[Chimera-users] model recordings

pbuscemi pbuscemi at q.com
Wed Jun 7 11:23:48 PDT 2017


Thanks Elaine,

Your assumptions were correct..and I apologize for the poor description.

  If I were to open the two files as two models - surface and water - and select only water to run the simulation ( only water is active ) would the water  know the surface was present ?

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




> On Jun 6, 2017, at 5:42 PM, P. Buscemi Ph.D. <pbuscemi at q.com> wrote:
> 
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> Dear Users groups.
>  
> I’ve been struggling  with this issue for some weeks.  I will describe the problem and then as what information I should supply to help me solve the issue.
>  
> It’s a prototype adsorption experiment. Water onto polyethylene oxide.  Each component, when run individually in a simulation will complete in a normal fashion with a good recorded video. All simulations were run with live presentation.   However when the two models are run together, the story is different.
>  
> The sequence below represents 1) the two loaded files ( water and PEO)  2) the PEO selected for later constraint  ( control drag)  3) moving the water into positon.  At this state the “ live”  simulation aappears normal.  The peo does not move, and the water more or less jiggles into position on the PEO.  However, in running the movie,  molecules of the PEO are disrupted (4)  and occupy the space in fragments  originally occupied by the water molecules when it was first loaded.  The same phenomenon occurs with a PE surface and with models of EtOH.  
>  
> The temperature is set to 0->100K,  Hydrogents added Gasteiger charge calculation, 0 charge total, no periodic box.  Again, I do not expect any suggestions ( although none would be refused !) only to ask the proper channels and information needed to approach the issue.
>  
> Regards
> Paul Buscemi
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