Margin Error

From: Hsing Pao (hpao_at_ucsd.edu)
Date: Fri Aug 10 2007 - 12:43:20 CDT

Hi everyone. Right now I am getting this error message when I try
equilibration.
Here's my error message:

OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Margin is too small for 156 atoms during timestep 5.
ERROR: Incorrect nonbonded forces and energies may be calculated!
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.

And here's my NAMD script file:

set inpname 1JSO-pH-apo-salt-min_4
set outname 1JSO-pH-apo-salt_eq_1
firsttimestep 0

# input
amber yes
parmfile 1JSO-pH-apo-salt.prmtop
ambercoor 1JSO-pH-apo-salt.inpcrd
readexclusions yes
BinCoordinates $inpname.restart.coor
#BinVelocities $inpname.restart.vel
ExtendedSystem $inpname.xsc

# Harmonic constraint part
constraints on
consRef restrain_backbone_ref.pdb
consKFile restrain_backbone_ref.pdb
consKCol O
constraintScaling 1.0

# force field parameters
exclude scaled1-4
1-4scaling 0.833333
cutoff 18
switching On
switchdist 12
pairlistdist 20
margin 2.5

rigidBonds all
rigidTolerance 0.0005

# integrator params
timestep 2.0
numsteps 5000000
nonbondedFreq 2
PME yes
PMEGridSizeX 70
PMEGridSizeY 86
PMEGridSizeZ 156
FullElectFrequency 2
stepspercycle 20
langevin on # do langevin dynamics
#langevinFile tempfile.pdb
#langevinCol O
langevinTemp 300.15 # bath temperature
langevinDamping 5 # damping coefficient (gamma) of 5/ps
langevinHydrogen no # don't couple langevin bath to
hydrogens
temperature 300.15

# Pressure Control for NPT ensemble
useFlexibleCell no
langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 300.15

#PBC
#cellBasisVector1 67.705 0.0 0.0
#cellBasisVector2 0.0 82.089 0.0
#cellBasisVector3 0.0 0.0 153.304
#cellOrigin 34.991 42.629 78.834
wrapWater on
wrapAll on
wrapNearest on
xstFile $outname.xst
xstFreq 10000

# output
outputname $outname
dcdfile $outname.dcd
restartname $outname.restart
restartfreq 500
dcdfreq 500
binaryoutput yes
outputEnergies 500

I am not quite sure how to fix this problem. I have tried increasing
the margin and increasing the PME grid size.

Thanks,

Hsing

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