A CUDA based solute Interaction Calculation of Biomolecular Simulation for GROMOS
Molecular dynamics is an important computational tool to simulate and understand biochemical processes at atomic level. However, large system simulations with many atoms and numerous time steps require huge amount of calculation and in traditional CPU, it is time-consuming. During the past few years, graphics processing units have become an important computing platform in many scientific fields, especially in high performance computing community. In this paper,implementation of solute-solute and solutesolvent interaction calculation with NVIDIAS Tesla C1060 will be presented. Therefore, the implementation enables users of GROMOS software for biomolecular simulation to run the whole nonbonded interaction evaluation on the GPU. Our experimental results are ten to twenty times faster than the conventional sequential implementation running on the CPU core.
GPU Molecular dynamics CUDA nonbonded parallel computation.
Xiaoli Jin Lei Zhao Jiwen Yang
School of Computer Science and Technology, Soochow University
国际会议
哈尔滨
英文
820-824
2011-12-24（万方平台首次上网日期，不代表论文的发表时间）