Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x.
Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland bstrickland@drew.edu wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc http://heating.nc/ files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland bstrickland@drew.edu wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Sorry, I'm kind of stumped. This does not happen for me. When I run solvated MD on 2gbp, it uses all of my cores (4) for all phases of the computation. Also, the trajectory updates continuously. You should be aware that the frame-to-frame motion is very slow and easy to miss -- though once bonds start crossing the periodic box it becomes more obvious as the long cross-box bonds appear and disappear every half-dozen frames or so.
Not sure why things would behave differently on your machine.
--Eric
On Jun 29, 2020, at 11:05 AM, Benjamin Strickland bstrickland@drew.edu wrote:
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland <bstrickland@drew.edu mailto:bstrickland@drew.edu> wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc http://heating.nc/ files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I will give it another try, perhaps I set something up incorrectly? But when saving in "MMTK updating coordinates" for example definitely only one core is being utilized
Regards, Benjamin
On Tue, Jun 30, 2020, 6:11 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Sorry, I'm kind of stumped. This does not happen for me. When I run solvated MD on 2gbp, it uses all of my cores (4) for all phases of the computation. Also, the trajectory updates continuously. You should be aware that the frame-to-frame motion is very slow and easy to miss -- though once bonds start crossing the periodic box it becomes more obvious as the long cross-box bonds appear and disappear every half-dozen frames or so.
Not sure why things would behave differently on your machine.
--Eric
On Jun 29, 2020, at 11:05 AM, Benjamin Strickland bstrickland@drew.edu wrote:
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland bstrickland@drew.edu wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
After it finishes actually computing the trajectory, there is a period of time where it only uses one CPU as it brings up the Movie dialog and finishes writing the trajectory files. This period of time can actually be awhile if you computed many trajectory steps.
--Eric
On Jun 30, 2020, at 9:55 PM, Benjamin Strickland bstrickland@drew.edu wrote:
I will give it another try, perhaps I set something up incorrectly? But when saving in "MMTK updating coordinates" for example definitely only one core is being utilized
Regards, Benjamin
On Tue, Jun 30, 2020, 6:11 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Sorry, I'm kind of stumped. This does not happen for me. When I run solvated MD on 2gbp, it uses all of my cores (4) for all phases of the computation. Also, the trajectory updates continuously. You should be aware that the frame-to-frame motion is very slow and easy to miss -- though once bonds start crossing the periodic box it becomes more obvious as the long cross-box bonds appear and disappear every half-dozen frames or so.
Not sure why things would behave differently on your machine.
--Eric
On Jun 29, 2020, at 11:05 AM, Benjamin Strickland <bstrickland@drew.edu mailto:bstrickland@drew.edu> wrote:
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland <bstrickland@drew.edu mailto:bstrickland@drew.edu> wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc http://heating.nc/ files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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I still believe something is weird with the calculation, this is only a single molecule and I left it overnight and it still did not finish updating, yet the actual minimization step in the beginning took approx. 30 seconds to compute. I attached a screenshot of where the program appears to hang up down below.
Regards, Benjamin
On Wed, Jul 1, 2020 at 12:20 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
After it finishes actually computing the trajectory, there is a period of time where it only uses one CPU as it brings up the Movie dialog and finishes writing the trajectory files. This period of time can actually be awhile if you computed many trajectory steps.
--Eric
On Jun 30, 2020, at 9:55 PM, Benjamin Strickland bstrickland@drew.edu wrote:
I will give it another try, perhaps I set something up incorrectly? But when saving in "MMTK updating coordinates" for example definitely only one core is being utilized
Regards, Benjamin
On Tue, Jun 30, 2020, 6:11 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Sorry, I'm kind of stumped. This does not happen for me. When I run solvated MD on 2gbp, it uses all of my cores (4) for all phases of the computation. Also, the trajectory updates continuously. You should be aware that the frame-to-frame motion is very slow and easy to miss -- though once bonds start crossing the periodic box it becomes more obvious as the long cross-box bonds appear and disappear every half-dozen frames or so.
Not sure why things would behave differently on your machine.
--Eric
On Jun 29, 2020, at 11:05 AM, Benjamin Strickland bstrickland@drew.edu wrote:
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland bstrickland@drew.edu wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Okay, sorry, but long bonds like that are not in the least bit normal. You need to use Help→Report A Bug to submit a bug report and attach the structure file of the compound you are running MD on. We can go from there.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 1, 2020, at 1:12 PM, Benjamin Strickland bstrickland@drew.edu wrote:
I still believe something is weird with the calculation, this is only a single molecule and I left it overnight and it still did not finish updating, yet the actual minimization step in the beginning took approx. 30 seconds to compute. I attached a screenshot of where the program appears to hang up down below.
Regards, Benjamin
On Wed, Jul 1, 2020 at 12:20 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: After it finishes actually computing the trajectory, there is a period of time where it only uses one CPU as it brings up the Movie dialog and finishes writing the trajectory files. This period of time can actually be awhile if you computed many trajectory steps.
