[gmx-users] Selecting specific atoms to find average energy of

Jennifer Casey jrcasey20 at gmail.com
Fri Jun 11 23:34:26 CEST 2010


I ran an md simulation, and I have graphed the total average energy of the
system by using g_energy to convert my binary .edr file into a text based
file.  What I want to do is to find the average energy between the solvent
molecules, excluding the energy between the solute-solvent molecules and the
solute-solute molecules.  I was unable to find a way to have g_energy give
me the energy between a specific group.  Is it possible to do this?  Or do I
need to rerun the simulation, and include something like energy monitor
groups?  There is probably a simple command for this that I am missing (or
at least I hope there is).  I would prefer not to have to rerun all of my md

Thanks in advance,
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