Computational Modeling of Molecular Mechanics for the Experimentally Inclined
Computational Modeling of Molecular Mechanics for the Experimentally Inclined
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DOI：
10.1021/acs.chemmater.2c00292
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发表时间：
2022-08
影响因子：
8.6
通讯作者：
Andrew T. Kleinschmidt;Alexander X. Chen;T. Pascal;D. Lipomi
中科院分区：
文献类型：
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作者：
Andrew T. Kleinschmidt;Alexander X. Chen;T. Pascal;D. Lipomi
现代计算机模拟可以为复杂材料系统提供独特的原子尺度的洞察，但对于非专业人士来说，进行模拟的方法可能看起来很模糊。该协议的目的是向实验研究人员介绍在原子模拟中使用的工具和方法，这些工具和方法可以阐明聚合物和纳米材料的结构、形态和动力学。特别是，它侧重于模拟的工作流程和后勤，其中的中心组件是不可分割的原子(与“量子”或“连续”方法相反的“原子论”)。我们介绍了描述原子位置的方法，例如蒙特卡罗(MC)和分子动力学(MD)模拟，以及建立、运行和分析模拟所需的过程。然而，本议定书中概述的许多术语和工作流程是通用的，因此适用于MC和MD以外的方法以及其他分子系统(例如蛋白质)。本议定书分为三个一般部分。首先，它描述了模拟所需的三种类型的信息：系统描述(即，“数据文件”)，模拟引擎的指令(即，“软件输入文件”)，以及硬件的指令，通常是超级计算基础设施(即，“硬件输入文件”)。数据文件通常描述系统的初始状态以及系统内原子如何相互作用的定义(通常表示为“力场”)。这三条信息一起用于运行模拟，然后产生研究人员可以分析的输出。我们希望该议定书将至少为实验者提供三件事：(1)解释计算数据的参照系，(2)促进与计算科学家的合作，以及(3)鼓励他们自己完成一些计算任务。
Modern computer simulations can provide unique atomic-scale insights into complex material systems, but the method of performing a simulation may seem obscure to the nonspecialist. The goal of this Protocol is to introduce to experimental researchers a description of the tools and methods used in atomic simulations which elucidate the structure, morphology, and dynamics of polymers and nanomaterials. In particular, it focuses on the workflow and logistics of simulations in which the central component is indivisible atoms (“atomistic” as opposed to “quantum” or “continuum” methods). We present methods which describe the positions of atoms, e.g., Monte Carlo (MC) and molecular dynamics (MD) simulations, along with the necessary processes by which simulations are set up, run, and analyzed. However, much of the terminology and workflow outlined in this Protocol is general and thus applies to methods beyond MC and MD as well as other molecular systems (e.g., proteins). This Protocol is separated into three general sections. First, it describes the three types of information that are required for a simulation: a description of the system (i.e., “data file”), instructions for the simulations engine (i.e., “software input file”), and instructions for the hardware, usually supercomputing infrastructure (i.e., “hardware input file”). The data file, generally, describes the initial state of the system as well as a definition of how the atoms within the system interact (usually denoted as a “force field”). Together, these three pieces of information are used to run a simulation, which then produces an output that can be analyzed by the researcher. We hope that this Protocol will provide at least three things for the experimentalist: (1) a frame of reference for the interpretation of computational data, (2) facilitation of collaboration with computational scientists, and (3) the encouragement to perform some computational tasks on their own.