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

要素：软件：NSCI：支持高效 GPU 的 QM/MM 计算：AMBER 与 QUICK 相结合

基本信息

批准号：
1835144
负责人：
Kenneth Merz
金额：
$ 60万
依托单位：
Michigan State University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-01 至 2024-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835144&HistoricalAwards=false
关键词：
Elements Software NSCI Efficient GPU

项目摘要

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.

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级问题。PI和他的合作者将开发开源软件，该软件将增强使用可持续模式解决化学和生物问题的能力。PI和他的合作者正在与NVIDIA在这个项目上合作，以帮助加快开发工作。最后，这里开展的项目将培训学生在形式理论、计算机编程、计算化学和生物学以及手稿准备/出版方面的培训，进一步加强美国的技术队伍。量子力学/分子力学(QM/MM)组合模型使人们在理解化学反应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方法对系统中要断裂和形成键的区域进行建模，而周围环境则使用经典模型进行处理。在QM/MM研究中最广泛使用的QM模型通常是半经验的，但最准确的使用密度泛函理论(DFT)、Hartree-Fock(HF)或后HF方法。当使用更精确的方法时，缺点是计算量大，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方法的性能有了很大的提高。本项目将重点关注两者：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，添加启用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将集成启用GPU的量子相互作用计算核(QUICK)程序与Amber程序套件中的SANDER和PMEMD分子动力学(MD)引擎。Amber是最受欢迎的模拟包之一，已经由Amber开发人员社区支持和维护了大约30年。这里建议的开发将通过AMBERTools完全提供给社区，AMBERTools使用开放源码模型发布(参见http://ambermd.org/AmberTools.php).这个项目得到了计算机与信息科学与工程局的高级网络基础设施办公室和数学与物理科学局的化学部的支持。这个奖项反映了NSF的法定使命，通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为是值得支持的。