Periodic cell has become too small for original patch grid!

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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