[gmx-users] GROMACS command for energy calculation

Justin Lemkul jalemkul at vt.edu
Sun Aug 26 23:09:34 CEST 2012

On 8/26/12 5:02 PM, Acoot Brett wrote:
> Dear All,
> After the production MD has been done, does GROMACS has a command which can calculate the interaction energy between any 2 residues in a frame of structure from the MD?

Assuming you have made proper use of energygrps in the .mdp file, you can 
extract nonbonded terms between these groups from the .edr file using g_energy. 
  If you have not set energygrps, you can create a new .tpr file and use mdrun 
-rerun to recalculate the energies from an existing trajectory or snapshot.



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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