[gmx-users] Re: energy group exclusions

[Sikandar Mashayak]

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>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>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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>
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