[gmx-developers] Geometry-dependent (non-spherically symmetric) potentials

[hess at sbc.su.se]

> On 11/01/11 16:32, hess at sbc.su.se wrote:
>> Hi,
>>
>> Are these 3 particles completely independent or are two of the particles
>> somehow bound together?
>> In the latter case you could use and modify the generic charge group
>> inner loops.
>
> Latter case. Thanks for the suggestion -can you elaborate on this, just
> to help me understanding why and how this is a viable opportunity? :)
> thanks!
>
> m.
>

Atoms in the same charge group are kept sequential in all circumstances
in Gromacs, in particular they end up sequentially in the neighbor list.

When you set the env.var. GMX_NBLISTCG interaction are calculated
charge group wise with plain C code in src/gmxlib/nonbonded/nb_generic_cg.c.
So you will then have access to all 3 coordinates at once.

Berk

>> Berk
>>
>>> Hi,
>>>
>>> While I understand that all non-bonded gmx potential shapes are
>>> intended
>>> to be spherically symmetric, for a project of mine it would be helpful
>>> to be able to have a non-bonded pair potential which is
>>> geometry-dependent (that is, depending on the angle between 3 atoms).
>>>
>>> Has anything -official or unofficial- of this kind ever been attempted
>>> on Gromacs and, if yes, are there code examples to look at?
>>>
>>> Any kind of advice is welcome!
>>>
>>> thanks,
>>> Massimo
>>>
>>> --
>>> Massimo Sandal, Ph.D.
>>> http://devicerandom.org
>>> --
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>>
>
>
> --
> Massimo Sandal, Ph.D.
> http://devicerandom.org
> --
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