A GPU Poisson–Fermi solver for ion channel simulations

Abstract

The Poisson–Fermi model is an extension of the classical Poisson–Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson–Boltzmann electrostatic calculations are essential but computationally very demanding for molecular dynamics or continuum simulations of complex systems in molecular biophysics and electrochemistry. The graphic processing unit (GPU) with enormous arithmetic capability and streaming memory bandwidth is now a powerful engine for scientific as well as industrial computing. We propose two parallel GPU algorithms, one for linear solver and the other for nonlinear solver, for solving the Poisson–Fermi equation approximated by the standard finite difference method in 3D to study biological ion channels with crystallized structures from the Protein Data Bank, for example. Numerical methods for both linear and nonlinear solvers in the parallel algorithms are given in detail to illustrate the salient features of the CUDA (compute unified device architecture) software platform of GPU in implementation. It is shown that the parallel algorithms on GPU over the sequential algorithms on CPU (central processing unit) can achieve 22.8× and 16.9× speedups for the linear solver time and total runtime, respectively.