[gmx-developers] Morse as non bonded (?)

[David van der Spoel]

Marcelo A. Carignano wrote:
> Salut,
> 
> Morse potentials are implemented in gromacs as a bond type.
> However, the potential has the interesting feature that allows an
> independent control
> of the depth, core size and range of the interactions (I need something
> like that).
> Therefore, using Morse potential as non-bonding will be useful for me,
> and possible others.
> 
> The question is how difficult would be to modify the code, using as base
> the Morse code
> for bonds, to write a Morse code for non-bonding. I am willing to
> attempt this, if I get some
> general indications (I can use also very detailed indications) from
> those of you who know
> the code with sufficient detail to provide some advise.
> 
> I know that I can use the tables, but that is not the solution I am
> looking for.
Why not? It is very efficient (much more efficient than analytical 
code). The bonded Morse code is quite simple (src/gmxlib/bondfree.c). 
There is also a generic nonbonded kernel (in C) for you to play with in 
src/gmxlib/nonbonded/nb_generic.c.

The real interesting thing in my opinion would be to have non-bonded 
three-body interactions...

> 
> Many thanks,
> 
> Marcelo Carignano
> --
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se