Collaborative Research: NSCI Framework: Software for Building a Community-Based Molecular Modeling Capability Around the Molecular Simulation Design Framework (MoSDeF)

合作研究：NSCI 框架：围绕分子模拟设计框架 (MoSDeF) 构建基于社区的分子建模能力的软件

• 批准号: 1835630
• 负责人: Edward Maginn
• 金额: $ 37.25万
• 依托单位: University of Notre Dame
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-10-01 至 2022-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835630&HistoricalAwards=false
• 关键词: Collaborative; Research; NSCI; Framework; Software

As molecular-based computer simulations of both naturally occurring and man-made (synthetic) materials become increasingly used to predict their properties, the reproducibility of these simulations becomes an increasingly important issue. These simulations are complex, require large amounts of computer time, and are usually performed manually - i.e., put together one at a time, from all the components that go into such a simulation, including the models for how molecules interact with each other (known as forcefields). In addition, there has been much interest in being able to perform such computational simulations on large sets of different but related systems in order to screen for desirable properties, leading to the discovery of new materials and their incorporation into applications twice as rapidly and at half the cost of existing, primarily experimental, methods. This ambition is the basis for the national Materials Genome Initiative (MGI), making reproducibility even more important. In this project, nine research groups from eight universities are combining their expertise to create a software environment, called the Molecular Simulation Design Framework (MoSDeF) that will enable the automation of molecular-based computer simulations of soft materials (such as fluids, polymers, and biological systems) and will enable MGI-style screening of such systems. MoSDeF is open source and the use of MoSDeF will enable reproducibility in molecular-based computer simulations, because all simulation steps, all input data, and all codes used will be publicly accessible to anyone to reproduce a published simulation. MoSDeF will contribute to reproducibility through standardization and maintaining the provenance of forcefields, one of the most common sources of irreproducibility in molecular-based simulations.Reproducibility in scientific research has become a prominent issue. Computational scientists, along with the rest of the scientific community, are grappling with the central question: How can a study be performed and published in such a way that it can be replicated by others? Answering this question is essential to the scientific enterprise and increasingly urgent, as reproducibility issues faced in small-scale studies will only be compounded as researchers look to harness the ever expanding computational power to perform large-scale Materials Genome Initiative (MGI) inspired screening studies, thus growing the number of simulations by orders of magnitude. Addressing the issues of reproducibility in soft matter simulation is particularly challenging, given the complexity of the simulation inputs and workflows, and the all-to-common usage of closed-source software. In this proposal, nine leading research groups (from Vanderbilt, U Michigan, Notre Dame U, U Delaware, Boise State U, U Houston, Wayne State U, and U Minnesota), representing a broad range of expertise, and an equally broad range of science applications, simulation codes, algorithms and analysis tools, along with computer scientists from Vanderbilt's Institute for Software Integrated Systems (ISIS), are committing to invest their expertise and capabilities to transform the mindset of molecular simulationists to perform and publish their simulations in such a way as to be Transparent, Reproducible, Usable by others, and Extensible (TRUE). Most of the investigators are recent or current holders of grants from the software program (i.e., S2I2, SSI or SSE grants); thus, the project builds upon, and brings synergy to, an existing large investment in molecular simulation software by NSF. To drive the community towards performing simulation that are TRUE, new software tools to facilitate best practices will be developed. Specifically, this will be achieved by expanding the capabilities of the open-source molecular simulation design framework (MoSDeF), which was initiated at Vanderbilt with support from two NSF grants. MoSDeF is a modular, scriptable Python framework that includes modules for programmatic system construction, encoding and applying force field usage rules, and workflow management, allowing the exact procedures used to setup and perform a simulation to be capture, version-controlled, and preserved. Continued development of the existing MoSDeF modules will be performed to support a wider range of force fields, molecular models, and open-source simulation engines. The creation of a plugin architecture for community extension, and the development of new modules for force field optimization, free energy calculations, and screening, will further allow MoSDeF can achieve these goals.This project is supported by the Office of Advanced Cyberinfrastructure in the Directorate for Computer & Information Science & Engineering and the Division of Materials Research and the Division of Chemistry in the Directorate of Mathematical and Physical Sciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

