[gmx-users] g_rdf -com

[David van der Spoel]

On 2011-11-27 12:27, mohammad agha wrote:
> Dear Prof.
>
> I have a question about g_rdf.
> I have a box consists of 500 surfactants that make 10 micelle. I want to
> compute rdf for surfactant relative to the center of mass of micelle.
> When I do g_rdf, the program ask me 2 groups that the first one is COM,
> but it is COM of molecules that I defined in index file.
> If I select the surfactant molecules as the first group for COM, this
> means the COM of micelle or just surfactants?
> If it select just COM of surfactants, then what do I do for selection of
> COM of micelle?
> Please help me.
>
> Best Regards
> Sara
>
>
you first have to define which surfactants belong together before g_rdf 
can do this - make an appropriate index file, maybe g_clustsize can help.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se