntNS2kFEA cZGhEKcGgXY0VCQ3Jpc2hnUkEQBxkaEQpwaBdkZU1nZWkTU2cYARAHGRoRCnBoF2RaWn9rGU1YS 1tEEAcZGhEKcGwXZx1EUE9JfBp4W2kQBxkaEQptfhcHGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 suspectscore=0 phishscore=0 adultscore=0 lowpriorityscore=0 clxscore=123 impostorscore=0 spamscore=0 bulkscore=0 malwarescore=0 mlxscore=0 priorityscore=712 mlxlogscore=519 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112130085 domainage_hfrom=9619 X-Spam-Score: 0 X-Spam-OrigSender: royrakesh8900@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Rakesh Roy --0000000000003fbf8205d306ec63 Content-Type: text/plain; charset="UTF-8" Hello I am Rakesh. I am currently running a constant pH simulation of a membrane protein system in NAMD with a system size of nearly 200,000 atoms. But when I am restarting the simulation it is showing a mismatch between the restart coordinates and the psf file FATAL ERROR: Incorrect atom count in binary file 3.5/cph0.restart.coor . What should I do ? thank you in advance.. -- Thanking You. *Rakesh Kumar Roy,* *Junior Research Fellow,* Department Of Applied Chemistry, IIT (ISM) Dhanbad, Dhanbad-826004, Jharkhand, INDIA. Contact no. 8709383084, 8877544146 email- royrakesh8900@gmail.com --0000000000003fbf8205d306ec63 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello I am Rakesh. I am currently running a constant = pH simulation of a membrane protein system in NAMD with a system size of ne= arly 200,000 atoms. But when I am restarting the simulation it is showing a= mismatch between the restart coordinates and the psf file
FATAL = ERROR: Incorrect atom count in binary file 3.5/cph0.restart.coor
= . What should I do ?
thank you in advance..



--

Thanking You.


Rakesh Kumar Roy,=
Junior Research Fellow,
Departmen= t Of Applied Chemistry,
IIT (ISM) Dhanbad,
Dhanbad-826004, Jharkhand, INDIA.
Cont= act no.=C2=A0
8709383084, 8877544146

email- royrakesh8900@gmail.com

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boundary="0000000000003a9eac05d3187d2a" X-Proofpoint-GUID: HTzXcFOmK8unmB7wq5l4FrOfs7IpN2_f X-Proofpoint-ORIG-GUID: HTzXcFOmK8unmB7wq5l4FrOfs7IpN2_f X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBkdEQpMehcbHhoRCllEF21TUHxHBUUfWRJnEQpYWBdlT35yU1lPXm9 pZBEKeE4Xbkl7G2JfeBtsHF4RCnlMF2F8aV5YZUVBHVgBEQpDSBcHEx0RCkNZFwccHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGBpxGwYZE3cGGxkSBhoGGgYSGgYacRoQGncGGgYaBhoGGgYaBhpxG hAadwYaEQpZXhdoY3kRCklGF19DX0l1QkVZXk9OEQpDThdiflBySWxlR2ESX0RHaB1dWx9GHmxY ZUxZHWNaZBh1TBEKWFwXHwQaBBgeGAUbGgQbGxoEHQQbGRkQGx4aHxoRCl5ZF3MdQmUbEQpNXBc bHBsRCkxaF2hpTWtrEQpCTxdgZGsfZ0QYcGYYWhEKQ1oXGBoTBBIfBBgYGAQeGBEKQl4XGxEKQk UXY05HQEBuS0VaZWcRCkJOF25JextiX3gbbBxeEQpCTBdlT35yU1lPXm9pZBEKQmwXY0hIAR9cR 11uQXsRCkJAF2hZfE1nYUxAaXsaEQpCWBdnc2VzQG5hYUxdYhEKTV4XBxsRClpYFxsRCnlDF29o GnB/HW56E00YEQpwaBdsf19TRGsZGRJNZxAHGRoRCnBoF2h8fFhvQ1obUmJjEAcZGhEKcGgXb0R kf2xkSFlbX0QQBxkaEQpwaBdteEdQUh1zG2BESBAHGRoRCnBoF24Fc3BAQG5oaEJQEAcZGhEKcG wXb3waZU9feVJcQ2sQBxkaEQptfhcHGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 adultscore=0 priorityscore=140 spamscore=0 mlxscore=0 bulkscore=0 malwarescore=0 clxscore=237 mlxlogscore=545 suspectscore=0 lowpriorityscore=0 impostorscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112140059 X-Spam-Score: 0 X-Spam-OrigSender: moumitasaharay@uohyd.ac.in X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Moumita Saharay --0000000000003a9eac05d3187d2a Content-Type: text/plain; charset="UTF-8" Dear all, I want to perform a constant velocity pulling experiment using Steered Molecular Dynamics (SMD). I used the following TCL script to mark the fixed and SMD atoms. It works well when there is only one atom to be fixed. But I want to fix the centroid of a collection of CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480. How do I do that ? Please help me to resolve this issue. TCL script: set allatoms [atomselect top all] $allatoms set beta 0 set fixedatom [atomselect top "resname GLU and resid 203 and name CA"] $fixedatom set beta 1 $allatoms set occupancy 0 set smdatom [atomselect top "index 10525"] $smdatom set occupancy 1 $allatoms writepdb smd_step5_01.ref set smdpos [lindex [$smdatom get {x y z}] 0] set fixedpos [lindex [$fixedatom get {x y z}] 0] vecnorm [vecsub $smdpos $fixedpos] Thanks, Moumita -- Dr. Moumita Saharay Assistant Professor, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India --0000000000003a9eac05d3187d2a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear all,

I want to pe= rform a constant velocity pulling experiment using
Steered Molecu= lar Dynamics (SMD). I used the following TCL
script to mark the f= ixed and SMD atoms. It works well when there is
only one atom to = be fixed. But I want to fix the centroid of a collection of=C2=A0
CA atoms,=C2=A0for example,=C2=A0CA atoms of GLU203, PHE257, and ASP480.= =C2=A0
How do I do that ? Please help me to resolve this issue.= =C2=A0=C2=A0

TCL script:
set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top "resname GLU and resid 203 and name CA= "]
$fixedatom set beta 1
$allatoms set occupancy 0=
set smdatom [atomselect top "index 10525"]
$= smdatom set occupancy 1
$allatoms writepdb smd_step5_01.ref
=
set smdpos [lindex [$smdatom get {x y z}] 0] =C2=A0
set fixedpos [lindex [$fixedatom get {x y z}= ] 0] =C2=A0
vecnorm [vecsu= b $smdpos $fixedpos]

Thanks,
Moumi= ta
--
=
Dr. Moumita Saharay
Assistant Professor,=C2=A0
Department of = Systems and Computational Biology,=C2=A0
School of Life Sciences,= =C2=A0
University of Hyderabad,=C2=A0
Gachibowli, Hyder= abad, India
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boundary="0000000000002ac21a05d319220c" X-Proofpoint-ORIG-GUID: DotqU6IT9XSF81M6Q_mpErTaBklbUW4Q X-CLX-Shades: MLX X-Proofpoint-GUID: DotqU6IT9XSF81M6Q_mpErTaBklbUW4Q X-CLX-Response: 1TFkXGx8YEQpMehcTHxEKWUQXYExEZH9gckBCHlMRClhYF2BDSVgTHXgeUBJ hEQp4ThdvGBIbTAVFQWdoehEKeUwXbB5fYFgfH0xra0MRCkNIFwcYHBsRCkNZFwceHxEKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhsZGHEYGhAadwYYGgYaEQpZXhdsbHkRCklGF19DX0l1Q kVZXk9OEQpDThduRV5bfxxjfhNyeWwSG2cce3VHWm9YfktoQUZIf30eexEKWFwXHwQaBBgeGAUb GgQbGhoEHQQbHhgQGx4aHxoRCl5ZF3MdQhxtEQpNXBcHHhoRCkxaF3hpTWtrEQpFWRdvaxEKTF8 XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XaFheUEkFElx7ZHsRCkNaFxgaEwQSHwQYGBsEHx sRCkJeFxsRCkReFxgRCkJcFxsRCl5OFxsRCkJLF28YEhtMBUVBZ2h6EQpCSRdvGBIbTAVFQWdoe hEKQkUXZ2JFYXsYeEgTc0ERCkJOF28YEhtMBUVBZ2h6EQpCTBdgQ0lYEx14HlASYREKQmwXYFAY fVJgXkZDUkIRCkJAF2Bbc0dNUnNtWXpIEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUM XbUN9YAVafFltGUwRCllLFx0TEhkRCnBnF21deW5mHk1lb1JTEBkaEQpwaBdsf19TRGsZGRJNZx AZGhEKcGgXYFxIYB16U0dcfXIQGRoRCnBoF2wYWkB/S01fWR9vEBkaEQpwaBdtGUkBBUt5bXhPe xAZGhEKcGgXbXhHUFIdcxtgREgQGRoRCnB9F2F6S29CU2loARJHEBkaEQpwfxdlGXlmXkdpG2RP cxAdEhEKcF8Xa1pYclhiY0JpRUIQGRoRCnBsF2NQGWFDbHsZbFp4EBkaEQptfhcbEQpYTRdLESA = X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=152 malwarescore=0 bulkscore=0 spamscore=0 adultscore=0 impostorscore=0 mlxscore=0 priorityscore=95 lowpriorityscore=0 suspectscore=0 phishscore=0 mlxlogscore=766 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112140064 domainage_hfrom=7983 X-Spam-Score: 0 X-Spam-OrigSender: anup.prasad@monash.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Anup Prasad --0000000000002ac21a05d319220c Content-Type: text/plain; charset="UTF-8" Hi Dr. Moumita, I don't think that there is any straightforward command for fixing the centroid of a group of atoms. Instead of it you can try the "distance colvar" module. You have to calculate the centre of mass (com) of the group of atoms and create the dummy atom at this com. Then apply distance colvar between "group of atoms" and "dummy atoms" along with SMD simulation. Fix the dummy atom in SMD instead of a group of atoms. https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html Cheers Anup On Tue, 14 Dec 2021 at 15:52, Moumita Saharay wrote: > Dear all, > > I want to perform a constant velocity pulling experiment using > Steered Molecular Dynamics (SMD). I used the following TCL > script to mark the fixed and SMD atoms. It works well when there is > only one atom to be fixed. But I want to fix the centroid of a collection > of > CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480. > How do I do that ? Please help me to resolve this issue. > > TCL script: > set allatoms [atomselect top all] > $allatoms set beta 0 > set fixedatom [atomselect top "resname GLU and resid 203 and name CA"] > $fixedatom set beta 1 > $allatoms set occupancy 0 > set smdatom [atomselect top "index 10525"] > $smdatom set occupancy 1 > $allatoms writepdb smd_step5_01.ref > set smdpos [lindex [$smdatom get {x y z}] 0] > set fixedpos [lindex [$fixedatom get {x y z}] 0] > vecnorm [vecsub $smdpos $fixedpos] > > Thanks, > Moumita > -- > Dr. Moumita Saharay > Assistant Professor, > Department of Systems and Computational Biology, > School of Life Sciences, > University of Hyderabad, > Gachibowli, Hyderabad, India > --0000000000002ac21a05d319220c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Dr. Moumita,
I don't think that there is any st= raightforward command for fixing the centroid=C2=A0of a group of atoms. Ins= tead of it you can try the "distance colvar" module. You have to = calculate the centre=C2=A0of mass (com)=C2=A0of the group of atoms and crea= te the dummy atom at this com. Then apply distance colvar between "gr= oup of atoms" and "dummy atoms" along with SMD simulation. F= ix the dummy atom in SMD instead of a group of atoms.

<= div>h= ttps://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html

=
Cheers
Anup


On Tue, 14 Dec 202= 1 at 15:52, Moumita Saharay <moumitasaharay@uohyd.ac.in> wrote:
Dear all,
I want to perform a constant velocity pulling experiment u= sing
Steered Molecular Dynamics (SMD). I used the following TCL
script to mark the fixed and SMD atoms. It works well when there i= s
only one atom to be fixed. But I want to fix the centroid of a = collection of=C2=A0
CA atoms,=C2=A0for example,=C2=A0CA atoms of = GLU203, PHE257, and ASP480.=C2=A0
How do I do that ? Please help = me to resolve this issue.=C2=A0=C2=A0

= TCL script:
set allatoms [atomselect top all]
$all= atoms set beta 0
set fixedatom [atomselect top "resname GLU = and resid 203 and name CA"]
$fixedatom set beta 1
= $allatoms set occupancy 0
set smdatom [atomselect top "index= 10525"]
$smdatom set occupancy 1
$allatoms writep= db smd_step5_01.ref
set smdpos [lindex [$smdatom get {x y z}] 0]<= span style=3D"white-space:pre-wrap"> =C2=A0
set fixedpos [= lindex [$fixedatom get {x y z}] 0] =C2=A0
vecnorm [vecsub $smdpos $fixedpos]
Thanks,
Moumita
--
Dr. Moumita Saharay
Assistant Professor,=C2=A0
Depar= tment of Systems and Computational Biology,=C2=A0
School of Life = Sciences,=C2=A0
University of Hyderabad,=C2=A0
Gachibow= li, Hyderabad, India
--0000000000002ac21a05d319220c-- From owner-namd-l@halifax.ks.uiuc.edu Tue Dec 14 08:11:00 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BEEB0II008678; Tue, 14 Dec 2021 08:11:00 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BEEB0Y1008677; Tue, 14 Dec 2021 08:11:00 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BEEAxOd008672; Tue, 14 Dec 2021 08:10:59 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BEEAxLQ008671; Tue, 14 Dec 2021 08:10:59 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BEEAgXJ008661 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 14 Dec 2021 08:10:42 -0600 (CST) Received: from pps.filterd (m0166259.ppops.net [127.0.0.1]) by mx0b-00007101.pphosted.com (8.16.1.2/8.16.1.2) with ESMTP id 1BEDaTfq021403 for ; Tue, 14 Dec 2021 14:10:41 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=henin@ibpc.fr; dmarc=none Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by mx0b-00007101.pphosted.com (PPS) with ESMTPS id 3cxuth0e02-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 14 Dec 2021 14:10:41 +0000 Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id 817201E42925; Tue, 14 Dec 2021 15:10:39 +0100 (CET) Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id bXUt7rhuIrfY; Tue, 14 Dec 2021 15:10:38 +0100 (CET) Received: from localhost (localhost.localdomain [127.0.0.1]) by raba.ibpc.fr (Postfix) with ESMTP id AE7B21E42932; Tue, 14 Dec 2021 15:10:38 +0100 (CET) X-Virus-Scanned: amavisd-new at ibpc.fr Received: from raba.ibpc.fr ([127.0.0.1]) by localhost (raba.ibpc.fr [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id 1SKkL9NDMrqm; Tue, 14 Dec 2021 15:10:38 +0100 (CET) Received: from raba.ibpc.fr (mail1.ibpc.fr [193.49.234.221]) by raba.ibpc.fr (Postfix) with ESMTP id 2D4BE1E4291F; Tue, 14 Dec 2021 15:10:38 +0100 (CET) Date: Tue, 14 Dec 2021 15:10:25 +0100 (CET) From: =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= To: NAMD list , Anup Prasad Cc: Moumita Saharay Message-ID: <1200681246.11603279.1639491025330.JavaMail.zimbra@ibpc.fr> In-Reply-To: References: Subject: Re: namd-l: SMD: Fixing centroid MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_14aaa0ab-5636-4cf2-9b08-ccc599e51744" X-Originating-IP: [172.27.1.46] X-Mailer: Zimbra 8.8.15_GA_4018 (ZimbraWebClient - GC84 (Linux)/8.8.15_GA_4026) Thread-Topic: namd-l: SMD: Fixing centroid Thread-Index: 0rDCatNkMe3CRwLgDBAkarCv1Fit0w== X-CLX-Shades: MLX X-Proofpoint-GUID: 9h42czOaGfCOETyztPGUIlrrv297n-Vu X-Proofpoint-ORIG-GUID: 9h42czOaGfCOETyztPGUIlrrv297n-Vu X-CLX-Response: 1TFkXGxIeEQpMehcaEQpZRBdjGXgcaXBNE3xASREKWFgXehJnaWBZeUZBT2U RCnhOF2VPfhJDaWZZHAFpEQp5TBdtb2hMaGhNEh9MZBEKQ0gXBxsdGBEKQ1kXBx4fEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwecR4ZEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOFxNCHhhJUGVLbUxpZW9+U1Beem1/Y0ZYWFwYEx1EB3xfEQpYXBcfBBoEGB4YBRsa BBsbGgQdBBsZGxAbHhofGhEKXlkXcx1BWhIRCk1cFxgcExEKTFoXeG1rTU0RCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXbGtrEQpCTxdoQEVIGBh8a1t6GREKQ1oXGxMZBB4TBBgZHgQYGBsRCk JeFxsRCkReFxgRCkRJFxsRCkJFF2RYXFxNflJJG2VJEQpCThdlT34SQ2lmWRwBaREKQkwXehJna WBZeUZBT2URCkJsF2ESEk9PTE1/Tx4FEQpCQBdgW3NHTVJzbVl6SBEKQlgXZ3Nlc0BuYWFMXWIR Ck1eFxsRClpYFxgRCnlDF21DfWAFWnxZbRlMEQpwZxdtXXluZh5NZW9SUxAeEhEKcGgXZ0l4HVx vYEB/bWsQGRoRCnBoF2h8fFhvQ1obUmJjEBoRCnBoF2d4UnJtbmNNQUIaEBkaEQpwaBduYGF5bX 1zYWdoRRAZGhEKcGgXbE9LR39sfHhJTEwQGRoRCnB9F2F6S29CU2loARJHEB4SEQpwfxdlGXlmX kdpG2RPcxAdGhEKcF8Xa1pYclhiY0JpRUIQHhIRCnBsF2ZgE2RcTRpnT3pQEBkaEQpwTBdtaGUZ QVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 adultscore=0 spamscore=0 lowpriorityscore=0 mlxlogscore=714 bulkscore=0 malwarescore=0 clxscore=184 priorityscore=0 mlxscore=0 suspectscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112140082 X-Spam-Score: 0 X-Spam-OrigSender: henin@ibpc.fr X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?B?SsOpcsO0bWUgSMOpbmlu?= --=_14aaa0ab-5636-4cf2-9b08-ccc599e51744 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi all,=20 Adding to the answer by Anup: if you pull on a distance colvar, there is pr= obably no need for fixing (or restraining) any group of atoms. However, if = you want to pull along a specific direction, you can use the "distanceZ" fu= nction, specifying that the axis is not z but x.=20 Cheers,=20 J=C3=A9r=C3=B4me=20 ----- On 14 D=C3=A9c 21, at 12:02, Anup Prasad wro= te:=20 > Hi Dr. Moumita, > I don't think that there is any straightforward command for fixing the ce= ntroid > of a group of atoms. Instead of it you can try the "distance colvar" modu= le. > You have to calculate the centre of mass (com) of the group of atoms and = create > the dummy atom at this com. Then apply distance colvar between "group of = atoms" > and "dummy atoms" along with SMD simulation. Fix the dummy atom in SMD in= stead > of a group of atoms. > [ https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html | > https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html ] > Cheers > Anup > On Tue, 14 Dec 2021 at 15:52, Moumita Saharay < [ > mailto:moumitasaharay@uohyd.ac.in | moumitasaharay@uohyd.ac.in ] > wrote: >> Dear all, >> I want to perform a constant velocity pulling experiment using >> Steered Molecular Dynamics (SMD). I used the following TCL >> script to mark the fixed and SMD atoms. It works well when there is >> only one atom to be fixed. But I want to fix the centroid of a collectio= n of >> CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480. >> How do I do that ? Please help me to resolve this issue. >> TCL script: >> set allatoms [atomselect top all] >> $allatoms set beta 0 >> set fixedatom [atomselect top "resname GLU and resid 203 and name CA"] >> $fixedatom set beta 1 >> $allatoms set occupancy 0 >> set smdatom [atomselect top "index 10525"] >> $smdatom set occupancy 1 >> $allatoms writepdb smd_step5_01.ref >> set smdpos [lindex [$smdatom get {x y z}] 0] >> set fixedpos [lindex [$fixedatom get {x y z}] 0] >> vecnorm [vecsub $smdpos $fixedpos] >> Thanks, >> Moumita >> -- >> Dr. Moumita Saharay >> Assistant Professor, >> Department of Systems and Computational Biology, >> School of Life Sciences, >> University of Hyderabad, >> Gachibowli, Hyderabad, India --=_14aaa0ab-5636-4cf2-9b08-ccc599e51744 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi all,

Adding to the answer by Anup: if = you pull on a distance colvar, there is probably no need for fixing (or res= training) any group of atoms. However, if you want to pull along a specific= direction, you can use the "distanceZ" function, specifying that the axis = is not z but x.

Cheers,
J=C3=A9r=C3=B4me

----- On 14 D=C3=A9c 21, at 12:02, Anup Prasad <anup.= prasad@monash.edu> wrote:
Hi Dr. Moumit= a,
I don't think that there is any straightforward command for fixing t= he centroid of a group of atoms. Instead of it you can try the "distan= ce colvar" module. You have to calculate the centre of mass (com) = ;of the group of atoms and create the dummy atom at this com. Then apply d= istance colvar between "group of atoms" and "dummy atoms" along with SMD si= mulation. Fix the dummy atom in SMD instead of a group of atoms.

<= div>https://www.ks.uiuc.e= du/Research/namd/2.13/ug/node55.html

Cheers
Anu= p


On Tue, 14 Dec 2021 at 15:52, Moumita Saharay <moumitasaharay@uohyd.ac.in> wrote:
Dear all,
I want to perform a constant velocity pulling e= xperiment using
Steered Molecular Dynamics (SMD). I used the foll= owing TCL
script to mark the fixed and SMD atoms. It works well w= hen there is
only one atom to be fixed. But I want to fix the cen= troid of a collection of 
CA atoms, for example, C= A atoms of GLU203, PHE257, and ASP480. 
How do I do that ? P= lease help me to resolve this issue.  

