From: Sadegh Faramarzi Ganjabad (
Date: Tue Mar 22 2016 - 11:35:24 CDT


I have a trajectory of a micelle in a water box. For each frame, I want to
get center of mass (COM) of the micelle and calculate the density of water
molecules from (COM) to the sides of the water box. Does anybody know what
is the best way to do that? from what I learned from VMD mailing list, VMD
does not do the entire process. However, I was wondering whether somebody
has dealt with such an issue before.