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For many macromolecular systems the accurate sampling of the relevant regionson the potential energy surface cannot be obtained by a single, long MolecularDynamics (MD) trajectory. New approaches are required to promote more efficientsampling. We present the design and implementation of the Extensible Toolkitfor Advanced Sampling and analYsis (ExTASY) for building and executing advancedsampling workflows on HPC systems. ExTASY provides Python based "templatedscripts" that interface to an interoperable and high-performance pilot-basedrun time system, which abstracts the complexity of managing multiplesimulations. ExTASY supports the use of existing highly-optimised parallel MDcode and their coupling to analysis tools based upon collective coordinateswhich do not require a priori knowledge of the system to bias. We describe twoworkflows which both couple large "ensembles" of relatively short MDsimulations with analysis tools to automatically analyse the generatedtrajectories and identify molecular conformational structures that will be usedon-the-fly as new starting points for further "simulation-analysis" iterations.One of the workflows leverages the Locally Scaled Diffusion Maps technique; theother makes use of Complementary Coordinates techniques to enhance sampling andgenerate start-points for the next generation of MD simulations. We show thatthe ExTASY tools have been deployed on a range of HPC systems including ARCHER(Cray CX30), Blue Waters (Cray XE6/XK7), and Stampede (Linux cluster), and thatgood strong scaling can be obtained up to 1000s of MD simulations, independentof the size of each simulation. We discuss how ExTASY can be easily extended ormodified by end-users to build their own workflows, and ongoing work to improvethe usability and robustness of ExTASY.

ExTASY: Scalable and Flexible Coupling of MD Simulations and Advanced Sampling Techniques