The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________
From: Chimera-users on behalf of K Jan <10dunajkr@gmail.com>
Sent: Wednesday, February 24, 2021 1:53:36 PM
To: chimera-users@cgl.ucsf.edu
Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
