From: Albert (mailmd2011_at_gmail.com)
Date: Fri Apr 06 2012 - 07:39:09 CDT
hello:
here is my log and I think with non-cuda, the minimization goes well:
ENERGY: 9990 6076.8951 6641.4338 7651.7002
55.3422 -208798.7611 16034.3467 0.0000
22.7461 0.0000 -172316.2969 0.0000
-172316.2969 -172316.2969 0.0000 -2751.5067
-2760.3487 593110.5555 -2751.5067 -2760.3487
LINE MINIMIZER BRACKET: DX 0.000116279 0.00010365 DU -0.1493 0.118129
DUDX -2585.91 11.3695 2326.51
ENERGY: 9991 6076.8569 6641.4126 7651.6998
55.3500 -208798.6868 16034.3254 0.0000
22.7459 0.0000 -172316.2961 0.0000
-172316.2961 -172316.2961 0.0000 -2751.4834
-2760.3142 593110.5555 -2751.4834 -2760.3142
LINE MINIMIZER BRACKET: DX 1.16279e-05 0.00010365 DU -0.000775158
0.118129 DUDX -248.332 11.3695 2326.51
ENERGY: 9992 6076.8912 6641.4317 7651.7002
55.3430 -208798.7537 16034.3446 0.0000
22.7461 0.0000 -172316.2970 0.0000
-172316.2970 -172316.2970 0.0000 -2751.5043
-2760.3453 593110.5555 -2751.5043 -2760.3453
LINE MINIMIZER BRACKET: DX 1.04651e-05 1.16279e-06 DU -0.000842925
6.77668e-05 DUDX -248.332 -14.6015 11.3695
ENERGY: 9993 6076.8916 6641.4319 7651.7002
55.3429 -208798.7544 16034.3448 0.0000
22.7461 0.0000 -172316.2969 0.0000
-172316.2969 -172316.2969 0.0000 -2751.5044
-2760.3455 593110.5555 -2751.5044 -2760.3455
LINE MINIMIZER BRACKET: DX 1.04651e-05 1.16481e-07 DU -0.000842925
7.84995e-05 DUDX -248.332 -14.6015 -12.0018
ENERGY: 9994 6076.8912 6641.4317 7651.7002
55.3430 -208798.7537 16034.3446 0.0000
22.7461 0.0000 -172316.2970 0.0000
-172316.2970 -172316.2970 0.0000 -2751.5043
-2760.3453 593110.5555 -2751.5043 -2760.3453
LINE MINIMIZER REDUCING GRADIENT FROM 4625.04 TO 4.62504
ENERGY: 9995 6079.5796 6642.0233 7651.5411
55.3408 -208803.0093 16034.6699 0.0000
22.7501 0.0000 -172317.1046 0.0000
-172317.1046 -172317.1046 0.0000 -2755.9541
-2760.1986 593110.5555 -2755.9541 -2760.1986
ENERGY: 9996 6082.4662 6642.6954 7652.0333
55.3584 -208807.2713 16035.0258 0.0000
22.7541 0.0000 -172316.9380 0.0000
-172316.9380 -172316.9380 0.0000 -2760.5698
-2760.0597 593110.5555 -2760.5698 -2760.0597
LINE MINIMIZER BRACKET: DX 0.000278591 0.000278591 DU -0.807588 0.166576
DUDX -4625.04 -1149.83 2330.75
ENERGY: 9997 6080.5072 6642.2355 7651.6311
55.3444 -208804.4058 16034.7836 0.0000
22.7514 0.0000 -172317.1526 0.0000
-172317.1526 -172317.1526 0.0000 -2757.4503
-2760.1482 593110.5555 -2757.4503 -2760.1482
LINE MINIMIZER BRACKET: DX 9.16412e-05 1.8695e-06 DU -0.0480941
0.000182354 DUDX -1149.83 -5.51214 17.8342
colvars: Writing the state file
"step6.1_equilibration_a.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step6.1_equilibration_a.colvars.traj".
colvars: Saving collective variables state to
"step6.1_equilibration_a.colvars.state".
