[gmx-developers] residue-residue interaction energies

aar2163 at columbia.edu aar2163 at columbia.edu
Sat Nov 16 04:02:22 CET 2013

Hi Mark,

Thanks for the reply. This energy decomposition will actually be part
of an automated analysis protocol which will be applied in a very large
number of cases, so I do not want to generate the edr files for all
possible pairs of residues and have the extra step of extracting  
averages from these files. I have already done the "script writing"  
approach and I think it is worth the effort to have this implemented  
in a faster way. Any further advice will be appreciated.

Thank you,

Quoting Mark Abraham <mark.j.abraham at gmail.com>:

> 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!
> Mark
> 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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