= TCL script:
set allatoms [atomselect top all]
$all= atoms set beta 0
set fixedatom [atomselect top "resname GLU and r= esid 203 and name CA"]
$fixedatom set beta 1
$allatoms = set occupancy 0
set smdatom [atomselect top "index 10525"]
<= div>$smdatom set occupancy 1
$allatoms writepdb smd_step5_01.ref<= /div>
set smdpos [lindex [$smdatom get {x y z}] 0]=09 
set fixedpos [lindex [$fixedatom= get {x y z}] 0]=09 
=
vecnorm [vecsub $smdpos $fixedpos]

Thanks,
Moumita
--
Dr. Moumita S= aharay
Assistant Professor, 
Department of Systems and Comput= ational Biology, 
School of Life Sciences, 
U= niversity of Hyderabad, 
Gachibowli, Hyderabad, India

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Wed, 15 Dec 2021 09:15:41 -0800 (PST) From: Hsubo Luo X-Google-Original-From: Hsubo Luo Content-Type: multipart/alternative; boundary="Apple-Mail=_243F5AE2-F227-4B4B-95D0-CA18556DD951" Subject: namd-l: Lone pair forces Message-Id: Date: Wed, 15 Dec 2021 11:15:40 -0600 To: namd-l@ks.uiuc.edu X-Mailer: Apple Mail (2.3693.40.0.1.81) X-CLX-Shades: MLX X-Proofpoint-GUID: oEEi7qt53WuVwtqTtRgUNBww0dfXjH6X X-Proofpoint-ORIG-GUID: oEEi7qt53WuVwtqTtRgUNBww0dfXjH6X X-CLX-Response: 1TFkXGxwdEQpMehcZHhMRCllEF3ocR1JQGBkYbht5EQpYWBdoUlJzExpoehJ SaREKeE4XY1Nja3sTWH4aX14RCnlMF2FscHBOXhxpfEsaEQpDSBcHHhkbEQpDWRcHEhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxgbcRsGHht3BhsaEgYaBhoGGRMGGnEaEBp3BhoGGgYaBhoGGgYac RoQGncGGhEKWV4XbGx5EQpJRhdfQ19JdUJFWV5PThEKQ04XRW9vQx1bXh8ZfV98XV5bfl54TX9k aF1dGk5MckBiHHIRClhcFx8EGgQYHhgFGxoEGxsaBB0EGxkZEBseGh8aEQpeWRdzHRJOSxEKTVw XHRIRCkxaF2hpTWtrEQpMRhdva2tra2sRCkJPF3pMQ0lzaXkBW0B7EQpDWhcYGhMEEh8EGBsaBB 4dEQpCXhcbEQpCXBcbEQpeThcbEQpCSxdjU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF 2JDR2JCZmBhExlQEQpCThdjU2NrexNYfhpfXhEKQkwXaFJScxMaaHoSUmkRCkJsF3pFYHJeTFhJ UAVtEQpCQBd6TG5vE3NtUkATGhEKQlgXZ3Nlc0BuYWFMXWIRCk1eFwcbEQpaWBcYEQp5QxdvT39 tYWUFa058EhEKWUsXExwYGxEKcGgXax55cG5OQ3JiekYQBxkaEQpwaBdoWVNhcGhrYk5BHRAHGR oRCnBoF28dZBtpRhNPW0FvEAcZGhEKcGgXZX8dRGRARBtIcEgQBxkaEQpwaBdiXWdvUml7ZhlvW hAHGRoRCnB9F2QbSFJAWF1aXWJIEAcZGhEKcH8XbV1bSE97S1gcTXgQBxkaEQpwXxdvGXwYS2RZ YWBrWBAHGRoRCnBsF2l8X0ZaSxt4f2VoEAcZGhEKcEMXaE1+TUVtTmtfBUEQBxkaEQptfhcHGxE KWE0XSxEg MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 adultscore=0 spamscore=0 lowpriorityscore=0 mlxlogscore=919 bulkscore=0 malwarescore=0 clxscore=167 priorityscore=349 mlxscore=0 suspectscore=0 phishscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112150099 domainage_hfrom=9621 X-Spam-Score: 0 X-Spam-OrigSender: luohsubo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hsubo Luo --Apple-Mail=_243F5AE2-F227-4B4B-95D0-CA18556DD951 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: Quoted-printable Hello NAMD developers and users, I am new to NAMD but have some experience with other code (gromacs and lamm= ps). My project is to use CHARMM force field with lone pair enabled on the = halogen atom. My question is about how the force on the lone pair is distri= buted to the parent atoms. In my case, the force field topology has: LONEPAIR COLI LP1 BRH CZ1 DIST 1.8900 SCAL 0.0 In psf file, I have the lines: 96 288 !NUMLP NUMLPH 2 1 F 1.8900 0.0000 0.0000 2 4 F 1.8900 0.0000 0.0000 etc. So it is the collinear lone pair. Actually, I obtained some different results on gromacs with the virtual sit= es (https://urldefense.com/v3/__https://manual.gromacs.org/documentation/cu= rrent/reference-manual/functions/interaction-methods.html*virtual-interacti= on-sites__;Iw!!DZ3fjg!u_r9z3z0MKumqyfF9ZCGSoUocT3EFOFKdyjM23CZNxDZ20QaljsjY= vxUfx1-kdP_jQ$ ). So I am suspecting that the treatment of fo= rce on lone pair can be the difference. Can you please tell how NAMD deals = with this? I have searched on the web but no conclusion to date. Thank you = in advance.= --Apple-Mail=_243F5AE2-F227-4B4B-95D0-CA18556DD951 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: Quoted-printable Hello NAMD developers a= nd users,

I am new to N= AMD but have some experience with other code (gromacs and lammps). My proje= ct is to use CHARMM force field with lone pair enabled on the halogen atom.= My question is about how the force on the lone pair is distributed to the = parent atoms. In my case, the force field topology has:

LONEPAIR COLI LP1    BRH &= nbsp; CZ1    DIST 1.8900 SCAL 0.0

In psf file, I have the lines:

    &n= bsp;   96       288 !NUMLP NUMLPH
=        2        1 F     &= nbsp;    1.8900     0.0000     0.0000
       2        4 F &= nbsp;        1.8900     0.0000     = 0.0000
etc.

=
So it is the collinear lone pair.

Actually, I obtained some different = results on gromacs with the virtual sites (https://manual.gromacs.org/documentation/current/reference-manual/functio= ns/interaction-methods.html#virtual-interaction-sites). So I am su= specting that the treatment of force on lone pair can be the difference. Ca= n you please tell how NAMD deals with this? I have searched on the web but = no conclusion to date. Thank you in advance.
= --Apple-Mail=_243F5AE2-F227-4B4B-95D0-CA18556DD951-- From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 15 23:43:10 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BG5hA05001367; Wed, 15 Dec 2021 23:43:10 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BG5hAFq001366; Wed, 15 Dec 2021 23:43:10 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BG5h9g6001362; Wed, 15 Dec 2021 23:43:09 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BG5h9G9001361; Wed, 15 Dec 2021 23:43:09 -0600 (CST) Received: from mx0b-00007101.pphosted.com (mx0b-00007101.pphosted.com [148.163.139.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BG5gteF001353 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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boundary="000000000000c299f305d33ce411" --000000000000c299f305d33ce411 Content-Type: text/plain; charset="UTF-8" Hi, Based on my previously asked question on the namd forum ( https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/1532.html), I have written a tcl force script to apply harmonic constraints during constant pH MD run. While the script works fine with normal MD run, when constant pH option is turned on, NAMD crashes with "can't read "group1": no such variable" error. How can I modify my script so that it works during cphmd run. Thanks in advance. Tcl script can be found in attachment and a snippet of log file is as follows: TCL: namdcph) B:22:LYS : 7500 1.00 TCL: namdcph) B:27:GLU : 7500 1.00 TCL: namdcph) B:29:LYS : 7500 1.00 TCL: namdcph) ************************************************* psfgen) Info: writing psf file 5.5/namdcph.md.psf psfgen) total of 50849 atoms psfgen) total of 39142 bonds psfgen) total of 42635 angles psfgen) total of 43628 dihedrals psfgen) total of 376 impropers psfgen) total of 0 explicit exclusions psfgen) total of 54 cross-terms psfgen) Info: psf file complete. psfgen) Info: writing pdb file 5.5/namdcph.md.pdb psfgen) Info: pdb file complete. psfgen) Info: writing namdbin file 5.5/namdcph.md.coor psfgen) Info: writing velnamdbin file 5.5/namdcph.md.vel psfgen) Info: namdbin file complete. psfgen) Info: velnamdbin file complete. TCL: namdcph) clearing extraBondsFile 5.5/namdcph.sw.extrabonds TCL: Reloading molecular structure from file 5.5/namdcph.md.psf and pdb file 5.5/namdcph.md.pdb Info: TIME FOR READING PSF FILE: 5.84653 Info: READING EXTRA BONDS FILE 5.5/namdcph.sw.extrabonds Info: Reading pdb file 5.5/namdcph.md.pdb Info: TIME FOR READING PDB FILE: 0.0943979 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 50849 ATOMS Info: 39142 BONDS Info: 42635 ANGLES Info: 43628 DIHEDRALS Info: 376 IMPROPERS Info: 54 CROSSTERMS Info: 0 EXCLUSIONS Info: 44345 RIGID BONDS Info: 108202 DEGREES OF FREEDOM Info: 17989 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 17989 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 303558 amu Info: TOTAL CHARGE = 7.00001 e Info: MASS DENSITY = 1.00502 g/cm^3 Info: ATOM DENSITY = 0.101381 atoms/A^3 Info: ***************************** Info: ADDED 125405 IMPLICIT EXCLUSIONS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.6778e-33 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.71539e-17 AT 11.9974 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 9.34011e-27 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.98256e-17 AT 11.9974 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 TCL: Reinitializing atom data from files with basename 5.5/namdcph.md Info: Reading from binary file 5.5/namdcph.md.coor Info: Reading from binary file 5.5/namdcph.md.vel Info: REMOVING COM VELOCITY -0.0070921 0.0605137 -0.0096071 TCL: Minimizing for 100 steps TCL: Line Number 30 TCL: can't read "group1": no such variable -- Diship Srivastava SRF Department of Chemistry IIT(ISM) - Dhanbad India --000000000000c299f305d33ce411 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
Based on my previously asked question on the namd = forum (https://www.ks.uiuc.edu/Research/namd/mailing_list/na= md-l.2020-2021/1532.html), I have written a tcl force script to apply= =C2=A0harmonic constraints=C2=A0during constant pH MD run. While the script= works fine with normal MD run, when constant pH option is turned on, NAMD = crashes with "can't read "group1": no such variable"= ; error. How can I modify my script so=C2=A0that=C2=A0it works during cphmd= run.=C2=A0
Thanks in advance.=C2=A0

Tcl= script can be found in attachment and a snippet of log file is as follows:= =C2=A0

TCL: namdcph) B:22:LYS =C2=A0 =C2=A0 =C2=A0 : = =C2=A0 =C2=A0 7500 =C2=A0 =C2=A0 1.00
TCL: namdcph) B:27:GLU =C2=A0 =C2= =A0 =C2=A0 : =C2=A0 =C2=A0 7500 =C2=A0 =C2=A0 1.00
TCL: namdcph) B:29:LY= S =C2=A0 =C2=A0 =C2=A0 : =C2=A0 =C2=A0 7500 =C2=A0 =C2=A0 1.00
TCL: namd= cph) *************************************************
psfgen) Info: wri= ting psf file 5.5/namdcph.md.psf
psfgen) total of 50849 atoms
psfgen)= total of 39142 bonds
psfgen) total of 42635 angles
psfgen) total of = 43628 dihedrals
psfgen) total of 376 impropers
psfgen) total of 0 exp= licit exclusions
psfgen) total of 54 cross-terms
psfgen) Info: psf fi= le complete.
psfgen) Info: writing pdb file 5.5/namdcph.md.pdb
psfgen= ) Info: pdb file complete.
psfgen) Info: writing namdbin file 5.5/namdcp= h.md.coor
psfgen) Info: writing velnamdbin file 5.5/namdcph.md.vel
ps= fgen) Info: namdbin file complete.
psfgen) Info: velnamdbin file complet= e.
TCL: namdcph) clearing extraBondsFile 5.5/namdcph.sw.extrabonds
TC= L: Reloading molecular structure from file 5.5/namdcph.md.psf and pdb file = 5.5/namdcph.md.pdb
Info: TIME FOR READING PSF FILE: 5.84653
Info: REA= DING EXTRA BONDS FILE 5.5/namdcph.sw.extrabonds
Info: Reading pdb file 5= .5/namdcph.md.pdb
Info: TIME FOR READING PDB FILE: 0.0943979
Info: Info: ****************************
Info: STRUCTURE SUMMARY:
In= fo: 50849 ATOMS
Info: 39142 BONDS
Info: 42635 ANGLES
Info: 43628 D= IHEDRALS
Info: 376 IMPROPERS
Info: 54 CROSSTERMS
Info: 0 EXCLUSION= S
Info: 44345 RIGID BONDS
Info: 108202 DEGREES OF FREEDOM
Info: 17= 989 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 179= 89 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TO= TAL MASS =3D 303558 amu
Info: TOTAL CHARGE =3D 7.00001 e
Info: MASS D= ENSITY =3D 1.00502 g/cm^3
Info: ATOM DENSITY =3D 0.101381 atoms/A^3
I= nfo: *****************************
Info: ADDED 125405 IMPLICIT EXCLUSION= S
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TAB= LE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0= .000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE:= 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY:= 9.6778e-33 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: = 3.71539e-17 AT 11.9974
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE= : 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY:= 9.34011e-27 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY:= 2.98256e-17 AT 11.9974
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORC= E: 0.00150189 AT 0.251946
TCL: Reinitializing atom data from files with = basename 5.5/namdcph.md
Info: Reading from binary file 5.5/namdcph.md.co= or
Info: Reading from binary file 5.5/namdcph.md.vel
Info: REMOVING C= OM VELOCITY -0.0070921 0.0605137 -0.0096071
TCL: Minimizing for 100 step= s
TCL: Line Number 30
TCL: can't read "group1": no such= variable
--
Diship Srivastava=C2=A0
S= RF=C2=A0
Department of Chemistry
IIT(ISM) - Dhanbad
India
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[77.103.16.24]) by smtp.gmail.com with ESMTPSA id u12sm5021414wrf.60.2021.12.16.07.05.57 for (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Thu, 16 Dec 2021 07:05:57 -0800 (PST) To: namd-l@ks.uiuc.edu From: Luis Cebamanos Subject: namd-l: Best performance multi node GPU Message-ID: <7d27d04a-70ff-2897-86e4-010d0812226f@gmail.com> Date: Thu, 16 Dec 2021 15:05:56 +0000 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Content-Language: en-GB X-Proofpoint-GUID: c07uR822LwivPG1vPBV1m5bjwIePJETP X-CLX-Shades: MLX X-CLX-Response: 1TFkXGBsYEQpMehcZGB0RCllEF21fU2FAYBNGWl5nEQpYWBdsSB1sfFhBbWA TZBEKeE4XY1Nja3sTWH4aX14RCnlMF2kaR2FNZX5BeFwaEQpDSBcHHRwRCkNZFwcYExoRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbExhxGxwcEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0kaHV94EhgYZl1DXHptG1x6aHwbRx9IQF1jT3pgb356EQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGxAbHhofGhEKXlkXcxJ6WlARCk1cFxsbHBEKTFoXbGlNTWsRCkxGF29ra2t raxEKQk8XaH1BYENafXNHQRMRCkNaFxgaEwQSHwQbGBIEHxgRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXbWESR1l9eW9hRngRCkJOF2NTY2t7E 1h+Gl9eEQpCTBdsSB1sfFhBbWATZBEKQmwXbGR8GX1QWR1kcH4RCkJAF2MFHWhbX2tHAXt/EQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXelNtbl4eRmd6GVkRCllLFxMcGBgRCnBoF2F peXN7BVhQQV9fEBkaEQpwaBdiWRhMTHlraERdRBAZGhEKcGgXaXtrRhgcTkcfeE8QGRoRCnBoF2 Fof1x4eRhNf19DEBkaEQpwbBdtTmZhfxMSfRoFSxAZGhEKcEMXaE17cBoZXE9yG34QGRoRCm1+F xsRClhNF0sRIA== X-Proofpoint-ORIG-GUID: c07uR822LwivPG1vPBV1m5bjwIePJETP X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 spamscore=0 priorityscore=327 adultscore=0 mlxscore=0 impostorscore=0 phishscore=0 clxscore=212 bulkscore=0 suspectscore=0 lowpriorityscore=0 mlxlogscore=573 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112160085 domainage_hfrom=9622 X-Spam-Score: 0 X-Spam-OrigSender: luiceur@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Luis Cebamanos Hello, I am a bit confused about all the different builds that can be done and I was wondering if there is a clear winner to build when running on large number of nodes (4x GPU each) on Infiniband clusters. 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boundary="_000_77d6b35e3d7a482a8b99e608a6ac98b6uniduede_" --_000_77d6b35e3d7a482a8b99e608a6ac98b6uniduede_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I have a similar problem to Moumita, so I will follow the same thread. In my case, I have a complex of two proteins chains and I want to pull them= apart. The complex is aligned such as the vector between the chains COMs i= s parallel to the X-axis. I want to pull the protein's COMs along that vect= or in opposite directions. The complex is in a rectangular box of 210 x 118= x 118 A. I got a colvars configuration file (attached) from a colleague to modify ac= cording to my problem, which I did with the Colvars Dashboard plugin. The file has first a distance colvar to monitor the distance, and then some= others to define the application of the forces for each protein on each ax= is. If I understood well, the: ref { dummyAtom (X, Y, Z) } section should refer to the COM of each protein, right? The problem is that, if I put the COM of my proteins, it doesn't work, but = it does with the original values coming from a completely different system = (in the file). My COMs are: COM(A) =3D [-11.17, 0.40, -0.28] COM(B) =3D [36.67, -0.44, 0.97] In the harmonic definition section, the values are the ones in the original= file. Since I want to pull the COMs in opposite direction along the X-axis= , I should put my COM_X values in the centers for pull_chainA_x and pull_ch= ainB_x, and larger values for the targetCenters, correct? Any help will be very appreciated, Best regards, Yasser ________________________________ From: owner-namd-l@ks.uiuc.edu on behalf of J=E9= r=F4me H=E9nin Sent: Tuesday, December 14, 2021 3:10:25 PM To: NAMD list; Anup Prasad Cc: Moumita Saharay Subject: Re: namd-l: SMD: Fixing centroid Hi all, Adding to the answer by Anup: if you pull on a distance colvar, there is pr= obably no need for fixing (or restraining) any group of atoms. However, if = you want to pull along a specific direction, you can use the "distanceZ" fu= nction, specifying that the axis is not z but x. Cheers, J=E9r=F4me ----- On 14 D=E9c 21, at 12:02, Anup Prasad wrote: Hi Dr. Moumita, I don't think that there is any straightforward command for fixing the cent= roid of a group of atoms. Instead of it you can try the "distance colvar" m= odule. You have to calculate the centre of mass (com) of the group of atoms= and create the dummy atom at this com. Then apply distance colvar between = "group of atoms" and "dummy atoms" along with SMD simulation. Fix the dummy= atom in SMD instead of a group of atoms. https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html Defining collective variables (NAMD 2.13 User's Guide) www.ks.uiuc.edu Defining collective variables (NAMD 2.13 User's Guide) Cheers Anup On Tue, 14 Dec 2021 at 15:52, Moumita Saharay > wrote: Dear all, I want to perform a constant velocity pulling experiment using Steered Molecular Dynamics (SMD). I used the following TCL script to mark the fixed and SMD atoms. It works well when there is only one atom to be fixed. But I want to fix the centroid of a collection o= f CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480. How do I do that ? Please help me to resolve this issue. TCL script: set allatoms [atomselect top all] $allatoms set beta 0 set fixedatom [atomselect top "resname GLU and resid 203 and name CA"] $fixedatom set beta 1 $allatoms set occupancy 0 set smdatom [atomselect top "index 10525"] $smdatom set occupancy 1 $allatoms writepdb smd_step5_01.ref set smdpos [lindex [$smdatom get {x y z}] 0] set fixedpos [lindex [$fixedatom get {x y z}] 0] vecnorm [vecsub $smdpos $fixedpos] Thanks, Moumita -- Dr. Moumita Saharay Assistant Professor, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India --_000_77d6b35e3d7a482a8b99e608a6ac98b6uniduede_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear all,


I have a similar problem to Moumita, so I will follow the same thread.


In my case, I have a complex of two proteins chains and I want to pull t= hem apart. The complex is aligned such as the vector between the chains COM= s is parallel to the X-axis. I want to pull the protein's COMs along that v= ector in opposite directions. The complex is in a rectangular box of= 210 x 118 x 118 A.

I got a colvars configuration file (attached) from a colleague to modify= according to my problem, which I did with the Colvars Dashboard plugin.


The file has first a distance colvar to monitor the distance, and then s= ome others to define the application of the forces for each protein on each= axis.


If I understood well, the:


ref {
  &nbs= p;  dummyAtom (X, Y, Z)
}

section should refer to the COM of each protein, right?

The problem is that, if I put the COM of my proteins, it doesn't work, but = it does with the original values coming from a completely different system = (in the file).

My COMs are:
COM(A) =3D [-11.17,= 0.40, -0.28]
COM(B) =3D [36.67,<= /span> -0.44, 0.97]

In the harmonic definition section, the values are the ones in the original= file. Since I want to pull the COMs in opposite direction along the X-axis= , I should put my COM_X values in the centers f= or pull_chainA_x and pull_chainB_x, and larger values for the targetCent= ers, correct?

Any help will be very appreciated,

Best regards,
Yasser



From: owner-namd-l@ks.uiu= c.edu <owner-namd-l@ks.uiuc.edu> on behalf of J=E9r=F4me H=E9nin <= jerome.henin@ibpc.fr>
Sent: Tuesday, December 14, 2021 3:10:25 PM
To: NAMD list; Anup Prasad
Cc: Moumita Saharay
Subject: Re: namd-l: SMD: Fixing centroid
 
Hi all,

Adding to the answer by Anup: if you pull on a distance colvar, there is pr= obably no need for fixing (or restraining) any group of atoms. However, if = you want to pull along a specific direction, you can use the "distance= Z" function, specifying that the axis is not z but x.