TIMING: 10000 CPU: 646.118, 0.0625219/step Wall: 646.118,
0.0625219/step, 0 hours remaining, 1574.234375 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: 10000 6080.5072 6642.2355 7651.6311
55.3444 -208804.4058 16034.7836 0.0000
22.7514 0.0000 -172317.1527 0.0000
-172317.1527 -172317.1527 0.0000 -2757.4503
-2760.1482 593110.5555 -2757.4503 -2760.1482
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE AT STEP 10000
WRITING COORDINATES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART VELOCITIES
TCL: Setting parameter numsteps to 90000000
TCL: Original numsteps 90000000 will be ignored.
TCL: Running for 2000000 steps
REASSIGNING VELOCITIES AT STEP 10000 TO 310 KELVIN.
colvars: Writing the state file
"step6.1_equilibration_a.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step6.1_equilibration_a.colvars.traj".
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 10000 462.8811 3364.7139 7651.6267
55.2352 -190736.0997 15641.0026 0.0000
22.7514 38451.3013 -125086.5876 310.9040
-163537.8889 -125091.9321 310.9040 643.6379
658.7199 593110.5555 643.6379 658.7199
colvars: Writing the state file
"step6.1_equilibration_a.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step6.1_equilibration_a.colvars.traj".
Info: Initial time: 24 CPUs 0.0539571 s/step 0.624504 days/ns 1574.23 MB
memory
colvars: Writing the state file
"step6.1_equilibration_a.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step6.1_equilibration_a.colvars.traj".
Info: Initial time: 24 CPUs 0.05284 s/step 0.611574 days/ns 1574.23 MB
memory
On 04/06/2012 09:59 AM, Francesco Pietra wrote:
> Hi:
> I wonder whether normal completion of minimization with no-cuda namd
> reported by Albert means successful minimization.
>
>
> I have now also tried Linux-x86_64-multicore (64-bit Intel/AMD single
> node), with the same files used beforewith the cuda 2.8 and 2.9b2
> versions. The requested 10,000 steps were completed without error
> messages, however there was no minimization at all, as shown by the
> starting and ending log below:
>
> TCL: Minimizing for 10000 steps
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 131511.9006 15951.4182 1089.1031
> 80.7094 -208755.0384 69052471.1297 0.0000
> 0.0000 0.0000 68992349.2227 0.0000
> 68992349.2227 68992349.2227 0.0000 28546289.9186
> 28560982.4534 672033.8185 28546289.9186 28560982.4534
>
> MINIMIZER SLOWLY MOVING 192 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY: 1 131687.0782 15972.6729 1093.8588
> 82.4127 -208979.1378 4016972.9223 0.0000
> 0.0000 0.0000 3956829.8071 0.0000
> 3956829.8071 3956829.8071 0.0000 1640862.7514
> 1655451.5178 672033.8185 1640862.7514 1655451.5178
>
> MINIMIZER SLOWLY MOVING 103 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY: 2 131746.9427 15987.1900 1096.4212
> 85.2803 -209095.4978 451409.8409 0.0000
> 0.0000 0.0000 391230.1773 0.0000
> 391230.1773 391230.1773 0.0000 165310.8297
> 179644.2803 672033.8185 165310.8297 179644.2803
> ...............................
> ...............................
