[gmx-users] Fw: Radial Density Profile

[Dallas Warren]

Apologies for mis-reading your question.

You need to look at the definition of what radial distribution function
actually means and calculates, the atom density falls out of that.

What they are asking for is the atom density, p(r)local, as a function of
distance r from the center of the vesicle. You can do that from the radial
distribution function, g(r).

p(r)local = g(r) * p(bulk)

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 Sat, 30 Nov 2019 at 03:37, elham <e.ghaedsharaf at yahoo.com> wrote:

>  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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