mra_bu at yahoo.com
Tue Jan 31 11:15:13 CET 2012
----- Forwarded Message -----
From: mohammad agha <mra_bu at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Sent: Tuesday, January 31, 2012 11:56 AM
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.
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