[Chimera-users] Chimera Molecular Dynamics

Wed Jul 1 15:29:05 PDT 2020

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