gabipb

This software package presents a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up our method, we take advantage of the parallel nature of the boundary integral formulation and parallelize the schemes within CUDA shared memory architecture on GPU. The schemes use only $11N+6N_c$ size-of-double device memory for a biomolecule with $N$ triangular surface elements and $N_c$ partial charges.

REFERENCE: W.H. Geng and F. Jacob, A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver, Comput. Phys. Commun. 184, 1490-1496 (2013).