Hi, My system is in the slab geometry; I have applied periodic boundary conditions along x and y, but none along z.
I frequently use the handy tool g_potential (using the -oc switch) to compute the (average) charge density (i.e., charge distribution or a "histogram of charges") along z for a particular group specified by an index file entry. Since the partial charges are discretely assigned to individual atoms, this means that the -oc switch of g_potential effectively gives me a sort of distribution of the atoms along z, although the units are charge density, of course. My question is, what if I have atoms with zero partial charge? Of course, such atoms do not contribute to the charge density. But what if I would still like to compute some sort of distribution of these atoms along z? One idea is to use g_traj to print all of the z-coordinates of a particular group over time to an .xvg file. Then, using a scripting language, I could "bin" the z-coordinates and then average over time. But is there already a Gromacs utility that does this? It seems that g_density, with the "-dens number" switch, may accomplish this. Is it true that the "-dens number" switch will lead to computation of the number density of _each_ atom which is specified in the index file entry? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
