VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 23 2004 - 15:46:26 CDT

Hi,
  You can read the coordinates of a loaded trajectory out of VMD using
simple Tcl scripting. This would allow you to write the coordinates to a
text file that would be more easily processed by your own code, or do whatever
you like with them. You'd do this using the "$sel get {x y z}" operations
one would use with the result of an 'atomselect' command. All of that is
mentioned in the User's Guide. We will be posting an energy evaluation
script/plugin written by Jan Saam soon, it may also help solve your problem.
I'll announce to VMD-L when it is posted for download.

  John

On Mon, May 17, 2004 at 02:28:40PM +0800, li wrote:
> Dear all:
> NAMD provides pairinteration function to analyze the dcd file,but i need the total energy of the molecule i am interested in.After long time molecular dynamic simulation of one or more molecules in aqueous solution, How to get the energy profiles of only those molecule(not the energy of the whole system).
> If I have to create a new program for this purpose, a module to read coordinates of every frames from the dcd file is a must,I guess it exists already,where can i find it out?
> Any comments welcome !
> Thank in advance!
> --
> USTC Alumni Email System
>
> 

-- 
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