[gmx-developers] residue-residue interaction energies

Mark Abraham mark.j.abraham at gmail.com
Sat Nov 16 01:26:26 CET 2013

Scripting writing an .mdp file, running grompp, running mdrun -rerun,
running gmxdump (or whatever) on the resulting .edr or .log file will solve
your problem a hundred times faster than trying to extend the number of
energy groups in mdrun. Whether that energy decomposition has a physical
interpretation and this method will measure it is another thing!


On Fri, Nov 15, 2013 at 11:49 PM, <aar2163 at columbia.edu> wrote:

> This is the second time I try to post this, but the first apparently did
> not work. I apologize if you receive it twice.
> Hi,
> I want to calculate inter-residue non-bonded interaction energies between
> all pairs of residues of a relatively large protein.
> Since most of these will be zero and I just want average values, I do not
> want to write the information to edr files. Furthermore, there seems to be
> a limit on the number of energygrps allowed.
> I'm going through the code of version 4.6.3 to try to make modifications
> that solve my problem. My plan would be to have grompp accept an arbitrary
> number of energygrps and mdrun -rerun store the values in a NxN matrix and
> print non-zero averages to a custom output file. Any help on where to look
> to accomplish any of this would be very welcome.
> Thanks.
> Andre.
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