ArticleThe Journal of chemical physics2020
Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian.
Article in The Journal of chemical physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field.The journal of physical chemistry letters · 2025Article
- Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Getting the intermolecular forces correct: introducing the ASTA strategy for a water model.RSC advances · 2024Article
- Simulating the Fluorescence of the Locally Excited State of DMABN in Solvents of Different Polarities.The journal of physical chemistry. B · 2024Article
- Simulating the Fluorescence of Di-8-ANEPPS in Solvents of Different Polarity.The journal of physical chemistry. B · 2024Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.Journal of chemical theory and computation · 2021Article
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
- Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control.The Journal of chemical physics · 2020Article
- Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.Journal of computer-aided molecular design · 2017Article
- All-atom polarizable force field for DNA based on the classical Drude oscillator model.Journal of computational chemistry · 2014Article
- Systematic improvement of a classical molecular model of water.The journal of physical chemistry. B · 2013Article
- Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field.Journal of computational chemistry · 2013Article
- Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.The journal of physical chemistry. B · 2012Article
- Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.The Journal of chemical physics · 2012Article
- Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems.Biochimica et biophysica acta · 2012Review
- Simulating polarizable molecular ionic liquids with Drude oscillators.The Journal of chemical physics · 2010Article
- Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models.The journal of physical chemistry. B · 2010Article
- Role of electrostatics in modulating hydrophobic interactions and barriers to hydrophobic assembly.The journal of physical chemistry. B · 2010Article
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4 authors.
Funding
Abstract
Polarizable force fields based on classical Drude oscillators offer a practical and computationally efficient avenue to carry out molecular dynamics (MD) simulations of large biomolecular systems. To treat the polarizable electronic degrees of freedom, the Drude model introduces a virtual charged particle that is attached to its parent nucleus via a harmonic spring. Traditionally, the need to relax the electronic degrees of freedom for each fixed set of nuclear coordinates is achieved by performing an iterative self-consistent field (SCF) calculation to satisfy a selected tolerance. This is a computationally demanding procedure that can increase the computational cost of MD simulations by nearly one order of magnitude. To avoid the costly SCF procedure, a small mass is assigned to the Drude particles, which are then propagated as dynamic variables during the simulations via a dual-thermostat extended Lagrangian algorithm. To help clarify the significance of the dual-thermostat extended Lagrangian propagation in the context of the polarizable force field based on classical Drude oscillators, the statistical mechanics of a dual-temperature canonical ensemble is formulated. The conditions for dynamically maintaining the dual-temperature properties in the case of the classical Drude oscillator are analyzed using the generalized Langevin equation.
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