On Tue, Nov 24, 2009 at 13:01, Omer Markovitch <[email protected]> wrote: > > On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek <[email protected]> > wrote: >> >> Dear all, >> >> I would like to understand better the way g_rdf performs >> normalization. I have two unexpected results: >> >> 1) In a simple simulation of atomic ions in water in a cubic box, I >> get RDFs that clearly reach a constant value at large enough >> distances, but that value is somewhat lower than one. The simulation >> is NpT, could that be a problem for the normalization? >> > g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure > water.
Indeed. However, see also Berk's remark. It seems to match very well for my system. > >> >> 2) In a simulation in a dodecahedron, I get an unexpected decrease in >> the RDF at larger distances (for free ions in solution). Is there some >> know problem with normalization in triclinic cells? Is the RDF perhaps >> not truncated "soon" enough? > > Try calculating it for much larger distances, if you have PBC this should > not be a problem even with the current docecahedron. Maybe I am missing something, but the range that g_rdf considers is hardwired - half the smallest box length with PBC, 3x the largest one without PBC. Is there a way to include contributions from multiple images of the unit cell? BTW, if g_rdf really only considers the box edge lengths and disregards angles, it would make sense that normalization is broken in general cells at larger distances, no? Ondrej > --Omer. > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
