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Hi,<br><br>g_rdf limits the distance to half the minimum periodic image distance.<br>So the volume normalization is always simply 4 pi r^2.<br>It uses the starting unit-cell with a factor of 0.99.<br>So you would only see strange effects when the box length reduces<br>more than 1% due to pressure coupling.<br><br>Berk<br><br>> Date: Tue, 24 Nov 2009 13:23:30 +0100<br>> Subject: Re: [gmx-users] Normalization in g_rdf<br>> From: ondrej.marsalek@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> On Tue, Nov 24, 2009 at 13:01, Omer Markovitch <omermar@gmail.com> wrote:<br>> ><br>> > On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek <ondrej.marsalek@gmail.com><br>> > wrote:<br>> >><br>> >> Dear all,<br>> >><br>> >> I would like to understand better the way g_rdf performs<br>> >> normalization. I have two unexpected results:<br>> >><br>> >> 1) In a simple simulation of atomic ions in water in a cubic box, I<br>> >> get RDFs that clearly reach a constant value at large enough<br>> >> distances, but that value is somewhat lower than one. The simulation<br>> >> is NpT, could that be a problem for the normalization?<br>> >><br>> > g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure<br>> > water.<br>> <br>> Indeed. However, see also Berk's remark. It seems to match very well<br>> for my system.<br>> <br>> ><br>> >><br>> >> 2) In a simulation in a dodecahedron, I get an unexpected decrease in<br>> >> the RDF at larger distances (for free ions in solution). Is there some<br>> >> know problem with normalization in triclinic cells? Is the RDF perhaps<br>> >> not truncated "soon" enough?<br>> ><br>> > Try calculating it for much larger distances, if you have PBC this should<br>> > not be a problem even with the current docecahedron.<br>> <br>> Maybe I am missing something, but the range that g_rdf considers is<br>> hardwired - half the smallest box length with PBC, 3x the largest one<br>> without PBC. Is there a way to include contributions from multiple<br>> images of the unit cell?<br>> <br>> BTW, if g_rdf really only considers the box edge lengths and<br>> disregards angles, it would make sense that normalization is broken in<br>> general cells at larger distances, no?<br>> <br>> Ondrej<br>> <br>> <br>> > --Omer.<br>> ><br>> ><br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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