>
> LINE MINIMIZER BRACKET: DX 1.88138e-301 3.76275e-301 DU -4.19171e-06
> 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> ENERGY: 9996 121119.4585 15410.7498 1102.0830
> 129.7461 -213732.3772 18984.3934 0.0000
> 0.0000 0.0000 -56985.9464 0.0000
> -56985.9464 -56985.9464 0.0000 -14603.1699
> -621.2528 672033.8185 -14603.1699 -621.2528
>
> LINE MINIMIZER BRACKET: DX 1.88138e-302 3.76275e-301 DU -1.14297e-05
> 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> ENERGY: 9997 121119.4585 15410.7498 1102.0830
> 129.7461 -213732.3772 18984.3934 0.0000
> 0.0000 0.0000 -56985.9464 0.0000
> -56985.9464 -56985.9464 0.0000 -14603.1699
> -621.2528 672033.8185 -14603.1699 -621.2528
>
> LINE MINIMIZER BRACKET: DX 1.88138e-303 3.76275e-301 DU -4.75305e-05
> 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> ENERGY: 9998 121119.4585 15410.7498 1102.0830
> 129.7461 -213732.3771 18984.3934 0.0000
> 0.0000 0.0000 -56985.9464 0.0000
> -56985.9464 -56985.9464 0.0000 -14603.1699
> -621.2528 672033.8185 -14603.1699 -621.2528
>
> LINE MINIMIZER BRACKET: DX 1.88138e-304 3.76275e-301 DU -5.37204e-05
> 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> ENERGY: 9999 121119.4585 15410.7498 1102.0830
> 129.7461 -213732.3772 18984.3934 0.0000
> 0.0000 0.0000 -56985.9464 0.0000
> -56985.9464 -56985.9464 0.0000 -14603.1700
> -621.2528 672033.8185 -14603.1700 -621.2528
>
> LINE MINIMIZER BRACKET: DX 1.88138e-305 3.76275e-301 DU -2.59996e-06
> 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> TIMING: 10000 CPU: 1566.85, 0.153887/step Wall: 1566.85,
> 0.153887/step, 0 hours remaining, 514.656250 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: 10000 121119.4585 15410.7498 1102.0830
> 129.7461 -213732.3772 18984.3934 0.0000
> 0.0000 0.0000 -56985.9464 0.0000
> -56985.9464 -56985.9464 0.0000 -14603.1699
> -621.2528 672033.8185 -14603.1699 -621.2528
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
> WRITING COORDINATES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART VELOCITIES
> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10000
> WRITING COORDINATES TO OUTPUT FILE AT STEP 10000
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 10000
> ====================================================
>
> WallClock: 1592.629395 CPUTime: 1592.629395 Memory: 514.656250 MB
> Program finished.
>
> *************
> The gradient:
>
> LINE MINIMIZER REDUCING GRADIENT FROM 4.52147e+08 TO 452147
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM 4.54669e+08 TO 454669
> ......................
> ......................
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM 4.54669e+08 TO 454669
> LINE MINIMIZER REDUCING GRADIENT FROM 4.54669e+08 TO 454669
> LINE MINIMIZER REDUCING GRADIENT FROM 4.54665e+08 TO 454665
> LINE MINIMIZER REDUCING GRADIENT FROM 4.54509e+08 TO 454509
> LINE MINIMIZER REDUCING GRADIENT FROM 4.54096e+08 TO 454096
>
> scores very badly, i.e., the minimizer was unable to deal with a badly
> parameterized system.
>
> I wonder whether Albert got the cuda error along a successful minimization.
>
> In my case, the two metal clusters reproduce nicely the crystal data
> and min-restart-coor after the attemped 10,000 step minimization do
> not show any wrong structural element at the naked eye. The ensemble
> is in a water box, which also does not show distortions. I was using
> 0.1fs ts and overall a min.conf that was successful in all previous
> cases of metalloproteins parameterized at home.
>
> My question was, and remains, how to get a clue abot atom-atom
> interactions that may explain the high (and un-minimizable) VDW and
> IMPR. My naive view is that once that adjustment in the input files is
> done, neither no-cuda, nor cuda will show problems any more. I regret
> to be unable to furnish more elements for debugging, however the
> software is not helping me by showing flying out atoms.
>
> Thanks for advice
>
> francesco
>
> On Fri, Apr 6, 2012 at 5:37 AM, Jim Phillips<jim_at_ks.uiuc.edu> wrote:
>> This is the real error:
>>
>> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over 101.085352
>> s on step 1778
>>
>> What it means is that NAMD has been waiting 101s for the CUDA event
>> indicating that the kernel has completed and NAMD is exiting rather than
>> likely hanging indefinitely. I've noticed that these errors were more
>> likely with energy evaluation (hence the connection to minimization),
>> certain compiler settings (-ftz), and particular devices on the Forge
>> cluster at NCSA that later crashed, suggesting this this is some kind of
>> hardware issue (GPU or PCIe bus) or driver/runtime/compiler fault. The
>> alternative is that I've missed a race condition that leads to an infinite
>> loop in the kernel.
>>
>> I'm really hoping someone will find a way to trigger this consistently since
>> in my experience it has been too rare to identify a cause.
