[gmx-users] Energy Group Exclusions

Berk Hess gmx3 at hotmail.com
Wed May 17 09:49:30 CEST 2006

>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 
>using energy group exclusions (energygrp_exl = substrate substrate) in my 
>file. I get the following warning upon running grompp.
>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 
>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

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


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