[gmx-users] Energy Group Exclusions

Bob Johnson robertjo at physics.upenn.edu
Tue May 16 21:08:02 CEST 2006

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.

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
Bob Johnson

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