Algorithms for GPU-Based Molecular Dynamics Simulations of Complex Fluids: Applications to Water, Mixtures, and Liquid Crystals

作者：Kazachenko Sergey^*; Giovinazzo Mark; Hall Kyle Wm; Cann Natalie M

来源：Journal of Computational Chemistry, 2015, 36(24): 1787-1804.

DOI：10.1002/jcc.24000

• graphics processing units
• molecular dynamics simulations
• water
• liquid crystals
• mixtures

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, Nose-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.

• 出版日期2015-9-15