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Convergence and time to solution of PyGBe with lysozyme molecule

dataset
posted on 15.09.2013 by Christopher D. Cooper, Jaydeep Bardhan, Lorena A. Barba

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. 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. 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.
http://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.

 

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