[gmx-users] GROMACS command for energy calculation

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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