Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
J Chem Inf Model. 2022 Jan 10;62(1):71-78. doi: 10.1021/acs.jcim.1c01206. Epub 2021 Dec 24.
We propose a new random number generation method, which is the fastest and the simplest of its kind, for use with molecular simulation. We also discuss the possibility of using this method with various other numerical calculations. To demonstrate the significant increases in calculation speeds that can be gained by using our method, we present a comparison with prior methods for dissipative particle dynamics (DPD) simulations. The DPD method uses random numbers to reproduce thermal fluctuations of molecules. As such, an efficient method to generate random numbers in parallel computing environments has been widely sought after. Several random number generation methods have been developed that use encryption. In this study, we establish for the first time that random numbers with desirable properties exist in the particle coordinates used in DPD calculations. We propose a method for generating random numbers without encryption that utilizes this source of randomness. This is an innovative method with minimal computational cost, since it is not dependent on a complicated random number generation algorithm or an encryption process. Furthermore, our method may lead to faster random number generation for many other physical and chemical simulations.
我们提出了一种新的随机数生成方法,它是同类方法中最快、最简单的,可用于分子模拟。我们还讨论了将这种方法应用于各种其他数值计算的可能性。为了展示使用我们的方法可以显著提高计算速度,我们将其与先前的耗散粒子动力学(DPD)模拟的方法进行了比较。DPD 方法使用随机数来再现分子的热波动。因此,在并行计算环境中生成随机数的有效方法已被广泛寻求。已经开发了几种使用加密的随机数生成方法。在这项研究中,我们首次证明在 DPD 计算中使用的粒子坐标中存在具有理想特性的随机数。我们提出了一种无需加密即可利用这种随机性生成随机数的方法。这是一种具有最小计算成本的创新方法,因为它不依赖于复杂的随机数生成算法或加密过程。此外,我们的方法可能会为许多其他物理和化学模拟带来更快的随机数生成。