From: Peter Jones (Peter.Jones-2_at_uts.edu.au)
Date: Mon May 31 2004 - 22:04:51 CDT
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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