[Chimera-users] model recordings

P. Buscemi Ph.D. pbuscemi at q.com
Thu Jun 8 12:37:58 PDT 2017


Elaine,

I found that placing all the components into one file helps tremendously.  The video shows a droplet of water forming on PE along with adsorption  of PVP.  None of the disruption, seen sing separate files, was noted in several trials.

 I think Chimera is up to the task.

Paul

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, June 07, 2017 12:03 PM
To: P. Buscemi Ph.D.
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] model recordings

Dear Paul,
You may be stretching the program far beyond what it was intended to do.  You might want to ask on CCL.net what might be a more appropriate program to simulate your system.

I assume you are still using the Molecular Dynamics Simulation tool to actually calculate the trajectory, and then using the MD Movie tool to view and record it as a movie file.  Your description is very confusing because it melds these two separate things into one.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

The first tool (simulation) requires specifying which model to use.  One idea is that the water and the PE surface may be two different models, which isn’t handled by the tool.  Another idea is that the hand-positioning generated a few overlapping atoms which gives  extremely large forces that can make molecules explode.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



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