[gmx-users] probability from COM of micelle

mohammad agha mra_bu at yahoo.com
Fri May 10 06:45:10 CEST 2013

Dear GROMACS Specialists,

Thank you very much from your answer, but I want to know plotting this curve from g_rdf.
May I ask you to give me one formula by this command, Please?

Best Regards

On 2013-05-09 20:15, Justin Lemkul wrote:
> On 5/9/13 10:15 AM, mohammad agha wrote:
>> Dear GROMACS Specialist,
>> I want to plot probability (nm^-1) distribution of micelle selected
>> atoms with respect to COM of the micelle (nm).
>> with respect to this definition, "Probability was defined as the
>> number of instances the selected atom was found within a spherical
>> shell of width 0.02 nm at a distance r from the micelle COM divided by
>> r", may I ask you to give me one formula to plot of this probability,
>> Please?
>> for example, to plot of density(nm^-3) with respect to COM of micelle
>> (nm), I do as following:
>> density = g(r) * (N/V)
> It sounds like all you need to do is create a histogram from data
> produced by g_dist.  You can make the histogram with g_analyze or any
> number of other programs.
> -Justin
How about g_rdf?

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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