Hi, g_rdf -surf mol counts the number of atoms within a distance r from the surface, i.e. the atoms which have a distance of less than r to the closest atom of the molecule. Since the surface can be complex and dynamic, normalization is difficult.
Berk From: ch...@nus.edu.sg To: gmx-users@gromacs.org Date: Tue, 28 Sep 2010 16:38:58 +0800 Subject: [gmx-users] g_rdf normalization Dear fellow Gromacs users Does anyone know how the “–surf mol” option works? I am trying to calculate the coordination number for a molecule in a slice (xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the integration of the RDF function if I use the center-of-mass option (-rdf mol_com), but I am more interested in calculating the coordination number with respect to the molecular surface. I have tried to use the “–surf mol” option together with “–cn “, and I get what I expected to get, namely N=2. However, when I import the rdf in Excel and do the integration, I get N=1. I should add that I have seen from the manual that the “-surf” option means that normalization cannot be used. Hence, in my calculations I do not normalize the integral with V/N. Does anyone have any suggestions? Best regards, Soren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
