Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE)
Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE)
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DOI：
10.1080/00268976.2020.1742938
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发表时间：
2020-03
影响因子：
1.7
通讯作者：
M. Thompson;Justin B. Gilmer;Ray A. Matsumoto;Co D. Quach;Parashara Shamaprasad;Alexander Yang;C. Iacovella;C. McCabe;P. Cummings
中科院分区：
文献类型：
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作者：
M. Thompson;Justin B. Gilmer;Ray A. Matsumoto;Co D. Quach;Parashara Shamaprasad;Alexander Yang;C. Iacovella;C. McCabe;P. Cummings
由软物质（如液体、聚合物、泡沫、凝胶、胶体和大多数生物材料）组成的系统在科学和工程中无处不在，但此类系统的分子模拟提出了特定的计算挑战，需要在长模拟轨迹上收集时间和/或整体平均数据以进行属性评估。执行软物质系统的分子模拟涉及多个步骤，这些步骤传统上由研究人员以“定制”方式执行，导致许多已发表的软物质模拟无法根据出版物中提供的信息进行重现。为了解决再现性问题并提供计算筛选工具，我们一直在开发开源分子模拟和设计框架（MoSDEF）软件套件。在本文中，我们提出了一套原则，以创建透明的，可复制的，可供他人使用的，可扩展的（真正的）分子模拟。MoSDEF通过自动化分子模拟中的许多关键步骤，促进了TRUE模拟的出版和传播，从而提高了其可重复性a。我们提供了几个真实分子模拟的例子：从模拟中创建、运行和提取属性的所有步骤都分布在开源平台上（在MoSDEF和GitHub上），因此符合真实模拟的定义。图形摘要
ABSTRACT Systems composed of soft matter (e.g. liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a ‘bespoke’ fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibilitya. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations. GRAPHICAL ABSTRACT