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

SRINIVAS MUSHNOORI scm177 at scarletmail.rutgers.edu
Wed Nov 22 17:57:19 CET 2017

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?


Srinivas Mushnoori
Dept of Chemical and Biochemical Engineering
Rutgers University

More information about the gromacs.org_gmx-users mailing list