VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
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...
On Tue, Nov 26, 2013 at 07:26:51PM -0500, Mihaela Drenscko wrote:
> 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,
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/