[gmx-users] using gmx density for making a radial density plot of a vesicle

[SRINIVAS MUSHNOORI]

Dear gromacs users,

I'm trying to make a radial density profile function (NOT an rdf) from the
center of my vesicle. I'm trying to use the following command:

gmx density -f vesicle.gro -o density.xvg -s vesicle.tpr -center

I want it to make a radial density profile from the center of mass of the
vesicle along an outward pointing radial vector. But the result I get with
the above command is incorrect, it appears as a monomodal bell curve. Since
it is a bilayered vesicle, it should be a bimodal distribution. I know that
this functionality exists for a flat bilayer along the normal vector to the
bilayer surface, but unsure how to do this for a spherical vesicle. Please
assist in helping me figure out what the right way to do this is?

Thanks!

Sincerely
Srinivas Mushnoori
Dept of Chemical and Biochemical Engineering
Rutgers University