Cheers,
J=E9r=F4me

----- On 14 D=E9c 21, at 12:02, Anup Prasad <anup.pra= sad@monash.edu> wrote:
Hi Dr. Moumita,
I don't think that there is any straightforward command for fixing the= centroid of a group of atoms. Instead of it you can try the "dis= tance colvar" module. You have to calculate the centre of mass (c= om) of the group of atoms and create the dummy atom at this com. Then apply distance colvar between "group of atoms"= and "dummy atoms" along with SMD simulation. Fix the dummy atom = in SMD instead of a group of atoms.

www.ks.uiuc.edu
Defining collective variables (NAMD 2.13 User's Guide)

Cheers
Anup


On Tue, 14 Dec 2021 at 15:52, Moumita= Saharay <moumitasaharay@uohyd.ac.in> w= rote:
Dear all,
I want to perform a constant velocity pulling experiment using
Steered Molecular Dynamics (SMD). I used the following TCL
script to mark the fixed and SMD atoms. It works well when there is
only one atom to be fixed. But I want to fix the centroid of a collect= ion of 
CA atoms, for example, CA atoms of GLU203, PHE257, and ASP48= 0. 
How do I do that ? Please help me to resolve this issue.  
TCL script:
set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top "resname GLU and resid 203 and name= CA"]
$fixedatom set beta 1
$allatoms set occupancy 0
set smdatom [atomselect top "index 10525"]
$smdatom set occupancy 1
$allatoms writepdb smd_step5_01.ref
set smdpos [lindex [$smdatom get {x y z}] 0]  
set fixedpos [lindex [$fixedatom get {x y z}] 0]  
vecnorm [vecsub $smdpos $fixedpos]

Thanks,
Moumita
--
Dr. Moumita Saharay
Assistant Professor, 
Department of Systems and Computational Biology, 
School of Life Sciences, 
University of Hyderabad, 
Gachibowli, Hyderabad, India

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Mon, 20 Dec 2021 10:17:54 -0800 (PST) Content-Type: multipart/alternative; boundary=Apple-Mail-9A863160-E55E-481C-8DBD-7F2AF8C2EC1B Content-Transfer-Encoding: 7bit From: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= Mime-Version: 1.0 (1.0) Subject: Re: namd-l: SMD: Fixing centroid Date: Mon, 20 Dec 2021 13:17:48 -0500 Message-Id: References: <77d6b35e3d7a482a8b99e608a6ac98b6@uni-due.de> In-Reply-To: <77d6b35e3d7a482a8b99e608a6ac98b6@uni-due.de> To: namd-l@ks.uiuc.edu, =?utf-8?Q?"Almeida-Hern=C3=A1ndez,_Yasser,_Dr."?= X-Mailer: iPhone Mail (18B92) X-Proofpoint-ORIG-GUID: CkQdfe6cU5q6W0towBiuuJkqofmdR0be X-CLX-Shades: MLX X-Proofpoint-GUID: CkQdfe6cU5q6W0towBiuuJkqofmdR0be X-CLX-Response: 1TFkXGxIfEQpMehcZHh4RCllEF25afGAfbFtJYx9AEQpYWBd6HmNBHl5cHB9 ySxEKeE4XY1Nja3sTWH4aX14RCnlMF2xeQBxjehtpQWBgEQpDSBcHHx8ZEQpDWRcHHxIRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB9xHh4QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XaUF7TkxPHEl/H1scfRpeRV1oQ19fYEFbRUxHTngaSE8RClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4YEBseGh8aEQpeWRdzE0cbXBEKTVwXGR8YEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2tsa2sRCkJPF2tBU0weElpvTxJsEQpDWhcYGhMEEh8EGxwaBB sdHREKQl4XGxEKRF4XGBEKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdmS21YRhhPY0VDQBEKQk4XY1Nja3sTWH4aX14RCkJMF3oeY0EeXlwcH3JLEQpCbBdv T2RBWkJQbWZrWREKQkAXYFtzR01Sc21ZekgRCkJYF2dzZXNAbmFhTF1iEQpaWBceEQp5QxdtQ31 gBVp8WW0ZTBEKWUsXExwYHBEKcGcXbEhyYmJbHnlMS2gQGRoRCnBoF20eY1pEa05NaXsZEB0YEQ pwaBdhZxsTcGkTThNbehAcGhEKcGgXYml7aBxpE3xoHm8QHB8RCnBoF2N7Qn1jW3BzfBseEBwaE QpwaBdkHnseZmR8XWZ8HxAZGhEKcGcXbUdha01jGUxTaW4QHBoRCnBnF2VCTWZ7HBxHWhpMEBka EQpwZxdkHR1EWmVnb1p5UhAZGhEKcH0XYXpLb0JTaWgBEkcQHBoRCnBnF21deW5mHk1lb1JTEBw aEQpwfxdlGXlmXkdpG2RPcxATGhEKcF8Xa1pYclhiY0JpRUIQGRoRCnBsF2doQ2tzEnkYTWJcEB kaEQpwQxduTm5ZZn9rHFAeYBAZGhEKbX4XGhEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 clxscore=185 priorityscore=344 mlxscore=0 phishscore=0 lowpriorityscore=0 spamscore=0 suspectscore=0 impostorscore=0 malwarescore=0 bulkscore=0 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112200102 domainage_hfrom=9626 X-Spam-Score: 0 X-Spam-OrigSender: biodano.geo@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= --Apple-Mail-9A863160-E55E-481C-8DBD-7F2AF8C2EC1B Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear, Use dummy as 0. 0. 0. , why it help to calculate distance to be moved, direc= tion of pulling (-x, o +x) axis is calculate based into center and target c= enters. Best,=20 Geo.=20 Enviado desde mi iPhone > El 20 dic. 2021, a la(s) 8:04 a. m., Almeida-Hern=C3=A1ndez, Yasser, Dr. <= yasser.almeida-hernandez@uni-due.de> escribi=C3=B3: >=20 > =EF=BB=BF > Dear all, >=20 >=20 >=20 > I have a similar problem to Moumita, so I will follow the same thread. >=20 >=20 >=20 > In my case, I have a complex of two proteins chains and I want to pull the= m apart. The complex is aligned such as the vector between the chains COMs i= s parallel to the X-axis. I want to pull the protein's COMs along that vecto= r in opposite directions. The complex is in a rectangular box of 210 x 118 x= 118 A. >=20 > I got a colvars configuration file (attached) from a colleague to modify a= ccording to my problem, which I did with the Colvars Dashboard plugin.=20 >=20 >=20 >=20 > The file has first a distance colvar to monitor the distance, and then som= e others to define the application of the forces for each protein on each ax= is.=20 >=20 >=20 >=20 > If I understood well, the: >=20 >=20 >=20 > ref { > dummyAtom (X, Y, Z) > } >=20 > section should refer to the COM of each protein, right? >=20 > The problem is that, if I put the COM of my proteins, it doesn't work, but= it does with the original values coming from a completely different system (= in the file). >=20 > My COMs are: > COM(A) =3D [-11.17, 0.40, -0.28] > COM(B) =3D [36.67, -0.44, 0.97] >=20 > In the harmonic definition section, the values are the ones in the origina= l file. Since I want to pull the COMs in opposite direction along the X-axis= , I should put my COM_X values in the centers for pull_chainA_x and pull_cha= inB_x, and larger values for the targetCenters, correct? >=20 > Any help will be very appreciated, >=20 > Best regards, > Yasser >=20 >=20 > From: owner-namd-l@ks.uiuc.edu on behalf of J=C3= =A9r=C3=B4me H=C3=A9nin > Sent: Tuesday, December 14, 2021 3:10:25 PM > To: NAMD list; Anup Prasad > Cc: Moumita Saharay > Subject: Re: namd-l: SMD: Fixing centroid > =20 > Hi all, >=20 > Adding to the answer by Anup: if you pull on a distance colvar, there is p= robably no need for fixing (or restraining) any group of atoms. However, if y= ou want to pull along a specific direction, you can use the "distanceZ" func= tion, specifying that the axis is not z but x. >=20 > Cheers, > J=C3=A9r=C3=B4me >=20 > ----- On 14 D=C3=A9c 21, at 12:02, Anup Prasad wr= ote: > Hi Dr. Moumita, > I don't think that there is any straightforward command for fixing the cen= troid of a group of atoms. Instead of it you can try the "distance colvar" m= odule. You have to calculate the centre of mass (com) of the group of atoms a= nd create the dummy atom at this com. Then apply distance colvar between "gr= oup of atoms" and "dummy atoms" along with SMD simulation. Fix the dummy ato= m in SMD instead of a group of atoms. >=20 > https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html > Defining collective variables (NAMD 2.13 User's Guide) > www.ks.uiuc.edu > Defining collective variables (NAMD 2.13 User's Guide) >=20 > Cheers > Anup >=20 >=20 >> On Tue, 14 Dec 2021 at 15:52, Moumita Saharay wrote: >> Dear all, >> I want to perform a constant velocity pulling experiment using >> Steered Molecular Dynamics (SMD). I used the following TCL >> script to mark the fixed and SMD atoms. It works well when there is >> only one atom to be fixed. But I want to fix the centroid of a collection= of=20 >> CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480.=20 >> How do I do that ? Please help me to resolve this issue. =20 >>=20 >> TCL script: >> set allatoms [atomselect top all] >> $allatoms set beta 0 >> set fixedatom [atomselect top "resname GLU and resid 203 and name CA"] >> $fixedatom set beta 1 >> $allatoms set occupancy 0 >> set smdatom [atomselect top "index 10525"] >> $smdatom set occupancy 1 >> $allatoms writepdb smd_step5_01.ref >> set smdpos [lindex [$smdatom get {x y z}] 0] >> =20 >> set fixedpos [lindex [$fixedatom get {x y z}] 0] >> =20 >> vecnorm [vecsub $smdpos $fixedpos] >>=20 >> Thanks, >> Moumita >> --=20 >> Dr. Moumita Saharay >> Assistant Professor,=20 >> Department of Systems and Computational Biology,=20 >> School of Life Sciences,=20 >> University of Hyderabad,=20 >> Gachibowli, Hyderabad, India >=20 > --Apple-Mail-9A863160-E55E-481C-8DBD-7F2AF8C2EC1B Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear,

Use dummy as 0. 0.= 0. , why it help to calculate distance to be moved, direction of pulling (-= x, o +x)  axis is calculate based into center and target centers.
=


Best, 

Geo.=  

Enviado desde mi iPhone

El 20 dic. 2021, a la(s) 8:04 a. m., Alm= eida-Hern=C3=A1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-due.de>= escribi=C3=B3:

=EF=BB=BF
ref {=
   = ;  dummyAtom (X, Y, Z)
}

section should refer to the COM of each protein, right?

The problem is that, if I put the COM of my proteins, it doesn't work, but i= t does with the original values coming from a completely different system (i= n the file).

My COMs are:
COM(A) =3D [-11.17, 0.40, -0.28]
COM(B) =3D [36.67, -0.44, 0.97
In the harmonic definition section, the values are the ones in the original f= ile. Since I want to pull the COMs in opposite direction along the X-axis, I= should put my COM_X values in the centers fo= r pull_chainA_x and pull_chainB_x, and larger values for the targetCente= rs, correct?

Any help will be very appreciated,

Best regards,
Yasser



From: owner-namd-l@ks.uiuc.ed= u <owner-namd-l@ks.uiuc.edu> on behalf of J=C3=A9r=C3=B4me H=C3=A9nin &= lt;jerome.henin@ibpc.fr>
Sent: Tuesday, December 14, 2021 3:10:25 PM
To: NAMD list; Anup Prasad
Cc: Moumita Saharay
Subject: Re: namd-l: SMD: Fixing centroid
 
Hi all,

Adding to the answer by Anup: if you pull on a distance colvar, there is pro= bably no need for fixing (or restraining) any group of atoms. However, if yo= u want to pull along a specific direction, you can use the "distanceZ" funct= ion, specifying that the axis is not z but x.

Cheers,
J=C3=A9r=C3=B4me

----- On 14 D=C3=A9c 21, at 12:02, Anup Prasad <anup.p= rasad@monash.edu> wrote:
Hi Dr. Moumita,
I don't think that there is any straightforward command for fixing the c= entroid of a group of atoms. Instead of it you can try the "distance co= lvar" module. You have to calculate the centre of mass (com) of th= e group of atoms and create the dummy atom at this com. Then apply distance colvar between "group of atoms" and "dummy= atoms" along with SMD simulation. Fix the dummy atom in SMD instead of a gr= oup of atoms.


Cheers
Anup


On Tue, 14 Dec 2021 at 15:52, Moumita S= aharay <moumitasaharay@uohyd.ac.in> wrote= :
Dear all,
I want to perform a constant velocity pulling experiment using
Steered Molecular Dynamics (SMD). I used the following TCL
script to mark the fixed and SMD atoms. It works well when there is
only one atom to be fixed. But I want to fix the centroid of a collecti= on of 
CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480= . 
How do I do that ? Please help me to resolve this issue.  
TCL script:
set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top "resname GLU and resid 203 and name CA"]<= /div>
$fixedatom set beta 1
$allatoms set occupancy 0
set smdatom [atomselect top "index 10525"]
$smdatom set occupancy 1
$allatoms writepdb smd_step5_01.ref
set smdpos [lindex [$smdatom get {x y z}] 0]  
set fixedpos [lindex [$fixedatom get {x y z}] 0]  
vecnorm [vecsub $smdpos $fixedpos]

Thanks,
Moumita
--
Dr. Moumita Saharay
Assistant Professor, 
Department of Systems and Computational Biology, 
School of Life Sciences, 
University of Hyderabad, 
Gachibowli, Hyderabad, India

