[gmx-users] Energy per residue

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 12 19:20:01 CET 2010

afsaneh maleki wrote:
> Dear gromacs users,
> Is there a way to get energy values (Vdw,..) per residue at the end of 
> MD prosses?

Yes and no.  You won't be able to get, for instance, the absolute van der Waals 
energy of a residue.  That doesn't really make any sense, since vdW interactions 
take place between particles.  There may be some 1-4 type interactions within a 
residue that you could quantify, but not much else.

You can decompose short-range residue-residue energies using energygrps in the 
.mdp file, and re-running the trajectory with the new .tpr file (mdrun -rerun), 
but the .edr file can quickly get out of hand in terms of disk usage, depending 
on how many groups you have (since you will then have essentially N^2 energy 
terms to write out, where N is the number of energygrps).


> I would really appreciate any help.
> Afsaneh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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