Re: Margin Value in NAMD

From: johan strumpfer (
Date: Wed Aug 31 2011 - 22:56:39 CDT

Hi Andrea,

The margin helps determine which atoms are assigned to which computing
patches. The error you're getting from removing the patch command is
likely because your simulation is changing size, maybe as it adapts to
a different box size or pressure.


Johan Strumpfer:
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA

On Wed, Aug 31, 2011 at 10:42 PM, Andrea Holfelder
<> wrote:
> I am not sure the importance of Margin value while running a PBC simulation.
> My cell basis vectors are around 100 for each of x y z and when I keep
> margin =2.5  the simulation runs quite welll but when I remove the margin
> from the config file ,I get an error after some time into the simulation
> which says something like   "the grid patch has become too small etc. etc. "
> What role is the Margin playing here?
> What does Margin do?

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