TY  - RPRT
AU  - O'Cais, Alan
AU  - Bialczak, Milosz
AU  - Swenson, David
AU  - Uchronsk, Mariusz
AU  - Wlodarczyk, Adam
TI  - Intelligent HTC for Committor Analysis
VL  - 297
IS  - PRACE WP297
M1  - FZJ-2021-00035
M1  - PRACE WP297
T2  - PRACE White Paper
SP  - 8 p.
PY  - 2020
AB  - 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.
LB  - PUB:(DE-HGF)3 ; PUB:(DE-HGF)15
DO  - DOI:10.5281/ZENODO.4382017
UR  - https://juser.fz-juelich.de/record/889105
ER  -