Thanks! Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a sufficiently large range?
2008/5/8 Berk Hess <[EMAIL PROTECTED]>: > Hi, > > The integrated rdf's never go to 1, since your box has corners which fall > out of a sphere. > The normalization should be ok. > Some time ago the normalization was slightly different, g_rdf normalized > with the number > of atoms - 1, if both groups were identical. I removed this in, I think, > 3.3.2. > > Berk. > > > > ------------------------------ > Date: Thu, 8 May 2008 15:18:47 +0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: g_rdf: normalization issues? > > > Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the > molecule); still, the integrated RDF values seem to deviate from what > ithey're supposed to be... > > 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>: > > Hi, > > I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in > water. What puzzles me is that sometimes in, e.g., two sequential runs, I > get two RDF's with one of them having *uniformly* larger values than the > other. Given the fact that the RDF should in principle be normalized, this > seems very strange. In fact, the intergrated values of RDFs that I get seem > smaller than 1*Rmax. How is this possible? Is this due to some finite box > size effect or something else that I'm unaware of? > > Best regards, Vasilii > > > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 gmx-users@gromacs.org http://www.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