From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 20 2007 - 13:44:46 CDT
Hi Todd,
as long as you're just analyzing a normal run, you can use the
namdenergy plugin that is bundled with VMD to do this; you need to
define one group as your atom of interest, and the other as the rest of
the system (this is just a frontend for namd's builtin pair interaction
calculations: http://www.ks.uiuc.edu/Research/namd/2.6/ug/node38.html).
Note that while this is set up as postprocessing, it still does take
significant amounts of time because force evaluations have to be
performed. Also, external forces like tclforces will *not* be included;
this is just the forcefield interactions with other atoms.
Peter
Todd Trimble wrote:
> Hi,
>
> Can anyone tell me if it is possible to extract the force on a given
> atom from a dcd file? I can get the force from an actual run using a
> tcl forces script, but is there a way that I can use a script like this
> in an analysis of a dcd file? Thanks in advance,
>
> Todd
>
> **********************************************************************
> Dr. Todd M. Trimble
> Center for Applied Nanobioscience at the Biodesign Institute
> Arizona State University
>
> todd.trimble_at_asu.edu
> work: 480-727-0435
> fax: 480-727-8283
> **********************************************************************
>
>
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