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.
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@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.
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#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@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.
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: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> I hope this helps, Elaine ---------- 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@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
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. Paul -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, May 31, 2017 2:12 PM To: P. Buscemi Cc: chimera-users@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: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> I hope this helps, Elaine ---------- 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@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
Not that I know of, sorry. Elaine
On May 31, 2017, at 2:57 PM, P. Buscemi <busce004@umn.edu> wrote:
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.
Paul
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Elaine Meng -
P. Buscemi