[gmx-users] Re: energy group exclusions

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 19 07:04:49 CEST 2011

On 4/19/2011 2:57 PM, Sikandar Mashayak wrote:
> so that means if I define a index group GRP and energy exclusion GRP 
> GRP then all the non-boned interactions between atoms belonging to GRP 
> group are excluded?

What does manual 7.3.19 say?


> On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     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.
>     Mark
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