Periodic cell has become too small

From: santanu chatterjee (santanu_c10_at_yahoo.co.in)
Date: Sun May 28 2006 - 17:42:29 CDT

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Hi,
   I am running equilibration for a box of 683 water
molecules. I have minimized the box first and then I
am using the output files of minimization to
equilibrate the water box. I am getting the following
error message:

OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: Periodic cell has become too small for
original patch grid!
There are probably many margin violations already
reported.
Possible solutions are to restart from a recent
checkpoint,
increase margin, or disable useFlexibleCell for liquid
simulation.
------------- Processor 0 Exiting: Called CmiAbort
------------
Reason: FATAL ERROR: Periodic cell has become too
small for original patch grid!
There are probably many margin violations already
reported.
Possible solutions are to restart from a recent
checkpoint,
increase margin, or disable useFlexibleCell for liquid
simulation.

I am using the following config file:

#structure ../minimize/ubq_wb.psf
structure ../minimize/water_683.psf
#coordinates ../minimize/ubq_wb.pdb
coordinates ../minimize/water_683.pdb
bincoordinates ../minimize/water_min.coor
binvelocities ../minimize/water_min.vel

#set temperature 2110
#set outputname water_eq

firsttimestep 0
numsteps 10000

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

# Input
paraTypeCharmm on
parameters ../minimize/SPCE.prm
#temperature 376

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 9.
switching on
switchdist 9.0
pairlistdist 10

# Integrator Parameters
seed 1234
timestep 2.0 # 2fs/step
rigidBonds water # needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on # do langevin dynamics
langevinDamping 5 # damping coefficient
(gamma) of 5/ps
#langevinTemp $temperature
langevinTemp 376
langevinHydrogen off # don't couple langevin
bath to hydrogens

margin 50.0

# Periodic Boundary Conditions
cellBasisVector1 34. 0. 0.
cellBasisVector2 0. 35. 0.
cellBasisVector3 0. 0 33.5
cellOrigin -0.1443 0.03841 0.213

#wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 24
PMEGridSizeY 24
PMEGridSizeZ 24

# Constant Pressure Control (variable volume)
useGroupPressure yes # needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
#langevinPistonTemp $temperature
langevinPistonTemp 376

# Output
outputName water_eq

restartfreq 500 # 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

I found that one way to get away with this problem is
to start simulation with a large margin. I tried that,
but it doesnt work.
It will be very helpful if anyone can point me to what
I am doing wrong.

Thanks,
-S

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