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

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 12 03:10:40 CEST 2010

Quoting Jennifer Casey <jrcasey20 at gmail.com>:

> Hello,
> 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
> simulations.

You will have to rerun your simulations using a new .tpr file with the desired
energygrps defined.  The good news is that you simply have to rerun the
trajectory using mdrun -rerun, which is substantially faster than recalculating
the whole thing from scratch.


> Thanks in advance,
> Jennifer


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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