You want to calculate the RDF between the center of mass of an appropriate group that will be at the center of the vesicle (probably the surfactant, or alkane chain of the surfactant, and need to ensure that you only have a single vesicle that perform the calculation on) to the center of mass of each surfactant head group (or a particular atom of the head group). Below link will help with the selection syntax required.
http://manual.gromacs.org/documentation/current/onlinehelp/selections.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 29 Nov 2019 at 20:52, 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.
