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首页> 外文期刊>Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological >Computationally Efficient Canonical Molecular Dynamics Simulations by Using a Multiple Time-Step Integrataor Algorithm Combined with the Particle Mesh Ewald Method and with the Fast Multipole Method
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Computationally Efficient Canonical Molecular Dynamics Simulations by Using a Multiple Time-Step Integrataor Algorithm Combined with the Particle Mesh Ewald Method and with the Fast Multipole Method

机译：多时间步积分算法与粒子网格Ewald方法和快速多极方法相结合的计算有效的规范分子动力学模拟

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摘要

An efficient implementation f the canonical molecular dynamics simulation using the reversible reference system propagator algorithm (r-RESPA) combined with the particle mesh Ewald method (PMEM) and with the macroscopic expansion of the fast multipole method (MEFMM) was examined. The performance of the calculations was evaluated for systems with 3000,9999,30,000,60,000,and 99,840 particles. For a given accuracy, the optimal conditions for minimizing the CPU time for the implementation of the Ewald method, the PMEM, and the MEFMM were first analyzed. Using the optimal conditions, we evaluated the performance and the reliability of the integrated methods. For all the systems examined, the r-RESPA with the PMEM was about twice as fast as the r-RESPA with the MEFMM.The difference arose from the difference in the numerical complexities of the fast Fourier transform in the PMEM and from the transformation of the multipole moments into the coefficients of the local field expansion in the MEFMM. Compared with conventional methods, such as the velocity-verlet algorithm with the Ewald method, sighnificant speedups were obtained by the integrated methods;the speedup of the calculation was a function of system sizae, and was a factor of 100 for a system with 3000 particles and increased to a factor of 700 for a system with 99,840 particles. These integrated calculations are, therefore, promising for realizing large-scale molecular dynamics simulations for complex systems.
机译：研究了使用可逆参考系统传播算法（r-RESPA）结合粒子网格Ewald方法（PMEM）和快速多极方法的宏观扩展（MEFMM）进行的经典分子动力学模拟的有效实现。对于具有3000,9999,30,000,60,000和99,840个粒子的系统，评估了计算的性能。对于给定的精度，首先分析了用于最小化CPU时间以实现Ewald方法，PMEM和MEFMM的最佳条件。使用最佳条件，我们评估了集成方法的性能和可靠性。对于所有检查的系统，使用PMEM的r-RESPA大约是使用MEFMM的r-RESPA的两倍。差异是由于PMEM中快速傅里叶变换的数值复杂性不同以及将多极矩转化为MEFMM中局部场扩展的系数。与常规方法相比，例如采用Ewald方法的速度-Verlet算法，通过集成方法获得了显着的加速;计算的加速是系统sizae的函数，对于具有3000个粒子的系统，计算的加速是100倍对于具有99,840个粒子的系统，该系数增加到700倍。因此，这些综合计算有望为复杂系统实现大规模分子动力学模拟。

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