[gmx-users] Re: energy group exclusions

[Sikandar Mashayak]

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>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>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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