[gmx-users] Fw: Radial Density Profile

[elham]

 Dear Dr. Dallas Warren,
Many thanks for your response. I calculated the radial distribution function of atoms on the surface of vesicles relative to the vesicle center of mass. I submitted my paper and the referees asked me to calculate the radial density profile instead of radial distribution function.I can plot the density profile versus X, Y and Z direction.My question is, how can I plot the density profile of an atom versus r?Best regards 



   ----- Forwarded Message ----- From: Dallas Warren <dallas.warren at monash.edu>To: GROMACS users <gmx-users at gromacs.org>; elham <e.ghaedsharaf at yahoo.com>Sent: Friday, November 29, 2019, 11:41:07 AM UTCSubject: Re: [gmx-users] Radial Density Profile
 You want to calculate the RDF between the center of mass of an appropriate group that will be at the center of the vesicle (probably the surfactant, or alkane chain of the surfactant, and need to ensure that you only have a single vesicle that perform the calculation on) to the center of mass of each surfactant head group (or a particular atom of the head group).  Below link will help with the selection syntax required.
http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Fri, 29 Nov 2019 at 20:52, elham <e.ghaedsharaf at yahoo.com> wrote:

Dear all, I am working on vesicle structure of surfactants in water. I want to calculate the radial density profile of surfactant headgroup atoms versus r. The head group atoms are located on the vesicle surface.How can I plot the radial density profile of headgroup atoms from the center of vesicle versus r ?
 Best regards
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