[gmx-users] spatial distribution function

[Nguyen Hoang Phuong]

On Mon, 10 Mar 2003, Christoph Freudenberger wrote:

> Hi there,
>
> I would like to analyse SDF's from gromacs trjectories.
> AFAIK there is no SDF-tool provided in offical gromacs (yet)...
>
> Has anybody already done that and could give some tips/code?

you can expand the distribution function in term of spherical harmonics
(for linear molecule) or in term of the rotation matrix (for any
molecule). i.e., you separate the distance dependence and angles
dependence. For distance dependent part, you can use g_rdf. For the
angles dependent part, basically, you can do the same.

Reference: Journal of Chemical Physics 115, 7227-7234 (2001).

Hope it helps.

Phuong
>
> I figured the easiest way to write a tool would be to alter/extend
> the code for r_rdf.
> I this allowed? I mean would I violate the GPL by doing it?
> (reading tons of manuals is ok for me, but i hate this legal
> stuff ;-)
> Ok, I suppose this is no problem from the legal pov:
> Would you prefer another option (like -sdf 3d.dat) for the
> g_rdf tool or should I better write a standalone version
> (like g_sdf)?
>
> regards
> --
> Christoph Freudenberger
> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
>
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