d(r) = (N/V)*g(r) Catch ya,
Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of mohammad agha Sent: Thursday, 2 February 2012 3:48 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf 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 <[email protected]<mailto:[email protected]>> To: Discussion list for GROMACS users <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected]<mailto:[email protected]> [mailto:[email protected]] On Behalf Of mohammad agha Sent: Tuesday, 31 January 2012 7:26 PM To: [email protected]<mailto:[email protected]> 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 -- gmx-users mailing list [email protected]<mailto:[email protected]> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]<mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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