[gmx-users] g_rdf normalization

Berk Hess gmx3 at hotmail.com
Tue Sep 28 11:21:54 CEST 2010


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.


From: chees at nus.edu.sg
To: gmx-users at 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,


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