From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Mon Aug 08 2011 - 17:20:56 CDT
Hi Bjoern
I did not use Periodic Boundary Conditions in the equilibartion script because I use "extendedSystem dppc_cal300.xsc".
First I minimized the system, then I heated it to 300 K. "dppc_cal300.xsc" is the xsc output file obtained from heating.
Exactly what do you mean with "restart files to continue from"?
Thanks for your help.
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/
> From: namdlist_at_googlemail.com
> To: andresmoralesn2_at_hotmail.com
> Subject: Re: namd-l: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid!
> Date: Mon, 8 Aug 2011 09:57:08 +0200
> CC: namd-l_at_ks.uiuc.edu
>
> 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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