[gmx-developers] residue-residue interaction energies

André Assunção S. T. Ribeiro aastr at yahoo.com.br
Fri Nov 15 22:41:25 CET 2013


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.

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