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

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Mon Aug 08 2011 - 21:12:39 CDT

Bilayers can be a little tricky to get going, especially if you are
allowing the XY box sides to move independently of the z. If your
system is relatively stable, meaning it isn't exploding due to overlaps
or imploding because there isn't enough water, the solution is to dump a
few frames before NAMD spits patch grid error and then use one of those
frames to restart your simulation. After a couple iterations, your
system should be good to go. If you can't get NAMD to give you a few
frames, you can try a smaller time step (0.5-1.0ns).

In some cases, I have found running a short (<1.0 ns) NVT simulation
before NPT helps, since it gives the tails a chance to reorient before
the box starts moving.

Despite a number of posts on namd-l that suggest using "margin", I
haven't found this to be much help.

Regards,
Jeff

On 8/7/2011 10:00 PM, 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/
> <http://www.ciencias.epn.edu.ec/%7Ebiomod/>
>

-- 
======================================================================
Jeffrey J. Potoff			  jpotoff_at_chem1.eng.wayne.edu
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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