Chapter 4. Fast Molecular Electrostatics Algorithms on GPUs
David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues and Klaus Schulten
In this chapter, we present GPU kernels for calculating electrostatic potential maps, which are of practical importance to modeling biomolecules. Calculations on a structured grid containing a large amount of fine-grained data parallelism make this problem especially well suited to GPU computing and a worthwhile case study. We discuss in detail the effective use of the hardware memory subsystems, kernel loop optimizations, and approaches to regularize the computational work performed by the GPU, all of which are important techniques for achieving high performance.