VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 18 2005 - 13:36:52 CDT

Hi,
  Are you having your simulation package wrap the atom coordinates
during the course of simulation, or are they left unwrapped in the
trajectory(ies) you're loading into VMD? If you're using non-wrapped
coordinates, you should see the residues and the nearby waters move
together. If you have coordinate wrapping enabled, then you may see
the waters wrap before residues do. Another way to solve this problem
is simply to enable the periodic cell display feature in VMD so you're
seeing multiple PBC cells next to each other, that should eliminate the
issue of the waters wrapping before the residues do, or vice-versa.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 18, 2005 at 08:44:34AM +0000, Cetin Baloglu wrote:
> Hi,
>
> I use periodic boundary conditions in my simulations and during the
> simulations, the side chains are moving out of the box as expected.
> However I want to make sure when a big conformational change occurs
> the water interacts with residues that are buried previously. Is
> there a trick to see residues moving out of the box, with the expected
> water.
>
> Cetin Baloglu 

-- 
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