afsaneh maleki wrote:
Dear Justin,
I want to get energy per residue not time. if i use mdrun -rerun with
energygrps in md.mdp then g_energy i obtain enery per time not residue.
at last, i don't understand how to get Energy per residue .
As I said before, as an absolute, "energy per residue" is not a straightforward
term, and even if it was, likely has no physical meaning. The potential energy
function is complicated, depending upon the positions of all the particles in
the system; that is, nearby particles will interact via Coulombic and vdW
interactions, but you can't simply extract out either of these terms for any
specific residue. There are numerous useful posts in the list archive on
similar topics, for example:
http://lists.gromacs.org/pipermail/gmx-users/2007-October/030425.html
-Justin
Best wishes,
Afsaneh
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 <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
========================================
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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