Minimization/Equilibrium problem, atoms moving too fast

From: Adrian (adpala_at_hotmail.com)
Date: Thu Jul 18 2013 - 15:28:10 CDT

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

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