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Abstrakt
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, under- developed 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 obtainead from simpler fixed partial charge force fields.
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Autorzy (20)
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Alex Albaugh
- University of California, Berkeley Department of Chemical and Biomolecular Engineering
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Henry Boateng
- Bates College Department of Mathematics
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Richard Bradshaw
- University of Southampton School of Chemistry
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Omar Demerdash
- University of California, Berkeley Department of Chemistry
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Yuezhi Mao
- University of California, Berkeley Department of Chemistry
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Daniel Margul
- New York University Department of Chemistry
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Jason Swails
- Rutgers University Department of Chemistry and Chemical Biology
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Qiao Zeng
- National Institutes of Health, Bethesda, Maryland Laboratory of Computational Biology, National Heart, Lung and Blood Institute
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David Case
- Rutgers University Department of Chemistry and Chemical Biology
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Peter Eastman
- Stanford University Department of Chemistry
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Jonathan Essex
- University of Southampton School of Chemistry
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Martin Head-Gordon
- University of California, Berkeley Department of Chemistry
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Vijay Pande
- Stanford University Department of Chemistry
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Jay Ponder
- Washington University in St. Louis Department of Chemistry
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Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California .
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Chris-Kriton Skylaris
- University of Southampton School of Chemistry
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Ilian Todorov
- STFC Daresbury Laborator .
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Mark Tuckerman
- New York University Department of Chemistry
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Teresa Head-Gordon
- University of California, Berkeley Department of Chemistry
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Pełna treść
- Wersja publikacji
- Accepted albo Published Version
- DOI:
- Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1021/acs.jpcb.6b06414
- Licencja
- Copyright (2016 American Chemical Society)
Słowa kluczowe
Informacje szczegółowe
- Kategoria:
- Publikacja w czasopiśmie
- Typ:
- artykuł w czasopiśmie wyróżnionym w JCR
- Opublikowano w:
-
JOURNAL OF PHYSICAL CHEMISTRY B
nr 120,
strony 9811 - 9832,
ISSN: 1520-6106 - Język:
- angielski
- Rok wydania:
- 2016
- Opis bibliograficzny:
- Albaugh A., Boateng H., Bradshaw R., Demerdash O., Dziedzic J., Mao Y., Margul D., Swails J., Zeng Q., Case D., Eastman P., Essex J., Head-Gordon M., Pande V., Ponder J., Shao Y., Skylaris C., Todorov I., Tuckerman M., Head-Gordon T.: Advanced Potential Energy Surfaces for Molecular Simulation// JOURNAL OF PHYSICAL CHEMISTRY B. -Vol. 120, nr. 37 (2016), s.9811-9832
- DOI:
- Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1021/acs.jpcb.6b06414
- Weryfikacja:
- Politechnika Gdańska
wyświetlono 131 razy
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