Data · dataset · 2013
Convergence and time to solution of PyGBe with lysozyme molecule
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This file bundle includes data, figures and plotting scripts of convergence and time-to-solution versus error for PyGBe and APBS using a lysozyme molecule.
Description
The errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba.
Comput. Phys. Comm. , 185 (3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution.
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It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods . Christopher Cooper, Lorena A. Barba. figshare. dx.doi.org/10.6084/m9.figshare.154331 Acknowledgement: This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356.
LAB also acknowledges support from NSF CAREER award OCI-1149784.
Links
Where it is published
- Repository landing page figshare.com/articles/dataset/Convergence_and_time_to_solution_of_PyGBe_wit… ↗
landing page · from DataCite
- Repository landing page figshare.com/articles/dataset/Convergence_and_time_to_solution_of_PyGBe_wit… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.799702 ↗
DOI / persistent id · from DataCite
- DOI doi.org/10.6084/m9.figshare.799702.v1 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 4
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.799702.v1 ↗
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- DataCite API api.datacite.org/dois/10.6084/m9.figshare.799702 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.799702.v1 ↗
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- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.799702 ↗
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Topics
- Stated by source
- Mechanical engineering · Mechanical engineering
Provenance · 2 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.799702 | 13 d ago | JSON v1 |
| DataCite | 10.6084/m9.figshare.799702.v1 | 13 d ago | JSON v1 |
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