From: Gurpreet Kaur Dhindsa (el2275_at_wayne.edu)
Date: Sun Jun 22 2014 - 17:32:16 CDT
Dear All,
I am running simulation contains carbon with water box. It showed me this error message
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
It stopped 2-3 times because water box was shrinking but now I looked at the
water box size is good enough. I looked in the mailing list peopled had this problem
but I didn't find in my conf file what I can change to get rid of that problem.
Appreciate for your suggestions.
Here is my configuration file
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
margin 2.5
structure ../common/ND_water4.psf
coordinates ../common/5ND_water.restart.pdb
set temperature 300
set outputname 5ND_water
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 2.0 ;# 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 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 325.0 0.0 0.0
cellBasisVector2 0.0 205.0 0.0
cellBasisVector3 0.0 0.0 145.0
cellOrigin -34.23 5.37 0.12
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#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 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 25000 ;# 50ps
reinitvels $temperature
run 3000000 ;# 6ns
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