Computational protein folding has historically relied on long-running
simulations of single molecules. Although many such simulations can run
be at once, they are statistically likely to sample the same common
configurations of the molecule, rather than exploring the many possible
states it may have. To address this, a team of researchers from the
University of Notre Dame and Stanford University designed a system that
combined the Adaptive Weighted Ensemble technique to run thousands of short Gromacs and Protomol simulations in parallel with periodic resampling to explore the rich state space of a molecule. Using the Work Queue
framework, these simulations were distributed across thousands of CPUs
and GPUs drawn from the Notre Dame, Stanford, and commercial cloud
providers. The resulting system effectively simulates the behavior of a
protein at 500 ns/hour, covering a wide range of behavior in days
rather than years.- Jesus Izaguirre, University of Notre Dame and Eric Darve, Stanford University
