[gmx-users] residue-residue interaction energies

Justin Lemkul jalemkul at vt.edu
Sat Oct 6 04:54:43 CEST 2012

On 10/5/12 1:40 PM, federico vaglio wrote:
> Dear all,
> I would like to extract the interaction energies (LJ
> and electrostatic) between each residue pairs from my trajectory.
> The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
> LJ-SRemat.xpm, totalemat.xpm) but not a "data" file with
> the residue-residue interaction energies I'm looking for.
> Is there a way to get these numbers? Or have I to read the xpm "matrix" and
> convert all those letters to the corresponding energy values?

Yes, you have to map it out based on the .xpm labels.

> Finally, is there a way to get pairwise residue-residue interaction energy
> values from each snapshot of my trajectory ?

Probably by analyzing them individually with mdrun -rerun to recalculate each 
frame.  Tedious, but can be easily scripted.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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