Re: Margin Value in NAMD

From: Andrea Holfelder (
Date: Wed Aug 31 2011 - 23:57:36 CDT

Thanks Johan

 Should I then keep using Margin command ?
 Is it good to keep the margin command ?
 I am using Margin 2.5 when my Cell basis vector is around 100 in x y z direction.

 From what I understand by ur explanation is that ,Margin value gives the pbc unit flexibity by 2.5 units in each direction(x,y,z) to change and adapt to new size.
 Is it ?

 Is it physiologically relevant to use margin ?

 What is the recommended value of margin when cell basis vector is aroun 100 in x y z direction.

----- Original Message -----
From: johan strumpfer
Sent: 09/01/11 09:26 AM
To: Andrea Holfelder
Subject: Re: namd-l: Margin Value in NAMD

 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. Cheers, Johan ------------------------------------------------------------------------------------------------------ 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 f
ile ,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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