[gmx-users] Sphericity

[Dallas Warren]

>1. I wonder how I can prove that the core part looks like a sphere? or how
>can I measure the Sphericity of the core part? Does Gromacs offer a tool
>for that?

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-gyrate.html

Then compare rx, ry, rz and/or eccentricity

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 Thu, 8 Nov 2018 at 02:59, Alex <alexanderwien2k at gmail.com> wrote:
>
> Dear all,
> I have two types of molecules (molecule number from each 56 and 29
> respectively) in water, the MD simulation gives me a core-shell like system
> in which the core part contain one of the molecule type and the shell is
> the another one that accumulate around the surface of the core.
>
> Regarding the system explained above I have below two questions on which
> your comments would be highly appreciated;
>
> 1. I wonder how I can prove that the core part looks like a sphere? or how
> can I measure the Sphericity of the core part? Does Gromacs offer a tool
> for that?
>
> 2. If am not wrong the gmx density gives the density only along the X or Y
> or Z direction, how I can calculate the density of each of the molecules in
> the core-shell system along radius of the sphere , r ?
>
> Thanks
> Alex
> P.S. Sorry, do not rely on the spelling auto-correction! :-)
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