ADL: Long Simulation Time (~180 hrs)

Joey Farrell jpfarrell at uchicago.edu
Tue Oct 27 20:03:14 PDT 2020


Greetings,

I am running a flexible docking job with files generated by AutoDockTools using Autodock Vina as the simulation-driving software.

The grid space size is 40 x 40 x 48, and I believe I have already exceeded the efficient ratio of CPU to exhaustivity. Are there any natural suggestions to make this job more feasibly runnable (i.e. ~ 36 hours runtime)? Currently, it seems projected to run for about 180 hours. I suppose the most natural idea might be to subdivide this grid into smaller grid simulations; if this is the case, is there any recommended software to automatically splice this volume into N disjoint subgrids for use with Vina?

Thank you in advance.

Best,
Joey


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