--Eric
On Jun 30, 2020, at 9:55 PM, Benjamin Strickland <bstrickland@drew.edu mailto:bstrickland@drew.edu> wrote:
I will give it another try, perhaps I set something up incorrectly? But when saving in "MMTK updating coordinates" for example definitely only one core is being utilized
Regards, Benjamin
On Tue, Jun 30, 2020, 6:11 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Sorry, I'm kind of stumped. This does not happen for me. When I run solvated MD on 2gbp, it uses all of my cores (4) for all phases of the computation. Also, the trajectory updates continuously. You should be aware that the frame-to-frame motion is very slow and easy to miss -- though once bonds start crossing the periodic box it becomes more obvious as the long cross-box bonds appear and disappear every half-dozen frames or so.
Not sure why things would behave differently on your machine.
--Eric
On Jun 29, 2020, at 11:05 AM, Benjamin Strickland <bstrickland@drew.edu mailto:bstrickland@drew.edu> wrote:
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland <bstrickland@drew.edu mailto:bstrickland@drew.edu> wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc http://heating.nc/ files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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<Annotation 2020-07-01 160814.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear help: In running an MD on an aromatic dipeptide from Chimera installed on my Mac, the minimization step within the Run Parameters does not add required Hs even though that option is checked, resulting in a n equilibration error message re missing Hs. However, if I choose to minimize outside of MD simulation (Tools—> structure editing—> minimize structure), Hs are successfully added, and are visible on the model. Returning to MD simulation, I am able to proceed to equilibration and production successfully. Laura J Sent from my iPad
On Jun 30, 2020, at 6:12 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
CAUTION: This email is from outside BC, so examine it closely before opening attachments or clicking on links
Sorry, I'm kind of stumped. This does not happen for me. When I run solvated MD on 2gbp, it uses all of my cores (4) for all phases of the computation. Also, the trajectory updates continuously. You should be aware that the frame-to-frame motion is very slow and easy to miss -- though once bonds start crossing the periodic box it becomes more obvious as the long cross-box bonds appear and disappear every half-dozen frames or so.
Not sure why things would behave differently on your machine.
--Eric
On Jun 29, 2020, at 11:05 AM, Benjamin Strickland <bstrickland@drew.edumailto:bstrickland@drew.edu> wrote:
Thank you for the quick response!
I have 24 cores on the CPU and selected the multi CPU option. Running the initial minimization and heating of a ligand molecule took approximately 20minutes and all cores were used after which the molecule became a mess of lines which I read is normal and is representative of the moved atoms? However, after this point it appears the software is only using one core on the CPU rather then all 24.
Additionally despite checking live trajectory I do not see the image updating only the final mess of lines image.
Regards, Benjamin
On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen <pett@cgl.ucsf.edumailto:pett@cgl.ucsf.edu> wrote: Hi Benjamin, MD calculation is a slow process, particularly for a large solvated system. If you want visual feedback as the calculation progresses, check the "Live trajectory" box in the "other runtime options" setting under the "Run Parameters" tab. To speed things (assuming you have multiple CPUs) you should also check the "Use multiple CPUs" box on that same page.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2020, at 9:49 PM, Benjamin Strickland <bstrickland@drew.edumailto:bstrickland@drew.edu> wrote:
Hello,
I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nchttp://heating.nc/ files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi Laura, You would need to use menu: Help... Report a Bug and attach the specific structure or a session file, so we could try to reproduce the problem. If we can't reproduce it, it is unlikely we could do anything about it! Also it would be great if you did that when you got the error, because then the report would include the error. There is a "Report Bug" button on the bottom of the error window that opens the same reporter dialog as from the Help menu.
I tried a small peptide and didn't have the problem. When I clicked the Run button on Molecular Dynamics Simulation, the Dock Prep tool appeared, hydrogens were added, charges assigned, etc. as normal and minimization was successful. Minimization needs hydrogens and charges, so it does not make sense for minimization to work and then equilibration to fail, unless the reason for the equilibration problem was something else (not because of missing hydrogens and charges).
In the bug report please describe what you did and what happened, attach data (the peptide structure or a session file allowing the error to be reproduced), and include your e-mail address if you want feedback. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2020, at 8:20 AM, Laura Juszczak LJuzak@brooklyn.cuny.edu wrote:
Dear help: In running an MD on an aromatic dipeptide from Chimera installed on my Mac, the minimization step within the Run Parameters does not add required Hs even though that option is checked, resulting in a n equilibration error message re missing Hs. However, if I choose to minimize outside of MD simulation (Tools—> structure editing—> minimize structure), Hs are successfully added, and are visible on the model. Returning to MD simulation, I am able to proceed to equilibration and production successfully. Laura J
participants (4)
-
Benjamin Strickland -
Elaine Meng -
Eric Pettersen -
Laura Juszczak