high performance computing on graphics processing units: hgpu.org

We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of intermolecular force and torque are parallelized on the GPU using the cell-list method, and an efficient algorithm to update the cell lists was proposed. Some important issues in the implementation of computations that involve a large number of arithmetic operations and data on the GPU that has limited high-speed memory resources are addressed extensively. Despite the relatively low GPU occupancy in the calculation of intermolecular force and torque, the computation on a recent GPU is about 50 times faster than that on a single core of a recent CPU, thus simulations involving a large number of molecules using a personal computer are possible. The GPU-based simulation should allow an extensive investigation of the molecular-level mechanisms underlying various macroscopic flow phenomena in fluids with anisotropic molecules.