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: 1835874
• 负责人: Peter Cummings
• 金额: $ 108.95万
• 依托单位: Vanderbilt University
• 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=1835874&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.

随着对天然材料和人造（合成）材料的基于分子的计算机模拟越来越多地用于预测其特性，这些模拟的可重复性成为一个日益重要的问题。这些模拟很复杂，需要大量的计算机时间，并且通常是手动执行的 - 即一次将进入此类模拟的所有组件组合在一起，包括分子如何相互作用的模型（已知作为力场）。此外，人们对能够在大量不同但相关的系统上执行此类计算模拟以筛选所需的特性非常感兴趣，从而使新材料的发现及其融入应用的速度提高两倍和一半现有方法（主要是实验方法）的成本。这一雄心壮志是国家材料基因组计划 (MGI) 的基础，使得可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将他们的专业知识结合起来创建一个软件环境，称为分子模拟设计框架（MoSDeF），它将实现软材料（例如流体、聚合物、和生物系统），并将实现对此类系统的 MGI 式筛选。 MoSDeF 是开源的，MoSDeF 的使用将实现基于分子的计算机模拟的可重复性，因为所有模拟步骤、所有输入数据和所有使用的代码都可供任何人公开访问，以重现已发布的模拟。 MoSDeF 将通过标准化和维护力场的来源来促进可重复性，力场是分子模拟中最常见的不可重复性来源之一。科学研究​​中的可重复性已成为一个突出问题。计算科学家以及科学界的其他成员正在努力解决一个核心问题：如何才能以可以被其他人复制的方式进行和发表一项研究？回答这个问题对于科学事业至关重要，而且越来越紧迫，因为当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) 启发的筛选研究时，小规模研究中面临的重现性问题只会变得更加复杂。 ，从而使模拟数量增加几个数量级。考虑到模拟输入和工作流程的复杂性以及闭源软件的普遍使用，解决软物质模拟中的再现性问题尤其具有挑战性。在这项提案中，九个领先的研究小组（来自范德比尔特大学、密歇根大学、圣母大学、特拉华大学、博伊西州立大学、休斯顿大学、韦恩州立大学和明尼苏达大学）代表了广泛的专业知识和同样广泛的领域科学应用、模拟代码、算法和分析工具以及范德比尔特软件集成系统研究所 (ISIS) 的计算机科学家致力于投入他们的专业知识和能力，以改变分子模拟学家执行和发布模拟的思维方式以透明、可复制、可供他人使用和可扩展（TRUE）的方式。大多数研究人员最近或当前获得了软件程序的资助（即 S2I2、SSI 或 SSE 资助）；因此，该项目建立在 NSF 对分子模拟软件现有大量投资的基础上，并为其带来协同效应。为了推动社区执行真实的模拟，将开发新的软件工具来促进最佳实践。具体来说，这将通过扩展开源分子模拟设计框架 (MoSDeF) 的功能来实现，该框架是范德比尔特大学在两项 NSF 拨款的支持下发起的。 MoSDeF 是一个模块化、可编写脚本的 Python 框架，包括用于编程系统构建、编码和应用力场使用规则以及工作流管理的模块，允许捕获、版本控制和保留用于设置和执行模拟的确切程序。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。创建用于社区扩展的插件架构，以及开发用于力场优化、自由能计算和筛选的新模块，将进一步使 MoSDeF 能够实现这些目标。该项目得到了该局高级网络基础设施办公室的支持计算机与信息科学与工程以及数学和物理科学理事会的材料研究部和化学部。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响进行评估，认为值得支持审查 标准。

项目成果

MoSDeF, a Python Framework Enabling Large-Scale Computational Screening of Soft Matter: Application to Chemistry-Property Relationships in Lubricating Monolayer Films

MoSDeF，一种能够对软物质进行大规模计算筛选的 Python 框架：在润滑单层薄膜中的化学性质关系的应用

• DOI: 10.1021/acs.jctc.9b01183
• 发表时间: 2020-03
• 期刊: Journal of Chemical Theory and Computation
• 影响因子: 5.5
• 作者: Summers, Andrew Z.;Gilmer, Justin B.;Iacovella, Christopher R.;Cummings, Peter T.;MCabe, Clare
• 通讯作者: MCabe, Clare

Formalizing atom-typing and the dissemination of force fields with foyer

通过门厅形式化原子类型和力场传播

• DOI: 10.1016/j.commatsci.2019.05.026
• 发表时间: 2018-12-07
• 期刊: Computational Materials Science
• 影响因子: 3.3
• 作者: Christoph Klein;Andrew Z. Summers;M. Thompson;Justin B. Gilmer;C. McCabe;P. Cummings;J. Sallai
• 通讯作者: J. Sallai

Open-source molecular modeling software in chemical engineering

化学工程中的开源分子建模软件

• DOI: 10.1016/j.coche.2019.03.008
• 发表时间: 2019-03
• 期刊: Current Opinion in Chemical Engineering
• 影响因子: 6.6
• 作者: Cummings, Peter T;Gilmer, Justin B
• 通讯作者: Gilmer, Justin B

Influence of Single-Stranded DNA Coatings on the Interaction between Graphene Nanoflakes and Lipid Bilayers

单链 DNA 涂层对石墨烯纳米片与脂质双层相互作用的影响

• DOI: 10.1021/acs.jpcb.9b04042
• 发表时间: 2019-08
• 期刊: The Journal of Physical Chemistry B
• 作者: Moore, Timothy C.;Yang, Alexander H.;Ogungbesan, Olu;Hartkamp, Remco;Iacovella, Christopher R.;Zhang, Qi;McCabe, Clare
• 通讯作者: McCabe, Clare

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: 2021-04
• 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.