[gmx-users] Re: energy group exclusions

[Mark Abraham]

On 4/20/2011 4:14 AM, Sikandar Mashayak wrote:
> I just did 2 tests in first I do md rerun with SOL SOL exclusions 
> along with PME option then I get forces on water atoms but in second 
> case when I use Cut-Off for electrostatic forces are zero... not sure 
> why PME introduces forces despite using energy exclusion group...

Because that's how PME works. Part of the electrostatic non-bonded 
contribution is done in reciprocal space, and that can't be readily 
decomposed into group-wise contributions.

Mark

> On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak 
> <symashayak at gmail.com <mailto:symashayak at gmail.com>> wrote:
>
>     Also, in the case of spc/e bulk water when I do md rerun with SOL
>     SOL exlcusion I see forces on water atoms, however I was expecting
>     it to be zero.
>
>
>     On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak
>     <symashayak at gmail.com <mailto:symashayak at gmail.com>> wrote:
>
>         Yes, 7.3.19 says that all non-nonbonded interactions are
>         excluded within energy_exclusion groups.
>
>         What I really trying is to get forces on water atoms only
>         because of water water interactions and I want force on
>         protein atoms to be zero, so I do md rerun with
>         energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also
>         remove any bond interaction information from .top file for
>         protein, but still I get force values on protein atoms. Not
>         sure whats going wrong?
>
>         thanks
>         sikandar
>
>
>         On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham
>         <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>             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?
>
>             Mark
>
>
>>             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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