[gmx-users] Specificity

Alex alexanderwien2k at gmail.com
Wed Nov 7 16:50:55 CET 2018

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 specificity 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 ?


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