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
Sara
________________________________
From: Dallas Warren <dallas.war...@monash.edu>
To: Discussion list for GROMACS users <gmx-users@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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Tuesday, 31 January 2012 7:26 PM
To: gmx-users@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
Sara
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