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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>If you expect a dilute homogeneous distribution and you make an rdf between<br>a group and itself, it should go to 1-1/N.<br></div>But for for instance liquid water it would go to 1, since the (N-1)/N molecules<br>can sample the whole volume minus the volume of one molecule.<br><br>Berk.<br><br><br><blockquote><hr id="EC_stopSpelling">Date: Thu, 8 May 2008 16:34:34 +0400<br>From: darth.vasya@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] Re: g_rdf: normalization issues?<br><br>Thanks!<br><br>Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a sufficiently large range?<br><br><div class="EC_gmail_quote">2008/5/8 Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>>:<br>
<blockquote class="EC_gmail_quote" style="padding-left: 1ex;">
<div><div style="text-align: left;">Hi,<br><br>The integrated rdf's never go to 1, since your box has corners which fall out of a sphere.<br>The normalization should be ok.<br>Some time ago the normalization was slightly different, g_rdf normalized with the number<br>
of atoms - 1, if both groups were identical. I removed this in, I think, <a href="http://3.3.2." target="_blank">3.3.2.</a><br><br>Berk.<br><br></div><br><br><blockquote><hr>Date: Thu, 8 May 2008 15:18:47 +0400<br>From: <a href="mailto:darth.vasya@gmail.com">darth.vasya@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] Re: g_rdf: normalization issues?<div><div></div><div class="EC_Wj3C7c"><br><br>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...<br>
<br><div>2008/5/8 Vasilii Artyukhov <<a href="mailto:darth.vasya@gmail.com">darth.vasya@gmail.com</a>>:<br>
<blockquote style="padding-left: 1ex;">Hi,<br><br>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 <i>uniformly</i> 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?<br>
<br>Best regards, Vasilii<br>
</blockquote></div><br>
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