From: David A Case <>
Date: Tue, 10 Apr 2012 07:58:51 -0400

On Tue, Apr 10, 2012, Fernando Martín García wrote:
> We are performing a long MD and we have observe a perturbation in one
> residue that have been stable during the whole simulation, until it has
> reached the limit of the water box (we are using PBC isotropic
> conditions) and we are asking if the change of the conformation could
> have been provoked by a pressure change in the limit of the box.

No: under periodic boundary conditions, there is no "limit" to the box, and
the edge of the box is no different than the middle, etc. For example, you
could use the "center" and "image" commands in ptraj to make it look like
any part of your molecule is at the very center of the box.


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Received on Tue Apr 10 2012 - 05:00:06 PDT
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