DeFever Ryan S, Matsumoto Ray A, Dowling Alexander W, Cummings Peter T, Maginn Edward J
Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, USA.
Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA.
J Comput Chem. 2021 Jul 5;42(18):1321-1331. doi: 10.1002/jcc.26544. Epub 2021 Apr 30.
We introduce a new Python interface for the Cassandra Monte Carlo software, molecular simulation design framework (MoSDeF) Cassandra. MoSDeF Cassandra provides a simplified user interface, offers broader interoperability with other molecular simulation codes, enables the construction of programmatic and reproducible molecular simulation workflows, and builds the infrastructure necessary for high-throughput Monte Carlo studies. Many of the capabilities of MoSDeF Cassandra are enabled via tight integration with MoSDeF. We discuss the motivation and design of MoSDeF Cassandra and proceed to demonstrate both simple use-cases and more complex workflows, including adsorption in porous media and a combined molecular dynamics - Monte Carlo workflow for computing lateral diffusivity in graphene slit pores. The examples presented herein demonstrate how even relatively complex simulation workflows can be reduced to, at most, a few files of Python code that can be version-controlled and shared with other researchers. We believe this paradigm will enable more rapid research advances and represents the future of molecular simulations.
我们为卡珊德拉蒙特卡罗软件（分子模拟设计框架MoSDeF卡珊德拉）引入了一种新的Python接口。MoSDeF卡珊德拉提供了简化的用户界面，与其他分子模拟代码具有更广泛的互操作性，能够构建可编程且可重现的分子模拟工作流程，并构建了高通量蒙特卡罗研究所需的基础设施。MoSDeF卡珊德拉的许多功能是通过与MoSDeF紧密集成来实现的。我们讨论了MoSDeF卡珊德拉的动机和设计，并继续展示简单的用例和更复杂的工作流程，包括多孔介质中的吸附以及用于计算石墨烯狭缝孔中横向扩散率的分子动力学 - 蒙特卡罗联合工作流程。本文给出的示例展示了即使是相对复杂的模拟工作流程最多也能简化为几个可进行版本控制并与其他研究人员共享的Python代码文件。我们相信这种范式将推动更快速的研究进展，并代表了分子模拟的未来。
