Abstract: Molecular Dynamics Simulation is an important method for acquiring liquid and solid atoms' properties. this method has been widely used in the fields of chemistry, physics, biology, medicine and materials. hhe complexity and accuracy demand causes enormous workloads. Parallel computing is a feasible way to speedup large-scale molecular dynamics simulation. With hundreds of GFlops or even hFlops performance, GPU can speed up computing-intensive applicanons. This paper presented a parallel algorithm named oApT-AD, and we implemented it on GPU under OpenCL and CUDA Framework. The experiment results show that the oApT-A7)algorithm can achieve 120 speedup on UPU Tesla 01060 under OpenCL Framework, compared to that on CPU. And we also implemented the oApT-Al)algorithm on GPU under CUDA Framework. hhe implement under OpenCI. Framework provides almost the same performance as the implement under CUDA Framework. Moreover, our algorithm can be extended to two or more(:PUs, with good scalability.

Key words: Molecular dynamics, GPU, OpenCL, CUDA, Atom decomposition