Re: extracting forces from dcd files

From: Peter Freddolino (
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
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.

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
> work: 480-727-0435
> fax: 480-727-8283
> **********************************************************************

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