>>
>> -Jim
>>
>>
>> On Thu, 5 Apr 2012, Norman Geist wrote:
>>
>>> I guess the developers will fix this soon as 2.9b2 is a beta, bugs are
>>> expected. And reports a wished.
>>>
>>>
>>>
>>> Norman Geist.
>>>
>>>
>>>
>>> Von: Albert [mailto:mailmd2011_at_gmail.com]
>>> Gesendet: Donnerstag, 5. April 2012 08:16
>>> An: Norman Geist; namd-l_at_ks.uiuc.edu
>>> Betreff: Re: AW: namd-l: CUDA problem?
>>>
>>>
>>>
>>> Hello:
>>> thank you very much for kind messages.
>>> Is there an solution for this problem?
>>>
>>> best
>>> A
>>>
>>> On 04/05/2012 08:12 AM, Norman Geist wrote:
>>>
>>> Hi,
>>>
>>>
>>>
>>> there seems to be something wrong within the new gpu accelerated
>>> minimization as Francesco posted the same issue and I answered him a few
>>> second ago. I first thought this could also be an hardware issue of a single
>>> gpu, but two people with a broken gpu is really unlikely. So it’s the
>>> developers turn.
>>>
>>>
>>>
>>> Best wishes
>>>
>>>
>>>
>>> Norman Geist.
>>>
>>>
>>>
>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
>>> von Albert
>>> Gesendet: Mittwoch, 4. April 2012 21:03
>>> An: namd-l_at_ks.uiuc.edu
>>> Betreff: namd-l: CUDA problem?
>>>
>>>
>>>
>>> Dear:
>>> I've built a membrane system from CHARMM GUI and use the equilibration
>>> protocol to relax my system. Everything goes well if I use the default
>>> setting and it was finished under CUDA mode. However, there is a ligand in
>>> my system and I would like to restrain it during step 6.1(see below of the
>>> file). Here is what I did to add constrain for my ligand
>>>
>>> set sel [atomselect top all]
>>> $sel set beta 0
>>> set fix [atomselect top "protein and backbone or (resname LIG and not
>>> hydrogen)"]
>>> $fix set beta 1
>>> $sel writepdb bb_rmsd.ref
>>>
>>>
>>>
>>> after that I am trying to run this 6.1.inp by command:
>>>
>>> charmrun ++local +p4 namd2 +idlepoll step6.1_equilibration.inp> log
>>>
>>>
>>>
>>>
>>> a few minutes later, it stopped with following logs:
>>>
>>>
>>> ---------log----------------
>>> LINE MINIMIZER BRACKET: DX 7.96611e-05 0.000159322 DU -84.715 50.7203 DUDX
>>> -1.52698e+06 -592619 1.21989e+06
>>> ENERGY: 1776 5819.8403 10258.1721 9471.5998 94.8591 -182114.5405
>>> 16169.6595 0.0000 3.2133 0.0000 -140297.1965 0.0000 -140297.1965
>>> -140297.1965 0.0000 3492.2283 3770.7578 593110.5555 3492.2283 3770.7578
>>>
>>> LINE MINIMIZER BRACKET: DX 5.18225e-05 0.0001075 DU -15.3777 66.098 DUDX
>>> -592619 3098.88 1.21989e+06
>>> ENERGY: 1777 5817.4042 10259.2760 9467.1949 94.8526 -182109.7937
>>> 16170.7783 0.0000 3.2124 0.0000 -140297.0753 0.0000 -140297.0753
>>> -140297.0753 0.0000 3495.3068 3772.9724 593110.5555 3495.3068 3772.9724
>>>
>>> LINE MINIMIZER BRACKET: DX 5.18225e-06 0.0001075 DU -0.121147 66.098 DUDX
>>> -56148.6 3098.88 1.21989e+06
>>> ------------- Processor 2 Exiting: Called CmiAbort ------------
>>> Reason: FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
>>> 101.085352 s on step 1778
>>>
>>> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
>>> 101.085352 s on step 1778
>>> Charm++ fatal error:
>>> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
>>> 101.085352 s on step 1778
>>>
>>>
>>> However, if I don't use CUDA mode, everthing goes well.... and the
>>> simulation can be finished without any error.... Would you please give me
>>> some advices for this?
