From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jul 18 2013 - 20:15:47 CDT
oh I see, never mind then it certainly won't help in that case.
On Thu, Jul 18, 2013 at 9:12 PM, adrian palacios <adpala_at_hotmail.com> wrote:
> Yeah, but I tried to center my molecule's pdb before all preparations, so
> the actual system origin should be the same as the coordinates origin (0 0
> 0), but I will do it anyways, IŽll let you know what happens tomorrow.
>
>
> Thanks for your help!
>
> Adrian Palacios
>
>
>
> ------------------------------
> Date: Thu, 18 Jul 2013 21:05:53 -0400
>
> Subject: Re: namd-l: Minimization/Equilibrium problem, atoms moving too
> fast
> From: broomsday_at_gmail.com
> To: adpala_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
>
> I'm not super familiar with exactly how NAMD does the periodic stuff or
> again what that VWD Boundary term means, but I wonder what would happen in
> your original larger simulation if you replaced:
>
> "cellOrigin 0 0 0"
>
> with
>
> "cellOrigin 80.5 73.0 72.0"
>
> Maybe nothing, but worth testing since it's a quick change.
>
>
> On Thu, Jul 18, 2013 at 8:58 PM, adrian palacios <adpala_at_hotmail.com>wrote:
>
> Well, my procedure to define the cell dimensions is running the "measure
> minmax $sel" where sel is the selection of the water box and using the
> diference between those vectors as each of the cell dimensions, for
> example, if it gives me {-80.5 . .} and {80.4 . .} I give a cell vector
> {161 0 0} as I did in my configuration file, trying to give numbers
> rounded to the greater integer. And sorry for my incorrect expression, I
> was thinking of the absolute value of energy, but you are correct in that
> point.
>
> Before you answered I looked for the vdw "NAMD Plot" from the minimization
> log file and it does represent the greater contribution to this
> unstability, but how could I fix this? I tried running a similar system in
> a smaller box and it worked, but still is the second time I have this
> problem related to CaCl Ionization neutralizing the system.
>
>
> Thanks for your reply, it was very accurate.
>
> Adrian Palacios
>
>
> ------------------------------
> Date: Thu, 18 Jul 2013 17:12:32 -0400
> Subject: Re: namd-l: Minimization/Equilibrium problem, atoms moving too
> fast
> From: broomsday_at_gmail.com
> To: adpala_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
>
>
> From the log, your energies actually go crazy low after minimization, not
> crazy high. And this seems to result from the ' VDW BOUNDARY' term. I'm
> not sure what this term applies to, but how confident are you in the cell
> dimensions you gave the system?
>
>
> On Thu, Jul 18, 2013 at 4:28 PM, Adrian <adpala_at_hotmail.com> wrote:
>
> Hello,
>
> I have been receiving an error during equilibration that says:
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Atom 224 velocity is -3.36524e+09 -5.3944e+10 -6.93782e+10 (limit
> is 14000, atom 76 of 587 on patch 328 pe 7)
> ERROR: Atom 226 velocity is 5548.87 -31899.4 21857.1 (limit is 14000, atom
> 78 of 587 on patch 328 pe 7)
> ERROR: Atom 231 velocity is 4.01192e+10 6.43101e+11 8.27101e+11 (limit is
> 14000, atom 83 of 587 on patch 328 pe 7)
> ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on
> patch 328 pe 7).
> ERROR: Exiting prematurely; see error messages above.
>
>
> But I have seen that this velocity problems arise from the minimization,
> which only runs for 100 steps and suddenly energies goes crazy high (see
> below).
>
> I have searched in namd-l and even in gromacs forums (they seem to have
> this problem too sometimes) and the only solutions I found are given for
> equilibration, such as gradual heat, which I tried but doesn't work (and
> shouldn't) as my systems becomes unstable from minimization...
>
> what could I do?
