Calculating Potential Energy for an atom selection

From: Aron Broom (
Date: Fri Aug 17 2012 - 15:49:38 CDT


I'd like to pull out the standard energy terms VDW, Elect, etc.. for a
selection of atoms during a simulation. I initially thought this should be
a simple task, but perhaps not? I see there is an NAMD energy plugin for
VMD, but this doesn't suit my needs because I'm interested in running
Generalized Born implicit solvent calculations, and it doesn't appear to
currently support this, so the Born and SASA contributions to the Elect
energy would be missing.

I thought there might be a simple Tcl method of scripting this into an NAMD
run, but I can't figure out how that might be done based on the command
options I'm seeing. Is something like this possible at the moment in a
simple manner, or would I need to look at either adding it to the NAMD
source, or more simply, trying to get the Generalized Born contributions
added to the NAMD Energy plugin?



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:55 CST