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

[Vitaly V. Chaban]

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...