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Hi,<br><br>If you have N molecules with total volume which is significantly less than the unit-cell,<br>as is the case for ions in solvent, the RDF of the N molecules againt themselves<br>will converge to (N-1)/N.<br><br>Berk<br><br>> Date: Tue, 24 Nov 2009 01:27:27 +0100<br>> From: ondrej.marsalek@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Normalization in g_rdf<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>> 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>> If these should work better than they do for me, I will of course<br>> check my simulations again. I would just like to check first if this<br>> is to be expected.<br>> <br>> Thanks,<br>> Ondrej<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 />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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