FATAL ERROR: Periodic cell has become too small for original patch grid!

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Wed Apr 22 2009 - 01:44:45 CDT

Hello,

I am running simulation as follows: first em, then heating from 1K to
300K, then 10 ns at 300K.

My configuration file is at the bottom.

When heating starts I receive the following error:

------------- Processor 124 Exiting: Called CmiAbort ------------
Reason: 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.

This must be related with the pressure coupling since it worked fine without it.

Any suggestions? Thanks. I appreciate your time
SDA

#############################################################
## JOB DESCRIPTION ##
#############################################################

# STRMB in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure ./strmb.s.charmm.psf
coordinates ./strmb.s.charmm.pdb

set start_temperature 1
set hold_temperature 300
set outputname strmb.md.charmm.namd

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ./par_all27_prot_lipid.inp
temperature $start_temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 15.
switching on
switchdist 10.

# 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
langevinTemp $start_temperature
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $start_temperature

# Periodic Boundary Conditions
cellBasisVector1 108 0. 0.
cellBasisVector2 0. 102 0.
cellBasisVector3 0. 0 105.
cellOrigin 63.87940979 13.3578186035 32.2524185181

wrapAll on

#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 125
PMEGridSizeY 115
PMEGridSizeZ 120

# Output
outputName $outputname

restartfreq 10000
dcdfreq 2000
xstFreq 2000
outputEnergies 2000
outputPressure 10000

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 5000

#Heat
for { set TEMP $start_temperature } { $TEMP < $hold_temperature } {
incr TEMP 25 } {
        reassignTemp $TEMP
        langevinPistonTemp $TEMP
        langevinTemp $TEMP
        run 5000
}

reassignTemp $hold_temperature
langevinTemp $hold_temperature
langevinPistonTemp $hold_temperature
run 5000000

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