From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 10 2008 - 17:05:18 CDT

Hi Irene,
if you run namd with one pairInteraction group instead of two, you'll
end up getting internal energies (including dihedrals), which you should
then be able to parse to pull out the dihedral energy. Please note that
pairInteractions may behave in slightly unintuitive ways if you are
calculating bonded interactions for only a subset of a segment; for
example, if you have a set of bonded atoms 1-2-3 and you use atoms 1 and
2 in the pair interaction group, you will end up getting energies for
both the 1-2 and 2-3 bonds. Similar logic extends to dihedrals. If you
want to have more fine grained control to measure a single dihedral
(rather than a dihedral energy for a chunk of your structure) you may
instead want to use vmd's measure energy command with bigdcd.
Best,
Peter

Irene Newhouse wrote:
> Using the sample config file at
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node42.html I've been able
> to compute interaction energies
> for a trajectory in batch mode. I'd like to do the analogous thing for
> dihedral energies of certain parts of my structure, but I'm not sure
> how to modify the sample config file appropriately - what do I use in
> place of the pairIneraction lines? I don't want to call the namdenergy
> plugin through VMD because my trajectories are too long to load into
> VMD - not enough memory per node.
>
> Thanks!
> Irene Newhouse
>
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