Re: Calculating Potential Energy for an atom selection

From: Axel Kohlmeyer (
Date: Fri Aug 17 2012 - 15:57:41 CDT

On Fri, Aug 17, 2012 at 10:49 PM, Aron Broom <> wrote:
> Hi,
> 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.

what the namdenergy plugin does is simply building custom input,
then run NAMD and grab the output. if you are a little proficient in
VMD scripting, it shouldn't be too difficult to either rip out the guts
of this procedure and make it work for your needs, or - even better -
add the hooks for what you need in addition.

> 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?

i don't see how this would work in a general NAMD run.
the Tcl scripting support in NAMD has a very different
design and purpose as to what VMD does.


> Thanks,
> ~Aron
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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