论文标题
分子动力学模拟简介
Introduction to molecular dynamics simulations
论文作者
论文摘要
在玻璃的Kob-Andersen模型的背景下，我们提供了分子动力学模拟的介绍。我们介绍了一组完整的工具，用于进行和分析固定NVE和NVT的模拟结果。本文的模块化格式使读者可以选择满足其需求的部分。我们从独立于编程语言的分子动力学介绍开始，然后介绍使用Python，然后再使用Python，然后是免费提供的开源软件包软件包LAMMPS。我们还描述了该程序在其开发过程中快速测试的分析工具，并使用Python和LAMMPS计算径向分布函数和均方根位移。
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular format of the paper allows readers to select sections that meet their needs. We start with an introduction to molecular dynamics independent of the programming language, followed by introductions to an implementation using Python and then the freely available open source software package LAMMPS. We also describe analysis tools for the quick testing of the program during its development and compute the radial distribution function and the mean square displacement using both Python and LAMMPS.
