Convergence of PyGBE with Kirkwood sphere
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This file bundle includes data, figures and plotting scripts of convergence results for PyGBe and APBS using a spherical molecule of radius 4 Armstrong with a centered charge of –1e. 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 and is open-source under MIT license.
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.
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.