Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular dynamics simulations which are major tools for problems at the nano-/micro- scale. Various algorithms are developed to calculate the pairwise Coulomb interactions to a linear scaling but the poor scalability limits the size of simulated systems. Here, we conduct an efficient molecular dynamics algorithm with the random batch Ewald method on all-atom systems where the complete Fourier components in the Coulomb interaction are replaced by randomly selected mini-batches. By simulating the $N$-body systems up to 100 million particles using $10$ thousand CPU cores, we show that this algorithm furnishes $O(N)$ complexity, almost perfect scalability and an order of magnitude faster computational speed when compared to the existing state-of-the-art algorithms. Further examinations of our algorithm on distinct systems, including pure water, micro-phase-separated electrolyte and protein solution demonstrate that the spatiotemporal information on all time and length scales investigated and thermodynamic quantities derived from our algorithm are in perfect agreement with those obtained from the existing algorithms. Therefore, our algorithm provides a breakthrough solution on scalability of computing the Coulomb interaction. It is particularly useful and cost-effective to simulate ultra-large systems, which was either impossible or very costing to conduct using existing algorithms, thus would benefit the broad community of sciences.
翻译:库伦互动,在逆平方方形的力量法下,量化了两个固定和电荷粒子之间的强度。库伦互动的远程性质对分子动态模拟提出了重大挑战,这些模拟是纳米/微缩规模问题的主要工具。我们开发了各种算法,以计算对称库伦互动的线性缩放,但缩放性差限制了模拟系统的规模。在这里,我们用随机批量的埃瓦尔德方法,在全方位系统上进行高效的分子动态算法,使库伦互动中完整的Fourier组件被随机选择的小型科学棒所取代。通过利用10 000美元的CPU核心模拟高达1亿美元的分子动态模拟。我们显示,这种算法提供了美元(N)的复杂度,几乎完美的缩放性,而且比现有的实用性算法速度要快得多。我们关于不同系统的算法,包括纯水、微平档的电磁波和蛋白质互动的全方形互动法,或者通过从我们现有的成本和蛋白质的算法分析,使得我们现有的系统能够从现在的快速的算算算算算算算算算到现在的系统。