[Chimera-users] Chimera Molecular Dynamics

Benjamin Strickland bstrickland at drew.edu
Mon Jun 29 11:05:29 PDT 2020

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.


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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