PyGBe: Python, GPUs and Boundary elements for biomolecular electrostatics. PyGBe—pronounced pigbē—is a Python code to apply the boundary element method for molecular-electrostatics calculations in a continuum model. It computes solvation energies for proteins modeled with any number of dielectric regions. The mathematical formulation follows Yoon and Lenhoff (1990) for solving the Poisson-Boltzmann equation of the implicit-solvent model in integral form. PyGBe achieves both algorithmic and hardware acceleration. The solution algorithm uses a Barnes-Hut treecode to accelerate each iteration of a GMRES solver to O(N logN), for N unknowns. It exploits NVIDIA GPU hardware on the most computationally intensive parts of the code using CUDA kernels in the treecode, interfacing with PyCUDA. Some parts of the code are written in C++, wrapped using SWIG.
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References in zbMATH (referenced in 5 articles )
Showing results 1 to 5 of 5.
- Timo Betcke; Matthew W. Scroggs: Bempp-cl: A fast Python based just-in-time compiling boundary element library (2021) not zbMATH
- Zhang, Bo; Debuhr, Jackson; Niedzielski, Drake; Mayolo, Silvio; Lu, Benzhuo; Sterling, Thomas: DASHMM accelerated adaptive fast multipole Poisson-Boltzmann solver on distributed memory architecture (2019)
- Zhou, S.: Effective electrostatic interactions between two overall neutral surfaces with quenched charge heterogeneity over atomic length scale (2017)
- Cooper, Christopher D.; Barba, Lorena A.: Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textscPyGBecode (2016)
- Cooper, Christopher D.; Bardhan, Jaydeep P.; Barba, L. A.: A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers (2014)