busce004 at umn.edu
Wed May 31 03:25:56 PDT 2017
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.
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
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:
Other programs may be better suited for simulating your system (faster, more options for solids or interfaces), although I don’t have specific suggestions.
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:
> 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 ?
> Paul Buscemi, Ph.D.
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