[Chimera-users] Chimera Molecular Dynamics

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 29 09:13:37 PDT 2020

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 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 <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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