Vitaly V. Chaban wrote:
On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Vitaly V. Chaban wrote:
Hi,
Is there a way to output only intramolecular interaction (LJ and
Coulomb but not bond, angle, etc) energies (with a respect of
exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in
g_energy include all interaction, both inter- and intramolecular ones.
Use energygrps in the .mdp file.
-Justin
This will evidently work with one molecule. One group (MOL) contains
the atoms of one molecule and then one calculates MOL-MOL interactions
with g_energy. Is there no automatic way to perform such
calculations with all molecules in the system? Maybe it's not
principal as the single molecule intramolecular energies should be
very close...
To get the intermolecular energies decomposed among many species, you would
still use energygrps, but if you have many species, the .edr file can
potentially get very large since the intermolecular interactions are then
calculated for each pair of energygrps, unless you use energygrp_excl.
-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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