From: John Stone (
Date: Tue Nov 26 2013 - 19:04:21 CST

  Have you look at using PBCtools to wrap your waters back to the
original unit cell? You can search the VMD-L list for many
discussions of the use of pbctools...

  John Stone

On Tue, Nov 26, 2013 at 07:26:51PM -0500, Mihaela Drenscko wrote:
> Hi,
> When I run water on graphite simulation, my water bulk drifts towards next
> cell, such that at the end of the simulation I have part of the water in
> one cell and part in another.
> I have to do an analysis of the trajectories and the program I use doe not
> read the part of the water molecules that are in the adjacent cell.
> What can I do to keep all water molecule centered in one cell, such that
> my program can real all trajectories?
> Thank you,
> Mihaela

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