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Advanced Potential Energy Surfaces for Molecular Simulation.
Albaugh, Alex; Boateng, Henry A; Bradshaw, Richard T; Demerdash, Omar N; Dziedzic, Jacek; Mao, Yuezhi; Margul, Daniel T; Swails, Jason; Zeng, Qiao; Case, David A; Eastman, Peter; Wang, Lee-Ping; Essex, Jonathan W; Head-Gordon, Martin; Pande, Vijay S; Ponder, Jay W; Shao, Yihan; Skylaris, Chris-Kriton; Todorov, Ilian T; Tuckerman, Mark E; Head-Gordon, Teresa.
Afiliação
  • Boateng HA; Department of Mathematics, Bates College , 2 Andrews Road, Lewiston, Maine 04240, United States.
  • Bradshaw RT; School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom.
  • Dziedzic J; School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom.
  • Mao Y; Faculty of Applied Physics and Mathematics, Gdansk University of Technology , 80-223 Gdansk, Poland.
  • Zeng Q; Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8066, United States.
  • Case DA; Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
  • Eastman P; Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8066, United States.
  • Wang LP; Department of Chemistry, Stanford University , Stanford, California 94305, United States.
  • Essex JW; Department of Chemistry, Stanford University , Stanford, California 94305, United States.
  • Head-Gordon M; School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom.
  • Ponder JW; Department of Chemistry, Stanford University , Stanford, California 94305, United States.
  • Shao Y; Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States.
  • Skylaris CK; Q-Chem Inc. , 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States.
  • Todorov IT; School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom.
  • Tuckerman ME; STFC Daresbury Laboratory , Keckwick Lane, Daresbury, Warrington WA4 4AD, United Kingdom.
  • Head-Gordon T; NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai , Shanghai 200062, China.
J Phys Chem B ; 120(37): 9811-32, 2016 09 22.
Article em En | MEDLINE | ID: mdl-27513316
ABSTRACT
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 (GPUs). 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.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Teoria Quântica / Algoritmos / Gráficos por Computador / Software / Simulação de Dinâmica Molecular Idioma: En Ano de publicação: 2016 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Teoria Quântica / Algoritmos / Gráficos por Computador / Software / Simulação de Dinâmica Molecular Idioma: En Ano de publicação: 2016 Tipo de documento: Article