Convergence and time to solution of PyGBe with lysozyme molecule

dataset

posted on 2013-09-15, 02:56 authored by Christopher D. Cooper, Jaydeep Bardhan, Lorena A. BarbaLorena 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.