<pulling_colvars_test.in>
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[77.103.16.24]) by smtp.gmail.com with ESMTPSA id o64sm2017274wme.28.2021.12.22.06.39.58 for (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Wed, 22 Dec 2021 06:39:59 -0800 (PST) Subject: namd-l: How to run on multi-node environment From: Luis Cebamanos To: namd-l@ks.uiuc.edu References: <7d27d04a-70ff-2897-86e4-010d0812226f@gmail.com> Message-ID: <9e745885-f588-c246-2c4c-cff30ca84dd4@gmail.com> Date: Wed, 22 Dec 2021 14:39:58 +0000 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 MIME-Version: 1.0 In-Reply-To: <7d27d04a-70ff-2897-86e4-010d0812226f@gmail.com> Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: en-GB X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0YEQpMehcZHBsRCllEF21fU2FAYBNGWl5nEQpYWBdsSB1sfFhBbWA TZBEKeE4XY1Nja3sTWH4aX14RCnlMF2kaR2FNZX5BeFwaEQpDSBcHExgRCkNZFwcYGxgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxhxHB8QGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XZV5jSFN+fURIT1oZTkIZG3hoB3BPRBNCfV9wQUtPT1wRClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4ZEBseGh8aEQpeWRdzAWQbSREKTVwXGBsfEQpMWhdoaU1NaxEKTEYXb2trbGt rEQpCTxdofUFgQ1p9c0dBExEKQ1oXGBoTBBIfBBsYEgQeEhEKQl4XGxEKQlwXGxEKXk4XGxEKQk sXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+Gl9eEQpCRRdtYRJHWX15b2FGeBEKQk4XY1Nja3sTW H4aX14RCkJMF2xIHWx8WEFtYBNkEQpCbBdsZHwZfVBZHWRwfhEKQkAXaE1JH3sfQFNcfXsRCkJY F2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5Qxdob0JvSEhtc19pexEKWUsXExwYEhEKcGgXaB8 dHWtwQR9JTk4QGRoRCnBoF2V7bhpibEBpR2BeEBkaEQpwaBdvchMFW2lQQhhhaRAZGhEKcGgXb1 JCQRJ/e2NDRU0QGRoRCnBoF2FQTkRJGGt/XRJgEBkaEQpwbBdtTmZhfxMSfRoFSxAZGhEKcEMXa E17cBoZXE9yG34QGRoRCm1+FxsRClhNF0sRIA== X-Proofpoint-GUID: OtIbyTWnbep3dh31RB-Zen9hWuZkaeev X-Proofpoint-ORIG-GUID: OtIbyTWnbep3dh31RB-Zen9hWuZkaeev X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=888 impostorscore=0 adultscore=0 spamscore=0 clxscore=172 malwarescore=0 lowpriorityscore=0 mlxscore=0 suspectscore=0 bulkscore=0 phishscore=0 priorityscore=361 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112220081 domainage_hfrom=9628 X-Spam-Score: 0 X-Spam-OrigSender: luiceur@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Luis Cebamanos Hello all, Trying to run on a multinode/multi-GPU environment (namd built with Charm-verbs, cuda SMP and Intel). Each node with 4 GPUs, 40 CPUs: charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9 namd2 +devices 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll +pemap 1-9,11-19,21-29,31-39 +comm ap 0,10,20,30 stmv.namd where my nodeListFile.txt looks like: group main host andraton11 host andraton12 ++cpus 40 ++shell ssh I am getting the following error: FATAL ERROR: Number of devices (4) is not a multiple of number of processes (8).  Sharing devices between processe s is inefficient.  Specify +ignoresharing (each process uses all visible devices) if not all devices are visible t o each process, otherwise adjust number of processes to evenly divide number of devices, specify subset of devices  with +devices argument (e.g., +devices 0,2), or multiply list shared devices (e.g., +devices 0,1,2,0). If not using +ignoresharing, how should I run this correctly? Regards, From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 22 08:56:19 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMEuJdj021730; Wed, 22 Dec 2021 08:56:19 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMEuJpr021729; Wed, 22 Dec 2021 08:56:19 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMEuIxO021725; Wed, 22 Dec 2021 08:56:18 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMEuIeG021724; Wed, 22 Dec 2021 08:56:18 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMEu5lS021716 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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charset="utf-8" Content-ID: MIME-Version: 1.0 X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: CH2PR12MB4892.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 45c9a81e-fe14-4e12-f075-08d9c55b2cf1 X-MS-Exchange-CrossTenant-originalarrivaltime: 22 Dec 2021 14:56:03.5618 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: GIThFNNek7aV25sOXQtLa7enus7mFqUCUKu3JCSS7t4R7+ZblEoeYtVHwbXmA4HztDrB3tQ+yNR2VmstzN3DLA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: CH2PR12MB5018 X-Proofpoint-GUID: QNe9oNCAyLp4ZqqF-ZiF5ve5o3Jb2mLX X-Proofpoint-ORIG-GUID: QNe9oNCAyLp4ZqqF-ZiF5ve5o3Jb2mLX X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwSEQpMehceEhEKWUQXaXtSfmRsGVBgYWQRClhYF29hWBMaS10bQ0F lEQp4Thdob0xmAXJmZEtdEhEKeUwXYGVTYE0dTx5nGFwRCkNIFwcbHRoRCkNZFwcbEhMRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHhJxGBMQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04Xe2RPE0VkaWtTZloecFtbbAdwQ2wfXE8fRRlgSBhHZnIRClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4ZEBseGh8aEQpeWRdzAWVvTREKTVwXGx4SEQpMWhd4aU1NaxEKRVkXb2sRCkx fF3oFBQUFBQUFBQVvEQpMRhdva2trbGtrEQpCTxdtcmlebk9ME1IfHBEKQ1oXHhoEGxodBBgeHg QcGxEKQl4XGxEKRF4XGREKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCTBdvYVgTG ktdG0NBZREKQmwXYXkcHxJce09aaUIRCkJAF2ZGAU9yfmF7WB1zEQpCWBdnc2VzQG5hYUxdYhEK TV4XGxEKWlgXGBEKeUMXaU5Ef2USY3IFBUsRCllLFxsYHB4TEQpwZxdtR2FrTWMZTFNpbhAeEhE KcGgXZXtuGmJsQGlHYF4QHhIRCnBoF2l4QUleG0AZc0ZAEBkaEQpwaBduc0QZTlNFHVhSaBAZGh EKcGgXYmNAY1NrZklBYU0QGRoRCnBoF2VvRBJfXGlIEmNvEBkaEQpwfRdnWhhSSWtfflhbHhAZG hEKcH8XZRl5Zl5HaRtkT3MQExoRCnBfF2taWHJYYmNCaUVCEB4SEQpwbBdneBpAYhhJGn55TRAZ GhEKbX4XGxEKWE0XSxEg X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 bulkscore=0 mlxlogscore=999 adultscore=0 phishscore=0 clxscore=168 priorityscore=48 suspectscore=0 malwarescore=0 impostorscore=0 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112220084 domainage_hfrom=12649 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by halifax.ks.uiuc.edu id 1BMEu6lR021717 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" That nodelist looks funky to me. I'm betting NAMD expects them to be one per line, only sees 1 line (as in the user guide https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes that you only have 1 node. It then nicely generates the configuration you generated on a single node, and goes about its merry way... Until it realizes that you've assigned 8 tasks to 4 GPUs, and warns you that it doesn't like sharing. -Josh On 12/22/21, 9:46 AM, "owner-namd-l@ks.uiuc.edu on behalf of Luis Cebamanos" wrote: Hello all, Trying to run on a multinode/multi-GPU environment (namd built with Charm-verbs, cuda SMP and Intel). Each node with 4 GPUs, 40 CPUs: charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9 namd2 +devices 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll +pemap 1-9,11-19,21-29,31-39 +comm ap 0,10,20,30 stmv.namd where my nodeListFile.txt looks like: group main host andraton11 host andraton12 ++cpus 40 ++shell ssh I am getting the following error: FATAL ERROR: Number of devices (4) is not a multiple of number of processes (8). Sharing devices between processe s is inefficient. Specify +ignoresharing (each process uses all visible devices) if not all devices are visible t o each process, otherwise adjust number of processes to evenly divide number of devices, specify subset of devices with +devices argument (e.g., +devices 0,2), or multiply list shared devices (e.g., +devices 0,1,2,0). If not using +ignoresharing, how should I run this correctly? Regards, From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 22 09:33:31 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMFXV0L023778; Wed, 22 Dec 2021 09:33:31 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMFXU3w023777; Wed, 22 Dec 2021 09:33:30 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMFXURg023773; Wed, 22 Dec 2021 09:33:30 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMFXUcM023772; Wed, 22 Dec 2021 09:33:30 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMFXLbG023763 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 22 Dec 2021 09:33:21 -0600 (CST) Received: from pps.filterd (m0166256.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with ESMTP id 1BMEO2UM019861 for ; Wed, 22 Dec 2021 15:33:20 GMT Authentication-Results: ppops.net; spf=pass smtp.mailfrom=luiceur@gmail.com; dkim=pass header.d=gmail.com header.s=20210112; dmarc=pass header.from=gmail.com Received: from mail-wr1-f52.google.com (mail-wr1-f52.google.com [209.85.221.52]) by mx0a-00007101.pphosted.com (PPS) with ESMTPS id 3d41j42hrh-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128 verify=NOT) for ; Wed, 22 Dec 2021 15:33:20 +0000 Received: by mail-wr1-f52.google.com with SMTP id t18so5632427wrg.11 for ; Wed, 22 Dec 2021 07:33:20 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=subject:to:references:from:message-id:date:user-agent:mime-version :in-reply-to:content-transfer-encoding:content-language; bh=7a3bLs8FquPWGJ8BLBCiKGPrD34X/P8ZcL2LiT/x+No=; b=RuomGGinNZ9PDr/cjQfGwbIU2S8sGFWIYvmvgMGAZCy4BZmhvFvXQiwJnLqaDkjll9 pWdBcr+LvRJfwayiGnCxEIFl6oHD7SEdiHqZmMySqcdN5slO9+baQZNZhSeNiO2OpsPj +vIMmhjLnGRSkW5ArQoXD9s52Sea7DqWZSd3BECXwsQ2BV3vXdNpp8XwFV2z2114Eoql 4kblRy7wNkpW/jczIWgFsD4x/DgDY6FZbc5OCHXldUBu2RoLlRZhb2c0el5BMSFisCNW ZIDp6oO21z9oFAMz/5Nfrf6dEYOWTCGEd1CYCr+60FbYLNU8/c9ixJcLFLrkfsEo4Bkq OssA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:subject:to:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-transfer-encoding :content-language; bh=7a3bLs8FquPWGJ8BLBCiKGPrD34X/P8ZcL2LiT/x+No=; b=hfY0/Itf0Z795a/w65PV9wrVyFuV7IFrwffK9hTAnu67TPeIfKUwKpBCxSMVMhQlSi bQs2zXW1dqALD4tQsn2zYpul22QiJJ9DjgSaj4qlmaqcBVKpAlwBGWocvw6BFbdZsj2E uWAXVobyqHtG6Z2HKCNxk0ij0kUqZOn7Gtk4xOkhSVq7RbQdQhrSqI8Gydvo5nyFuGkT cGexcnF5zXbcJxvfE00eLPY0b3cE40L4LJnCbhCJFDT+I/gMm5rH2Q3REk4NOc6dgFfX ldzFunrad0FGR092tOaMyvxnU+68PU6WVEhvreKRaANwL91DXlfHVAUDjrYQWvSmmA0Y NkZw== X-Gm-Message-State: AOAM533FLORe8mH1SnEdf6wVGBPyV49TaCfohS3ZILWihpFnNiOLBFkx G10PlhbN3yB/wBacnEkUnnmvWWlip3G/a1Hn X-Google-Smtp-Source: ABdhPJw3yHM1ab4NMDo2KiOrXHe/AxbbUvvag7hDRYXHMxxZQG5HEvSa9mbcA9aKNJNpyj80vDaFBQ== X-Received: by 2002:adf:de84:: with SMTP id w4mr2385314wrl.67.1640187198713; Wed, 22 Dec 2021 07:33:18 -0800 (PST) Received: from macca.local (cpc102380-sgyl38-2-0-cust23.18-2.cable.virginm.net. [77.103.16.24]) by smtp.gmail.com with ESMTPSA id o11sm3679647wmq.15.2021.12.22.07.33.17 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Wed, 22 Dec 2021 07:33:17 -0800 (PST) Subject: Re: namd-l: How to run on multi-node environment To: "Vermaas, Josh" , "namd-l@ks.uiuc.edu" References: <7d27d04a-70ff-2897-86e4-010d0812226f@gmail.com> <9e745885-f588-c246-2c4c-cff30ca84dd4@gmail.com> From: Luis Cebamanos Message-ID: <59defffc-adb2-3f20-fd77-d1f0375d7a59@gmail.com> Date: Wed, 22 Dec 2021 15:33:16 +0000 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: en-GB X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0ZEQpMehcZGxwRCllEF21fU2FAYBNGWl5nEQpYWBdsSB1sfFhBbWA TZBEKeE4XY1Nja3sTWH4aX14RCnlMF2kaR2FNZX5BeFwaEQpDSBcHGxwfEQpDWRcHGxITEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8ZcRkZEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF24HZxxbfG1+bnxYXh1TdWR/UhxIY3tQWXJgBxsdbF9YEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGRAbHhofGhEKXlkXcwFlREgRCk1cFxkSHBEKTFoXe2lNTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdoWF5QSQUSXHtkexEKQ1oXGBoTBBIfBBgYGw QfGBEKQl4XGxEKRF4XGREKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdtYRJHWX15b2FGeBEKQk4XY1Nja3sTWH4aX14RCkJMF2xIHWx8WEFtYBNkEQpCbBds ZHwZfVBZHWRwfhEKQkAXZkYBT3J+YXtYHXMRCkJYF2dzZXNAbmFhTF1iEQpaWBcYEQp5QxdpTkR /ZRJjcgUFSxEKWUsXExwYEhEKcGcXbUdha01jGUxTaW4QHhIRCnBoF2FiGV9QBU19R0N8EBoRCn BoF2sTWhoSa2BjbU1lEBoRCnBoF25zRBlOU0UdWFJoEBkaEQpwaBdiY0BjU2tmSUFhTRAZGhEKc GgXZW9EEl9caUgSY28QGRoRCnB9F2daGFJJa19+WFseEBkaEQpwfxdlGXlmXkdpG2RPcxATGhEK cF8Xa1pYclhiY0JpRUIQHhIRCnBsF21OZmF/ExJ9GgVLEBkaEQpwQxdoTXtwGhlcT3IbfhAZGhE KbX4XGhEKWE0XSxEg X-Proofpoint-GUID: D-M6qVGTDVrt7y_NUx6bIQzsXJ-17Fur X-Proofpoint-ORIG-GUID: D-M6qVGTDVrt7y_NUx6bIQzsXJ-17Fur X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 mlxlogscore=999 impostorscore=0 adultscore=0 spamscore=0 clxscore=173 malwarescore=0 lowpriorityscore=0 mlxscore=0 suspectscore=0 bulkscore=0 phishscore=0 priorityscore=316 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112220088 domainage_hfrom=9628 X-Spam-Score: 0 X-Spam-OrigSender: luiceur@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Luis Cebamanos Ah! That make sense! If I create the nodelist as expected I get this for each of the Pe FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file src/ComputePmeCUDAMgr.C, function alloc_, line 54  on Pe 8 (g424 device 0 pci 0:60:0): out of memory FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in file src/CudaUtils.C, function reallocate_host_T, line 164  on Pe 9 (g424 device 1 pci 0:61:0): out of memory FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in file src/CudaUtils.C, function reallocate_host_T, line 164  on Pe 9 (g424 device 1 pci 0:61:0): out of memory FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in file src/CudaUtils.C, function reallocate_host_T, line 164  on Pe 54 (g425 device 2 pci 0:88:0): out of memory Is there a reason for this? L On 22/12/2021 14:56, Vermaas, Josh wrote: > That nodelist looks funky to me. I'm betting NAMD expects them to be one per line, only sees 1 line (as in the user guide https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes that you only have 1 node. It then nicely generates the configuration you generated on a single node, and goes about its merry way... Until it realizes that you've assigned 8 tasks to 4 GPUs, and warns you that it doesn't like sharing. > > -Josh > > On 12/22/21, 9:46 AM, "owner-namd-l@ks.uiuc.edu on behalf of Luis Cebamanos" wrote: > > Hello all, > > Trying to run on a multinode/multi-GPU environment (namd built with > Charm-verbs, cuda SMP and Intel). Each node with 4 GPUs, 40 CPUs: > > charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9 namd2 +devices > 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll +pemap > 1-9,11-19,21-29,31-39 +comm > ap 0,10,20,30 stmv.namd > > where my nodeListFile.txt looks like: > > group main > host andraton11 host andraton12 ++cpus 40 ++shell ssh > > I am getting the following error: > > FATAL ERROR: Number of devices (4) is not a multiple of number of > processes (8). Sharing devices between processe > s is inefficient. Specify +ignoresharing (each process uses all visible > devices) if not all devices are visible t > o each process, otherwise adjust number of processes to evenly divide > number of devices, specify subset of devices > with +devices argument (e.g., +devices 0,2), or multiply list shared > devices (e.g., +devices 0,1,2,0). > > > If not using +ignoresharing, how should I run this correctly? > > Regards, > > From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 22 10:38:16 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMGcGsD025962; Wed, 22 Dec 2021 10:38:16 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMGcG6D025961; Wed, 22 Dec 2021 10:38:16 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMGcFNn025957; 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Wed, 22 Dec 2021 08:38:03 -0800 (PST) References: <7d27d04a-70ff-2897-86e4-010d0812226f@gmail.com> <9e745885-f588-c246-2c4c-cff30ca84dd4@gmail.com> <59defffc-adb2-3f20-fd77-d1f0375d7a59@gmail.com> In-Reply-To: <59defffc-adb2-3f20-fd77-d1f0375d7a59@gmail.com> From: Axel Kohlmeyer Date: Wed, 22 Dec 2021 11:37:52 -0500 Message-ID: Subject: Re: namd-l: How to run on multi-node environment To: NAMD list , Luis Cebamanos Cc: "Vermaas, Josh" Content-Type: multipart/alternative; boundary="000000000000e67e2505d3bebed0" X-Proofpoint-GUID: nGYnfzEhXY1zouzSruIrDyQxHj_EHCHD X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxwfEQpMehcZHx8RCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGxITEQpDWRcHGxITEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx4fcRgdEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0Rtc0RMUG9CcnMbUEVfUHlYX2NYblN7UmJAdW9iaWJuEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGBAbHhofGhEKXlkXcwF6QWMRCk1cFx4SHxEKTFoXaXhpa01rEQpFWRdvaxE KTF8XegUFBQUFBQUFBW8RCkxGF29ra2xraxEKQk8XaFheUEkFElx7ZHsRCkNaFxgaEwQSHwQYGB sEHhgRCkJeFxsRCkReFxgRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXYGBLGWZEY15eUHgRCkJOF2NTY2t7E1h+Gl9eEQpCTBd6WGtMY2VdWwVE cBEKQmwXZnhufhhkZUESWH8RCkJAF2ZGAU9yfmF7WB1zEQpCWBdnc2VzQG5hYUxdYhEKWlgXGRE KeUMXaU5Ef2USY3IFBUsRCllLFxMcGBIRCnBnF21HYWtNYxlMU2luEB0aEQpwaBdrE1oaEmtgY2 1NZRAeEhEKcGgXbnNEGU5TRR1YUmgQHRoRCnBoF2dvYBxbHW1ecm0eEBkaEQpwaBdiY0BjU2tmS UFhTRAdGhEKcGgXZW9EEl9caUgSY28QHRoRCnB9F2daGFJJa19+WFseEB0aEQpwfRdgGEUbAUga Exp5UhAZGhEKcH0XYRxoHFtkSBJ/H3IQGRoRCnB/F2UZeWZeR2kbZE9zEBIfEQpwXxdrWlhyWGJ jQmlFQhAdGhEKcH8XaHpfYh5+WwVkUhsQGxocEQpwXxdgExlmS05sTkVTexAZGhEKcGwXYGlHZ2 lSX39feEwQGRoRCnBMF21oZRlBUn17GEVSEBoRCm1+FxoRClhNF0sRIA== X-Proofpoint-ORIG-GUID: nGYnfzEhXY1zouzSruIrDyQxHj_EHCHD MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 impostorscore=0 lowpriorityscore=0 bulkscore=0 priorityscore=355 suspectscore=0 malwarescore=0 phishscore=0 mlxlogscore=944 clxscore=165 mlxscore=0 adultscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112220094 domainage_hfrom=9628 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --000000000000e67e2505d3bebed0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable As the error message states, you are obviously running out of memory on the corresponding GPUs. On Wed, Dec 22, 2021 at 10:34 AM Luis Cebamanos wrote: > Ah! That make sense! If I create the nodelist as expected I get this for > each of the Pe > > FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file > src/ComputePmeCUDAMgr.C, function alloc_, line 54 > on Pe 8 (g424 device 0 pci 0:60:0): out of memory > FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in > file src/CudaUtils.C, function reallocate_host_T, line 164 > on Pe 9 (g424 device 1 pci 0:61:0): out of memory > FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in > file src/CudaUtils.C, function reallocate_host_T, line 164 > on Pe 9 (g424 device 1 pci 0:61:0): out of memory > FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in > file src/CudaUtils.C, function reallocate_host_T, line 164 > on Pe 54 (g425 device 2 pci 0:88:0): out of memory > > Is there a reason for this? > L > > On 22/12/2021 14:56, Vermaas, Josh wrote: > > That nodelist looks funky to me. I'm betting NAMD expects them to be one > per line, only sees 1 line (as in the user guide > https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes > that you only have 1 node. It then nicely generates the configuration you > generated on a single node, and goes about its merry way... Until it > realizes that you've assigned 8 tasks to 4 GPUs, and warns you that it > doesn't like sharing. > > > > -Josh > > > > =EF=BB=BFOn 12/22/21, 9:46 AM, "owner-namd-l@ks.uiuc.edu on behalf of L= uis > Cebamanos" > wrote: > > > > Hello all, > > > > Trying to run on a multinode/multi-GPU environment (namd built with > > Charm-verbs, cuda SMP and Intel). Each node with 4 GPUs, 40 CPUs: > > > > charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9 namd2 +devices > > 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll +pemap > > 1-9,11-19,21-29,31-39 +comm > > ap 0,10,20,30 stmv.namd > > > > where my nodeListFile.txt looks like: > > > > group main > > host andraton11 host andraton12 ++cpus 40 ++shell ssh > > > > I am getting the following error: > > > > FATAL ERROR: Number of devices (4) is not a multiple of number of > > processes (8). Sharing devices between processe > > s is inefficient. Specify +ignoresharing (each process uses all > visible > > devices) if not all devices are visible t > > o each process, otherwise adjust number of processes to evenly > divide > > number of devices, specify subset of devices > > with +devices argument (e.g., +devices 0,2), or multiply list > shared > > devices (e.g., +devices 0,1,2,0). > > > > > > If not using +ignoresharing, how should I run this correctly? > > > > Regards, > > > > > > --=20 Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!vH4dfU-_ILd6ZyEN1u_BrQvuvnXEVJBaAkveWUPG2DVzvDUNGHPo= MJDmp_UBjccKUA$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. --000000000000e67e2505d3bebed0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
As the error message states, you are obviously running out of mem= ory on the corresponding GPUs.

On Wed, Dec 22, 2021 at 10:34 AM Luis C= ebamanos <luiceur@gmail.com>= wrote:
Ah! That= make sense! If I create the nodelist as expected I get this for
each of the Pe

FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file
src/ComputePmeCUDAMgr.C, function alloc_, line 54
=C2=A0=C2=A0on Pe 8 (g424 device 0 pci 0:60:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 9 (g424 device 1 pci 0:61:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 9 (g424 device 1 pci 0:61:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 54 (g425 device 2 pci 0:88:0): out of memory

Is there a reason for this?
L

On 22/12/2021 14:56, Vermaas, Josh wrote:
> That nodelist looks funky to me. I'm betting NAMD expects them to = be one per line, only sees 1 line (as in the user guide https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes that you only have 1 node. It then nicely generates the con= figuration you generated on a single node, and goes about its merry way... = Until it realizes that you've assigned 8 tasks to 4 GPUs, and warns you= that it doesn't like sharing.
>
> -Josh
>
> =EF=BB=BFOn 12/22/21, 9:46 AM, "
owner-namd-l@ks.uiuc.edu on behalf of Luis= Cebamanos" <owner-namd-l@ks.uiuc.edu on behalf of luiceur@gmail.com> wrote:
>
>=C2=A0 =C2=A0 =C2=A0 Hello all,
>
>=C2=A0 =C2=A0 =C2=A0 Trying to run on a multinode/multi-GPU environment= (namd built with
>=C2=A0 =C2=A0 =C2=A0 Charm-verbs, cuda SMP and Intel). Each node with 4= GPUs, 40 CPUs:
>
>=C2=A0 =C2=A0 =C2=A0 charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9= namd2 +devices
>=C2=A0 =C2=A0 =C2=A0 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll = +pemap
>=C2=A0 =C2=A0 =C2=A0 1-9,11-19,21-29,31-39 +comm
>=C2=A0 =C2=A0 =C2=A0 ap 0,10,20,30 stmv.namd
>
>=C2=A0 =C2=A0 =C2=A0 where my nodeListFile.txt looks like:
>
>=C2=A0 =C2=A0 =C2=A0 group main
>=C2=A0 =C2=A0 =C2=A0 host andraton11 host andraton12 ++cpus 40 ++shell = ssh
>
>=C2=A0 =C2=A0 =C2=A0 I am getting the following error:
>
>=C2=A0 =C2=A0 =C2=A0 FATAL ERROR: Number of devices (4) is not a multip= le of number of
>=C2=A0 =C2=A0 =C2=A0 processes (8).=C2=A0 Sharing devices between proce= sse
>=C2=A0 =C2=A0 =C2=A0 s is inefficient.=C2=A0 Specify +ignoresharing (ea= ch process uses all visible
>=C2=A0 =C2=A0 =C2=A0 devices) if not all devices are visible t
>=C2=A0 =C2=A0 =C2=A0 o each process, otherwise adjust number of process= es to evenly divide
>=C2=A0 =C2=A0 =C2=A0 number of devices, specify subset of devices
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 with +devices argument (e.g., +devices 0,2)= , or multiply list shared
>=C2=A0 =C2=A0 =C2=A0 devices (e.g., +devices 0,1,2,0).
>
>
>=C2=A0 =C2=A0 =C2=A0 If not using +ignoresharing, how should I run this= correctly?
>
>=C2=A0 =C2=A0 =C2=A0 Regards,
>
>



