# RE: Minimization/Equilibrium problem, atoms moving too fast

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Jul 18 2013 - 20:23:35 CDT

The cell origin should be the center of mass of your system:

measure center \$all.

Unless you have used the "rotate to minimize volume" option in Solvate, your center could easily be tens or hundreds of Angstroms from {0 0 0} and your simulation will go crazy trying to move the system there.

If you're using the built-in solvate and ionize GUI tools in VMD, you should be able to just type:

pbc get

to get the box dimensions.

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Aron Broom
Sent: Friday, 19 July 2013 11:06 AM
To: adrian palacios
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Minimization/Equilibrium problem, atoms moving too fast

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<mailto: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<mailto:broomsday_at_gmail.com>
To: adpala_at_hotmail.com<mailto:adpala_at_hotmail.com>
CC: namd-l_at_ks.uiuc.edu<mailto: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<mailto: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
```

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