Advanced Potential Energy Surfaces for Molecular Simulation

被引:72
作者
Albaugh, Alex [3 ]
Boateng, Henry A. [9 ]
Bradshaw, Richard T. [1 ]
Demerdash, Omar N. [2 ]
Dziedzic, Jacek [1 ,5 ]
Mao, Yuezhi [2 ]
Margul, Daniel T. [6 ]
Swails, Jason [10 ]
Zeng, Qiao [8 ]
Case, David A. [10 ]
Eastman, Peter [11 ]
Wang, Lee-Ping [11 ]
Essex, Jonathan W. [1 ]
Head-Gordon, Martin [2 ]
Pande, Vijay S. [11 ]
Ponder, Jay W. [12 ]
Shao, Yihan [13 ]
Skylaris, Chris-Kriton [1 ]
Todorov, Ilian T. [14 ]
Tuckerman, Mark E. [6 ,7 ,15 ]
Head-Gordon, Teresa [2 ,3 ,4 ]
机构
[1] Univ Southampton, Sch Chem, Southampton SO17 1BJ, Hants, England
[2] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA
[3] Univ Calif Berkeley, Dept Chem & Biomol Engn, Berkeley, CA 94720 USA
[4] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA
[5] Gdansk Univ Technol, Fac Appl Phys & Math, PL-80223 Gdansk, Poland
[6] NYU, Dept Chem, New York, NY 10003 USA
[7] NYU, Courant Inst Math Sci, New York, NY 10003 USA
[8] NHLBI, Lab Computat Biol, NIH, Bethesda, MD 20892 USA
[9] Bates Coll, Dept Math, 2 Andrews Rd, Lewiston, ME 04240 USA
[10] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA
[11] Stanford Univ, Dept Chem, Stanford, CA 94305 USA
[12] Washington Univ, Dept Chem, St Louis, MO 63130 USA
[13] Q Chem Inc, 6601 Owens Dr,Suite 105, Pleasanton, CA 94588 USA
[14] STFC Daresbury Lab, Keckwick Lane, Warrington WA4 4AD, Cheshire, England
[15] NYU, Ctr Computat Chem, NYU ECNU, Shanghai 200062, Shanghai, Peoples R China
基金
英国工程与自然科学研究理事会; 美国国家科学基金会; 美国国家卫生研究院;
关键词
POLARIZABLE FORCE-FIELD; DENSITY-FUNCTIONAL THEORY; GENERALIZED GRADIENT APPROXIMATION; PARTICLE MESH EWALD; NONCOVALENT INTERACTIONS; DECOMPOSITION ANALYSIS; PERTURBATION-THEORY; QUANTUM-CHEMISTRY; EFFICIENT IMPLEMENTATION; ELECTRONIC POLARIZATION;
D O I
10.1021/acs.jpcb.6b06414
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate Models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC). architectures, such as multicore CPUs and modern graphics processing units (CPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware-platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory-while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
引用
收藏
页码:9811 / 9832
页数:22
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