The weighted ensemble (WE) �scripting level� strategy for orchestrating an ensemble of simulations can parallelize stochastic dynamics run with any package, such as for biomolecular or systems biology simulations.  WE can exhibit super-linear parallel scaling, sometimes yielding one or more orders of magnitude of speedup in estimating equilibrium or non-equilibrium observables compared to standard simulation - and accounting for the total simulation time of all trajectories.  Nevertheless, like other simulation approaches, WE has limitations that must be appreciated (e.g., trajectory correlations and the sampling of coordinates orthogonal to binning coordinates).  We report on challenges and progress in applying WE to increasingly complex biological systems using the WESTPA software package.

Weighted ensemble simulation methodology: Progress and challenges

247th National Meeting (2014)

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