Cyberinfrastructure and Research Facilities: Tools for Ab Initio Molecular Dynamics and Simulation Analysis

伊利诺伊大学的Todd Martinez和爱荷华州立大学的Mark Gordon、Brett Bode、Ricky Kendall和Masha Sosonkina得到了美国国家科学基金会化学和共享网络基础设施部门的支持，隶属于网络基础设施和研究设施项目。该项目将把最先进的分子动力学技术与电子结构方法结合起来，以公开的计算机代码提供给对确定化学反应机制感兴趣的专家和非专家使用。图形用户界面将允许快速模拟设置，数据库驱动的分析工具将自动存档结果与复杂的多维分析相结合。反应机理的确定是化学中的一项重要活动，用于解释现有的实验数据以及评估新实验的可行性。该项目的成果包括公开可用的软件工具，以及一个传播研讨会，这将允许反应速率估计，超快速实验的模拟，局部极小值的枚举和稳态光谱的自动生成。

Todd Martinez of the University of Illinois, and Mark Gordon, Brett Bode, Ricky Kendall, and Masha Sosonkina of Iowa State University are supported by the NSF Divisions of Chemistry and Shared Cyberinfrastructure, under the Cyberinfrastructure and Research Facilities Program. This project will link state-of-the-art molecular dynamics techniques with electronic structure methods in a publicly available computer code, for use by both experts and non-experts interested in determining chemical reaction mechanisms. A graphical user interface will allow fast simulation setups, and a database-driven analysis tool will couple automated archived results with sophisticated multi-dimensional analysis. The determination of reaction mechanisms is a major activity in chemistry, and is used to explain existing experimental data as well to assess the feasibility of new experiments. Outcomes of this project include publicly available software tools, along with a workshop for dissemination, that will allow for reaction rate estimation, simulation of ultra-fast experiments, enumeration of local minima, and automatic generation of steady-state spectra.