[gmx-users] Energy contribution of individual residues

Erik Marklund erik.marklund at chem.ox.ac.uk
Fri Jul 3 10:28:28 CEST 2015

Dear Seema,

You do not need to run the simulation anew, you can make use of mdrun -rerun, which uses an existing trajectory but a new tpr file, with new energy groups for instance.

That said, it is often impossible to decompose the energy exactly into separate contributions from, say, individual residues.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

> On 3 Jul 2015, at 05:50, Dr. Seema Mishra <seema_uoh at yahoo.com> wrote:
> Hello Gromacs users,
> I have run several 50 ns production runs using Gromacs. Can anyone tell me how to calculate interaction energy of indvidual protein residues with ligand? I had set energygrps as "Protein LIG" (LIG for ligand). I have gone through the archives, but these do not tell much and say that the results may not be accurate, and because of shortage of time, I cannot do the production run again with setting energygrps for individual residues. Do you happen to know any other good tool? 
> Thanks. ---
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