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

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Aug 08 2011 - 02:57:08 CDT

Hi Andres,

looks lke you didn't specify the box size.
You probably want to add something like this:
# Periodic Boundary Conditions
cellBasisVector1 X Y Z
cellBasisVector2 X Y Z
cellBasisVector3 X Y Z
cellOrigin 0. 0. 0.

But if you already minimized your System (using NAMD?) you should have restart
files to continue from.

Cheers,
Bjoern

On Monday 08 August 2011 04:00:38 Andres Morales N wrote:
> 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/

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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