VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 24 2008 - 18:01:20 CST

Hi,
  You can load any scalar quantity you like into the per-atom-per-timestep
"User" fields in VMD via scripts, and then use those values as the basis
for coloring structural representations quite easily. Beyond that, you
could go further and use some of the existing scripts people have written
for drawing arrows and draw force arrows if that's something you're
interested in. These sorts of things are all done via scripting as none
of the standard simulation trajectory formats I'm aware of provide
fields for storing these things. The main challenge here is just getting
your force data into a file that you can then read into VMD using the
scripts I mention above. Check out Axel's CPMD/VMD tutorial (linked to from
the VMD tutorials page), as he's got some nice examples for
drawing arrows and doing some of the items I've just described.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 24, 2008 at 06:16:14PM -0500, Yinglong Miao wrote:
> Hi, VMD users/developers,
>
> Can anyone tell me whether VMD can visualize forces or not? I have some
> force data calculated from a "pairInteraction" NAMD simulation and I'd like
> to see how the forces on atom groups evolve as the simulation goes.
>
> Thanks in advance,
> Long
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981 

-- 
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