[gmx-users] g_rdf

mohammad agha mra_bu at yahoo.com
Tue Jan 31 09:26:07 CET 2012

Dear Prof.

I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf. Then I count the number of atoms in the shells around the COM of special group by " trjorder -com -nshell -r " , next I use from this formula for compute the density:
density = (dN/4*pi*dr*r^2)*g(r), where dN, dr, r and g(r) are the number of atoms in each shell, wide of shell, radius of COM of special group, and averaged RDF in each shell, respectively.
While the plot of g(r) is consistent with published previous results but density has not consistence with them, I think that I am wrong in compute the density.
Please help me.

Best Regards
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