[gmx-users] g_rdf -com

mohammad agha mra_bu at yahoo.com
Mon Nov 28 11:29:47 CET 2011

Dear Prof. Spoel

Thanks for your reply. 

I used g_clustsize and after it, I used g_rdf but it is not true, because the plot of g(r) for tails of surfactants relative to COM of micelle starts from 0 but it is not true!

Best Regards

 From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, November 27, 2011 3:08 PM
Subject: Re: [gmx-users] g_rdf -com
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
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