VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 19 2007 - 10:53:00 CDT

Hi,
  Yes, and you can easily graph the bond length over time. The trivial
interactive way of doing this is to press the "2" key while the mouse focus
is in the OpenGL graphics window, and then select the two atoms that you want
to monitor distances for. From there you can open the Labels window and
there you'll be able to make plots etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 19, 2007 at 11:33:22AM +0200, Adilah Hussien wrote:
> Hi there,
>
> Does anyone know whether it is possible to use VMD to track the changes
> in bond length during a simulation run?
>
> By this I mean, for example, the length between, say, Atom 1 and Atom 2
> at every x timesteps (controlled by what one inputs as the dcdfreq in
> the NAMD).
>
>
> Thanks!
> Adilah. 

-- 
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