A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

Zeta Potential Determination from Molecular Simulations

(2020) Denys Biriukov et al.   Journal of Physical Chemistry C

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

(2020) Abhishek A. Kognole et al.   JOURNAL OF MOLECULAR MODELING

Surface Potential and Interfacial Water Order at the Amorphous TiO2 Nanoparticle/Aqueous Interface

(2020) Marie Bischoff et al.   Journal of Physical Chemistry C

Scaled charges at work: Salting out and interfacial tension of methane with electrolyte solutions from computer simulations

(2020) S. Blazquez et al.   FLUID PHASE EQUILIBRIA

Electronic continuum correction without scaled charges

(2020) Milan Předota et al.   JOURNAL OF MOLECULAR LIQUIDS

Oxalic acid adsorption on rutile: Experiments and Surface Complexation Modeling to 150°C

(2019) Michael L. Machesky et al.   LANGMUIR

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

(2019) Dmitry Bedrov et al.   CHEMICAL REVIEWS

Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions

(2019) Damien Laage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics

(2019) Philip E Mason et al.   Journal of Physical Chemistry Letters

Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations

(2019) Denys Biriukov et al.   LANGMUIR

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

(2019) Alexei Nikitin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Surface Characterization of Colloidal Silica Nanoparticles by Second Harmonic Scattering: Quantifying the Surface Potential and Interfacial Water Order

(2019) Arianna Marchioro et al.   Journal of Physical Chemistry C

A force field of Li+, Na+, K+, Mg2+, Ca2+, Cl−, and SO42− in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions

(2019) I. M. Zeron et al.   JOURNAL OF CHEMICAL PHYSICS

Charge Scaling Manifesto: A Way of Reconciling the Inherently Macroscopic and Microscopic Natures of Molecular Simulations

(2019) Brian J. Kirby et al.   Journal of Physical Chemistry Letters

Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization

(2019) Josef Melcr et al.   Journal of Chemical Theory and Computation

Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections

(2019) D. A. Tolmachev et al.   Journal of Chemical Theory and Computation

Force field development and simulations of intrinsically disordered proteins

(2018) Jing Huang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

(2018) Tomas Martinek et al.   JOURNAL OF CHEMICAL PHYSICS

Does an electronic continuum correction improve effective short-range ion-ion interactions in aqueous solution?

(2018) Ellen E. Bruce et al.   JOURNAL OF CHEMICAL PHYSICS

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2+

(2018) Francesco Villa et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations

(2018) Elise Duboué-Dijon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization

(2018) Josef Melcr et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions

(2018) Kyungreem Han et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calcium Sensing by Recoverin: Effect of Protein Conformation on Ion Affinity

(2018) Štěpán Timr et al.   Journal of Physical Chemistry Letters

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

(2018) Huiying Chu et al.   MOLECULAR PHYSICS

New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

(2018) Jejoong Yoo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

(2018) Louis Lagardère et al.   Chemical Science

How well do force fields capture the strength of salt bridges in proteins?

(2018) Mustapha Carab Ahmed et al.   PeerJ

Modeling of solid–liquid interfaces using scaled charges: rutile (110) surfaces

(2018) Denys Biriukov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Many-body effect determines the selectivity for Ca2+and Mg2+in proteins

(2018) Zhifeng Jing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polarizable force field for RNA based on the classical drude oscillator

(2018) Justin A. Lemkul et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation

(2018) Kevin R. DeMarco et al.   JOURNAL OF PHYSIOLOGY-LONDON

Interatomic potentials of Mg ions in aqueous solutions: structure and dehydration kinetics

(2018) Xinxing Zhang et al.   EUROPEAN JOURNAL OF MINERALOGY

A potential model for sodium chloride solutions based on the TIP4P/2005 water model

(2017) A. L. Benavides et al.   JOURNAL OF CHEMICAL PHYSICS

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

(2017) Hui Li et al.   Journal of Chemical Theory and Computation

Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges

(2017) Ondřej Kroutil et al.   JOURNAL OF MOLECULAR MODELING

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations

(2017) Elise Duboué-Dijon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Prediction of the Hydration Free Energies of 20 Salts through Adaptive Force Matching and the Proper Comparison with Experimental References

(2017) Jicun Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers

(2017) Matti Javanainen et al.   LANGMUIR

A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids

(2017) Huiying Chu et al.   MOLECULES

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

(2017) Sadra Kashefolgheta et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

(2016) Seonghoon Kim et al.   BIOPHYSICAL JOURNAL

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

(2016) Jejoong Yoo et al.   BIOPOLYMERS

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

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Complex refractive index of normal and malignant human colorectal tissue in the visible and near-infrared

(2016) Panagiotis Giannios et al.   Journal of Biophotonics

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

(2016) Karl T. Debiec et al.   Journal of Chemical Theory and Computation

Sodium Chloride, NaCl/ϵ: New Force Field

(2016) Raúl Fuentes-Azcatl et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Concepts and protocols for electrostatic free energies

(2016) Thomas Simonson et al.   MOLECULAR SIMULATION

Molecular electrometer and binding of cations to phospholipid bilayers

(2016) Andrea Catte et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Visible to near-infrared refractive properties of freshly-excised human-liver tissues: marking hepatic malignancies

