Re: [gmx-users] Fw: probability from COM of micelle
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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fw: probability from COM of micelle
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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
