[gmx-users] Re: energy group exclusions

Sikandar Mashayak symashayak at gmail.com
Mon Apr 18 05:43:19 CEST 2011

Also, what about non-bonded interactions within the protein? Does exclusion
group only exclude the non-bonded interactions between two different
molecules and non-bonded interactions within the single molecule atoms are
still computed?

On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak <symashayak at gmail.com>wrote:

> Hi
> When we define energy group exclusions e.g. like in manual energygrp excl
> = Protein Protein SOL SOL
> and do md rerun, then only non-bonded interactions between Protein and SOL
> are computed. I am wondering what happens to bonded interactions within the
> protein, do they contribute to energies even though we have excluded
> protein-protein interactions?
> thanks
> sikandar
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