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

SUBMITTER: Lemkul JA 

PROVIDER: S-EPMC4865892 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature