[gmx-users] g_rdf

mohammad agha mra_bu at yahoo.com
Wed Feb 1 17:48:09 CET 2012

Dear Prof.

Thank you very much from your reply.
Is your mean that "density=(N/V)*g(r)", where N is the number of total atoms in box not in the shell and V is the volume of box not in the shell?

Best Regards

 From: Dallas Warren <Dallas.Warren at monash.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, February 1, 2012 2:12 AM
Subject: RE: [gmx-users] g_rdf

An RDF is normalised to the density for the entire box, so you should simply be using that.
Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.
From:gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of mohammad agha
Sent: Tuesday, 31 January 2012 7:26 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] g_rdf
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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