From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Mon Aug 08 2011 - 21:12:24 CDT
Hi,
If you look at your script you will see that the PMEGridSpacing is set to 1.0 plus manual definition of the grid. This may generate a conflict into the grid calculation.
Try one option at once.
If you use PMEGridSpacing 1.0, then coment # the three lines above. If the problem persist, try the contrary.
Flavio
--- On Mon, 8/8/11, Andres Morales N <andresmoralesn2_at_hotmail.com> wrote:
From: Andres Morales N <andresmoralesn2_at_hotmail.com>
Subject: namd-l: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid!
To: "NAMD" <namd-l_at_ks.uiuc.edu>
Date: Monday, August 8, 2011, 3:00 AM
solvate dppc.psf dppc.pdb -z 5 +z 30 -o dppc_water
## 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.
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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