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.
[email protected] http://folding.bmc.uu.se
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