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The formation of biomolecular materials via dynamical interfacial processessuch as self-assembly and fusion, for diverse compositions and externalconditions, can be efficiently probed using ensemble Molecular Dynamics.However, this approach requires a large number of simulations wheninvestigating a large composition phase space. In addition, there is difficultyin predicting whether each simulation is yielding biomolecular materials withthe desired properties or outcomes and how long each simulation will run for.These difficulties can be overcome by rules-based management systems whichinclude intermittent inspection, variable sampling, premature termination andextension of the individual Molecular Dynamics simulations. The automation ofsuch a management system can significantly reduce the overhead of managinglarge ensembles of Molecular Dynamics simulations. To this end, ahigh-throughput workflows-based computational framework, Pipeline forAutomating Compliance-based Elimination and Extension (PACE2), for biomolecularmaterials simulations is proposed. The PACE2 framework encompassesSimulation-Analysis Pipelines. Each Pipeline includes temporally separatedsimulation and analysis tasks. When a Molecular Dynamics simulation completes,an analysis task is triggered which evaluates the Molecular Dynamics trajectoryfor compliance. Compliant Molecular Dynamics simulations are extended to thenext Molecular Dynamics phase with a suitable sample rate to allow additional,detailed analysis. Non-compliant Molecular Dynamics simulations are eliminated,and their computational resources are either reallocated or released. Theframework is designed to run on local desktop computers and high performancecomputing resources. In the future, the framework will be extended to addressgeneralized workflows and investigate other classes of materials.

Pipeline for Automating Compliance-based Elimination and Extension  (PACE2): A Systematic Framework for High-throughput Biomolecular Material  Simulation Workflows