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

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Jan 30 2008 - 10:42:06 CST

I am try to equilibrate a system, by first using harmonic constraints
(restraints) on the protein atoms. I run a short simulation in which I
hold the protein atoms and let the water and ions go as I slowly heat
the system using progressive temperature rescaling without any thermo-
or barostats. Once I reach 300K, I try to run another simulation where
I relax the restraints on the non-backbone atoms of the protein in the
NPT ensemble, but the simulation immediately crashes out giving the
error:

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.

I tried increasing the margin to 2.0, but it does the same thing.
useFlexibleCell is off already. If I turn off the barostat (NVT), the
simulation runs fine and if I remove the constraints completely, NPT
runs fine. I'm not sure how the barostat and the constraints are
interacting to cause this problem. I'm including the input script below.

Any suggestions would be appreciated.

Josh

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

structure ../2sub2.psf
coordinates ../2sub2.pdb
outputName 2s2-equil4

set temperature 300.0

# Continuing a job from the restart files
set inputname 2s2-equil3
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc

set xscfile $inputname.restart.xsc

#########################################################
proc get_first_ts { xscfile } {
   set fd [open $xscfile r]
   gets $fd
   gets $fd
   gets $fd line
   set ts [lindex $line 0]
   close $fd
   return $ts
}

set firstts [get_first_ts $xscfile]
########################################################

firsttimestep $firstts

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

# Input
paraTypeCharmm on
parameters ../par_all27_prot_na.prm

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
#cellBasisVector1 119.5 0. 0.
#cellBasisVector2 0. 87. 0.
#cellBasisVector3 0. 0 111.9
cellOrigin 0. 0. 0.

wrapWater on
wrapAll off

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
COMmotion yes
margin 2.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

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

# Restraints
constraints on
consref 1VYM_2sub2_restrained.pdb
conskfile 1VYM_2sub2_restrained.pdb
conskcol B

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

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

restartfreq 500 ;# 1000steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

#protocol
run 5000

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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