[gmx-users] Energy Group Exclusions

[Berk Hess]

>From: Bob Johnson <robertjo at physics.upenn.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: GROMACS Mailing List <gmx-users at gromacs.org>
>Subject: [gmx-users] Energy Group Exclusions
>Date: Tue, 16 May 2006 15:08:02 -0400
>
>Hello everyone,
>I'm simulating a nanotube on a substrate. My substrate is just a simple
>impenetrable wall of closely packed atoms. To restrict the substrate to a
>planar geometry I am using position restraints on substrate atoms as well 
>as
>using energy group exclusions (energygrp_exl = substrate substrate) in my 
>input
>file. I get the following warning upon running grompp.
>
>WARNING:
>Can not exclude the lattice Coulomb energy between energy groups
>
>The substrate atoms are uncharged and only have the C12 value defined in my
>topology file. Is this warning generated by default when using any kind of
>energy group exclusions whatsoever? It's obvious to me that if my substrate 
>were
>charged it would also contribute to the PME calculation. Thus, the Coulomb
>energy of the substrate would be impossible to get rid of. Is my thinking
>correct?

Yes.
We didn't go through the effort of writing code that would check
if all the particles in an excluded group are uncharged.

Berk.