PyGBe swMATH ID: 17642 Software Authors: Cooper, Christopher D.; Barba, Lorena A. Description: 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. Homepage: https://github.com/barbagroup/pygbe Source Code: https://github.com/barbagroup/pygbe Related Software: tabipb; Python; TABI; MIBPB; PyCUDA; APBS; PDB2PQR; CUDA; NanoShaper; exafmm; meshio; HyENA; Numba; SciPy; Gmsh; abem; FEniCS; BETL; Bempp-cl; VCMM Cited in: 5 Documents all top 5 Cited by 14 Authors 2 Barba, Lorena A. 2 Cooper, Christopher D. H. 1 Bardhan, Jaydeep P. 1 Chen, Jiahui 1 Debuhr, Jackson 1 Geng, Weihua 1 Hu, Jingzhen 1 Krasny, Robert 1 Lu, Benzhuo 1 Mayolo, Silvio 1 Niedzielski, Drake 1 Sterling, Thomas Lawrence 1 Wilson, Leighton 1 Zhang, Bo Cited in 4 Serials 2 Computer Physics Communications 1 Journal of Statistical Physics 1 Communications in Information and Systems 1 Communications in Computational Physics all top 5 Cited in 6 Fields 4 Optics, electromagnetic theory (78-XX) 3 Biology and other natural sciences (92-XX) 2 Numerical analysis (65-XX) 1 Computer science (68-XX) 1 Quantum theory (81-XX) 1 Statistical mechanics, structure of matter (82-XX) Citations by Year