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<style>.hmmessage P{margin:0px;padding:0px}body.hmmessage{FONT-SIZE: 10pt;FONT-FAMILY:Tahoma}</style>Hi Berk, thanks for the answearing.<br><br>Here is my command line:<br><br>g_rdf -f file.xtc -s file.tpr -n index.ndx -com -rdf mol_com -xy<br><br>then i select 'Protein' as reference group and 'upper-leaf_&_P8' (just the P8 atoms from the upper-leaflet) in the 1 group option.<br><br>The value of the g_rdf at the half of the box is roughly 0.5 - 0.6<br><br>In the attachment is de g(r) that i got.<br><br>Thanks in advance!<br><hr>From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] periodic boundary conditions in g_rdf<br>Date: Mon, 3 Nov 2008 10:20:08 +0100<br><br><meta http-equiv="Content-Type" content="text/html; charset=unicode"><meta name="Generator" content="Microsoft SafeHTML"><style>.ExternalClass .EC_hmmessage P{padding:0px;}.ExternalClass body.EC_hmmessage{font-size:10pt;font-family:Tahoma;}</style><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_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><style>.ExternalClass .EC_hmmessage P{padding:0px;}.ExternalClass body.EC_hmmessage{font-size:10pt;font-family:Tahoma;}</style><br><style>.ExternalClass .EC_hmmessage P{padding:0px;}</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><br><hr>Conoce el perfil completo de todos tus amigos de Windows Live Messenger justo aquí: <a href="http://home.services.spaces.live.com/" target="_blank">Windows Live Spaces</a><br><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a><br /><hr />Conoce el perfil completo de todos tus amigos de Windows Live Messenger justo aquí: <a href='http://home.services.spaces.live.com/' target='_new'>Windows Live Spaces</a></body>
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