Lipid bilayer equilibration: Periodic cell has become too small for original patch grid!

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Sun Aug 07 2011 - 21:00:38 CDT

Dear NAMD Users:
 
 
I am working with a dppc lipid bilayer system. I solvated the lipids using the commands:
 
package require solvate
solvate dppc.psf dppc.pdb -z 5 +z 30 -o dppc_water
 
I had no problems neither at system minimization nor at systme heating. But when I was running sytem equilibration it appeared the follwing mistake:
 
 

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.
[0] Stack Traceback:
[0] _ZN9HomePatch14positionsReadyEi+0x6e [0x8404a6e]
[1] _ZN9Sequencer17runComputeObjectsEii+0xc3 [0x8491eb3]
[2] _ZN9Sequencer9integrateEv+0x1074 [0x848ed88]
[3] _ZN9Sequencer9algorithmEv+0x327 [0x848bd7b]
 
 
I used the following configuration file for the equilibration:
 
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure dppc.psf
coordinates dppc.pdb
bincoordinates dppc_cal300.coor
binvelocities dppc_cal300.vel
set outputname dppc_eq1ns
firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_lipid27.rtf

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
margin 0
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
PMEGridSizeX 70
PMEGridSizeY 70
PMEGridSizeZ 95
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# 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 200.
langevinPistonDecay 50.
langevinPistonTemp 300
# Output
outputName $outputname
dcdfreq 1000
outputEnergies 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Boundary conditions
extendedSystem dppc_cal300.xsc
wrapWater on
wrapAll on

# Restrains
fixedAtoms on
fixedAtomsCol B
fixedAtomsForces on
 
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Equilibración
run 1000000
 
 
 
I have tried some solutions:
 
1) I increased margin to 1, 2, 3, 5 and 8
2) Also I disabled useFlexibleCell in the simulation
 
But none of them worked.
 
Also I looked at dcd output file using VMD and there is nothing unusual in the vizualization.
I checked the log output file and there is no critical increasing or decriasing of energy. It seems a pretty normal equilibration process.

I wait someone could help me with some solution.
 
 
Thank a lot.
 
 
 
 Hernán Andrés Morales Navarrete

Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/

                                                

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