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

该项目的总体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方面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及其合作者正在与NVIDIA就该项目进行合作，以帮助加快开发工作。最后，在这里进行的项目将训练学生的形式理论，计算机编程，计算化学和生物学，以及手稿准备/出版，进一步增强美国的技术劳动力。量子力学/分子力学（QM/MM）组合模型在理解化学反应性和分子间相互作用方面取得了重大进展。这种方法允许使用精确的QM方法对系统中键断裂和形成的区域进行建模，而使用经典模型对周围环境进行处理。QM/MM研究中最广泛使用的QM模型通常是半经验的，但最准确的是使用密度泛函理论（DFT）， Hartree-Fock （HF）或post HF方法。使用更精确的方法时的缺点是计算费用大，这限制了QM/MM分子动力学模拟的程度。多年来，通过算法和硬件的改进，QM方法的性能得到了极大的提高。该项目将重点关注这两个方面：对于前者，PI将增加处理QM/MM计算中的远程相互作用的能力，添加支持GPU的相关方法并创建通用的电子排斥相互作用（ERI）引擎，而对于后者，PI将集成GPU支持的量子相互作用计算内核（QUICK）程序与AMBER程序套件中的Sander和PMEMD分子动力学（MD）引擎。AMBER是最流行的模拟包之一，已经被AMBER开发者社区支持和维护了大约30年。这里提出的开发将通过AMBERTools完全提供给社区，AMBERTools使用开源模型发布（参见http://ambermd.org/AmberTools.php）。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和数学与物理科学理事会的化学部门提供支持。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。

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.