Re: NPT calculations in NAMD

From: Leandro Martinez (lmartinez_at_iqm.unicamp.br)
Date: Tue Jun 01 2004 - 07:17:58 CDT

   Maybe that was not the problem for Gavin, but I have seen that many
people get this error. I was having that error also, but the
error was that my pairlistdist was equal to my cellBasisVector in
length. Once I changed pairlistdist to a value significantly smaller
than the cellbasisvectors, the problem disappeared. Maybe this
simple error was the problem for other people.
  Leandro.

On Tuesday 01 June 2004 12:04, you wrote:
> Hi,
>
>
> as I understand it NAMD assigns atoms to a patch grid based on the
> system volume defined by the periodic cell definitions. If the volume
> of the cell alters too much as the system equilibrates and evolves,
> then this error occurs. My solution is to look at the cell volume
> shown on the NAMD output just before the error, and alter the cell
> dimensions (cellBasisVector1,2,3) so that the cell volume is closer
> to this equilibrated volume. I cannot vouch for the correctness of
> this solution, but it certainly should be OK to rerun the simulation
> from t=0, using the new (equilibrated) cell dimensions,
>
> good luck,
>
> Peter Jones
>
>
>
> On Tuesday, June 1, 2004, at 02:06 AM, Hui-Hsu (Gavin) Tsai [contr]
>
> wrote:
> > Hi,
> >
> > I am trying to run membrane calculations with NPT ensemble.
> > The initial membrane structure was generated from the membrane
> > plugin from
> > VMD. However, NAMD keeps on giving me these error messages:
> >
> > ****************************************************************
> > 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.
> > ------------- Processor 11 Exiting: Called CmiAbort ------------
> > Reason: 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.
> > *******************************************************************
> >*
> >
> > My setup for NPT calculations are as below:
> >
> > langevin on
> > langevinDamping 10
> > langevinTemp 300.0
> >
> > # Constant Pressure Control (variable volume)
> > useGroupPressure yes ;# needed for rigidBonds
> > useFlexibleCell no
> > useConstantArea no
> >
> > langevinPiston on
> > langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> > langevinPistonPeriod 100.
> > langevinPistonDecay 50.
> > langevinPistonTemp 300.0
> >
> > Is there anyone who has experience could give me some
> > advice/comments?
> > Thanks.
> >
> > Gavin
> >
> >
> >
> >
> >
> >
> > -------------------------------------------------
>
> Peter Jones Ph.D.
> Research Fellow
> Department of Cell and Molecular Biology
> University of Technology Sydney
> Westbourne Street
> Gore Hill N.S.W. 2065
> Australia
>
> Tel: 61-2-9514 4105
> FAX: 61-2-9514 4026
> email: Peter.Jones-2_at_uts.edu.au

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