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
--
========================================
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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