[gmx-users] Re: energy group exclusions

[Sikandar Mashayak]

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?

On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham <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
> > 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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