Book/Internal Report

FZJ-2021-00035

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Intelligent HTC for Committor Analysis

O'Cais, A. (Corresponding author)FZJ* ; Bialczak, M. ; Swenson, D. ; Uchronsk, M. ; Wlodarczyk, A.

2020

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Please use a persistent id in citations: http://hdl.handle.net/2128/26664  doi:10.5281/ZENODO.4382017

Report No.: PRACE WP297

Abstract: 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.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. E-CAM - An e-infrastructure for software, training and consultancy in simulation and modelling (676531) (676531)
3. PRACE CoE Allocation E-CAM (prcoe02_20181001) (prcoe02_20181001)

Appears in the scientific report 2020

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