Re: [AMBER] Question about AMBER energy decomposition

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 4 Jul 2015 19:00:18 -0400

On Sat, Jul 4, 2015 at 9:41 AM, Lee-Ping Wang <leeping.stanford.edu> wrote:

> Thanks, Jason; I did something similar where I created a separate set of
> parameter files that zeros out the improper torsions; that allows me to
> isolate the improper torsion contribution to the energy. :)
>
> Since this was just for verifying the correctness of the AMBER-FB15
> parameter conversion, it didn't have to be efficient.
>

‚ÄčThat works equally well. On second thought, this could've been done
entirely within ParmEd (walk through the dihedrals, zero-out all impropers,
and pass the structure to either the sander API or OpenMM). You could do
the same thing with both the Gromacs and Amber representations.

Ah well -- an idea if you need to do something like this again, in any case.

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jul 04 2015 - 16:30:02 PDT
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