[Chimera-users] Chimera MD: minimization not adding Hs

[Laura Juszczak]

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 at cgl.ucsf.edu> wrote:


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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 at drew.edu<mailto:bstrickland at 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 at cgl.ucsf.edu<mailto:pett at 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 at drew.edu<mailto:bstrickland at 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.
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