Hi Berk, thanks for the answearing. Here is my command line:
g_rdf -f file.xtc -s file.tpr -n index.ndx -com -rdf mol_com -xy then i select 'Protein' as reference group and 'upper-leaf_&_P8' (just the P8 atoms from the upper-leaflet) in the 1 group option. The value of the g_rdf at the half of the box is roughly 0.5 - 0.6 In the attachment is de g(r) that i got. Thanks in advance! From: [EMAIL PROTECTED] To: [email protected] Subject: RE: [gmx-users] periodic boundary conditions in g_rdf Date: Mon, 3 Nov 2008 10:20:08 +0100 Hi, To what value does your rdf go then? You have pbc in your system, so running with -nopbc is incorrect. The rdf will then stop at half the box, since you molecules are in the box and your peptide is probably in the middle, leading to a longest distance of roughly half the box. Berk From: [EMAIL PROTECTED] To: [email protected] Date: Fri, 31 Oct 2008 16:55:54 -0600 Subject: [gmx-users] periodic boundary conditions in g_rdf Hi everybody. 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. Any help will be appreciated. Thanks in advance. Conoce el perfil completo de todos tus amigos de Windows Live Messenger justo aquí: Windows Live Spaces Express yourself instantly with MSN Messenger! MSN Messenger _________________________________________________________________ Live Search premia tus búsquedas, llévate hasta ¡Un Auto! http://www.ganabuscando.com/Default.aspx
<<attachment: gdr_upperleaf_and_P8-COM_Prot.png>>
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