Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density?
On Mon, May 18, 2015 at 11:25 AM, mah maz <mahma...@gmail.com> wrote: > Hi Justin > The fact is I want to calculate water density in the system. If I select > group1: oxygen and group2: oxygen, g_rdf command gives me very large > numbers. Is it the number of atoms that should be changed to g/cm3? > Besides, what does it calculate, each O is a reference atom during > calculation? > Thanks a lot! > > On Sun, May 17, 2015 at 2:17 PM, mah maz <mahma...@gmail.com> wrote: > >> Dear all, >> I want to calculate the radial distribution function of water molecules >> in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers >> which is not logical I suppose. Is it meaningful if I separate oxygen and >> hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is >> reference atom necessary to get RDF? >> Thanks! >> > > -- 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.
