From: saman amiri (saman_amiri00_at_yahoo.com)
Date: Fri Jun 17 2011 - 16:07:14 CDT
Hi all,
I am goingt to simulate SWM4 water molecules using drude
polarizable force field. Unfortunately after minimization it is crashed.
The following error is presented:
FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small.
Increasing
cutoff and/or pairlistdist is not helpful. On the other hand, looking
at trajectories indicates that during minimization, water molecules
would like to break and form some chemical bonds which is so strange.
Would it be possible to look at CONF file (see bellow) and let me know what is the problem?
structure ../swm4_drude.xplor.psf
coordinates ../swm4_drude.pdb
outputName swm4_drude-1
set temperature 248
firsttimestep 0
# Input
paraTypeCharmm on
drude on
parameters toppar_drude_master_c36a1.STR
drudeTemp
1
temperature $temperature
if {1} {
cellBasisVector1 25.80 0. 0.
cellBasisVector2 0. 25.80 0.
cellBasisVector3 0. 0. 25.80
cellOrigin -0.05 0.05 0.08
}
wrapWater on
wrapAll on
COMmotion no
# Force-Field Parameters
exclude scaled1-4
1-4scaling
1.0
cutoff 10.
switching on
switchdist 8.
pairlistdist 12.
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX
27
PMEGridSizeY 27
PMEGridSizeZ 27
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen off
# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp
$temperature
restartfreq 1000
dcdfreq 100
xstFreq 1000
outputEnergies 1000
outputPressure 1000
# Minimization
if {1} {minimize 5000
reinitvels $temperature
}
run 100000
thanks,
Saman
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