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@cgl.ucsf.edu] Sent: Thursday, May 25, 2017 11:24 AM To: P. Buscemi Cc: chimera-users@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#constra...> 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@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.