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

随着基于分子的计算机模拟自然发生和人造（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一个越来越重要的问题。这些模拟是复杂的，需要大量的计算机时间，并且通常是手动执行的——也就是说，一次一个地将所有进入这种模拟的组件组合在一起，包括分子如何相互作用的模型（称为力场）。此外，人们对能够在大量不同但相关的系统上执行这种计算模拟非常感兴趣，以便筛选理想的特性，从而发现新材料并将其纳入应用，速度是现有实验方法的两倍，成本是现有方法的一半。这一雄心壮志是国家材料基因组计划（MGI）的基础，使可重复性变得更加重要。在这个项目中，来自8所大学的9个研究小组正在结合他们的专业知识创建一个名为分子模拟设计框架（MoSDeF）的软件环境，该环境将实现基于分子的软材料（如流体、聚合物和生物系统）计算机模拟的自动化，并将实现mgi式的系统筛选。MoSDeF是开源的，使用MoSDeF可以实现基于分子的计算机模拟的再现性，因为任何人都可以公开访问所有模拟步骤、所有输入数据和所有使用的代码来重现已发布的模拟。MoSDeF将通过标准化和维护力场的来源来促进再现性，力场是基于分子的模拟中最常见的不可再现性来源之一。可重复性在科学研究中已成为一个突出的问题。计算科学家和其他科学界人士都在努力解决一个核心问题：一项研究如何才能以一种可以被其他人复制的方式进行和发表？回答这个问题对科学事业至关重要，而且越来越紧迫，因为小规模研究中面临的可重复性问题只会变得更加复杂，因为研究人员希望利用不断扩大的计算能力来进行大规模的材料基因组计划（MGI）启发的筛选研究，从而以数量级增加模拟的数量。考虑到模拟输入和工作流程的复杂性，以及对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。在这份提案中，9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，以及同样广泛的科学应用、模拟代码、算法和分析工具，以及来自范德比尔特软件集成系统研究所（ISIS）的计算机科学家，正致力于投入他们的专业知识和能力，以改变分子模拟学家的思维方式，以透明、可复制、可被他人使用和可扩展的方式执行和发布他们的模拟（TRUE）。大多数研究人员是软件项目（即S2I2， SSI或SSE资助）的最近或当前持有人；因此，该项目建立在美国国家科学基金会对分子模拟软件的现有大笔投资的基础上，并带来协同效应。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，该框架是在范德比尔特大学发起的，得到了两项NSF拨款的支持。MoSDeF是一个模块化的，可脚本化的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，允许用于设置和执行模拟的确切过程被捕获，版本控制和保存。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。为社区扩展创建插件架构，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。该项目由计算机与信息科学与工程理事会的先进网络基础设施办公室以及数学与物理科学理事会的材料研究司和化学司提供支持。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.