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

伊利诺伊大学的托德马丁内斯和爱荷华州州立大学的马克戈登、布雷特博德、里奇肯德尔和玛莎索松金娜在网络基础设施和研究设施计划下得到了NSF化学和共享网络基础设施部门的支持。 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在一个公开可用的计算机代码中，供对确定化学反应机理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主要活动，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提供的软件工具，沿着一个讲习班以供传播，这将允许反应速率估计、超快实验模拟、局部最小值计数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.