--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://= goo.gl/1wk0
College of Science & Technology, Temple University, = Philadelphia PA, USA
International Centre for Theoretical Physics, Tries= te. Italy.
--000000000000e67e2505d3bebed0-- From owner-namd-l@halifax.ks.uiuc.edu Wed Dec 22 11:04:20 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMH4KKW027946; Wed, 22 Dec 2021 11:04:20 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMH4KbO027945; Wed, 22 Dec 2021 11:04:20 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMH4Jh1027941; Wed, 22 Dec 2021 11:04:19 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BMH4Jte027940; Wed, 22 Dec 2021 11:04:19 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BMH49FF027933 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=K27Oz2bJwtqsHT43gcHgOTwZaH17hxr+R3USadMOXWk=; b=Ob1sSjPkwBCllLVFctkGTyFUsQJ6R37i4bGGiBdOn+95S3A5O8mvaR8jsgvcVU31Rc bhVgoNCN+vQfTqt8Ad+Ajb4miUxrigPO71M/1oAW21vkHRkk8yNFOxZJIH0osnWZv5VP UNEaogENcOI4YnNqEVh1iDAqcUg0bN1K0evtXu5IYjutu4MA4KFWqGFpDNDEfAZDrJ53 J87wWITfphlUSjpyVh3C5DPwP/RPzW3sA38XblA5BNZMISQWJYNgWJLXMah8nKk7h+la jgdsLT3JcWRDUhGK59oVoIdyzqM2+uXPndOoTgdEQEfYJhy+u6aeVYcUwpYOTkUQ3UMB A4Ww== X-Gm-Message-State: AOAM533nsTOFtwgc9ab+CYP9J1shOma/xKKkC1KCKLAjdUXxBvoGBFT8 C8TrffJMh2e5C9JNIJvay3G/97q1s+tRK9NJPjcbSkkS X-Google-Smtp-Source: ABdhPJzGNrKFQN0ZShNoQITvCHtyjFqxNkmiNazGs+8JuwtZaIf8gcMZ0vTE19WYhf6FuRg6F4QV+MyAwXH2jnG5xkM= X-Received: by 2002:a25:8609:: with SMTP id y9mr5433468ybk.50.1640192647977; Wed, 22 Dec 2021 09:04:07 -0800 (PST) References: <7d27d04a-70ff-2897-86e4-010d0812226f@gmail.com> <9e745885-f588-c246-2c4c-cff30ca84dd4@gmail.com> <59defffc-adb2-3f20-fd77-d1f0375d7a59@gmail.com> In-Reply-To: From: Giacomo Fiorin Date: Wed, 22 Dec 2021 12:03:32 -0500 Message-ID: Subject: Re: namd-l: How to run on multi-node environment To: NAMD list , Axel Kohlmeyer Cc: Luis Cebamanos , "Vermaas, Josh" Content-Type: multipart/alternative; boundary="000000000000255ee705d3bf1cf8" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: hNakCpxrMAjenbXkULW0_B6hnrPBDK9Y X-CLX-Response: 1TFkXGxIYEQpMehcZHhoRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHGxMfEQpDWRcHGxMaEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwYcR4bEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0JkS0FpWlJYZ2tAT0RIckF/Zn0adWgcQkRYemhuYRNzEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGRAbHhofGhEKXlkXcwF6EkERCk1cFxsTGhEKTFoXe2lrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRwRCkJeFxsRCkReFxgRCkRJFxgRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU 2NrexNYfhpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4 YBEKQmwXYV96UxlDRBp6G34RCkJAF2ZGAU9yfmF7WB1zEQpCWBdnc2VzQG5hYUxdYhEKTV4XGxE KWlgXHREKeUMXaU5Ef2USY3IFBUsRCllLFxMcGBIRCnBnF21HYWtNYxlMU2luEB0aEQpwaBdpSW YdG1leGVgcHRAZGhEKcGgXaxNaGhJrYGNtTWUQHhIRCnBoF2dvYBxbHW1ecm0eEB4SEQpwaBdiY 0BjU2tmSUFhTRAcGhEKcGgXZW9EEl9caUgSY28QHBoRCnB9F2daGFJJa19+WFseEBwaEQpwfRdg GEUbAUgaExp5UhAZGhEKcH0XbgV8aFhdUkxMGF4QHhIRCnB9F2EcaBxbZEgSfx9yEB4SEQpwfRd hW2NQcEV/Xm9nWBAeEhEKcH8XZRl5Zl5HaRtkT3MQGxoeEQpwXxdrWlhyWGJjQmlFQhAdGhEKcH 8XaHpfYh5+WwVkUhsQGxoTEQpwXxdgExlmS05sTkVTexAZGhEKcH8XbURfRkVtfUh5GW4QGx4aE QpwXxdrRksTeWhpbnwTeBAbGh0RCnB/F2Fmb1saZ2RCSB1bEBsZGhEKcF8XY2ISUEhjeB98Qn0Q ExIRCnBsF2Yfe1hcYgVLWGQfEBkaEQpwTBdtaGUZQVJ9exhFUhAZGhEKbX4XGxEKWE0XSxEg X-Proofpoint-GUID: hNakCpxrMAjenbXkULW0_B6hnrPBDK9Y MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=999 impostorscore=0 clxscore=182 spamscore=0 adultscore=0 bulkscore=0 suspectscore=0 priorityscore=340 mlxscore=0 malwarescore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112220095 domainage_hfrom=9628 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --000000000000255ee705d3bf1cf8 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable What GPU models are these, though? For a 4-GPU run of STMV I get between 1 and 1.5 GB of memory usage per GPU, more or less (depends on NAMD 2.x vs. 3.0 alpha). It's been quite a while since Nvidia put out GPUs with less than 2 GB of memory. Giacomo On Wed, Dec 22, 2021 at 11:39 AM Axel Kohlmeyer wrote: > As the error message states, you are obviously running out of memory on > the corresponding GPUs. > > On Wed, Dec 22, 2021 at 10:34 AM Luis Cebamanos wrote: > >> Ah! That make sense! If I create the nodelist as expected I get this for >> each of the Pe >> >> FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file >> src/ComputePmeCUDAMgr.C, function alloc_, line 54 >> on Pe 8 (g424 device 0 pci 0:60:0): out of memory >> FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in >> file src/CudaUtils.C, function reallocate_host_T, line 164 >> on Pe 9 (g424 device 1 pci 0:61:0): out of memory >> FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in >> file src/CudaUtils.C, function reallocate_host_T, line 164 >> on Pe 9 (g424 device 1 pci 0:61:0): out of memory >> FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in >> file src/CudaUtils.C, function reallocate_host_T, line 164 >> on Pe 54 (g425 device 2 pci 0:88:0): out of memory >> >> Is there a reason for this? >> L >> >> On 22/12/2021 14:56, Vermaas, Josh wrote: >> > That nodelist looks funky to me. I'm betting NAMD expects them to be >> one per line, only sees 1 line (as in the user guide >> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes >> that you only have 1 node. It then nicely generates the configuration you >> generated on a single node, and goes about its merry way... Until it >> realizes that you've assigned 8 tasks to 4 GPUs, and warns you that it >> doesn't like sharing. >> > >> > -Josh >> > >> > =EF=BB=BFOn 12/22/21, 9:46 AM, "owner-namd-l@ks.uiuc.edu on behalf of = Luis >> Cebamanos" >> wrote: >> > >> > Hello all, >> > >> > Trying to run on a multinode/multi-GPU environment (namd built wi= th >> > Charm-verbs, cuda SMP and Intel). Each node with 4 GPUs, 40 CPUs: >> > >> > charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9 namd2 +devices >> > 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll +pemap >> > 1-9,11-19,21-29,31-39 +comm >> > ap 0,10,20,30 stmv.namd >> > >> > where my nodeListFile.txt looks like: >> > >> > group main >> > host andraton11 host andraton12 ++cpus 40 ++shell ssh >> > >> > I am getting the following error: >> > >> > FATAL ERROR: Number of devices (4) is not a multiple of number of >> > processes (8). Sharing devices between processe >> > s is inefficient. Specify +ignoresharing (each process uses all >> visible >> > devices) if not all devices are visible t >> > o each process, otherwise adjust number of processes to evenly >> divide >> > number of devices, specify subset of devices >> > with +devices argument (e.g., +devices 0,2), or multiply list >> shared >> > devices (e.g., +devices 0,1,2,0). >> > >> > >> > If not using +ignoresharing, how should I run this correctly? >> > >> > Regards, >> > >> > >> >> > > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http:= //goo.gl/1wk0__;!!DZ3fjg!v2gNE_oWbQfPwMorCSUyU2Z8a8eXO8uQuaQxhWoVBP0YQCXZo6= etUjz7VKPkx0yo6g$=20 > > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy. > --000000000000255ee705d3bf1cf8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
What GPU models are these, though?=C2=A0 For a 4-GPU run o= f STMV I get between=C2=A01 and 1.5 GB of memory usage per GPU, more or les= s (depends on NAMD 2.x vs. 3.0 alpha).

It's been quite a wh= ile since Nvidia put out GPUs with less than 2 GB of memory.

=
Giacomo

On Wed, Dec 22, 2021 at 11:39 AM Axel Kohlmeyer <= ;akohlmey@gmail.com> wrote:
<= div class=3D"gmail_default" style=3D"font-family:arial,sans-serif">As the e= rror message states, you are obviously running out of memory on the corresp= onding GPUs.

On Wed, Dec 22, 2021 at 10:34 AM Luis Cebamanos <luiceur@gmail.com>= wrote:
Ah! That= make sense! If I create the nodelist as expected I get this for
each of the Pe

FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file
src/ComputePmeCUDAMgr.C, function alloc_, line 54
=C2=A0=C2=A0on Pe 8 (g424 device 0 pci 0:60:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 9 (g424 device 1 pci 0:61:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 9 (g424 device 1 pci 0:61:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 54 (g425 device 2 pci 0:88:0): out of memory

Is there a reason for this?
L

On 22/12/2021 14:56, Vermaas, Josh wrote:
> That nodelist looks funky to me. I'm betting NAMD expects them to = be one per line, only sees 1 line (as in the user guide https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes that you only have 1 node. It then nicely generates the con= figuration you generated on a single node, and goes about its merry way... = Until it realizes that you've assigned 8 tasks to 4 GPUs, and warns you= that it doesn't like sharing.
>
> -Josh
>
> =EF=BB=BFOn 12/22/21, 9:46 AM, "
owner-namd-l@ks.uiuc.edu on behalf of Luis= Cebamanos" <owner-namd-l@ks.uiuc.edu on behalf of luiceur@gmail.com> wrote:
>
>=C2=A0 =C2=A0 =C2=A0 Hello all,
>
>=C2=A0 =C2=A0 =C2=A0 Trying to run on a multinode/multi-GPU environment= (namd built with
>=C2=A0 =C2=A0 =C2=A0 Charm-verbs, cuda SMP and Intel). Each node with 4= GPUs, 40 CPUs:
>
>=C2=A0 =C2=A0 =C2=A0 charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9= namd2 +devices
>=C2=A0 =C2=A0 =C2=A0 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll = +pemap
>=C2=A0 =C2=A0 =C2=A0 1-9,11-19,21-29,31-39 +comm
>=C2=A0 =C2=A0 =C2=A0 ap 0,10,20,30 stmv.namd
>
>=C2=A0 =C2=A0 =C2=A0 where my nodeListFile.txt looks like:
>
>=C2=A0 =C2=A0 =C2=A0 group main
>=C2=A0 =C2=A0 =C2=A0 host andraton11 host andraton12 ++cpus 40 ++shell = ssh
>
>=C2=A0 =C2=A0 =C2=A0 I am getting the following error:
>
>=C2=A0 =C2=A0 =C2=A0 FATAL ERROR: Number of devices (4) is not a multip= le of number of
>=C2=A0 =C2=A0 =C2=A0 processes (8).=C2=A0 Sharing devices between proce= sse
>=C2=A0 =C2=A0 =C2=A0 s is inefficient.=C2=A0 Specify +ignoresharing (ea= ch process uses all visible
>=C2=A0 =C2=A0 =C2=A0 devices) if not all devices are visible t
>=C2=A0 =C2=A0 =C2=A0 o each process, otherwise adjust number of process= es to evenly divide
>=C2=A0 =C2=A0 =C2=A0 number of devices, specify subset of devices
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 with +devices argument (e.g., +devices 0,2)= , or multiply list shared
>=C2=A0 =C2=A0 =C2=A0 devices (e.g., +devices 0,1,2,0).
>
>
>=C2=A0 =C2=A0 =C2=A0 If not using +ignoresharing, how should I run this= correctly?
>
>=C2=A0 =C2=A0 =C2=A0 Regards,
>
>



--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://goo.gl/1wk0
College= of Science & Technology, Temple University, Philadelphia PA, USA
In= ternational Centre for Theoretical Physics, Trieste. Italy.
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boundary="00000000000081864d05d3bf72ca" X-Proofpoint-GUID: hYptmRNPJ6oJ8sof3YYWBpPcgaPcOPem X-Proofpoint-ORIG-GUID: hYptmRNPJ6oJ8sof3YYWBpPcgaPcOPem X-CLX-Shades: MLX X-CLX-Response: 1TFkXGxIcEQpMehcZHxwRCllEF256bwFzbn8SbHBGEQpYWBd6WGtMY2VdWwV EcBEKeE4XY1Nja3sTWH4aX14RCnlMF2lTc2VbXhlQQmJhEQpDSBcHGxMcEQpDWRcHGxITEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwccR4fEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0JzWl5HeGR6YBxFYBJZRUwZc3N9aFp6SU1Lekllek9HEQpYXBcfBBoEGB4Y BRsaBBsaGgQdBBseGBAbHhofGhEKXlkXcwF7fmURCk1cFxkSGxEKTFoXeGlrTWsRCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdofUFgQ1p9c0dBExEKQ1oXGBoTBBIfBBsYEg QfGhEKQl4XGxEKREkXGREKQlwXGxEKXk4XGxEKQksXY1Nja3sTWH4aX14RCkJJF2NTY2t7E1h+G l9eEQpCRRdgYEsZZkRjXl5QeBEKQk4XY1Nja3sTWH4aX14RCkJMF3pYa0xjZV1bBURwEQpCbBdm eG5+GGRlQRJYfxEKQkAXZkYBT3J+YXtYHXMRCkJYF2dzZXNAbmFhTF1iEQpaWBcdEQp5QxdpTkR /ZRJjcgUFSxEKWUsXExwYEhEKcGcXbUdha01jGUxTaW4QHRoRCnBoF2FrU2gcbl0cRHNlEBkaEQ pwaBdrE1oaEmtgY21NZRAdGhEKcGgXZ29gHFsdbV5ybR4QHBoRCnBoF25QQ1pwfn1jRkV6EBkaE QpwaBdlb0QSX1xpSBJjbxAdGhEKcH0XZ1oYUklrX35YWx4QHRoRCnB9F2AYRRsBSBoTGnlSEBka EQpwfRduBXxoWF1STEwYXhAcGhEKcH0XYRxoHFtkSBJ/H3IQHBoRCnB9F2FbY1BwRX9eb2dYEBw aEQpwfxdlGXlmXkdpG2RPcxATHxEKcF8Xa1pYclhiY0JpRUIQHRoRCnB/F2h6X2IeflsFZFIbEB saHhEKcF8XYBMZZktObE5FU3sQGRoRCnB/F21EX0ZFbX1IeRluEBseHREKcF8Xa0ZLE3loaW58E 3gQGxoYEQpwfxdhZm9bGmdkQkgdWxAbGRkRCnBfF2NiElBIY3gffEJ9EBMfEQpwbBdgaUdnaVJf f194TBAeEhEKcEwXbWhlGUFSfXsYRVIQGRoRCm1+FxoRClhNF0sRIA== MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 lowpriorityscore=0 bulkscore=0 mlxlogscore=890 adultscore=0 phishscore=0 clxscore=186 priorityscore=356 suspectscore=0 malwarescore=0 impostorscore=0 mlxscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112220096 domainage_hfrom=9628 X-Spam-Score: 0 X-Spam-OrigSender: akohlmey@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Axel Kohlmeyer --00000000000081864d05d3bf72ca Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable On second thought, it could be on the memory/address space on the host that is lacking (cudaHostAlloc()!). There could be a number of reasons including other processes hogging resources. On Wed, Dec 22, 2021 at 12:04 PM Giacomo Fiorin wrote: > What GPU models are these, though? For a 4-GPU run of STMV I get > between 1 and 1.5 GB of memory usage per GPU, more or less (depends on NA= MD > 2.x vs. 3.0 alpha). > > It's been quite a while since Nvidia put out GPUs with less than 2 GB of > memory. > > Giacomo > > On Wed, Dec 22, 2021 at 11:39 AM Axel Kohlmeyer > wrote: > >> As the error message states, you are obviously running out of memory on >> the corresponding GPUs. >> >> On Wed, Dec 22, 2021 at 10:34 AM Luis Cebamanos >> wrote: >> >>> Ah! That make sense! If I create the nodelist as expected I get this for >>> each of the Pe >>> >>> FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file >>> src/ComputePmeCUDAMgr.C, function alloc_, line 54 >>> on Pe 8 (g424 device 0 pci 0:60:0): out of memory >>> FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in >>> file src/CudaUtils.C, function reallocate_host_T, line 164 >>> on Pe 9 (g424 device 1 pci 0:61:0): out of memory >>> FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in >>> file src/CudaUtils.C, function reallocate_host_T, line 164 >>> on Pe 9 (g424 device 1 pci 0:61:0): out of memory >>> FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in >>> file src/CudaUtils.C, function reallocate_host_T, line 164 >>> on Pe 54 (g425 device 2 pci 0:88:0): out of memory >>> >>> Is there a reason for this? >>> L >>> >>> On 22/12/2021 14:56, Vermaas, Josh wrote: >>> > That nodelist looks funky to me. I'm betting NAMD expects them to be >>> one per line, only sees 1 line (as in the user guide >>> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and >>> assumes that you only have 1 node. It then nicely generates the >>> configuration you generated on a single node, and goes about its merry >>> way... Until it realizes that you've assigned 8 tasks to 4 GPUs, and wa= rns >>> you that it doesn't like sharing. >>> > >>> > -Josh >>> > >>> > =EF=BB=BFOn 12/22/21, 9:46 AM, "owner-namd-l@ks.uiuc.edu on behalf of= Luis >>> Cebamanos" >>> wrote: >>> > >>> > Hello all, >>> > >>> > Trying to run on a multinode/multi-GPU environment (namd built >>> with >>> > Charm-verbs, cuda SMP and Intel). Each node with 4 GPUs, 40 CPUs: >>> > >>> > charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9 namd2 +devices >>> > 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll +pemap >>> > 1-9,11-19,21-29,31-39 +comm >>> > ap 0,10,20,30 stmv.namd >>> > >>> > where my nodeListFile.txt looks like: >>> > >>> > group main >>> > host andraton11 host andraton12 ++cpus 40 ++shell ssh >>> > >>> > I am getting the following error: >>> > >>> > FATAL ERROR: Number of devices (4) is not a multiple of number of >>> > processes (8). Sharing devices between processe >>> > s is inefficient. Specify +ignoresharing (each process uses all >>> visible >>> > devices) if not all devices are visible t >>> > o each process, otherwise adjust number of processes to evenly >>> divide >>> > number of devices, specify subset of devices >>> > with +devices argument (e.g., +devices 0,2), or multiply list >>> shared >>> > devices (e.g., +devices 0,1,2,0). >>> > >>> > >>> > If not using +ignoresharing, how should I run this correctly? >>> > >>> > Regards, >>> > >>> > >>> >>> >> >> -- >> Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http= ://goo.gl/1wk0__;!!DZ3fjg!v0OUIYvy7_OVLSXUeINGDA7TrMOoWh2PUQvHU6Pw34DnIPHKM= GuqZchQ-1HLmgsAAg$=20 >> >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >> > --=20 Dr. Axel Kohlmeyer akohlmey@gmail.com https://urldefense.com/v3/__http://= goo.gl/1wk0__;!!DZ3fjg!v0OUIYvy7_OVLSXUeINGDA7TrMOoWh2PUQvHU6Pw34DnIPHKMGuq= ZchQ-1HLmgsAAg$=20 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. --00000000000081864d05d3bf72ca Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
On second thought, it could be on the memory/address space on the= =C2=A0host that is lacking (cudaHostAlloc()!).=C2=A0
There could be a number = of reasons including other processes hogging resources.

On Wed, Dec 22= , 2021 at 12:04 PM Giacomo Fiorin <giacomo.fiorin@gmail.com> wrote:
What GPU models are these= , though?=C2=A0 For a 4-GPU run of STMV I get between=C2=A01 and 1.5 GB of = memory usage per GPU, more or less (depends on NAMD 2.x vs. 3.0 alpha).
=
It's been quite a while since Nvidia put out GPUs with less th= an 2 GB of memory.

Giacomo

On Wed, Dec 22, 20= 21 at 11:39 AM Axel Kohlmeyer <akohlmey@gmail.com> wrote:
As the error message states, you= are obviously running out of memory on the corresponding GPUs.
=
On Wed= , Dec 22, 2021 at 10:34 AM Luis Cebamanos <luiceur@gmail.com> wrote:
Ah! That make sense! If I create= the nodelist as expected I get this for
each of the Pe

FATAL ERROR: CUDA error cudaMallocHost(&p, size) in file
src/ComputePmeCUDAMgr.C, function alloc_, line 54
=C2=A0=C2=A0on Pe 8 (g424 device 0 pci 0:60:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 9 (g424 device 1 pci 0:61:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 9 (g424 device 1 pci 0:61:0): out of memory
FATAL ERROR: CUDA error cudaHostAlloc(pp, sizeofT*(*curlen), flag) in
file src/CudaUtils.C, function reallocate_host_T, line 164
=C2=A0=C2=A0on Pe 54 (g425 device 2 pci 0:88:0): out of memory

Is there a reason for this?
L

On 22/12/2021 14:56, Vermaas, Josh wrote:
> That nodelist looks funky to me. I'm betting NAMD expects them to = be one per line, only sees 1 line (as in the user guide https://www.ks.uiuc.edu/Research/namd/2.14/ug/node103.html), and assumes that you only have 1 node. It then nicely generates the con= figuration you generated on a single node, and goes about its merry way... = Until it realizes that you've assigned 8 tasks to 4 GPUs, and warns you= that it doesn't like sharing.
>
> -Josh
>
> =EF=BB=BFOn 12/22/21, 9:46 AM, "
owner-namd-l@ks.uiuc.edu on behalf of Luis= Cebamanos" <owner-namd-l@ks.uiuc.edu on behalf of luiceur@gmail.com> wrote:
>
>=C2=A0 =C2=A0 =C2=A0 Hello all,
>
>=C2=A0 =C2=A0 =C2=A0 Trying to run on a multinode/multi-GPU environment= (namd built with
>=C2=A0 =C2=A0 =C2=A0 Charm-verbs, cuda SMP and Intel). Each node with 4= GPUs, 40 CPUs:
>
>=C2=A0 =C2=A0 =C2=A0 charmrun ++nodelist nodeListFiletxt ++p 72 ++ppn 9= namd2 +devices
>=C2=A0 =C2=A0 =C2=A0 0,1,2,3 +isomalloc_sync +setcpuaffinity +idlepoll = +pemap
>=C2=A0 =C2=A0 =C2=A0 1-9,11-19,21-29,31-39 +comm
>=C2=A0 =C2=A0 =C2=A0 ap 0,10,20,30 stmv.namd
>
>=C2=A0 =C2=A0 =C2=A0 where my nodeListFile.txt looks like:
>
>=C2=A0 =C2=A0 =C2=A0 group main
>=C2=A0 =C2=A0 =C2=A0 host andraton11 host andraton12 ++cpus 40 ++shell = ssh
>
>=C2=A0 =C2=A0 =C2=A0 I am getting the following error:
>
>=C2=A0 =C2=A0 =C2=A0 FATAL ERROR: Number of devices (4) is not a multip= le of number of
>=C2=A0 =C2=A0 =C2=A0 processes (8).=C2=A0 Sharing devices between proce= sse
>=C2=A0 =C2=A0 =C2=A0 s is inefficient.=C2=A0 Specify +ignoresharing (ea= ch process uses all visible
>=C2=A0 =C2=A0 =C2=A0 devices) if not all devices are visible t
>=C2=A0 =C2=A0 =C2=A0 o each process, otherwise adjust number of process= es to evenly divide
>=C2=A0 =C2=A0 =C2=A0 number of devices, specify subset of devices
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 with +devices argument (e.g., +devices 0,2)= , or multiply list shared
>=C2=A0 =C2=A0 =C2=A0 devices (e.g., +devices 0,1,2,0).
>
>
>=C2=A0 =C2=A0 =C2=A0 If not using +ignoresharing, how should I run this= correctly?
>
>=C2=A0 =C2=A0 =C2=A0 Regards,
>
>



--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://goo.gl/1wk0
College= of Science & Technology, Temple University, Philadelphia PA, USA
In= ternational Centre for Theoretical Physics, Trieste. Italy.


