title: Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals.
abstract: A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup.
authors.affiliation: Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
authors.forename: Sergey
authors.initials: S
authors.lastname: Kazachenko
authors.affiliation: Department of Mechanical and Materials Engineering, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Giovinazzo
authors.affiliation: Department of Chemistry, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
authors.forename: Kyle Wm
authors.initials: KW
authors.lastname: Hall
authors.affiliation: Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
authors.forename: Natalie M
authors.initials: NM
authors.lastname: Cann
keywords: graphics processing units; liquid crystals; mixtures; molecular dynamics simulations; water