Hi Elham, In general to calculate the radial density profile of a droplet-like object one should do binning (histogram) in spherical coordinate along radius. That means you should define a series of shell each with thickness of dr and all centered on center of the vesicle. And then you could count how many atoms of your interest are withing each shell so that you would get something like \rho (r) at the end.
Regards, Salman On Fri, Nov 29, 2019 at 4:52 AM elham <e.ghaedsha...@yahoo.com> wrote: > Dear all, I am working on vesicle structure of surfactants in water. I > want to calculate the radial density profile of surfactant headgroup atoms > versus r. The head group atoms are located on the vesicle surface.How can I > plot the radial density profile of headgroup atoms from the center of > vesicle versus r ? > Best regards > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