(2016) Panagiotis Giannios et al.   Scientific Reports

The complex nature of calcium cation interactions with phospholipid bilayers

(2016) Adéla Melcrová et al.   Scientific Reports

Dependence of Refractive Index on Concentration and Temperature in Electrolyte Solution, Polar Solution, Nonpolar Solution, and Protein Solution

(2015) Chan-Yuan Tan et al.   JOURNAL OF CHEMICAL AND ENGINEERING DATA

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

(2015) Pengfei Li et al.   Journal of Chemical Theory and Computation

Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

(2015) Maria T. Panteva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering

(2015) Miriam Kohagen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring Ion–Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering

(2015) Miriam Kohagen et al.   Journal of Physical Chemistry Letters

Understanding Nucleic Acid–Ion Interactions

(2014) Jan Lipfert et al.   Annual Review of Biochemistry

Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets. 1. NMR and MD Characterization of the Complex between the c-Crk N-SH3 Domain and the Peptide Sos

(2014) Yi Xue et al.   BIOCHEMISTRY

Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

(2014) Manjeet Kumar et al.   CHEMPHYSCHEM

Transmembrane helix assembly and the role of salt bridges

(2014) Torsten H Walther et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions

(2014) Z. R. Kann et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models

(2014) Igor V. Leontyev et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

(2014) Karl T. Debiec et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions

(2014) Miriam Kohagen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

(2014) Fernanda Duarte et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

(2014) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

(2014) Jing Huang et al.   Journal of Physical Chemistry Letters

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization

(2014) Miriam Kohagen et al.   Journal of Physical Chemistry Letters

Hydration of the chloride ion in concentrated aqueous solutions using neutron scattering and molecular dynamics

(2014) Eva Pluhařová et al.   MOLECULAR PHYSICS

Specific Binding of Chloride Ions to Lipid Vesicles and Implications at Molecular Scale

(2013) Volker Knecht et al.   BIOPHYSICAL JOURNAL

Competition among Metal Ions for Protein Binding Sites: Determinants of Metal Ion Selectivity in Proteins

(2013) Todor Dudev et al.   CHEMICAL REVIEWS

A Polarizable Force-Field for Cholesterol and Sphingomyelin

(2013) David Robinson   Journal of Chemical Theory and Computation

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Ion Pairing in Aqueous Lithium Salt Solutions with Monovalent and Divalent Counter-Anions

(2013) Eva Pluhařová et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

(2013) Janamejaya Chowdhary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data

(2013) Richard M. Venable et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protonation and pK changes in protein–ligand binding

(2013) Alexey V. Onufriev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Force Fields for Studying the Structure and Dynamics of Ionic Liquids: A Critical Review of Recent Developments

(2012) Florian Dommert et al.   CHEMPHYSCHEM

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

(2012) Maria Fyta et al.   JOURNAL OF CHEMICAL PHYSICS

An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes

(2012) Joakim P. M. Jämbeck et al.   Journal of Chemical Theory and Computation

Polarizable Mean-Field Model of Water for Biological Simulations with AMBER and CHARMM Force Fields

(2012) Igor V. Leontyev et al.   Journal of Chemical Theory and Computation

Simulating GTP:Mg and GDP:Mg with a simple force field: A structural and thermodynamic analysis

(2012) Thomas Simonson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accurate Description of Aqueous Carbonate Ions: An Effective Polarization Model Verified by Neutron Scattering

(2012) Philip E. Mason et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids

(2012) Joakim P. M. Jämbeck et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization

(2012) Mario Vazdar et al.   Journal of Physical Chemistry Letters

Solvation and ion-pairing properties of the aqueous sulfate anion: explicit versus effective electronic polarization

(2012) Luís Pegado et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides

(2011) Moon Bae Gee et al.   Journal of Chemical Theory and Computation

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Polarizability versus mobility: atomistic force field for ionic liquids

(2011) Vitaly Chaban   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Accounting for electronic polarization in non-polarizable force fields

(2011) Igor Leontyev et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulating water with rigid non-polarizable models: a general perspective

(2011) Carlos Vega et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Histidine in continuum electrostatics protonation state calculations

(2011) Vernon Couch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Electronic Polarizability and the Effective Pair Potentials of Water

(2010) I. V. Leontyev et al.   Journal of Chemical Theory and Computation

Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules

(2010) I. V. Leontyev et al.   Journal of Chemical Theory and Computation

Solvation of Magnesium Dication: Molecular Dynamics Simulation and Vibrational Spectroscopic Study of Magnesium Chloride in Aqueous Solutions

(2010) Karen M. Callahan et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Ionic Charge Reduction and Atomic Partial Charges from First-Principles Calculations of 1,3-Dimethylimidazolium Chloride

(2010) Jochen Schmidt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electronic continuum model for molecular dynamics simulations

(2009) I. V. Leontyev et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of the charge profile in the KcsA selectivity filter using ab initio calculations and molecular dynamics simulations

(2009) Sebastian Kraszewski et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Cation specific binding with protein surface charges

(2009) B. Hess et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA