From: rohan uttarwar (rohan.uttarwar_at_wayne.edu)
Date: Fri Mar 04 2011 - 15:53:56 CST
Hi NAMD Users,
I am trying to make a residue-based CG model of PMMA polymer system in
vaccum. I succeeded in building the CG model from my atomistic model. But,
when I try to run the equilibration (NPT), it wont let me go beyond a
timestep of 6fs. Any bigger timestep beyond 6fs gives me one of the two
errors either "Bad Global Exclusion Count" or "Periodic cell has become too
small for original patch grid".
Below is my configuration file. Any suggestion would be highly appreciated.
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Bulk hydrogen sulfide
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ok_pmma.psf
coordinates ok_pmma.pdb
set temperature 500.0
#reassignFreq 1000
#reassignTemp 10
#reassignIncr 10
#reassignHold 300
set outputname dmp_equil
set inputname dmp_temp
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.restart.xsc
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_cg_hain1.inp
#temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 25.0
switching on
switchdist 10.
pairlistdist 45.5
# margin 2.5
# Integrator Parameters
timestep 6.0 ;# 2fs/step
# rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
# fullElectFrequency 2
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen on ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 80. 0. 0.
cellBasisVector2 0. 80. 0.
cellBasisVector3 0. 0. 80.
cellOrigin 39.76119613647461 42.538482666015625 39.87489318847656
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 80
PMEGridSizeY 80
PMEGridSizeZ 80
# 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
restartfreq 5000 ;# 500steps = every 1ps
dcdfreq 5000
xstFreq 5000
outputEnergies 5000
outputPressure 5000
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
#minimize 1000
#reinitvels $temperature
run 1000000 ;# 5ps
#for { set TEMP 50 } { $TEMP < 300 } { incr TEMP 50 } {
# run 1000
# reassignTemp $TEMP
#}
-- Rohan G. Uttarwar PhD Student Dept. of Chemical Engg & Material Science, Wayne State University, Detroit, MI.
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