[gmx-users] Re: energy group exclusions

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 19 02:43:58 CEST 2011

On 4/18/2011 1:43 PM, Sikandar Mashayak wrote:
> 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?

The sets of atoms for energy groups and such exclusions are defined by 
the index groups, not molecules. See manual 7.3 and wherever it talks 
about groups in an early chapter.

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

Bonded interactions are unaffected, as you will see if you try it.


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