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.