--
Dr. Axel Kohlmeyer =C2=A0akohlmey@gmail.com =C2=A0http://= goo.gl/1wk0
College of Science & Technology, Temple University, = Philadelphia PA, USA
International Centre for Theoretical Physics, Tries= te. Italy.
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boundary="000000000000145f1d05d3d054b4" X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: 7MjAjXjWtncwsYaxcOrGVuy_CU8IRDC3 X-CLX-Response: 1TFkXGx0TEQpMehcZGB4RCllEF2VfSHNJAWRtZBMSEQpYWBdoSFxZYXtJch0 bfBEKeE4XY1Nja3sTWH4aX14RCnlMF2JHGxtSaUJsE2xbEQpDSBcHGx0RCkNZFwcYEh0RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHxNxGRIQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XHWdAa0ByQH1eREldWXNLUkllWG18X1N1aX8SY3huaRkRClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4YEBseGh8aEQpeWRdzAUNrbBEKTVwXExMRCkxaF2hpTU1rEQpMRhdva2tra2s RCkJPF2Bkax9nRBhwZhhaEQpDWhcYGhMEEh8EGBgYBB8YEQpCXhcbEQpCXBcbEQpeThcbEQpCSx djU2NrexNYfhpfXhEKQkkXY1Nja3sTWH4aX14RCkJFF2QSZXtvGVpFH1NhEQpCThdjU2NrexNYf hpfXhEKQkwXaEhcWWF7SXIdG3wRCkJsF2B+Wl0dTQVBEllyEQpCQBdheFpFbnNEaHABTBEKQlgX Z3Nlc0BuYWFMXWIRCk1eFxsRClpYFxgRCnlDF29+ZWYbGBNfUGZoEQpZSxcTHBgTEQpwaBd6f3p BcHxcWhtERxAZGhEKcGgXbGZsaVIeS2lHGmwQGRoRCnBoF2lSGU1GAXJifE5CEBkaEQpwaBdpBU l7UAV+fH1pXRAZGhEKcGgXYEZBGWB7ewV+GlkQGRoRCnBsF2t9aUVSXUZzYF9TEBsaGhEKbX4XG xEKWE0XSxEg X-Proofpoint-GUID: 7MjAjXjWtncwsYaxcOrGVuy_CU8IRDC3 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 phishscore=0 mlxlogscore=603 impostorscore=0 clxscore=179 spamscore=0 adultscore=0 bulkscore=0 suspectscore=0 priorityscore=324 mlxscore=0 malwarescore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112230073 domainage_hfrom=9629 X-Spam-Score: 0 X-Spam-OrigSender: yogesh.rma13@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Yogesh Sharma --000000000000145f1d05d3d054b4 Content-Type: text/plain; charset="UTF-8" Hi all, I was using ABF for PMF calculation. But during simulation run my protein and membrane is moving a bit in z direction. Will it effect PMF estimate? For future reference should I restrain some atoms to avoid this behaviour? Looking forward for your suggestions. Thanks in advance. --000000000000145f1d05d3d054b4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,

I wa= s using ABF for PMF calculation. But during simulation run my protein and m= embrane is moving a bit in z direction. Will it effect PMF estimate? For fu= ture reference should I restrain some atoms to avoid this behaviour?=C2=A0<= /div>
=C2=A0Looking forward for your suggestions.=C2=A0
Thanks in advance.=C2=A0
--000000000000145f1d05d3d054b4-- From owner-namd-l@halifax.ks.uiuc.edu Sun Dec 26 18:41:56 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BR0fuVv013943; Sun, 26 Dec 2021 18:41:56 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BR0fuWe013942; Sun, 26 Dec 2021 18:41:56 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BR0ftrR013938; Sun, 26 Dec 2021 18:41:55 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BR0ftMl013937; Sun, 26 Dec 2021 18:41:55 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BR0fjeY013925 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; 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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=QgDm4DUvnDU9sMol+byl8OveeEcpCPFMCg+snaS6eLg=; b=AytNu0DBqmW7QOt8/x1DQxQ8lxM2y4tVqkXnH3Q2sjda4tZUAy57rKRiOGV5717r2P 1CAiNaI/nMxCduuPEOu1cXTtgesp8VriE/4gQfETSEcSLJAVp26V7As3re8P353BZXuO viBTS4SrIAvv/1wygOP3D50NOzWAD4h+U9KcXPeuioeczfNK7HHc8S2f4w5Z6FQp9+qZ a15ShNGuli0k+ymTF3VgC+vHh6GHo9/kNtb6BPAmVVLf28egxZGW5LuTmWXt8qh3S9Jh l8leDnTNtoEXsOGWBbssPH7JgH15/43ZLlkjJQ5j5uADuZ/z1a/dLnzDn6U2+GNgPZCM GZcQ== X-Gm-Message-State: AOAM532Y+ytdKcyE43RP10NqUd6cyXcSsDW5OSORNn4sP4ey1HXhnEhO iljsszgkXC/2uNmNgDO0O038Epnt1+7fOmvFy3ajEgiFO16ipDWy X-Google-Smtp-Source: ABdhPJxuzyJyEsh+Uxz+xrRmQKMUyPLiFcp4gHd+PYX3kHL1qr5t/UnmQaDEsQmY+r+uhQ2UjfOdi5gMrNMdmf55QH4= X-Received: by 2002:a2e:9901:: with SMTP id v1mr12965334lji.61.1640565701909; Sun, 26 Dec 2021 16:41:41 -0800 (PST) MIME-Version: 1.0 From: Ahmad Alqaisi Date: Mon, 27 Dec 2021 02:41:30 +0200 Message-ID: Subject: namd-l: Question about CHARMM-GUI NAMD Inputs To: namd-l@ks.uiuc.edu Content-Type: multipart/alternative; boundary="000000000000e4a95305d415f730" X-CLX-Shades: MLX X-Proofpoint-GUID: Fwv5otkq4EWAdyoBjNv-ubpjtZU_EOFx X-Proofpoint-ORIG-GUID: Fwv5otkq4EWAdyoBjNv-ubpjtZU_EOFx X-CLX-Response: 1TFkXGxISEQpMehcaEQpZRBdtGVlmbEtEXnxoWBEKWFgXbUkSHkBPH2JzEgE RCnhOF2J4YnMBeVhmW0V/EQp5TBd6WWQbT2teeHJTXBEKQ0gXBxgZEhEKQ1kXBxgcGREKQ0kXGg QaGhoRCllNF2dmchEKWUkXGnEaEBp3BhscEnEeHRAadwYYGgYaEQpZXhdobnkRCklGF19DX0l1Q kVZXk9OEQpDThdsXVwfRV5BWx5vfWtOU0VoQGRcB19IWkBecH91b2VsUhEKWFwXHwQaBBgeGAUb GgQbGhoEHQQbHhgQGx4aHxoRCl5ZF3MFWGhAEQpNXBcYGx8RCkxaF2loaU1NTREKQk8Xa3xZUFg ZaV4YZloRCkNaFxgaEwQSHwQYGhIEGx0ZEQpCXhcbEQpCRRdvZ2JdHh0TZ3MaSBEKQk4XYnhicw F5WGZbRX8RCkJMF21JEh5ATx9icxIBEQpCbBdoZh1kHUQFaV54ehEKQkAXYBJGfVNaYVNBT04RC kJYF2dzZXNAbmFhTF1iEQpNXhcbEQpaWBcYEQp5QxdpWRthaU1gHnkdZhEKWUsXGxgfHRgRCnBo F2EaRBoBa21JfEBEEBoRCnBoF2JmYWxPTVtCRE9eEBoRCnBoF21/T0JzS2gYUGV8EBoRCnBoF2B cR2FDUFJDeXNfEBoRCnBoF2JrXm0FQX4bUAVaEBoRCnBsF2VEGlxAb2ViG1xMEBkaEQptfhcbEQ pYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 bulkscore=0 spamscore=0 lowpriorityscore=0 clxscore=188 impostorscore=0 mlxscore=0 priorityscore=0 mlxlogscore=491 phishscore=0 suspectscore=0 adultscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112270002 domainage_hfrom=12572 X-Spam-Score: 0 X-Spam-OrigSender: aalqais2@asu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Ahmad Alqaisi --000000000000e4a95305d415f730 Content-Type: text/plain; charset="UTF-8" Hello all, I have been using the CHARMM-GUI server to generate NAMD input files for MD simulations. I noticed that inputs from this server give bad results in many cases, especially in terms of RMSD values and simulation stability. Can you give any suggestion on how to improve the inputs generated by CHARMM-GUI to get better results? For example, the equilibration time in the CHARMM-GUi protocol is much smaller than other protocols like QwikMD. If I increase the equilibration time, would that give me better results? Also, can anyone give a description of the protocol that is carried in the CHARMM-GUI input files ? For example the file named step4_equilibration.inp, does it contain minimization, annealing and equilibration or only minimization and equilibration? Best, Ahmad Alqaisi --000000000000e4a95305d415f730 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello all,=C2=A0

I have been using the = CHARMM-GUI server to generate NAMD input files for MD simulations. I notice= d that inputs from this server give bad results in many cases, especially i= n terms of RMSD values and simulation stability.=C2=A0

=
Can you give any suggestion on how to improve the inputs generated by = CHARMM-GUI to get better results? For=C2=A0example, the equilibration=C2=A0= time in the CHARMM-GUi protocol is much smaller than=C2=A0other protocols l= ike QwikMD. If I increase the equilibration time, would that give me better= results?

Also, can anyone give a description of t= he protocol that is carried in the CHARMM-GUI input files ? For example the= file named step4_equilibration.inp, does it contain minimization, annealin= g and equilibration or only minimization and equilibration?=C2=A0

Best,
Ahmad Alqaisi
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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I am struggling with a SMD at constant velocity, where I want to pull two p= roteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 A/n= s, during 50 ns Below is the definition of the harmonic: harmonic { colvars pull_nter pull_cter pull_nter_y pull_cter_y pull_nt= er_z pull_cter_z centers -20.0 20.0 0.0 0.0 0.0 = 0.0 targetCenters -20.5 20.5 0.0 0.0 0.0 = 0.0 forceConstant 5. targetNumSteps 25000000 outputCenters yes outputAccumulatedWork yes } I have tried several centers and targetCenters to achieve the velocity, but= what happens is that the targetCenters are reached very fast and then the = proteins stay there. However, I write the centers during the simulation (w= ith outputCenters, x0_pull_nter and x0_pull_nter) and they change continuou= sly as expected until the end of the run. Am I missing something? Also, what are the units of the accumulated work written in the .traj file? Any help will be very much appreciated. Best, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universit=E4tsstr. 2, 45117 Essen Email: yasser.almeida-hernandez@uni-due.de Phone: +49 201 183 2457 --_000_d66272c00b9143d89cb597bc460c336funiduede_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear all,


I am struggling with a SMD at constant velocity, where I want to pull tw= o proteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 A/ns, during 50 ns


Below is the definition of the harmonic:


harmonic {<= /span>
   col= vars            pull_nter &nbs= p; pull_cter pull_nter_y pull_cter_y pull_nter_z pull_cter_z
   cen= ters            -20.0    =     20.0      0.0      &n= bsp;   0.0          0.0    &nb= sp;     0.0
   tar= getCenters   -20.5       20.5     = 0.0          0.0      &n= bsp;   0.0          0.0
   for= ceConstant 5.
   tar= getNumSteps 25000000
   out= putCenters yes
   out= putAccumulatedWork yes
}


I have tried several centers and targetCenters to achieve the velocity, but what happens is that the targetCenters are reached very fast and then the proteins stay there= .  However, I write the centers during the simulation (with outputCenters, x0_pull_nter<= span style=3D"font-family: Consolas, Courier, monospace;"> and x0_pull_nter= ) and they change continuously as expected until the en= d of the run.


Am I missing something?


Also, what are the units of the accumulated work written in the .traj fi= le?


Any help will be very much appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=E4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" target=3D"_blank" = rel=3D"noopener noreferrer" id=3D"LPNoLP">&nb= sp;yasser.almeida-hernandez@uni-due.de

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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello Ahmad, It is unclear what do you mean by simulation stability. CHARMM-GUI produces= fairly nice inputs but, of course, you may need to modify the input files = based on your requirements, especially the number of steps. One important a= spect to understand is that even if you use the same input files and run it= three times, the results will vary. This is because of the rounding-off of= the decimal places and the systems could diverge right from the first step= . So, a short run (say, 5 ns) will show differences in RMSD values. It would be a better idea to contact CHARMM-GUI team, they have a very shor= t turnaround time for any issues. Regards, Raman ________________________________ From: namd-l digest Sent: Monday, December 27, 2021, 1:30 PM To: namd-l-digest@ks.uiuc.edu Subject: namd-l digest V1 #3189 namd-l digest Monday, December 27 2021 Volume 01 : Number 318= 9 In this issue: namd-l: Question about CHARMM-GUI NAMD Inputs ---------------------------------------------------------------------- Date: Mon, 27 Dec 2021 02:41:30 +0200 From: Ahmad Alqaisi Subject: namd-l: Question about CHARMM-GUI NAMD Inputs Hello all, I have been using the CHARMM-GUI server to generate NAMD input files for MD simulations. I noticed that inputs from this server give bad results in many cases, especially in terms of RMSD values and simulation stability. Can you give any suggestion on how to improve the inputs generated by CHARMM-GUI to get better results? For example, the equilibration time in the CHARMM-GUi protocol is much smaller than other protocols like QwikMD. If I increase the equilibration time, would that give me better results? Also, can anyone give a description of the protocol that is carried in the CHARMM-GUI input files ? For example the file named step4_equilibration.inp, does it contain minimization, annealing and equilibration or only minimization and equilibration? Best, Ahmad Alqaisi ------------------------------ End of namd-l digest V1 #3189 ***************************** --_000_BMXPR01MB3526A29FDEDDEA60F6B54D85B3429BMXPR01MB3526INDP_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hello Ahmad,

It is unclear what do you mean by simulation stability. CHARMM-GUI produces= fairly nice inputs but, of course, you may need to modify the input files = based on your requirements, especially the number of steps. One important a= spect to understand is that even if you use the same input files and run it three times, the results will v= ary. This is because of the rounding-off of the decimal places and the syst= ems could diverge right from the first step. So, a short run (say, 5 ns) wi= ll show differences in RMSD values.

It would be a better idea to contact CHARMM-GUI team, they have a very shor= t turnaround time for any issues.

Regards,
Raman



From: namd-l digest <owner-na= md-l-digest@ks.uiuc.edu>
Sent: Monday, December 27, 2021, 1:30 PM
To: namd-l-digest@ks.uiuc.edu
Subject: namd-l digest V1 #3189


namd-l digest        Monday, December 27= 2021        Volume 01 : Number 3189



In this issue:

    namd-l: Question about CHARMM-GUI NAMD Inputs

----------------------------------------------------------------------

Date: Mon, 27 Dec 2021 02:41:30 +0200
From: Ahmad Alqaisi <aalqais2@asu.edu>
Subject: namd-l: Question about CHARMM-GUI NAMD Inputs

Hello all,

I have been using the CHARMM-GUI server to generate NAMD input files for MD=
simulations. I noticed that inputs from this server give bad results in
many cases, especially in terms of RMSD values and simulation stability.
Can you give any suggestion on how to improve the inputs generated by
CHARMM-GUI to get better results? For example, the equilibration time in the CHARMM-GUi protocol is much smaller than other protocols like QwikMD. If I increase the equilibration time, would that give me better results?
Also, can anyone give a description of the protocol that is carried in the<= br> CHARMM-GUI input files ? For example the file named
step4_equilibration.inp, does it contain minimization, annealing and
equilibration or only minimization and equilibration?

Best,
Ahmad Alqaisi

------------------------------

End of namd-l digest V1 #3189
*****************************


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1.0 (1.0) Subject: Re: namd-l: Initial force for steered MD simulations Date: Mon, 27 Dec 2021 10:46:23 -0500 Message-Id: <65D1051E-2FFD-410E-A340-6A8804B70B76@mix.wvu.edu> References: Cc: namd-l@ks.uiuc.edu In-Reply-To: To: =?utf-8?Q?"ROP=C3=93N-PALACIOS_G."?= X-Mailer: iPhone Mail (18H107) X-Proofpoint-ORIG-GUID: bCTgdEL5T5A_0Zxs5b3vj29kj59dhECc X-CLX-Response: 1TFkXGB8ZEQpMehcaEQpZRBdkS0JpTUJQQUBNGhEKWFgXbR9jbnNcXGtsS28 RCnhOF2x6UFlsfEJsRkgcEQp5TBducm9jY31wGGRcYREKQ0gXBx4fExEKQ1kXBxMaEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcbGXEbBhgfdwYYGhoGGgYaBhsaGgYacRoQGncGGgYaBhoGBxwaBhoGG nEaEBp3BhoRClleF2xseREKSUYXX0NfSXVCRVleT04RCkNOF0hpfk1Ob2Yffh9rdRpwUlkfSBlc QBgTQUAfE05Cb2lJEQpYXBcfBBoEGB4YBRsaBBsbGgQdBBsZGBAbHhofGhEKXlkXcwUeeF8RCk1 cFx4aHREKTFoXeGlNa2sRCkVZF29rEQpMXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdlaV BnYUZ9bBsFBREKQ1oXGBoTBBIfBBgYGAQbHRsRCkJeFxsRCkRJFxsRCkJcFxsRCkJLF2h4Q2NAE 0hgeVoeEQpCSRdselBZbHxCbEZIHBEKQkUXekNDXmVnX19SYnwRCkJOF2x6UFlsfEJsRkgcEQpC TBdtH2Nuc1xca2xLbxEKQmwXYwV5TGdSZH1ObxkRCkJAF2NHTFtmW0IaXWVeEQpCWBdnc2VzQG5 hYUxdYhEKTV4XBxsRClpYFxkRCnlDF2RPEl5AfxlLWnB/EQpZSxcbGhIaHxEKcGcXbB9Pek1zXG FtTl8QBxkaEQpwaBdrXBJSZ3xHU2NcUxAHGRoRCnBoF2leGUIZYR8deRlZEAcZGhEKcGgXaXtJT n8eckABZx4QBxkaEQpwaBdlQGNGS1hNRUx8HRAHGRoRCnBoF2ZGe2MZY3lyTGNPEAcZGhEKcH0X Z11rQlt6ZVhnZEkQBxkaEQpwfxdlGXlmXkdpG2RPcxAHGRoRCnBfF25FH2saTHx5Gh1eEAcZGhE KcGwXbhJaS0MbWl9iGGQQHBoRCnBDF2Z5Y3BBXB9gSRhoEAcZGhEKbX4XBxsRClhNF0sRIA== X-Proofpoint-GUID: bCTgdEL5T5A_0Zxs5b3vj29kj59dhECc X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=0 suspectscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 clxscore=253 spamscore=0 impostorscore=0 malwarescore=0 phishscore=0 mlxlogscore=999 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112270077 domainage_hfrom=10805 X-Spam-Score: 0 X-Spam-OrigSender: hrs00003@mix.wvu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Hannah Scott --Apple-Mail-98D9E3F6-C00C-4ACB-A39D-128CD4AE543F Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Just updating this to say that I have not found a solution to this problem. D= oes anyone have any suggestions? > On Dec 9, 2021, at 7:43 PM, ROP=C3=93N-PALACIOS G. = wrote: >=20 > =EF=BB=BFTry use Occupancy column and not beta=20 >=20 > In contrast with guide only atoms tagged Eith no-zero values into beta col= umn are used as pulling atoms. >=20 > https://www.ks.uiuc.edu/Research/namd/2.9/ug/node48.html >=20 > Enviado desde mi iPhone >=20 >> El 9 dic. 2021, a la(s) 3:41 p. m., Hannah Scott e= scribi=C3=B3: >>=20 >> =EF=BB=BF >> I am seeing an unusually high force being applied in the wrong direction w= hen applying constant velocity steered MD to my system. For this simulation I= am applying SMD to a single alpha-carbon in a helical peptide and pulling a= long the -z axis in an attempt to simulate insertion into a membrane bilayer= with a 1 fs timestep.=20 >>=20 >> When visualizing my system, I see that the peptide is being pulled in the= +z direction instead. The SMD output shows that the initial force applied i= s very large. What could be causing this and what do you recommend I try? >>=20 >> The following are the parameters I have set for the SMD simulation as wel= l as the output: >>=20 >> SMD on >> SMDFile ../current-parameters/rev-smd.ref ;# this is the pbd file wi= th b-column needs remade with different systems >> SMDk 10 ;#adjusted to pull on termius of= phlip >> SMDVel .00001 ;# 10 A/ns =3D .01 A/ps =3D .0000= 1 A/fs >> SMDDir 0 0 -1 >> SMDOutputFreq 100 >>=20 >>=20 >> SMD 0 5.801 -4.258 27.644 0 -0 27336.5 >> SMD 100 6.09131 -4.67441 31.9466 0 -0 24346.4 >> SMD 200 6.91383 -3.83161 34.0325 0 -0 22896.4 >> SMD 300 7.37256 -3.92352 36.4932 0 -0 21186.1 >> SMD 400 7.21118 -4.2608 39.8742 0 -0 18836.3 >> SMD 500 6.8234 -3.46171 43.0824 0 -0 16606.6 >> SMD 600 6.92947 -2.77978 46.19 0 -0 14446.8 >> SMD 700 7.27499 -2.5372 48.6056 0 -0 12767.7 >> SMD 800 8.21247 -2.39816 50.8552 0 -0 11204 >> SMD 900 8.02797 -1.72661 53.5881 0 -0 9304.52 >> SMD 1000 7.32698 -1.27389 55.6482 0 -0 7872.5 >>=20 >>=20 >>=20 >> Thank you in advance, >> Hannah --Apple-Mail-98D9E3F6-C00C-4ACB-A39D-128CD4AE543F Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Just updating this to say t= hat I have not found a solution to this problem. Does anyone have any sugges= tions?

On Dec 9, 2021, a= t 7:43 PM, ROP=C3=93N-PALACIOS G. <biodano.geo@gmail.com> wrote:
=EF=BB=BFTry us= e Occupancy column and not beta 

In contrast with gu= ide only atoms tagged Eith no-zero values into beta column are used as pulli= ng atoms.

https://www.ks.uiuc.edu/Research/namd/2.9/ug/nod= e48.html

Enviado desde mi iPhone

El 9 dic. 2021, a la(s) 3:41 p. m.,= Hannah Scott <hrs00003@mix.wvu.edu> escribi=C3=B3:

=EF=BB=BF
I am seeing an unusually high force being applied in the wrong di= rection when applying constant velocity steered MD to my system. For this si= mulation I am applying SMD to a single alpha-carbon in a helical peptide and= pulling along the -z axis in an attempt to simulate insertion into a membra= ne bilayer with a 1 fs timestep. 

When visuali= zing my system, I see that the peptide is being pulled in the +z direct= ion instead. The SMD output shows that the initial force applied is very lar= ge. What could be causing this and what do you recommend I try?

