[gmx-users] Re: intramolecular LJ and Coulomb interactions

Justin A. Lemkul jalemkul at vt.edu
Sat Dec 5 22:03:34 CET 2009

Vitaly V. Chaban wrote:
> On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul <jalemkul at 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 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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