Pipelines for automating compliance-based elimination and extension (PACE2): a systematic framework for high-throughput biomolecular materials simulation workflows

Abstract

The formation of biomolecular materials via dynamical interfacial processes, such as self-assembly and fusion, for diverse compositions and external conditions can be efficiently probed using ensemble Molecular Dynamics (MD). However, this approach requires many simulations when investigating a large composition phase space. In addition, there is difficulty in predicting whether each simulation will yield biomolecular materials with the desired properties or outcomes and how long each simulation will run. These difficulties can be overcome by rules-based management systems, including intermittent inspection, variable sampling, and premature termination or extension of the individual MD simulations. Automating such a management system can significantly improve runtime efficiency and reduce the burden of organizing large ensembles of MD simulations. To this end, a computational framework, the Pipelines for Automating Compliance-based Elimination and Extension (PACE2), is proposed for high-throughput ensemble biomolecular materials simulations. The PACE2 framework encompasses Candidate pipelines, where each pipeline includes temporally separated simulation and analysis tasks. When a MD simulation is completed, an analysis task is triggered, which evaluates the MD trajectory for compliance. Compliant simulations are extended to the next MD phase with a suitable sample rate to allow additional, detailed analysis. Non-compliant simulations are eliminated, and their computational resources are reallocated or released. The framework is designed to run on local desktop computers and high-performance computing resources. Preliminary scientific results enabled by the use of PACE2 framework are presented, which demonstrate its potential and validates its function. In the future, the framework will be extended to address generalized workflows and investigate composition-structure-property relations for other classes of materials.