[Chimera-users] (no subject)

Thomas Cheatham tec3 at utah.edu
Wed Feb 24 13:06:55 PST 2021

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-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0

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/


From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of K Jan <10dunajkr at gmail.com>
Sent: Wednesday, February 24, 2021 1:53:36 PM
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] (no subject)


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.?


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