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).
-Justin
I would really appreciate any help.
Afsaneh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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