From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Thu Aug 18 2005 - 17:35:21 CDT
Hi,
After minimization, the reinitializing of the temperature causes large
forces and energies and NAMD immediately crashes. In two other cases, it
didn't actually crash, but the box size was huge. It should have been
around 50 in that case, and it was 460!!
I have run this same exact script (minus the vdwGeometricSigma option) in
NAMD 2.5 (which I compiled myself) without any problems. Are there some
syntax changes that I haven't figured out?
Is there a problem with my configuration file (see below), or could it
just be that the binaries are not behaving properly on these two systems?
Thanks.
Joshua Moore
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# ethanol in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure 7ethanol64_w1991.psf
coordinates 7ethanol64_w1991.pdb
set temperature 295
#temperature: should only be set when starting from scratch
temperature $temperature
set outputname 7ethanol_out
firsttimestep 0
# continuing a run
#set inputname 7ethanol_in
#binCoordinates $inputname.coor
#binVelocities $inputname.vel
#extendedSystem $inputname.xsc
#firsttimestep 502000
#run stops when this step is reached
#numsteps 1250000
#set outputname 7ethanol_out
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters oplsaa_SPCE.prm
vdwGeometricSigma yes
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.5
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0
rigidBonds water
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: should only be used in starting a run
cellBasisVector1 42.5 0. 0.
cellBasisVector2 0. 42.5 0.
cellBasisVector3 0. 0. 42.5
cellOrigin 0. 0. 0.
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 48
PMEGridSizeY 48
PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
#binaryoutput no
restartfreq 500 ;# 500steps = every 1ps
#binaryrestart no
dcdfreq 250
xstFreq 250
outputEnergies 100
DCDUnitCell yes
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 2000
reinitvels $temperature
run 10000
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