VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 10 2010 - 13:22:07 CST

Edward,
  VMD doesn't presently have a timestep field for storing forces, but
one could conceivably load a trajectory file containing forces into the
atom coordinate fields in VMD and get away with abusing it for this purpose.
I don't know any of the details of the Desmond format, so I can't answer whether
this is practical for DTR files or not. The other question is whether the
DTR file itself and the VMD DTR plugin (written by D. E. Shaw Research)
have explicit support for storing/reading forces, or if it is just implemented
as an alternative use of the same field used for coordinates?
It might be simpler for us to add an optional per-timestep force vector
to VMD rather than go through playing games with the files themselves, but
we'd have to make sure the DTR plugin can parse them and load them into VMD
as well.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 05, 2010 at 10:03:55AM -0600, Edward Lyman wrote:
> Hi all,
>
> I am wondering if the dtr plugin can read trajectories of forces in binary
> desmond format. Anyone tried this, or know the status?
>
> Thx,
> Ed
> 

-- 
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