[gmx-users] g_rdf normalization

Enemark Soeren chees at nus.edu.sg
Tue Sep 28 10:38:58 CEST 2010

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,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100928/9e2ec539/attachment.html>

More information about the gromacs.org_gmx-users mailing list