>
>
>
>
>
>
> Below theres a part of the minimization log file where the energies
> suddendly jump an go crazy:
>
> ****************************************************************
> ********************************************
>
> LINE MINIMIZER BRACKET: DX 0 7.46617e-05 DU 0 804922 DUDX -1.17635e+11
> -1.17635e+11 9.89855e+09
> ENERGY: 98 82987.3409 32267.5604 378.1408 398.7799
> -1379409.6821 220635.2885 0.0000 0.0000 0.0000
> -1042742.5716 0.0000 -1042742.5716 -1042742.5716 0.0000
>
> LINE MINIMIZER BRACKET: DX 0 2.85182e-05 DU 0 648998 DUDX -1.17635e+11
> -1.17635e+11 -1.41585e+10
> ENERGY: 99 53742.1489 26794.8140 378.9026 391.4425
> -1379049.7368 88822.2874 0.0000 0.0000 0.0000
> -1208920.1414 0.0000 -1208920.1414 -1208920.1414 0.0000
>
> LDB: ============= START OF LOAD BALANCING ============== 12.3247
> LDB: Largest compute 8450 load 0.006281 is 0.4% of average load 1.470207
> LDB: Average compute 0.001140 is 0.1% of average load 1.470207
> LDB: Partitioning computes with target load 0.147021
> LDB: Increased migratable compute count from 3456 to 3456
> LDB: Largest unpartitionable compute is 0.006281
> LDB: ============== END OF LOAD BALANCING =============== 12.3267
> Info: useSync: 1 useProxySync: 0
> LDB: =============== DONE WITH MIGRATION ================ 12.3279
> LINE MINIMIZER BRACKET: DX 0 1.0893e-05 DU 0 482821 DUDX -1.17635e+11
> -1.17635e+11 -6.00576e+09
> Info: Initial time: 8 CPUs 0.0917141 s/step 1.06151 days/ns 545.605 MB
> memory
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
>
> ENERGY: 100 50712.3949 26491.2341 381.0279 384.0135
> -1378906.7507 153570.1053 0.0000 0.0000 0.0000
> -1147367.9752 0.0000 -1147367.9752 -1147367.9752 0.0000
>
> LINE MINIMIZER BRACKET: DX 0 4.16075e-06 DU 0 544373 DUDX -1.17635e+11
> -1.17635e+11 4.31289e+10
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE AT STEP 100
> The last position output (seq=100) takes 0.016 seconds, 545.797 MB of
> memory in use
> ENERGY: 101 50478.8814 26312.4298 378.2435 378.8770
> -1378841.8835 -9999999999.9999 0.0000 0.0000 0.0000
> -9999999999.9999 0.0000 -9999999999.9999 -9999999999.9999
> 0.0000
>
> LINE MINIMIZER BRACKET: DX 1.58927e-06 2.57149e-06 DU -1.38707e+11
> 1.38708e+11 DUDX -1.17635e+11 1.17012e+11 4.31289e+10
> ENERGY: 102 50518.8841 26374.8347 378.6484 378.0852
> -1378867.4574 -436743.2275 0.0000 0.0000 0.0000
> -1737960.2326 0.0000 -1737960.2326 -1737960.2326 0.0000
>
> LINE MINIMIZER BRACKET: DX 1.58927e-06 9.82221e-07 DU -1.38707e+11
> 1.38707e+11 DUDX -1.17635e+11 1.17012e+11 1.25833e+11
> ENERGY: 103 50481.9200 26279.3515 378.2880 379.4739
> -1378826.8819 -9999999999.9999 0.0000 0.0000 0.0000
> -9999999999.9999 0.0000 -9999999999.9999 -9999999999.9999
> 0.0000
>
>
> ****************************************************************
> *********************************************
>
>
>
>
> Here is my minimization configuration file:
>
> ##############################**##############################**#
> ## JOB DESCRIPTION ##
> ##############################**##############################**#
>
> # Minimization of 1AML_Ca2mM
>
>
> ##############################**##############################**#
> ## ADJUSTABLE PARAMETERS ##
> ##############################**##############################**#
>
> structure 1AML_Ca2mM.psf
> coordinates 1AML_Ca2mM.pdb
> outputname minCa2mM
>
> set temperature 298
>
> firsttimestep 0
>
>
> ##############################**##############################**#
> ## SIMULATION PARAMETERS ##
> ##############################**##############################**#
>
> # Input
> paraTypeCharmm on
> parameters /usr/local/lib/vmd/plugins/**noarch/tcl/readcharmmpar1.2/**
> par_all27_prot_lipid_na.inp
>
> temperature $temperature
>
>
> # Periodic Boundary conditions
> if {0} {
> cellBasisVector1 161 0 0
> cellBasisVector2 0 146 0
> cellBasisVector3 0 0 144
> cellOrigin 0 0 0
> }
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0 ;# already a default value
> cutoff 14.0
> switching on ;# already a default value
> switchdist 12.0
> pairlistdist 16.0
>
>
> # Integrator Parameters
> timestep 1.0
> rigidBonds water
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
>
> restartfreq 2000
> dcdfreq 100
> xstFreq 100
> outputEnergies 200
>
>
> ##############################**##############################**
> #################
> ## EXTRA PARAMETERS ##
> ##############################**##############################**
> #################
>
>
> binaryoutput no
> binaryrestart no
>
>
>
> ##############################**##############################**#
> ## EXECUTION SCRIPT ##
> ##############################**##############################**#
>
> minimize 1000
>
>
>
>
>
>
>
>
>
>
> Thanks for your attention
>
> Adrian Palacios
>
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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