This title appears in the Scientific Report :
2020
Please use the identifier:
http://hdl.handle.net/2128/26664 in citations.
Please use the identifier: http://dx.doi.org/10.5281/ZENODO.4382017 in citations.
Intelligent HTC for Committor Analysis
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 w...
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Personal Name(s): | O'Cais, Alan (Corresponding author) |
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Bialczak, Milosz / Swenson, David / Uchronsk, Mariusz / Wlodarczyk, Adam | |
Contributing Institute: |
Jülich Supercomputing Center; JSC |
Imprint: |
2020
|
Physical Description: |
8 p. |
DOI: |
10.5281/ZENODO.4382017 |
Document Type: |
Book Internal Report |
Research Program: |
PRACE CoE Allocation E-CAM An e-infrastructure for software, training and consultancy in simulation and modelling Computational Science and Mathematical Methods |
Series Title: |
PRACE White Paper
297 |
Link: |
OpenAccess |
Publikationsportal JuSER |
Please use the identifier: http://dx.doi.org/10.5281/ZENODO.4382017 in citations.
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. |