An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Printer-friendly versionPrinter-friendly versionPDF versionPDF version
TitleAn Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.
Publication TypeJournal Article
Year of Publication2016
AuthorsLemkul, JA, Huang, J, Roux, B, Mackerell, AD
JournalChem Rev
Volume116
Issue9
Pagination4983-5013
Date Published2016 05 11
ISSN1520-6890
KeywordsCarbohydrates, DNA, Lipids, Molecular Dynamics Simulation, Proteins
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.

DOI10.1021/acs.chemrev.5b00505
Alternate JournalChem. Rev.
PubMed ID26815602
PubMed Central IDPMC4865892
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
R01 GM070855 / GM / NIGMS NIH HHS / United States
F32 GM109632 / GM / NIGMS NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States