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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>To what value does your rdf go then?<br><br>You have pbc in your system, so running with -nopbc is incorrect.<br>The rdf will then stop at half the box, since you molecules are in the box<br>and your peptide is probably in the middle, leading to a longest distance<br>of roughly half the box.<br><br>Berk<br></div><br><br><br><hr id="EC_stopSpelling">From: ilhan_eins@live.com.mx<br>To: gmx-users@gromacs.org<br>Date: Fri, 31 Oct 2008 16:55:54 -0600<br>Subject: [gmx-users] periodic boundary conditions in g_rdf<br><br>
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</style>Hi everybody.<br>I'm working a system with a peptide embedded in a lipid bilayer and I try to get the two-dimentional g_rdf for the upper leaflet around the peptide with the -xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a used -nopbc i get almost the same result (just multiplied by a constant) and the RDF is always cutted at the half of size of the box.<br><br>Any help will be appreciated.<br><br>Thanks in advance.<br><br><a href="http://skydrive.live.com" target="_blank"></a>
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