为了提高分子动力学模拟计算在当前具有多级缓存(Cache)结构的处理器上的计算性能,对分子动力学模拟过程中缓存(Cache)的访问特征进行了分析与优化.通过对影响Cache命中率和模拟计算效率的因素进行测试与分析,提出一种Atomreorder算法.该方法通过重新调整粒子的顺序,使同一个或者相邻晶格的粒子在主存中的位置接近来增强程序的局部性,进而减少Cache的丢失.测试结果表明该方法对大体系模拟的Cache丢失有明显的优化,计算效率也相应提高了. In order to improve the computational performance of molecular dynamics simulations on current processors with multi-level cache, the cache access features in the process of molecular dynamics simulation are analyzed and optimized.Through the analysis of the impact on Cache hit Rate and simulation efficiency, an Atomreorder algorithm is proposed to enhance the locality of the program by readjusting the order of the particles and bringing the particles in the same or adjacent lattice close to each other in main memory , So as to reduce the loss of Cache.Experimental results show that the proposed method can significantly reduce the cache loss in large-scale system simulation and improve the computational efficiency accordingly.