[Chimera-users] surfaces

P. Buscemi busce004 at umn.edu
Wed May 31 03:25:56 PDT 2017


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 

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, May 25, 2017 11:24 AM
To: P. Buscemi
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] surfaces

Hi Paul,
Sorry, Chimera doesn’t have special handling (like wraparound display) for periodic boundary conditions.

The Molecular Dynamics Simulation tool does have a “Constraints Etc.” section.  All I know about it is in the documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#constraints>

Other programs may be better suited for simulating your system (faster, more options for solids or interfaces), although I don’t have specific suggestions.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

> On May 24, 2017, at 1:33 AM, P. Buscemi <busce004 at umn.edu> wrote:
> 
> Elaine,
> A conceptual question. 
> 
> I'm trying to work with surfaces - large flat surfaces that proteins 
> and polymers might adsorb. Think fibrinogen on medical devices.
> 
> Chimera does not seem to like large surfaces in box. IF a portion of 
> the surface slips outside the box, it goes to the other ( abnormal side).
> 
> Constraining a portion of the surface does not help. Constraining all of the
> surface has not been tried.   I'd like to use a box  to keep the solvent and
> protein local.  
> 
> Any suggestions on how to handle this, or point me to a URL ?  Can I 
> constrain only in two directions  perhaps ?  or use a box size 30,30, 
> infinite ?
> Best
> Paul Buscemi, Ph.D.





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