[Chimera-users] Chimera Molecular Dynamics

[Benjamin Strickland]

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> 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>
> 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> 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>
>> 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.
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