VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 18 2004 - 10:24:54 CDT

Hi,
  It should be possible for you to wrap coordinates after-the-fact without
modifying your .trr files at all. There's a script in the VMD script library
that does this for trajectories produced by NAMD, with a little work it
could be made to work for TRR files from Gromacs I suspect.
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

Probably the best thing would be to modify that script to get the
cell info from VMD rather than assuming the existence of an XST file
ala NAMD. If someone has already done this, please let me know, otherwise
perhaps I can take a look at doing this in a few weeks when I'm done
with some more pressing work.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 18, 2004 at 10:03:37AM -0500, Nitin Rathore wrote:
> Hi,
> I am trying to view the trajectories of my simulation that have been
> written in Gromacs ".trr" format. The periodic boundary conditions are
> giving me problems. Every time few sites of a molecule crosses one edge
> of the box and re-enters from the opposite edge, VMD tries to create
> bonds between the broken halves of the molecule. Since at any given time
> there are enough water molecules that exist in this broken
> configuration, VMD ends up creating a mesh of lines across the
> simulation box.
> Does anyone know how to fix this? Can anything be done without changing
> the .trr files?
>
> --Nitin
> ============================================
> Nitin Rathore
> Graduate Research Assistant
> Department of Chemical Engineering
> University of Wisconsin-Madison.
> http://www.cae.wisc.edu/~rathore
> ============================================
> 

-- 
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