From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Thu Apr 01 2010 - 09:27:16 CDT
Hi All,
I'm getting the above error with one of my simulations, I read the tips
given on here and have increased the margin (initially 0) to 2.5 and this
has made no difference. Unfortunately I can't restart at an earlier stage,
as this is the first step of my equilibration. Below is my input:
#Heating script, change according to correct molecule
# input
coordinates 2HKM_f_ionized.pdb
structure 2HKM_f_ionized.psf
binCoordinates 2HKM_f_therm.coor
binVelocities 2HKM_f_therm.vel
parameters par_ttw_namd.inp ;# parameter file for simulation
paratypecharmm on
extendedSystem 2HKM_f_therm.xsc
# output
set output 2HKM_f_eq1
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 50
xstFreq 50
binaryoutput yes
binaryrestart yes
outputEnergies 100
outputTiming 50
restartfreq 1000
# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
rigidBonds all
# Simulation space partitioning
switching on
switchdist 12
cutoff 14
pairlistdist 16
# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20
nonbondedFreq 2
fullElectFrequency 4
# PBC (commented out settings not needed with xsc)
#cellBasisVector1 82 0 0 ;#set correct basis vectors and origin
#cellBasisVector2 0 72 0
#cellBasisVector3 0 0 83
#cellOrigin 5.11 1.78 0.03
wrapAll on
wrapWater on
dcdUnitCell yes
useGroupPressure yes
useFlexibleCell no
useConstantRatio no
margin 2.5
#PME
PME on
PMEGridSpacing 1
#Langevin Settings
langevin on
langevinTemp 300
langevinDamping 3.0 # 3 for equilibration 1
langevinHydrogen off
langevinPiston on
langevinPistonTarget 1.00 ;# in bar.
langevinPistonPeriod 100 ;# in fs.
langevinPistonDecay 50
langevinPistonTemp 300 ;# set same as langevinTemp.
# Constraints
constraints on
consRef 2HKM_f_theq_const.pdb
consKFile 2HKM_f_theq_const.pdb
consKCol B
constraintScaling 10
run 100000 ; # run for 100 ps
constraintScaling 5
run 100000 ; # run for 100 ps
constraintScaling 2.5
run 100000
constraintScaling 1
run 100000
constraintScaling 0.5
run 100000
Any help would be appreciated, although I will continue to play with things
until then!
Philip Peartree
University of Manchester
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