4.2 Article

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Multidisciplinary

Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors

Brad A. Bauer et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

Arginine in Membranes: The Connection Between Molecular Dynamics Simulations and Translocon-Mediated Insertion Experiments

Eric V. Schow et al.

JOURNAL OF MEMBRANE BIOLOGY (2011)

Article Chemistry, Physical

Revised charge equilibration parameters for more accurate hydration free energies of alkanes

Joseph E. Davis et al.

CHEMICAL PHYSICS LETTERS (2010)

Article Chemistry, Physical

The electrostatics of solvent and membrane interfaces and the role of electronic polarizability

Igor Vorobyov et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

Article Chemistry, Physical

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

Christopher M. Baker et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

Haibo Yu et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

Variation of Ion Polarizability from Vacuum to Hydration: Insights from Hirshfeld Partitioning

Brad A. Bauer et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2010)

Article Chemistry, Physical

Role of Electrostatics in Modulating Hydrophobic Interactions and Barriers to Hydrophobic Assembly

Brad A. Bauer et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Physical

Current Status of the AMOEBA Polarizable Force Field

Jay W. Ponder et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Biochemistry & Molecular Biology

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

Erik Wallin et al.

PROTEIN SCIENCE (2010)

Article Chemistry, Physical

Permeability of Small Molecules through a Lipid Bilayer: A Multiscale Simulation Study

Mario Orsi et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Chemistry, Multidisciplinary

Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields

Sandeep Patel et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Review Multidisciplinary Sciences

Many-body effects and simulations of potassium channels

Christopher J. Illingworth et al.

PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2009)

Article Biophysics

Distribution of amino acids in a lipid bilayer from computer simulations

Justin L. MacCallum et al.

BIOPHYSICAL JOURNAL (2008)

Article Chemistry, Physical

Origin and control of superlinear polarizability scaling in chemical potential equalization methods

G. Lee Warren et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Biomolecular simulations of membranes:: Physical properties from different force fields

Shirley W. I. Siu et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Effect of structural parameters on the polarizabilities of methanol clusters: A hirshfeld study

Alisa Krishtal et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Multidisciplinary

Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models

Yang Zhong et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

Additive Empirical Force Field for Hexopyranose Monosaccharides

Olgun Guvench et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Chemistry, Physical

The polarizability of point-polarizable water models: Density functional theory molecular mechanics results

Bernhard Schropp et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Chemistry, Physical

Revised charge equilibration potential for liquid alkanes

Joseph E. Davis et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Chemistry, Physical

Vibrational analysis of N-acetyl-α-D-glucosamine and β-D-glucuronic acid

Attila Kovacs et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Multidisciplinary Sciences

Application of a polarizable force field to calculations of relative protein-ligand binding affinities

Oleg Khoruzhii et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Calculation of protein-ligand binding free energy by using a polarizable potential

Dian Jiao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Physiology

Structural determinants of water permeability through the lipid membrane

John C. Mathai et al.

JOURNAL OF GENERAL PHYSIOLOGY (2008)

Article Chemistry, Physical

Additive and classical drude polarizable force fields for linear and cyclic ethers

Igor Vorobyov et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Chemistry, Physical

Critical analysis and extension of the Hirshfeld atoms in molecules

Patrick Bultinck et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Review Chemistry, Physical

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

Pedro E. M. Lopes et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Multidisciplinary Sciences

On the thermodynamic stability of a charged arginine side chain in a transmembrane helix

Sudha Dorairaj et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Using cryo-EM to measure the dipole potential of a lipid membrane

Liguo Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Chemistry, Physical

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential

Dian Jiao et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Physical

A Hirshfeld partitioning of polarizabilities of water clusters

A. Krishtal et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Review Chemistry, Multidisciplinary

Aqueous solutions next to phospholipid membrane surfaces: Insights from simulations

ML Berkowitz et al.

CHEMICAL REVIEWS (2006)

Article Chemistry, Physical

Towards a force field based on density fitting

JP Piquemal et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

A polarizable model of water for molecular dynamics simulations of biomolecules

G Lamoureux et al.

CHEMICAL PHYSICS LETTERS (2006)

Article Chemistry, Multidisciplinary

Computer simulation of the distribution of hexane in a lipid bilayer: Spatially resolved free energy, entropy, and enthalpy profiles

JL MacCallum et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Review Biochemistry & Molecular Biology

Asparagine-linked protein glycosylation: from eukaryotic to prokaryotic systems

Eranthie Weerapana et al.

GLYCOBIOLOGY (2006)

Review Chemistry, Physical

Polarizable empirical force field for alkanes based on the classical drude oscillator model

IV Vorobyov et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Chemistry, Physical

Water concentration profiles in membranes measured by ESEEM of spin-labeled lipids

DA Erilov et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Chemistry, Multidisciplinary

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials

LR Olano et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Towards understanding the interaction between oligosaccharides and water molecules

A Almond

CARBOHYDRATE RESEARCH (2005)

Article Chemistry, Physical

Dependence of ion hydration on the sign of the ion's charge

A Grossfield

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Chemistry, Physical

Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator

VM Anisimov et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)

Article Biochemical Research Methods

Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study

RB Von Dreele

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)

Article Biophysics

Complexation of phosphatidylcholine lipids with cholesterol

SA Pandit et al.

BIOPHYSICAL JOURNAL (2004)

Review Biophysics

Theoretical and computational models of biological ion channels

B Roux et al.

QUARTERLY REVIEWS OF BIOPHYSICS (2004)

Article Chemistry, Multidisciplinary

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

S Patel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Multidisciplinary Sciences

Energetics of ion conduction through the gramicidin channel

TW Allen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Chemistry, Physical

Temperature and pressure dependence of the AMOEBA water model

PY Ren et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

Review Chemistry, Multidisciplinary

Ion solvation thermodynamics from simulation with a polarizable force field

A Grossfield et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Chemistry, Physical

A simple polarizable model of water based on classical Drude oscillators

G Lamoureux et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

Review Chemistry, Physical

Polarizable atomic multipole water model for molecular mechanics simulation

PY Ren et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2003)

Article Biophysics

Gramicidin A channel as a test ground for molecular dynamics force fields

TW Allen et al.

BIOPHYSICAL JOURNAL (2003)

Article Chemistry, Multidisciplinary

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF

JP Piquemal et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)

Article Chemistry, Multidisciplinary

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

PY Ren et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)

Article Biophysics

Membrane water-penetration profiles from spin labels

D Marsh

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2002)

Article Chemistry, Multidisciplinary

Water polarizability in condensed phase:: Ab initio evaluation by cluster approach

A Morita

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)

Article Biophysics

The ionization state and the conformation of Glu-71 in the KcsA K+ channel

S Bernèche et al.

BIOPHYSICAL JOURNAL (2002)

Review Biophysics

NMR structures of biomolecules using field oriented media and residual dipolar couplings

JH Prestegard et al.

QUARTERLY REVIEWS OF BIOPHYSICS (2000)

Review Chemistry, Physical

Molecular dynamics simulations of lipid bilayers

SE Feller

CURRENT OPINION IN COLLOID & INTERFACE SCIENCE (2000)

Article Chemistry, Physical

Electron distribution in water

YS Badyal et al.

JOURNAL OF CHEMICAL PHYSICS (2000)