[gmx-users] residue-residue specific energy plots

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 22 23:51:28 CEST 2009

Jonathan Reyles wrote:
> Is there any utility/tool out there that can take an outputted GROMACS
> trajectory, and output the energies (electric potential, VDW, etc.) of
> all residue-residue specific interactions as a function of time?  The
> g_energy utility does not give me the data I want, and it will not
> even allow you to index and compare two residues.

You can if you utilize energygrps in the .mdp file, listing all of the residues 
of interest.  This will, naturally, make the .edr file enormous, but you can 
then extract any or all of these residue-residue pairs using g_energy.


> Thanks,
> Jon
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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