The following are the parameters I have set for the S= MD simulation as well as the output:

SMD on
SMDFile .= ./current-parameters/rev-smd.ref      ;# this is the pbd file= with b-column   needs remade with different systems
SMDk 10   &= nbsp;                     &= nbsp;        ;#adjusted to pull on termius of phlip
S= MDVel .00001                   &= nbsp;       ;# 10 A/ns =3D .01 A/ps =3D .00001 A/fs
SMDDir= 0 0 -1
SMDOutputFreq 100


SMD  0 5= .801 -4.258 27.644 0 -0 27336.5
SMD  100 6.09131 -4.67441 31.9466 0 -= 0 24346.4
SMD  200 6.91383 -3.83161 34.0325 0 -0 22896.4
SMD &nbs= p;300 7.37256 -3.92352 36.4932 0 -0 21186.1
SMD  400 7.21118 -4.2608= 39.8742 0 -0 18836.3
SMD  500 6.8234 -3.46171 43.0824 0 -0 16606.6<= br>SMD  600 6.92947 -2.77978 46.19 0 -0 14446.8
SMD  700 7.2749= 9 -2.5372 48.6056 0 -0 12767.7
SMD  800 8.21247 -2.39816 50.8552 0 -= 0 11204
SMD  900 8.02797 -1.72661 53.5881 0 -0 9304.52
SMD  = 1000 7.32698 -1.27389 55.6482 0 -0 7872.5


<= /div>

Thank you in advance,
Hannah
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charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Hi Yasser, it sounds like the variables' values do not evolve as you expect them to, but the restraint centers do work as expected. This is not uncommon. Your initial and final centers differ by only 0.5 =C3=85, and assuming you = used the default width of 1, for a force constant of 5 kcal/mol you get 1/2=C3=975=C3=970.5^2 =3D 0.625 kcal/mol, roughly one kT unit. Not muc= h difference between those states as far as the restraint is concerned. Accumulated work, like all energies, is in the same unit of the MD engine that Colvars is distributed with, in this case NAMD: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:units__;Iw!!DZ3fjg!su6lmSqnhgVAVHfWHdtrvUBMPEiv= qbKcs7f2O7GJ8a_bQFffTnDHcgsqte-_nmnWtQ$=20 and NAMD uses kcal/mol. Giacomo On Mon, Dec 27, 2021 at 5:47 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < yasser.almeida-hernandez@uni-due.de> wrote: > Dear all, > > > I am struggling with a SMD at constant velocity, where I want to pull two > proteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 > A/ns, during 50 ns > > > Below is the definition of the harmonic: > > > harmonic { > colvars pull_nter pull_cter pull_nter_y pull_cter_y > pull_nter_z pull_cter_z > centers -20.0 20.0 0.0 0.0 0.0 > 0.0 > targetCenters -20.5 20.5 0.0 0.0 0.0 > 0.0 > forceConstant 5. > targetNumSteps 25000000 > outputCenters yes > outputAccumulatedWork yes > } > > > I have tried several centers and targetCenters to achieve the velocity, > but what happens is that the targetCenters are reached very fast and then > the proteins stay there. However, I write the centers during the > simulation (with outputCenters, x0_pull_nter and x0_pull_nter) and they > change continuously as expected until the end of the run. > > > Am I missing something? > > > Also, what are the units of the accumulated work written in the .traj fil= e? > > > Any help will be very much appreciated. > > > Best, > > Yasser > > > -- > Dr. Yasser Almeida-Hernandez > Postdoctoral Researcher > Computational Biochemistry group > T01 R03 D45 > Faculty of Biology > University of Duisburg-Essen > Universit=C3=A4tsstr. 2, 45117 Essen > Email: yasser.almeida-hernandez@uni-due.de > <%20yasser.almeida-hernandez@uni-due.de> > Phone: +49 201 183 2457 <+49%20201%20183%202457> > > --00000000000098507e05d42303f4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Hi Yasser, it sounds like the variables' values do not= evolve as you expect them to, but the restraint centers do work as expecte= d.=C2=A0 This is not uncommon.

Your initi= al and final centers differ by only 0.5 =C3=85, and assuming you used the d= efault width of 1, for a force constant of 5 kcal/mol you get=C2=A01/2=C3= =975=C3=970.5^2 =3D 0.625 kcal/mol, roughly=C2=A0one kT unit.=C2=A0 Not muc= h difference between those states as far as the restraint=C2=A0is concerned= .

Accumulated=C2=A0work, like all energies, is in t= he same unit of the MD engine that Colvars is distributed with, in this cas= e NAMD:
and NAMD uses kcal/mol.

Giacomo=

On Mon, Dec 27, 2021 at 5:47 AM Almeida-Hern=C3=A1ndez, Y= asser, Dr. <yasser.almeida-hernandez@uni-due.de> wrote:

Dear all,


I am struggling with a SMD at constant velocity, where I want to pull tw= o proteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 A/ns, during 50 ns


Below is the definition of the harmonic:


harmonic {
=C2=A0=C2=A0 colvars= =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 pull_nter=C2=A0=C2=A0 p= ull_cter pull_nter_y pull_cter_y pull_nter_z pull_cter_z
=C2=A0=C2=A0 centers= =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 -20.0 =C2=A0=C2=A0 =C2= =A0=C2=A0=C2=A0 20.0 =C2=A0=C2=A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2= =A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2= =A0=C2=A0=C2=A0 =C2=A0 0.0
=C2=A0=C2=A0 targetC= enters=C2=A0=C2=A0 -20.5 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 20.5 =C2=A0=C2=A0 =C2=A0 0.0 =C2= =A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2= =A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0 0.0
=C2=A0=C2=A0 forceCo= nstant 5.
=C2=A0=C2=A0 targetN= umSteps 25000000
=C2=A0=C2=A0 outputC= enters yes
=C2=A0=C2=A0 outputA= ccumulatedWork yes
}


I have tried several centers and t= argetCenters to achieve the velocity, but what happens is that the targetCenters are reached very fast and then the proteins stay there= .=C2=A0 However, I write the centers during the simulation (with outputCenters= ,=C2=A0x0_pull_nter and = x0_pull_nter)= and they change continuously as expected until the end of the= run.


Am I missing something?


Also, what are the units of the accumulated work written in the .traj fi= le?


Any help will be very much appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=C3=A4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" rel=3D"noopener no= referrer" id=3D"gmail-m_-8563912227759805556gmail-m_6632314740631305832LPNo= LP" target=3D"_blank">=C2=A0yasser.almeida-he= rnandez@uni-due.de
Phone:=C2=A0+49 201 183 2457=C2=A0

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boundary="000000000000b40ab005d42ad0e9" X-Proofpoint-ORIG-GUID: cFbcINlU3U8nDt5TleKE_VnxWBM5Brde X-Proofpoint-GUID: cFbcINlU3U8nDt5TleKE_VnxWBM5Brde X-CLX-Shades: MLX X-CLX-Response: 1TFkXGx0TEQpMehcZHhkRCllEF2FNfENOSXliE10TEQpYWBdmSUVSYUJ+GW5 QGxEKeE4XY1Nja3sTWH4aX14RCnlMF2F8UlptR1B4aUEBEQpDSBcHGBofEQpDWRcHGRoTEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx8TcRkSEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF0lsSEljZEZ/GX8SRG5eH35GT2FvdXxEUn1oZx9oWE5PEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGBAbHhofGhEKXlkXcGtrHkARCk1cFxwfEQpMWhdsaWtNaxEKTEYXb2tra2t rEQpCTxdtE2ATAWFaa21AEhEKQ1oXGBoTBBIfBBgbHwQbHRkRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZEBYG31oGn17eUERCkJOF2NTY2t7E 1h+Gl9eEQpCTBdmSUVSYUJ+GW5QGxEKQmwXbnxPU0VQb1kTYB4RCkJAF29fQ1tkbEB/ZX1pEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXb2JiXksYRFBIQn4RCllLFxMcGR4RCnBoF2h hbXlLYVBsfAVJEBkaEQpwaBdnYh1BcBsTZGMSHxAZGhEKcGgXYHgBQ21ueBJvXmMQGRoRCnBoF2 drHnBDRXxzW3tSEBkaEQpwaBdnRV5NT2YbRxh/EhAZGhEKcGwXZxtdE24SYR0aZhIQGRoRCnBMF 21oZRlBUn17GEVSEBkaEQptfhcbEQpYTRdLESA= X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 adultscore=0 clxscore=179 lowpriorityscore=0 malwarescore=0 mlxscore=0 suspectscore=0 spamscore=0 mlxlogscore=999 phishscore=0 priorityscore=343 impostorscore=0 bulkscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112280006 domainage_hfrom=9634 X-Spam-Score: 0 X-Spam-OrigSender: dhirajks@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Dhiraj Srivastava --000000000000b40ab005d42ad0e9 Content-Type: text/plain; charset="UTF-8" Hi All I want to simulate the protein-DNA complex whose structure I recently solved. However I want to simulate it with longer DNA than the one in crystal structure to see how protein binding potentially affects the conformation of nearby DNA sequence. The protein causes DNA bonding so I can not generate an ideal DNA structure and simply replace the crystallized DNA with the ideal one. Is there any way I can extend the bend DNA in both directions before starting the simulation? Thank you Dhiraj --000000000000b40ab005d42ad0e9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi All
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0I want to sim= ulate the protein-DNA complex whose structure I recently solved. However I = want to simulate it with longer DNA than the one in crystal structure to se= e how protein binding potentially affects the conformation of nearby DNA se= quence. The protein causes DNA bonding so I can not generate an ideal DNA s= tructure and simply replace the crystallized DNA with the ideal one.=C2=A0<= /div>
Is there any way I can extend the bend DNA in both directions bef= ore starting the simulation?

Thank you
D= hiraj=C2=A0
--000000000000b40ab005d42ad0e9-- From owner-namd-l@halifax.ks.uiuc.edu Tue Dec 28 04:45:23 2021 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BSAjN0E009781; Tue, 28 Dec 2021 04:45:23 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BSAjNWN009780; Tue, 28 Dec 2021 04:45:23 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BSAjMsb009776; Tue, 28 Dec 2021 04:45:22 -0600 (CST) Received: (from daemon@localhost) by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id 1BSAjMVN009775; Tue, 28 Dec 2021 04:45:22 -0600 (CST) Received: from mx0a-00007101.pphosted.com (mx0a-00007101.pphosted.com [148.163.135.28]) by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id 1BSAj5QA009767 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 28 Dec 2021 04:45:06 -0600 (CST) Received: from pps.filterd (m0166255.ppops.net [127.0.0.1]) by mx0a-00007101.pphosted.com (8.16.1.2/8.16.1.2) with ESMTP id 1BS6ifsL004294 for ; Tue, 28 Dec 2021 10:45:05 GMT Authentication-Results: ppops.net; spf=none smtp.mailfrom=yasser.almeida-hernandez@uni-due.de; dmarc=none Received: from mailoutzim.uni-due.de (mailoutzim.uni-due.de [134.91.56.37]) by mx0a-00007101.pphosted.com (PPS) with ESMTPS id 3d5ssxx8sk-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Tue, 28 Dec 2021 10:45:04 +0000 Received: from EX2.win.uni-due.de (ns1-owa.uni-duisburg-essen.de [132.252.183.35]) by mailoutzim.uni-due.de (8.14.7/8.14.7) with ESMTP id 1BSAj0K3024774 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Tue, 28 Dec 2021 11:45:00 +0100 Received: from EX3.win.uni-due.de (134.91.18.65) by EX2.win.uni-due.de (132.252.183.34) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2375.17; Tue, 28 Dec 2021 11:45:00 +0100 Received: from EX3.win.uni-due.de ([134.91.18.65]) by EX3.win.uni-due.de ([134.91.18.65]) with mapi id 15.01.2375.017; Tue, 28 Dec 2021 11:45:00 +0100 From: =?iso-8859-1?Q?Almeida-Hern=E1ndez=2C_Yasser=2C_Dr=2E?= To: Giacomo Fiorin , NAMD list Subject: Re: namd-l: SMD at constant velocity Thread-Topic: namd-l: SMD at constant velocity Thread-Index: AQHX+wwzgvt6eeEO1kekzY/fCsh7FKxGcuuAgAEgDi0= Date: Tue, 28 Dec 2021 10:45:00 +0000 Message-ID: <8eda062edcd44e23bb32aa77f544acdc@uni-due.de> References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [132.252.183.35] Content-Type: multipart/alternative; boundary="_000_8eda062edcd44e23bb32aa77f544acdcuniduede_" X-Virus-Scanned: Clam Anti Virus - http://www.clamav.net X-Spam-Scanned: SpamAssassin: 3.004000 - http://www.spamassassin.org X-Scanned-By: MIMEDefang 2.85 X-Proofpoint-GUID: ruCZ9wulLfVCx35UvFCobC5j8gNjGIM7 X-CLX-Response: 1TFkXGxIeEQpMehceEhEKWUQXbkt/R3kSXFheQEMRClhYF2h8RmdObnABWVl SEQp4ThdvfEJscE1CZ3hcWREKeUwXb0R5Y3JDWX5cWnwRCkNIFwceHxMRCkNZFwcbGh4RCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbHB5xHhkQGncGGBoGGhEKWV4XaG55EQpJRhdfQ19Jd UJFWV5PThEKQ04XWF9pcBNdX0ZmTHxpUhkff1xsaUVIaR9AEk1kQG1jZx0RClhcFx8EGgQYHhgF GxoEGxoaBB0EGx4YEBseGh8aEQpeWRdwa2MTZxEKTVwXGRMSEQpMWhd4aWtNaxEKRVkXf2sRCkx fF3oFBQUFBQUFBQFHEQpMRhdsaWsRCkJPF3pCXVJsYBsaWWxtEQpDWhcbGR4EExsEHxwEGR0RCk JeFxsRCkReFxgRCkJFF2FEGxJlTntsGFgYEQpCThdvfEJscE1CZ3hcWREKQkwXaHxGZ05ucAFZW VIRCkJsF2xGa1x8c2NTGnloEQpCQBdna2N7Em5jbxpcHBEKQlgXZ3Nlc0BuYWFMXWIRClpYFx4R CnlDF2xNSFpMY3xZQ0YeEQpwZxduQHkde2IdfUF6bBAeEhEKcGgXbQVscn5zG2lsHnIQGRoRCnB oF2x/EmBebm59eUZHEB4aEQpwaBdtHmNaRGtOTWl7GRAdEhEKcGgXaF9gUx9BW3tiXXIQGRoRCn BoF2ZZeERAXBxLSxJYEBkaEQpwfRdlZ3BzZWdPbksTSxAZGhEKcH8XYk4FAXBEXmlEe2UQGxsbE QpwXxdiGl9QTEYBRhwaUhAZGhEKcGwXbmFcbXhCaxoBAQEQGRoRCnBMF21oZRlBUn17GEVSEBka EQptfhcaEQpYTRdLESA= X-Proofpoint-ORIG-GUID: ruCZ9wulLfVCx35UvFCobC5j8gNjGIM7 X-CLX-Shades: MLX MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=48 lowpriorityscore=0 adultscore=0 clxscore=184 phishscore=0 mlxscore=0 mlxlogscore=999 malwarescore=0 suspectscore=0 bulkscore=0 impostorscore=0 spamscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112280048 X-Spam-Score: 0 X-Spam-OrigSender: yasser.almeida-hernandez@uni-due.de X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, =?iso-8859-1?Q?Almeida-Hern=E1ndez=2C_Yasser=2C_Dr=2E?= --_000_8eda062edcd44e23bb32aa77f544acdcuniduede_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable Dear Giacomo, Thank you for your reply. I've tried with different initial and final centers, up to 10 A apart, and= the same happens. The proteins reach the targetCenters very fast and stay = there, while the centers evolve linearly until the end of the simulation. What do you think could be the problem? Best, Yasser ________________________________ From: Giacomo Fiorin Sent: Monday, December 27, 2021 5:14:57 PM To: NAMD list; Almeida-Hern=E1ndez, Yasser, Dr. Subject: Re: namd-l: SMD at constant velocity Hi Yasser, it sounds like the variables' values do not evolve as you expect= them to, but the restraint centers do work as expected. This is not uncom= mon. Your initial and final centers differ by only 0.5 =C5, and assuming you use= d the default width of 1, for a force constant of 5 kcal/mol you get 1/2=D7= 5=D70.5^2 =3D 0.625 kcal/mol, roughly one kT unit. Not much difference bet= ween those states as far as the restraint is concerned. Accumulated work, like all energies, is in the same unit of the MD engine t= hat Colvars is distributed with, in this case NAMD: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:units__;Iw!!DZ3fjg!ui7KrEjvrrh8S5NdFLmRweKzpv7n= SplHV0Kz3XSw3lEZPGymuBhTEMo8XGnkNMJ7qQ$=20 and NAMD uses kcal/mol. Giacomo On Mon, Dec 27, 2021 at 5:47 AM Almeida-Hern=E1ndez, Yasser, Dr. > wro= te: Dear all, I am struggling with a SMD at constant velocity, where I want to pull two p= roteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 A/n= s, during 50 ns Below is the definition of the harmonic: harmonic { colvars pull_nter pull_cter pull_nter_y pull_cter_y pull_nt= er_z pull_cter_z centers -20.0 20.0 0.0 0.0 0.0 = 0.0 targetCenters -20.5 20.5 0.0 0.0 0.0 = 0.0 forceConstant 5. targetNumSteps 25000000 outputCenters yes outputAccumulatedWork yes } I have tried several centers and targetCenters to achieve the velocity, but= what happens is that the targetCenters are reached very fast and then the = proteins stay there. However, I write the centers during the simulation (w= ith outputCenters, x0_pull_nter and x0_pull_nter) and they change continuou= sly as expected until the end of the run. Am I missing something? Also, what are the units of the accumulated work written in the .traj file? Any help will be very much appreciated. Best, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universit=E4tsstr. 2, 45117 Essen Email: yasser.almeida-hernandez@uni-due.de Phone: +49 201 183 2457 --_000_8eda062edcd44e23bb32aa77f544acdcuniduede_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: Quoted-printable

Dear Giacomo,


Thank you for your reply.


I've tried with different initial and final centers, up to 10 A apart,&n= bsp; and the same happens. The proteins reach the targetCenters very fast a= nd stay there, while the centers evolve linearly until the end of the simul= ation.


What do you think could be the problem?


Best,

Yasser


From: Giacomo Fiorin <= giacomo.fiorin@gmail.com>
Sent: Monday, December 27, 2021 5:14:57 PM
To: NAMD list; Almeida-Hern=E1ndez, Yasser, Dr.
Subject: Re: namd-l: SMD at constant velocity
 
Hi Yasser, it sounds like the variables' values do not evo= lve as you expect them to, but the restraint centers do work as expected.&n= bsp; This is not uncommon.

Your initial and final centers differ by only 0.5 =C5, and assuming yo= u used the default width of 1, for a force constant of 5 kcal/mol you get&n= bsp;1/2=D75=D70.5^2 =3D 0.625 kcal/mol, roughly one kT unit.  Not= much difference between those states as far as the restraint is concerned.

Accumulated work, like all energies, is in the same unit of the MD eng= ine that Colvars is distributed with, in this case NAMD:
and NAMD uses kcal/mol.

Giacomo

On Mon, Dec 27, 2021 at 5:47 AM Almei= da-Hern=E1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-due.de> w= rote:

Dear all,


I am struggling with a SMD at constant velocity, where I want to pull tw= o proteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 A/ns, during 50 ns


Below is the definition of the harmonic:


harmonic {
   colvars=            pull_nter   p= ull_cter pull_nter_y pull_cter_y pull_nter_z pull_cter_z
   centers=            -20.0    &nbs= p;   20.0      0.0       =   0.0          0.0     &= nbsp;    0.0
   targetC= enters   -20.5       20.5      0.0 &nb= sp;        0.0        &nb= sp; 0.0          0.0
   forceCo= nstant 5.
   targetN= umSteps 25000000
   outputC= enters yes
   outputA= ccumulatedWork yes
}


I have tried several centers and targetCen= ters to achieve the velocity, but what happens is that the targetCenters are reached very fast and then the proteins stay there= .  However, I write the centers during the simulation (with outputCenters= , x0_pull_nter and = x0_pull_nter)= and they change continuously as expected until the end of the= run.


Am I missing something?


Also, what are the units of the accumulated work written in the .traj fi= le?


Any help will be very much appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=E4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" rel=3D"noopener no= referrer" id=3D"gmail-m_-8563912227759805556gmail-m_6632314740631305832LPNo= LP" target=3D"_blank"> yasser.almeida-he= rnandez@uni-due.de
Phone: +49 201 183 2457 

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boundary="0000000000000a99b305d432b402" X-Proofpoint-ORIG-GUID: s0iJUZ2ys6FcSIZufqUulCpOBpeNg5IU X-CLX-Response: 1TFkXGx8SEQpMehcZHBoRCllEF2VfSHNJAWRtZBMSEQpYWBdoSFxZYXtJch0 bfBEKeE4XY1Nja3sTWH4aX14RCnlMF2JHGxtSaUJsE2xbEQpDSBcHHRMRCkNZFwcZGhgRCkNJFx oEGhoaEQpZTRdnZnIRCllJFxpxGhAadwYbGRJxGBkQGncGGBoGGhEKWV4XbGx5EQpJRhdfQ19Jd UJFWV5PThEKQ04XWRpDYH9wGFNZHGxJeWNwX0xbf19GaVplaFpPZE0fY38RClhcFx8EGgQYHhgF GxoEGxsaBB0EGxkbEBseGh8aEQpeWRdwa2BgHxEKTVwXGxsSEQpMWhdoaU1NaxEKTEYXb2tra2t rEQpCTxd6QFp/WlhLcB9wXREKQ1oXGBoTBBIfBBgYGwQbHRkRCkJeFxsRCkJcFxsRCl5OFxsRCk JLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYfhpfXhEKQkUXZBJle28ZWkUfU2ERCkJOF2NTY2t7E 1h+Gl9eEQpCTBdoSFxZYXtJch0bfBEKQmwXYH5aXR1NBUESWXIRCkJAF2RDbH4de0ReUktfEQpC WBdnc2VzQG5hYUxdYhEKTV4XGxEKWlgXGBEKeUMXZ2tGRxgZfH5lUEERCllLFxMcGR4RCnBoF25 aAUVjRxpOfn9wEBkaEQpwaBdlUkYSZEBdUkFcbRAZGhEKcGgXbGRCUHNGUmIcYk8QGRoRCnBoF2 1dUl5fY0lPBXkdEBkaEQpwaBdmUG9CaEB4fX1/ehAZGhEKcGwXa31pRVJdRnNgX1MQHR8RCm1+F xsRClhNF0sRIA== X-Proofpoint-GUID: s0iJUZ2ys6FcSIZufqUulCpOBpeNg5IU X-CLX-Shades: MLX X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 priorityscore=360 suspectscore=0 adultscore=0 lowpriorityscore=0 bulkscore=0 clxscore=158 spamscore=0 impostorscore=0 malwarescore=0 phishscore=0 mlxlogscore=695 mlxscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112280050 domainage_hfrom=9634 X-Spam-Score: 0 X-Spam-OrigSender: yogesh.rma13@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Yogesh Sharma --0000000000000a99b305d432b402 Content-Type: text/plain; charset="UTF-8" Hi all, I am studying ligand transport through membrane protein but during longer simulation runs. I can see shift in membrane and protein system in z direction. Most probably due to forces applied on ligand. Can someone guide me through how can i avoid this ? Is it okay, if i restrain lipid head groups to avoid this movement and how likely is it that this shift in z will effect my pmf with respect to protein z coordinates ( since protein and membrane is getting displaced along z by the ligand). looking forward for your suggestions. --0000000000000a99b305d432b402 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,
I am studying ligand transport thro= ugh membrane protein but during longer simulation runs. I can see shift in = membrane and protein system in z direction. Most probably due to forces app= lied on ligand. Can someone guide me through how can i avoid this ?=C2=A0 I= s it okay, if i restrain lipid head groups to avoid this movement and how l= ikely is it that this shift in z will effect my pmf with respect to protein= z coordinates ( since protein and membrane is getting displaced along z by= the ligand).
=C2=A0looking forward for your suggestions.

