Elements: Software: NSCI: Efficient GPU Enabled QM/MM Calculations: AMBER Coupled with QUICK

该项目的首要目标是开发一个软件网络基础设施，旨在解决催化，药物设计和能量转换中的重要分子水平问题。PI和他的合作者将开发开源软件，以提高使用可持续模型解决化学和生物问题的能力。PI和他的合作者正在与NVIDIA就该项目进行合作，以帮助加速开发工作。最后，在这里进行的项目将培养学生的正式理论，计算机编程，计算化学和生物学，和手稿的准备/出版，进一步提高技术劳动力在美国。结合量子力学/分子力学（QM/MM）模型，使化学反应性和分子间相互作用的理解显着进步。这种方法允许使用精确的QM方法对系统中要断开和形成键的区域进行建模，而使用经典模型处理周围环境。QM/MM研究中最广泛使用的QM模型通常是半经验的，但最精确的采用密度泛函理论（DFT），Hartree-Fock（HF）或后HF方法。使用更精确的方法时的缺点是计算费用，这限制了QM/MM分子动力学模拟的范围。多年来，通过算法和硬件的改进，QM方法的性能得到了很大的提高。该项目将侧重于以下两个方面：对于前者，PI将增加在QM/MM计算中处理长程相互作用的能力，增加GPU支持的相关方法，并创建一个通用的电子排斥相互作用（ERI）引擎，而对于后者，PI将把支持GPU的量子相互作用计算内核（QUICK）程序与Sander和PMEMD分子动力学（MD）程序集成在一起引擎从琥珀套件的程序。AMBER是最受欢迎的模拟软件包之一，已经得到AMBER开发人员社区的支持和支持约30年。社区将通过AMBERTools全面获得此处提议的开发，AMBERTools使用开放源代码模式发布（见http：//ambermd.org/AmberTools.php）。该项目得到了计算机信息科学工程局高级网络基础设施办公室和数学与物理科学局化学部的支持。该奖项反映了NSF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。

The over-arching goal of this project is to develop a software cyberinfrastructure aimed at solving important molecular-level problems in catalysis, drug design, and energy conversion. The PI and his collaborators will develop open source software that will enhance the ability to tackle chemical and biological problems using a sustainable model. The PI and his collaborators are collaborating with NVIDIA on this project to help accelerate the development efforts. Finally, the projects undertaken here will train students in formal theory, computer programming, computational chemistry and biology, and manuscript preparation/publication further enhancing the technical workforce in the USA.Combined quantum mechanical/molecular mechanical (QM/MM) models have enabled significant advances in the understanding of chemical reactivity and intermolecular interactions. This approach allows regions of a system where bonds are to be broken and formed to be modeled using accurate QM methods, while the surrounding environment is treated using classical models. The most widely used QM models in QM/MM studies are generally semiempirical, but the most accurate employ density functional theory (DFT), Hartree-Fock (HF) or post HF methods. The shortcoming when using the more accurate methods is the computational expense, which limits the extent of QM/MM molecular dynamics simulations. The performance of QM methods has been greatly improved over the years through algorithmic and hardware improvements. This project will focus on both: for the former the PI will add the ability to handle long-range interactions in QM/MM calculations, add GPU enabled correlated methods and create an electron repulsion interaction (ERI) engine for general use, while for the latter the PI will integrate the GPU enabled Quantum Interaction Computational Kernel (QUICK) program with the Sander and PMEMD molecular dynamics (MD) engines from the AMBER suite of programs. AMBER is one of the most popular simulations packages and has been supported and sustained by the AMBER developer community for approximately 30 years. The developments proposed here will be fully available to the community via AMBERTools, which is released using an open source model (see http://ambermd.org/AmberTools.php). This project is supported by the Office of Advanced Cyberinfrastructure in the Directorate for Computer & Information Science & Engineering 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.