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Three-site and five-site fixed-charge water models compatible with AMOEBA force field.

Authors
  • Pan, Cong1
  • Liu, Chengwen2
  • Peng, Junhui1
  • Ren, Pengyu2
  • Huang, Xuhui1, 3
  • 1 Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong. , (Hong Kong SAR China)
  • 2 Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas.
  • 3 Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong. , (Hong Kong SAR China)
Type
Published Article
Journal
Journal of Computational Chemistry
Publisher
Wiley (John Wiley & Sons)
Publication Date
Apr 15, 2020
Volume
41
Issue
10
Pages
1034–1044
Identifiers
DOI: 10.1002/jcc.26151
PMID: 31976572
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

In a typical biomolecular simulation using Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, the vast majority molecules in the simulation box consist of water, and these water molecules consume the most CPU power due to the explicit mutual induction effect. To improve the computational efficiency, we here develop two new nonpolarizable water models (with flexible bonds and fixed charges) that are compatible with AMOEBA solute: the 3-site AW3C and 5-site AW5C. To derive the force-field parameters for AW3C and AW5C, we fit to six experimental liquid thermodynamic properties: liquid density, enthalpy of vaporization, dielectric constant, isobaric heat capacity, isothermal compressibility and thermal expansion coefficient, at a broad range of temperatures from 261.15 to 353.15 K under 1.0 atm pressure. We further validate our AW3C and AW5C water models by showing that they can well reproduce the radial distribution function g(r), self-diffusion constant D, and hydration free energy from the AMOEBA03 water model and the experimental observations. Furthermore, we show that our AW3C and AW5C water models can greatly accelerate (>5 times) the bulk water as well as biomolecular simulations when compared to AMOEBA water. Specifically, we demonstrate that the applications of AW3C and AW5C water models to simulate a DNA duplex lead to a threefold acceleration, and in the meanwhile well maintain the structural properties as the fully polarizable AMOEBA water. We expect that our AW3C and AW5C water models hold great promise to be widely applied to simulate complex bio-molecules using the AMOEBA force field. © 2020 Wiley Periodicals, Inc.

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