VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 06 2006 - 19:20:18 CST

Hi Michel,
  At present, the built-in PBC support in VMD is only used for graphics
and hasn't yet been extended for selections and the various built-in
measurement commands etc. Even if you use the PBC drawing features to
render multiple translated instances of the unit cell, this won't affect
the atom selection commands etc. Currently, the best way to do this sort
of thing is via custom scripting, as some others have suggested. Quite a few
people have already written such scripts, so with any luck if you're doing
something related to the things others already have scripts for, you'll
have something similar to start from.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 06, 2006 at 01:06:50AM +0100, L. Michel Espinoza-Fonseca wrote:
> Dear all,
>
> I've been trying to analyze the contacts between water and a given
> peptide from my trajectories. I used a nice script provided by one of
> the VMD users. Everything went well, except from the fact that VMD is
> not able to count the water molecules around my peptide from the image
> of my periodic box. I've read some issues related to the pbc and VMD
> (computation of hbonds, for instance), and according to what I read,
> there is not such handling of pbc in VMD. Do you have any suggestions?
> I tried to use some artifacts such as drawing images of the water box,
> but it didn't work.
>
> Thanks!
>
> Michel 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078