随着基于分子的计算机模拟天然发生和人造（合成）材料越来越多地用于预测其性质，这些模拟的可重复性成为越来越重要的问题。这些模拟是复杂的，需要大量的计算机时间，通常是手动执行的 - 即一次将一个组合起来，从所有进入此类模拟的组件中，包括分子如何相互作用的模型（称为Force Fields）。此外，人们有很大的兴趣能够在大量不同但相关的系统上进行此类计算模拟，以筛选出理想的属性，从而导致发现新材料及其在应用中的两倍和一半是现有实验性方法的一半，并将其纳入应用的一半。这种野心是国家材料基因组倡议（MGI）的基础，使重复性变得更加重要。在这个项目中，来自八所大学的九个研究小组正在将其专业知识结合起来，以创建一个称为分子模拟设计框架（MOSDEF）的软件环境，这些软件将能够自动化基于分子的软材料的计算机模拟（例如流体，聚合物和生物系统），并将启用此类系统的MGI式筛选。 MOSDEF是开源的，MOSDEF的使用将在基于分子的计算机模拟中启用可重复性，因为所有仿真步骤，所有输入数据以及所有使用的代码都可以公开访问任何人，以重现已发布的模拟。 MOSDEF将通过标准化和维持力场的出处来促进可重复性，这是基于分子的模拟中最常见的不可夸大性来源之一。科学研究​​中的可重复性已成为一个杰出的问题。计算科学家以及其余的科学界都在努力解决一个主要问题：如何以其他方式进行研究和发表研究？回答这个问题对于科学企业和越来越紧迫至关重要，因为研究人员希望利用不断扩展的计算能力来执行大规模材料基因组计划（MGI）启发的筛选研究，因此，仅通过幅度增长了模拟数量，因此小规模研究中面临的可重复性问题才会变得更加复杂。考虑到模拟输入和工作流程的复杂性以及封闭源软件的全面用法，解决软物质模拟中可重复性的问题特别具有挑战性。 In this proposal, nine leading research groups (from Vanderbilt, U Michigan, Notre Dame U, U Delaware, Boise State U, U Houston, Wayne State U, and U Minnesota), representing a broad range of expertise, and an equally broad range of science applications, simulation codes, algorithms and analysis tools, along with computer scientists from Vanderbilt's Institute for Software Integrated Systems (ISIS), are committing to invest their转变分子模拟主义者心态的专业知识和能力，以透明，可重现的，其他人可用且可扩展的方式执行和发布模拟。大多数调查人员是该软件计划（即S2I2，SSI或SSE赠款）的最新赠款或当前持有人；因此，该项目建立在NSF对分子模拟软件上的现有大量投资基础上。为了推动社区进行真实的模拟，将开发新的软件工具来促进最佳实践。具体而言，这将通过扩展开源分子仿真设计框架（MOSDEF）的能力来实现，该框架是在范德比尔特（Vanderbilt）启动的，并得到了两个NSF赠款的支持。 MOSDEF是一个模块化的，可脚本的Python框架，其中包括用于程序化系统构建，编码和应用力场使用规则和工作流程管理的模块，允许使用用于设置和执行模拟的确切过程，可以捕获，版本对照控制并保留。将继续开发现有的MOSDEF模块，以支持更广泛的力场，分子模型和开源模拟引擎。 The creation of a plugin architecture for community extension, and the development of new modules for force field optimization, free energy calculations, and screening, will further allow MoSDeF can achieve these goals.This project is supported by the Office of Advanced Cyber​​infrastructure in the Directorate for Computer & Information Science & Engineering and the Division of Materials Research and the Division of Chemistry in the Directorate of Mathematical and Physical Sciences.This award reflects NSF's statutory mission and使用基金会的知识分子优点和更广泛的审查标准，通过评估被认为值得支持。

项目成果

MoSDeF Cassandra: A complete Python interface for the Cassandra Monte Carlo software

MoSDeF Cassandra：Cassandra Monte Carlo 软件的完整 Python 接口

• DOI: 10.1002/jcc.26544
• 发表时间: 2021
• 期刊: Journal of Computational Chemistry
• 影响因子: 3
• 作者: DeFever, Ryan S.;Matsumoto, Ray A.;Dowling, Alexander W.;Cummings, Peter T.;Maginn, Edward J.
• 通讯作者: Maginn, Edward J.