[gmx-users] Normalization In RDF, GROMACS

Haiyang Zhao hzhao0203 at gmail.com
Tue Aug 5 21:49:06 CEST 2014

Hello Dear User,

I am confused about the normalization in the g_rdf command. It should be
noted that I understand the meaning of RDF but am not sure about the
definition of RDF in GROMACS in detail.

When I calculate the rdf of Hydrogen (HW) of water molecules around one
Oxygen (OW) of one water molecule, I do not want the normalized option, and
thus I use the -nonorm in g_rdf, which indicate that no Normalization is
conducted for volume and density.

I checked the results, namely the HW number distribution at different
radical distances (R), the minimum value is 500, which is quite
impossible.  What the meaning of these value? Are these value means the HW
numbers at different radical distance ? Additionally, all HW numbers are
integral times of 500.

In order to confirm this result, I normalize the data myself: dividing
these values by the volume of the shell layer (4*pi*R^2*dl) and the average
water density (33.4 N/nm^3). However, these calculated results is several
order higher than the normalized results by Gromacs with default -norm

Thanks in advance.


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