VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 22 2012 - 10:49:01 CDT

Hi,
  You can compute values like this by writing a script that computes
the distances you care about. You can then run the script over your
trajectory and compute the values, write them to files, plot them, etc.
I think that the best thing would be for you to begin by working through some
of the basic VMD atom selection and scripting tutorial sections and
from there you can probably get this done pretty easily:
  http://www.ks.uiuc.edu/Training/Tutorials/

Cheers,
  John
 
On Sat, Oct 20, 2012 at 05:44:13PM -0400, Eric Lovejoy wrote:
> Hi all,
> I should have included the end to end distance in my calculation but I did not. The calculation took several months to compute, so I don't want to recalculate. How can I get the end to end distance using the *.dcd trajectory files? I have several
> calculations where I forgot to compute the to end distance. Is there something that can do it automatically in vmd? What is the command? I am using a Linux based VMD if it matters.
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078