Salahub Dennis R, Noskov Sergei Yu, Lev Bogdan, Zhang Rui, Ngo Van, Goursot Annick, Calaminici Patrizia, Köster Andreas M, Alvarez-Ibarra Aurelio, Mejía-Rodríguez Daniel, Řezáč Jan, Cailliez Fabien, de la Lande Aurélien
Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
Molecules. 2015 Mar 16;20(3):4780-812. doi: 10.3390/molecules20034780.
The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.
密度泛函代码deMon2k始终采用拟合密度（辅助密度泛函理论），这在不牺牲必要精度的情况下提供了极大的速度优势。本文综述了强大的量子力学/分子力学（QM/MM）方法。在概述了deMon2k在保持精度的同时使其高效的基本特征之后，对三种QM/MM实现方式进行了比较和对比。第一种是将deMon2k与CHARMM分子力学代码（CHARMM-deMon2k）连接；第二种是将分子力学直接编码在deMon2k软件中；第三种是使用Ruby中的化学（Cuby）包装器来驱动计算。Cuby也用于受限密度泛函理论/分子力学计算。简要描述了每种实现方式；讨论了优缺点，并简要介绍了一些近期的应用。应用包括溶剂化离子和生物分子、在多聚谷氨酰胺神经退行性疾病中重要的多聚谷氨酰胺肽、铜单加氧酶以及隐花色素中的超快电子转移。
