[Chimera-users] MD analysis of ion position

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 24 13:22:02 PST 2021

Thanks, I agree that CPPTRAJ is a great solution for analyzing trajectories.  Looks like it can read several formats:

In Chimera, if you can view your trajectory in the MD Movie tool, you can also use that tool to calculate and display an occupancy map.  I think that's essentially the same thing that Tom mentioned, a density map on a grid that can be viewed as isosurfaces.

MD Movie help, click "Occupancy Analysis" in the left hand links:

Occupancy analysis is also covered in the last section of this Chimera tutorial:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3 at utah.edu> wrote:
> 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/
> --tec3
> ________________________________________
> 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)
> 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

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