>>>
>>>
>>> ----------step 6.1.inp-------------
>>> structure ../step5_assembly.xplor_ext.psf
>>> coordinates ../step5_assembly.pdb
>>>
>>> set temp 310;
>>> set outputname step6.1_equilibration;
>>>
>>> # read system values written by CHARMM (need to convert uppercases to
>>> lowercases)
>>> exec tr "\[:upper:\]" "\[:lower:\]"< ../step5_assembly.str | sed -e "s/ =
>>> //g"> step5_assembly.namd.str
>>> source step5_assembly.namd.str
>>>
>>> temperature $temp;
>>>
>>> outputName step6.1_equilibration_a; # base name for output from this run
>>> # NAMD writes two files at the end, final coord and vel
>>> # in the format of first-dyn.coor and first-dyn.vel
>>> firsttimestep 0; # last step of previous run
>>> restartfreq 500; # 500 steps = every 1ps
>>> dcdfreq 1000;
>>> 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 1000; # 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
>>>
>>> exec mkdir -p toppar
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ./toppar/par_all22_prot.prm>
>>> toppar/par_all22_prot.prm
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all27_na.prm>
>>> toppar/par_all27_na.prm
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ./toppar/par_all36_carb.prm>
>>> toppar/par_all36_carb.prm
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ./toppar/par_all36_lipid.prm
>>>> toppar/par_all36_lipid.prm
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ./toppar/par_all36_cgenff.prm
>>>> toppar/par_all36_cgenff.prm
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
>>> -e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
>>> ./toppar/toppar_water_ions.str> toppar/toppar_water_ions.str
>>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
>>> -e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
>>> ./toppar/toppar_all36_lipid_cholesterol.str>
>>> toppar/toppar_all36_lipid_cholesterol.str
>>>
>>> parameters toppar/par_all27_prot_na.prm;
>>> parameters toppar/par_all36_lipid.prm;
>>> parameters toppar/par_all22_prot.prm;
>>> parameters toppar/par_all27_na.prm;
>>> parameters toppar/par_all36_carb.prm;
>>> parameters toppar/par_all36_cgenff.prm;
>>> parameters toppar/par_all35_ethers.prm;
>>> parameters toppar/lig.prm;
>>>
>>>
>>> parameters toppar/toppar_water_ions.str;
>>> parameters toppar/toppar_all36_lipid_cholesterol.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.
>>> seed 1333525265 # Specifies a specific seed
>>>
>>> # 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;
>>>
>>> # Periodic Boundary conditions. Need this since for a start...
>>> cellBasisVector1 $a 0.0 0.0; # vector to the next image
>>> cellBasisVector2 0.0 $b 0.0;
>>> cellBasisVector3 0.0 0.0 $c;
>>> cellOrigin 0.0 0.0 $zcen; # the *center* of the cell
>>>
>>> wrapWater on; # wrap water to central cell
>>> wrapAll on; # wrap other molecules too
>>> wrapNearest off; # use for non-rectangular cells (wrap to the nearest
>>> image)
>>>
>>> # PME (for full-system periodic electrostatics)
>>> exec python ../checkfft.py $a $b $c> checkfft.str
>>> source checkfft.str
>>>
>>> PME yes;
>>> PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
>>> PMEGridSizeX $fftx; # should be close to the cell size
>>> PMEGridSizeY $ffty; # corresponds to the charmm input fftx/y/z
>>> PMEGridSizeZ $fftz;
>>>
>>> # 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 10
>>> langevinTemp $temp
>>> langevinHydrogen no
>>>
>>> # planar restraint
>>> colvars on
>>> exec sed -e "s/Constant \$fc/Constant 5/g" -e "s/\$bb/10.0/g" -e
>>> "s/\$sc/5.0/g" membrane_lipid_restraint.namd.col>
>>> restraints/$outputname.col
>>> colvarsConfig restraints/$outputname.col
>>>
>>> # dihedral restraint
>>> extraBonds yes
>>> exec sed -e "s/\$FC/500/g" restraints/dihe.txt>
>>> restraints/$outputname.dihe
>>> extraBondsFile restraints/$outputname.dihe
>>>
>>> minimize 10000
>>>
>>> numsteps 90000000
>>> run 3000000 ; 3ns
>>>
>>>
>>>
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