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

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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