[Chimera-users] surfaces

P. Buscemi busce004 at umn.edu
Wed May 31 14:57:26 PDT 2017

Thanks Elaine for all your help.

One small question.  Is there a way to stop a simulation without terminating the program as occurs by using  the command "stop" ?   You know,  in the rare event, things are not quite right.


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, May 31, 2017 2:12 PM
To: P. Buscemi
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] surfaces

Hi Paul,
Although I’ve done simulations in the past, I am not a simulations expert at this point, so for general MD questions you may want to consult other sources, ask on CCL.net, etc.   Reading the methods sections of reputable papers with simulations is another way to learn best practices. Generally people do some equilibration of the system before they start collecting data from the production run.  The purpose of the trajectory file is for viewing and analysis of what happened in that part of the simulation.

My understanding is that even if some atoms are constrained, they still exert forces.

The nc file is in the MMTK format, which is one of several formats that can be used as input to the trajectory-viewing tool, MD Movie. (menu Tools… MD/Ensemble Analysis… MD Movie) … click its Help button to see its documentation, or see the copy on our website:

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

> On May 31, 2017, at 3:25 AM, P. Buscemi <busce004 at umn.edu> wrote:
> Elaine,
> Thank you for the feedback.  As it turns out,  if I make a surface large enough and put everyone in a box (without periodic condition on ), the simulation is not bad.  I constrain the surface and assume that it is still "chemically" active while it is not permitted to move. i.e.  other molecules know the surface is there and its polarity , e.pot is still alive. ( correct ?  ).  
> I have saved the trajectory ( nc )  and restart files. I see that the restart is used for a production run.  Can I use the nc file to review the simulation later ? Or must  I save a series of pdb files.  What is the intended  purpose of the nc file and the "production run"
> Hope you had a great getaway weekend.
> Paul 

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