<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt"><div>Hi,</div><div><br></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;">I want to calculate inter-residue non-bonded interaction energies between all pairs of residues of a relatively large protein.</div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;">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.</div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;">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.</div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family:
HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;">Thanks.</div></div></body></html>