[gmx-users] About Potential energy calculation

Justin Lemkul jalemkul at vt.edu
Tue May 7 00:33:36 CEST 2013

On 5/6/13 5:58 PM, jhon michael espinosa duran wrote:
> Hi all
> I am doing an NVE simulation of a protein immersed in water, and I want
> to keep track of  the potential energy in the protein. Do you know how can I do it?.
> I tried saving the energy of the protein ( the protein as an energy group) in the .edr file, but when I checked the file with g_energy, it does not give me the option of potential energy only for the protein, it  gives me the total potential energy.

The potential energy of a subset of atoms is not stored in the .edr file; only 
short-range nonbonded interactions can be decomposed by using energygrps.  There 
are a variety of reasons for doing so.  The easiest way to get the quantity you 
want is to use tpbconv create a .tpr file that contains only the protein and 
then re-calculate energies using mdrun -rerun on the existing trajectory.



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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