[gmx-developers] Geometry-dependent (non-spherically symmetric) potentials
hess at sbc.su.se
hess at sbc.su.se
Tue Jan 11 17:55:43 CET 2011
> On 11/01/11 16:32, hess at sbc.su.se wrote:
>> 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? :)
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.
>>> While I understand that all non-bonded gmx potential shapes are
>>> 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!
>>> Massimo Sandal, Ph.D.
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-developers-request at gromacs.org.
> Massimo Sandal, Ph.D.
> gmx-developers mailing list
> gmx-developers at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
More information about the gromacs.org_gmx-developers