[gmx-users] Radial Density Profile

[Dallas Warren]

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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