[gmx-developers] residue-residue interaction energies

aar2163 at columbia.edu aar2163 at columbia.edu
Fri Nov 15 23:49:27 CET 2013

This is the second time I try to post this, but the first apparently  
did not work. I apologize if you receive it twice.


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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