<div dir="ltr">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!<div>
<br></div><div>Mark</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 15, 2013 at 11:49 PM, <span dir="ltr"><<a href="mailto:aar2163@columbia.edu" target="_blank">aar2163@columbia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">This is the second time I try to post this, but the first apparently did not work. I apologize if you receive it twice.<br>
<br>
Hi,<br>
<br>
I want to calculate inter-residue non-bonded interaction energies between all pairs of residues of a relatively large protein.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Thanks.<br>
<br>
Andre.<span class="HOEnZb"><font color="#888888"><br>
<br>
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