[gmx-users] Re: energy group exclusions

[Sikandar Mashayak]

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...

On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak <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>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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>>
>
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