Wednesday, August 10, 2016

Simulation of HP24stab with AWE and Work Queue

The villin headpiece subdomain "HP24stab" is a recently discovered 24-residue stable supersecondary structure that consists of two helices joined by a turn. Simulating 1μs of motion for HP24stab can take days or weeks depending on the available hardware, and folding events take place on a scale of hundreds of nanoseconds to microseconds.  Using the Accelerated Weighted Ensemble (AWE), a total of 19us of trajectory data were simulated over the course of two months using the OpenMM simulation package. These trajectories were then clustered and sampled to create an AWE system of 1000 states and 10 models per state. A Work Queue master dispatched 10,000 simulations to a peak of 1000 connected 4-core workers, for a total of 250ns of concurrent simulation time and 2.5μs per AWE iteration. As of August 8, 2016, the system has run continuously for 18 days and completed 71 iterations, for a total of 177.5μs of simulation time. The data gathered from these simulations will be used to report the mean first passage time, or average time to fold, for HP24stab, as well as the major folding pathways.  - Jeff Kinnison and Jesús Izaguirre, University of Notre Dame

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