Intelligent HTC for Committor Analysis

Committor analysis is a powerful, but computationally expensive, tool to study reaction mechanisms in complex systems. The committor can also be used to generate initial trajectories for transition path sampling, a less-expensive technique to study reaction mechanisms. The main goal of the project was to facilitate an implementation of committor analysis in the software application OpenPathSampling (http://openpathsampling.org/) that is performance portable across a range of HPC hardware and hosting sites. We do this by the use of hardware-enabled MD engines in OpenPathSampling coupled with a custom library extension to the data analytics framework Dask (https://dask.org/) that allows for the execution of MPI-enabled tasks in a steerable High Throughput Computing workflow. The software developed here is being used to generate initial trajectories to study a conformational change in the main protease of the SARS-CoV-2 virus, which causes COVID-19. This conformational change may regulate the accessibility of the active site of the main protease, and a better understanding of its mechanism could aid drug design.