From: Prija Ponnan (prija.ponnan_at_gmail.com)
Date: Fri May 21 2010 - 05:24:58 CDT
Hello
I have run simulation of GST as given in the "topology tutorial"
the configuration file is as follows
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Human Pi GST in a Water Box
# N, V, E simulation
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure gst_solv_ion.psf
coordinates gst_solv_ion.pdb
set temperature 298
set outputname gst_wb_mineq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
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 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 58.9 0. 0.
cellBasisVector2 0. 76.7 0.
cellBasisVector3 0. 0 68.2
cellOrigin 17.7 12.4 15.8
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 64
PMEGridSizeY 80
PMEGridSizeZ 74
# Output
outputName $outputname
restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 10
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
reinitvels $temperature
run 10000 ;# 10ps
After running the simulation i have encountered the following error
REINITIALIZING VELOCITIES AT STEP 100 TO 298 KELVIN.
TCL: Running for 10000 steps
ERROR: Atom 23573 velocity is -16230.5 -42310.9 16194.5 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 11717 velocity is -26595 352.88 35945.3 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 32740 velocity is 6234.49 -10573.8 3218.94 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 10811 velocity is 20760.9 47547.2 -18996.4 (limit is 12000)
ERROR: Atom 24548 velocity is 562.081 -1538.09 -21147.8 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 23541 velocity is -5318.93 2372.28 14141.1 (limit is 12000)
ERROR: Atom 25076 velocity is 19915.6 -32341.9 12263.8 (limit is 12000)
ERROR: Atom 25838 velocity is 80549.7 -36561.9 -219838 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 13300 velocity is 20625.6 13084.8 -2221.2 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 11828 velocity is 82687.7 -32277.6 43229 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 24167 velocity is -2496.97 7572.91 -10993.4 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 33196 velocity is -913.896 21848.3 -7693.01 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 12536 velocity is 18992.3 -35199.8 29699.8 (limit is 12000)
ERROR: Atom 27931 velocity is 2720.71 7220.98 -10991.5 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 9806 velocity is 63749.5 -334617 63478 (limit is 12000)
ERROR: Atom 14958 velocity is -3915.41 21516.5 -4112.67 (limit is 12000)
ERROR: Atom 24475 velocity is -17615.2 -6948.36 -35026.4 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 100 89080.0711 15192.4248 2209.5977
216.1183 302922.0085 9999999999.9999 0.0000
0.0000 30021.9274 9999999999.9999 299.5870 9999999999.9999
9999999999.9999 299.5870 42540284.6972 7734007.8743
308102.3660 42540284.6972 7734007.8743
ERROR: Exiting prematurely; see error messages above.
Please help me to solve the problem
Thanks
-- Prija Ponnan
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