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X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: b56_dYGR9lC3CGV370clcs4xv8CRsUfh MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=192 mlxscore=0 malwarescore=0 bulkscore=0 phishscore=0 mlxlogscore=999 spamscore=0 adultscore=0 lowpriorityscore=0 impostorscore=0 priorityscore=0 suspectscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112280063 domainage_hfrom=12655 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Josh Vermaas --------------72D6F5DEF60C6B3F65ABED83 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: Quoted-printable I'd invite you to try an experiment. Simulate a bilayer for a long time=20 without applied forces. It'll diffuse along the z dimension over long=20 periods of time. The applied force probably isn't helping, but for a=20 well-defined reaction coordinate, where you only care about the=20 *relative* position between the small molecule and the membrane,=20 diffusion along the membrane normal axis will not impact the PMF. -Josh On 12/28/21 5:58 AM, Yogesh Sharma wrote: > Hi all, > I am studying ligand transport through membrane protein but during=20 > longer simulation runs. I can see shift in membrane and protein system=20 > in z direction. Most probably due to forces applied on ligand. Can=20 > someone guide me through how can i avoid this ?=C2=A0 Is it okay, if i=20 > restrain lipid head groups to avoid this movement and how likely is it=20 > that this shift in z will effect my pmf with respect to protein z=20 > coordinates ( since protein and membrane is getting displaced along z=20 > by the ligand). > =C2=A0looking forward for your suggestions. > --=20 Josh Vermaas vermaasj@msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul= ar Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-= vermaas/__;!!DZ3fjg!ogEOfBmpNczC8nA5fttgYqbr9UrrPVit71e48xdVVwSenxyEjkWqozm= J3L19KOV7QA$=20 --------------72D6F5DEF60C6B3F65ABED83 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: Quoted-printable I'd invite you to try an experiment. Simulate a bilayer for a long time without applied forces. It'll diffuse along the z dimension over long periods of time. The applied force probably isn't helping, but for a well-defined reaction coordinate, where you only care about the *relative* position between the small molecule and the membrane, diffusion along the membrane normal axis will not impact the PMF.

-Josh

On 12/28/21 5:58 AM, Yogesh Sharma wrote:
=20=20=20=20=20=20
Hi all,
I am studying ligand transport through membrane protein but during longer simulation runs. I can see shift in membrane and protein system in z direction. Most probably due to forces applied on ligand. Can someone guide me through how can i avoid this ?  Is it okay, if i restrain lipid head groups to avoid this movement and how likely is it that this shift in z will effect my pmf with respect to protein z coordinates ( since protein and membrane is getting displaced along z by the ligand).
 looking forward for your suggestions.


--=20
Josh Vermaas

verm=
aasj@msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecul=
ar Biology
Michigan State University
https://prl.natsci=
.msu.edu/people/faculty/josh-vermaas/
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a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=+eZWqO4KnAzMNcr2ZRr74/OEjjvqDM0ihLiWYwEmfdk=; b=gjcoYvPCflKGH14j428s7cWnFUWR4DYVoZKs9EJOjOVVagn6sxfWoSYLpJOdxYZb2f bR/4PLZI4TaIwkuid8qeewDQAhl62Lyaj+g3ac7wB/oaKrg3gXCSjIDkerpGu+CsB/v0 gwpynY97JWe2ApQVEaAiGEulOfDXuGEHqjhzSjuHJ0eKbnthghU5xn62oG4feq3sY9dS glVUJpP3aSa6hu1rLeMsWKrwknzlzl0YDVxCSMNYrtIxB9jTNYhJHWfJKj58Nvax98G4 85VNbccRjbEtOHpyVpFOL65WkUhnKd+ZdRm/a3u8cwhSABIY1e0zqOh5yzk8Dk70qweq 84Qg== X-Gm-Message-State: AOAM530HncyJe18fr6wdqYd93XM89JMJx8+e5oKozsmnhlcD9dvofYol oMCSfCkNZtb7MDTs2sVPuXwUjYxbqB6hQMpSfpLU014tJW8= X-Google-Smtp-Source: ABdhPJxLfYeTMjZ7FuNcHPKUE9Udda+dgsTxL5cLtggvvAT7YzgmwYXvxRyxmlKOhr+6wURBzIB+ae1HchKr1bVi2/U= X-Received: by 2002:a25:3249:: with SMTP id y70mr17588483yby.486.1640707610070; Tue, 28 Dec 2021 08:06:50 -0800 (PST) References: <8eda062edcd44e23bb32aa77f544acdc@uni-due.de> In-Reply-To: <8eda062edcd44e23bb32aa77f544acdc@uni-due.de> From: Giacomo Fiorin Date: Tue, 28 Dec 2021 11:06:14 -0500 Message-ID: Subject: Re: namd-l: SMD at constant velocity To: =?UTF-8?Q?Almeida=2DHern=C3=A1ndez=2C_Yasser=2C_Dr=2E?= Cc: NAMD list Content-Type: multipart/alternative; boundary="00000000000047542d05d4370280" X-Proofpoint-ORIG-GUID: xjFqw3BrxDfc6Q6wwyFiIWBF5eOxu5ZA X-CLX-Shades: MLX X-Proofpoint-GUID: xjFqw3BrxDfc6Q6wwyFiIWBF5eOxu5ZA X-CLX-Response: 1TFkXGxMaEQpMehcZGBgRCllEF2wee1wBcwV/WRtsEQpYWBdnXVtyHW5sT1h 4YBEKeE4XY1Nja3sTWH4aX14RCnlMF2cfGHJ+GWR5enNbEQpDSBcHHxoYEQpDWRcHGxoYEQpDSR caBBoaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGx0acR4TEBp3BhgaBhoRClleF2xseREKSUYXX0NfS XVCRVleT04RCkNOF1JAbFtdGWhYUm5MSRx7HF1dU2xDY31obB9PZVJfH3BrEQpYXBcfBBoEGB4Y BRsaBBsbGgQdBBsZGRAbHhofGhEKXlkXcGtkWxsRCk1cFxkcExEKTFoXeGlrTU0RCkVZF29rEQp MXxd6BQUFBQUFBQUFbxEKTEYXb2trbGtrEQpCTxdhWRx5GEgFEhtCeBEKQ1oXGBoTBBIfBBgbEw QbHRkRCkJeFxsRCkRJFxsRCkJcFxsRCl5OFxsRCkJLF2NTY2t7E1h+Gl9eEQpCSRdjU2NrexNYf hpfXhEKQkUXbGVAUksbcmV5Tk0RCkJOF2NTY2t7E1h+Gl9eEQpCTBdnXVtyHW5sT1h4YBEKQmwX YV96UxlDRBp6G34RCkJAF2drY3sSbmNvGlwcEQpCWBdnc2VzQG5hYUxdYhEKWlgXGREKeUMXbE1 IWkxjfFlDRh4RCllLFxMcGR4RCnBnF2xIcmJiWx55TEtoEB4SEQpwaBdiR3tCaQFeY0FJWRAZGh EKcGgXaAFsYFxMQkV5REwQGRoRCnBoF20eSxpveh0ZZn9zEBkaEQpwaBducwVaXWQFRkJDbxAZG hEKcGgXbWMZS1xpQkt7eE4QHhIRCnB9F2MYQxJoH2tmeHNDEBkaEQpwfRdlZ3BzZWdPbksTSxAZ GhEKcGcXbkB5HXtiHX1BemwQHBoRCnB/F2JOBQFwRF5pRHtlEB8TEQpwXxdiGl9QTEYBRhwaUhA ZGhEKcGwXZh97WFxiBUtYZB8QGRoRCnBMF21oZRlBUn17GEVSEBkaEQptfhcaEQpYTRdLESA= MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=190 mlxscore=0 priorityscore=322 malwarescore=0 phishscore=0 bulkscore=0 suspectscore=0 mlxlogscore=999 spamscore=0 adultscore=0 impostorscore=0 lowpriorityscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112280074 domainage_hfrom=9634 X-Spam-Score: 0 X-Spam-OrigSender: giacomo.fiorin@gmail.com X-Spam-Bar: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, Giacomo Fiorin --00000000000047542d05d4370280 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable Impossible to say for sure without digging deeper into the details of your system, but there are a couple of common things to check. 1. Make sure that PBC wrapping is not an issue for your variables' definition: https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/c= olvars-refman-namd.html*sec:colvar_atom_groups_wrapping__;Iw!!DZ3fjg!tzT0ys= eWc4Avjl1Bm1eoiGGpw8eq0pRlRRfVwyQjM4z2JdJN-OYyETDC_fqIEfoFKA$=20 and test them individually. 2. Try an unbiased MD run first, i.e. defining just the variables but not the restraint to get an idea of how the initial force will act. Giacomo On Tue, Dec 28, 2021 at 5:45 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < yasser.almeida-hernandez@uni-due.de> wrote: > Dear Giacomo, > > > Thank you for your reply. > > > I've tried with different initial and final centers, up to 10 A apart, > and the same happens. The proteins reach the targetCenters very fast and > stay there, while the centers evolve linearly until the end of the > simulation. > > > What do you think could be the problem? > > > Best, > > Yasser > ------------------------------ > *From:* Giacomo Fiorin > *Sent:* Monday, December 27, 2021 5:14:57 PM > *To:* NAMD list; Almeida-Hern=C3=A1ndez, Yasser, Dr. > *Subject:* Re: namd-l: SMD at constant velocity > > Hi Yasser, it sounds like the variables' values do not evolve as you > expect them to, but the restraint centers do work as expected. This is n= ot > uncommon. > > Your initial and final centers differ by only 0.5 =C3=85, and assuming yo= u used > the default width of 1, for a force constant of 5 kcal/mol you > get 1/2=C3=975=C3=970.5^2 =3D 0.625 kcal/mol, roughly one kT unit. Not m= uch difference > between those states as far as the restraint is concerned. > > Accumulated work, like all energies, is in the same unit of the MD engine > that Colvars is distributed with, in this case NAMD: > > https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd= /colvars-refman-namd.html*sec:units__;Iw!!DZ3fjg!tzT0yseWc4Avjl1Bm1eoiGGpw8= eq0pRlRRfVwyQjM4z2JdJN-OYyETDC_fqwltreLw$=20 > and NAMD uses kcal/mol. > > Giacomo > > On Mon, Dec 27, 2021 at 5:47 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. < > yasser.almeida-hernandez@uni-due.de> wrote: > >> Dear all, >> >> >> I am struggling with a SMD at constant velocity, where I want to pull two >> proteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 >> A/ns, during 50 ns >> >> >> Below is the definition of the harmonic: >> >> >> harmonic { >> colvars pull_nter pull_cter pull_nter_y pull_cter_y >> pull_nter_z pull_cter_z >> centers -20.0 20.0 0.0 0.0 >> 0.0 0.0 >> targetCenters -20.5 20.5 0.0 0.0 0.0 >> 0.0 >> forceConstant 5. >> targetNumSteps 25000000 >> outputCenters yes >> outputAccumulatedWork yes >> } >> >> >> I have tried several centers and targetCenters to achieve the velocity, >> but what happens is that the targetCenters are reached very fast and >> then the proteins stay there. However, I write the centers during the >> simulation (with outputCenters, x0_pull_nter and x0_pull_nter) and they >> change continuously as expected until the end of the run. >> >> >> Am I missing something? >> >> >> Also, what are the units of the accumulated work written in the .traj >> file? >> >> >> Any help will be very much appreciated. >> >> >> Best, >> >> Yasser >> >> >> -- >> Dr. Yasser Almeida-Hernandez >> Postdoctoral Researcher >> Computational Biochemistry group >> T01 R03 D45 >> Faculty of Biology >> University of Duisburg-Essen >> Universit=C3=A4tsstr. 2, 45117 Essen >> Email: yasser.almeida-hernandez@uni-due.de >> <%20yasser.almeida-hernandez@uni-due.de> >> Phone: +49 201 183 2457 <+49%20201%20183%202457> >> >> --00000000000047542d05d4370280 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: Quoted-printable
Impossible to say for sure without digging deeper into the= details of your system, but there are a couple of common things to check.<= div>
1. Make sure that PBC wrapping is not an issue for your = variables' definition:
https://colvars.github.io/colvars-refman-namd/= colvars-refman-namd.html#sec:colvar_atom_groups_wrapping
and test th= em individually.

2. Try an unbiased MD run first, = i.e. defining just the variables but not the restraint to get an idea of ho= w the initial force will act.

Giacomo
<= br>
On Tue,= Dec 28, 2021 at 5:45 AM Almeida-Hern=C3=A1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-d= ue.de> wrote:

Dear Giacomo,


Thank you for your reply.


I've tried with different initial and final centers, up to 10 A apar= t,=C2=A0 and the same happens. The proteins reach the targetCenters very fa= st and stay there, while the centers evolve linearly until the end of the s= imulation.


What do you think could be the problem?


Best,

Yasser


From= : Giacomo Fiorin <giacomo.fiorin@gmail.com>
Sent: Monday, December 27, 2021 5:14:57 PM
To: NAMD list; Almeida-Hern=C3=A1ndez, Yasser, Dr.
Subject: Re: namd-l: SMD at constant velocity
=C2=A0
Hi Yasser, it sounds like the variables' values do not= evolve as you expect them to, but the restraint centers do work as expecte= d.=C2=A0 This is not uncommon.

Your initial and final centers differ by only 0.5 =C3=85, and assuming= you used the default width of 1, for a force constant of 5 kcal/mol you ge= t=C2=A01/2=C3=975=C3=970.5^2 =3D 0.625 kcal/mol, roughly=C2=A0one kT unit.= =C2=A0 Not much difference between those states as far as the restraint=C2= =A0is concerned.

Accumulated=C2=A0work, like all energies, is in the same unit of the MD eng= ine that Colvars is distributed with, in this case NAMD:
and NAMD uses kcal/mol.

Giacomo

On Mon, Dec 27, 2021 at 5:47 AM Almei= da-Hern=C3=A1ndez, Yasser, Dr. <yasser.almeida-hernandez@uni-due.de>= ; wrote:

Dear all,


I am struggling with a SMD at constant velocity, where I want to pull tw= o proteins continuously along the X-axis apart, at k =3D 5 kcal/mol at 0.5 A/ns, during 50 ns


Below is the definition of the harmonic:


harmonic {
=C2=A0=C2=A0 colvars= =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 pull_nter=C2=A0=C2=A0 p= ull_cter pull_nter_y pull_cter_y pull_nter_z pull_cter_z
=C2=A0=C2=A0 centers= =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 -20.0 =C2=A0=C2=A0 =C2= =A0=C2=A0=C2=A0 20.0 =C2=A0=C2=A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2= =A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2= =A0=C2=A0=C2=A0 =C2=A0 0.0
=C2=A0=C2=A0 targetC= enters=C2=A0=C2=A0 -20.5 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 20.5 =C2=A0=C2=A0 =C2=A0 0.0 =C2= =A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2= =A0 0.0 =C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0 0.0
=C2=A0=C2=A0 forceCo= nstant 5.
=C2=A0=C2=A0 targetN= umSteps 25000000
=C2=A0=C2=A0 outputC= enters yes
=C2=A0=C2=A0 outputA= ccumulatedWork yes
}


I have tried several centers and targetCen= ters to achieve the velocity, but what happens is that the targetCenters are reached very fast and then the proteins stay there= .=C2=A0 However, I write the centers during the simulation (with outputCenters= ,=C2=A0x0_pull_nter and = x0_pull_nter)= and they change continuously as expected until the end of the= run.


Am I missing something?


Also, what are the units of the accumulated work written in the .traj fi= le?


Any help will be very much appreciated.


Best,

Yasser


--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universit=C3=A4tsstr. 2, 45117 Essen
Email:<= a href=3D"mailto:%20yasser.almeida-hernandez@uni-due.de" rel=3D"noopener no= referrer" id=3D"gmail-m_-736950438922981945gmail-m_-8563912227759805556gmai= l-m_6632314740631305832LPNoLP" target=3D"_blank">=C2=A0yasser.almeida-hernandez@uni-due.de
Phone:=C2=A0+49 201 = 183 2457=C2=A0

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When I try to run the 1st simulation for lipid tail meting, I am getting the following error: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG324 CG321 OG301 (ATOMS 221060 221065 221066) The following atoms are present in my ligand- acetylcholine. Can someone help me with the same? 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charset="utf-8" Content-ID: X-OriginatorOrg: msu.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BL0PR12MB4881.namprd12.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: cbe93a8c-e135-453b-adad-08d9cba7da39 X-MS-Exchange-CrossTenant-originalarrivaltime: 30 Dec 2021 15:20:02.9405 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 22177130-642f-41d9-9211-74237ad5687d X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: 1EfuW+/u4kaep2lkpEhNOwQN23V1bFsjktKiuIKtF0WBBhrlpc/EUH6KfWXwUevRb3hH0Eg26R7aCK4NsHxUZA== X-MS-Exchange-Transport-CrossTenantHeadersStamped: MN2PR12MB3408 X-CLX-Response: 1TFkXGxIaEQpMehcaEQpZRBdpe1J+ZGwZUGBhZBEKWFgXb2FYExpLXRtDQWU RCnhOF2hvTGYBcmZkS10SEQp5TBdgZVNgTR1PHmcYXBEKQ0gXBxsdExEKQ1kXBxIaEQpDSRcaBB oaGhEKWU0XZ2ZyEQpZSRcacRoQGncGGxwacRkTEBp3BhgaBhoRClleF2hueREKSUYXX0NfSXVCR VleT04RCkNOF0YHe2JME2kYdR9ifGhyY3xdWWxkWHJIZ2JSaWNCXRhPEQpYXBcfBBoEGB4YBRsa BBsaGgQdBBseGBAbHhofGhEKXlkXcGsZZmgRCk1cFxgcExEKTFoXeGlNTWsRCkVZF29rEQpMXxd 6BQUFBQUFBQUFbxEKTEYXb2tra2xraxEKQk8XbntEGFt5ZhpHeAERCkNaFx4aBBsaHQQTHAQeHR EKQl4XGxEKRF4XGREKQkUXaG1rYHkSS0BaHn0RCkJOF2hvTGYBcmZkS10SEQpCTBdvYVgTGktdG 0NBZREKQmwXYXkcHxJce09aaUIRCkJAF2BiT0BDWFBIUBl+EQpCWBdnc2VzQG5hYUxdYhEKTV4X GxEKWlgXGREKeUMXYnAdWk5wT01PRV0RCllLFxsYHB8dEQpwaBd6cF9EYVtZfkl+RxAZGhEKcGg Xem0ZTn5PfFATSEgQGRoRCnBoF2ZmRx5GHVpaG3hJEBoRCnBoF2locnxJQQFGUFhtEBoRCnBoF2 BOWExYa0BhWWF/EBkaEQpwfRdrehxgUxkYb1BFYBAZGhEKcH8Xbh9nXX1eQBN4ZHkQGxsYEQpwX xdkY2htHn1Qa0xQYBAZGhEKcGwXZ3gaQGIYSRp+eU0QGRoRCm1+FxsRClhNF0sRIA== X-CLX-Shades: MLX X-Proofpoint-ORIG-GUID: l-QHf9C2_5HVBXIVwsFNrXbMHxCIhw2e X-Proofpoint-GUID: l-QHf9C2_5HVBXIVwsFNrXbMHxCIhw2e MIME-Version: 1.0 X-Spam-Details: rule=cautious_plus_nq_notspam policy=cautious_plus_nq score=0 clxscore=180 spamscore=0 bulkscore=0 phishscore=0 priorityscore=0 lowpriorityscore=0 suspectscore=0 mlxscore=0 impostorscore=0 adultscore=0 mlxlogscore=999 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2110150000 definitions=main-2112300088 domainage_hfrom=12657 X-Spam-Score: 0 X-Spam-OrigSender: vermaasj@msu.edu X-Spam-Bar: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by halifax.ks.uiuc.edu id 1BUFK740010388 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Reply-To: namd-l@ks.uiuc.edu, "Vermaas, Josh" Hi Pradeepti, The atoms might be present, but does NAMD know where to find parameters for those particular atomtypes? Atomtype CGsomething suggests that this is using CGenFF parameters. Did you perhaps forget to include a parameter file for something nonstandard? -Josh On 12/30/21 04:26, Pradeepti Kampani wrote: > Hello all, > > I prepared a liganded-protein system in a POPC membrane. When I try to > run the 1st simulation for lipid tail meting, I am getting the > following error: > > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG324 CG321 OG301 > (ATOMS 221060 221065 221066) > > The following atoms are present in my ligand- acetylcholine. > > Can someone help me with the same? > > Sincerely, > Pradeepti > -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology vermaasj@msu.edu https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!vQ5ZfVON1PTus9LVO2uted8pL3YUpmeQq2OtNBpEo9WbXy5V6w2g1uax5LdeU9nyGw$