title: An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.
abstract: Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Lemkul
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States.
authors.forename: Jing
authors.initials: J
authors.lastname: Huang
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
mesh_terms: D002241:Carbohydrates / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D008055:Lipids / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry
chemical_list: D002241:Carbohydrates; D008055:Lipids; D011506:Proteins; D004247:DNA
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