Modified Anderson Method for Accelerating 3D-RISM Calculations Using Graphics Processing Unit

作者：Maruyama Yutaka; Hirata Fumio^*

来源：Journal of Chemical Theory and Computation, 2012, 8(9): 3015-3021.

DOI：10.1021/ct300355r

A fast algorithm is proposed to solve the three-dimensional reference interaction site model (3D-RISM) theory on a graphics processing unit (GPU). 3D-RISM theory is a powerful tool for investigating biomolecular processes in solution; however, such calculations are often both memory-intensive and time-consuming. We sought to accelerate these calculations using GPUs, but to work around the problem of limited memory size in GPUs, we modified the less memory-intensive %26quot;Anderson method%26quot; to give faster convergence to 3D-RISM calculations. Using this method on a Tesla C2070 GPU, we reduced the total computational time by a factor of 8, 1.4 times by the modified Andersen method and 5.7 times by GPU, compared to calculations on an Intel Xeon machine (eight cores, 3.33 GHz) with the conventional method.

• 出版日期2012-9