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@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@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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users