[gmx-users] Re: number denisty calculation

Dr. Vitaly Chaban vvchaban at gmail.com
Wed Feb 13 12:21:50 CET 2013

> hi all,
> i am trying to find the coordination number using the rdf between two chains
> in the system .my box contains two polymer chains with water molecules.i know
> integrating 4*pi*r*r*g(r)*rho between 0 to first minima of rdf will give
> coordination number .the first minima value i took from the rdf between two
> chains. but for value of rho what shall i use .is that total number of
> atoms/volume of box or number of atoms in the two chains/volume of box. i have
> a doubt whether to include number of solvent atoms to calculate the number
> density or not .kindly clarify this doubt
> --

I do not understand what "RHO" is in your formula. If you want
coordination number, just issue "g_rdf -cn"

If you need a coordination number between two chain (as a whole)
rather than between atoms constituting those chains, you will
re-normalize the resulting integer number, as I assume.

All needed "corrections" are applied by default by g_rdf.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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