Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids

(2021) Yalun Yu et al.   Journal of Chemical Theory and Computation

How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes?

(2020) Ana West et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase

(2020) Marco Campetella et al.   JOURNAL OF CHEMICAL PHYSICS

Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids

(2020) Yalun Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

(2020) Marina P. Oliveira et al.   Journal of Chemical Theory and Computation

Computational Modeling of Realistic Cell Membranes

(2019) Siewert J. Marrink et al.   CHEMICAL REVIEWS

On the hydration of DOPE in solution

(2019) Natasha H. Rhys et al.   JOURNAL OF CHEMICAL PHYSICS

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

(2019) Joshua T. Horton et al.   Journal of Chemical Information and Modeling

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

(2019) Giray Enkavi et al.   CHEMICAL REVIEWS

Molecular Dynamics Simulations of Membrane Permeability

(2019) Richard M. Venable et al.   CHEMICAL REVIEWS

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

(2019) Alison N. Leonard et al.   CHEMICAL REVIEWS

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

(2019) Melanie P. Muller et al.   CHEMICAL REVIEWS

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

(2019) Andreas Krämer et al.   Journal of Chemical Theory and Computation

Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers

(2019) Hanne Antila et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Configuration-Sampling-Based Surrogate Models for Rapid Parameterization of Non-Bonded Interactions

(2018) Richard A. Messerly et al.   Journal of Chemical Theory and Computation

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations

(2018) Alison N. Leonard et al.   Journal of Chemical Theory and Computation

Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers

(2018) Alison N. Leonard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling Pseudomonas aeruginosa inner plasma membrane in planktonic and biofilm modes

(2018) Yalun Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields

(2018) Mohammad Mehdi Ghahremanpour et al.   Journal of Chemical Theory and Computation

Escaping Atom Types in Force Fields Using Direct Chemical Perception

(2018) David L. Mobley et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Ceramide and Ceramide-Phosphatidylcholine Bilayers

(2017) Eric Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Long-Range Dispersion Effects on the Water/Vapor Interface Simulated Using the Most Common Models

(2017) Marcello Sega et al.   JOURNAL OF PHYSICAL CHEMISTRY B

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations

(2016) Xiaohong Zhuang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field

(2016) Keri A. McKiernan et al.   Journal of Chemical Theory and Computation

A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers

(2016) Kristyna Pluhackova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties

(2015) Viviana Monje-Galvan et al.   BIOCHEMISTRY

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Mechanical properties of lipid bilayers from molecular dynamics simulation

(2015) Richard M. Venable et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Direct-Space Corrections Enable Fast and Accurate Lorentz–Berthelot Combination Rule Lennard-Jones Lattice Summation

(2015) Christian L. Wennberg et al.   Journal of Chemical Theory and Computation

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

(2015) Alexandru Botan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties

(2014) Xiaohong Zhuang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

(2014) Richard M. Venable et al.   BIOPHYSICAL JOURNAL

Cholesterol stabilizes fluid phosphoinositide domains

(2014) Zhiping Jiang et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Automated parameterization of intermolecular pair potentials using global optimization techniques

(2014) Andreas Krämer et al.   COMPUTER PHYSICS COMMUNICATIONS

A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations

(2014) Stefan Grimme   Journal of Chemical Theory and Computation

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain

(2014) Qufei Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

(2013) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

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

Activation and dynamic network of the M2 muscarinic receptor

(2013) Y. Miao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Influence of pH on Phosphatidylethanolamine Monolayer at the Air/Aqueous Solution Interface

(2012) Aneta Dorota Petelska et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions

(2012) Rolf E. Isele-Holder et al.   JOURNAL OF CHEMICAL PHYSICS

Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains

(2012) Jeffery B. Klauda 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

Divalent Cation-Induced Cluster Formation by Polyphosphoinositides in Model Membranes

(2012) Yu-Hsiu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism of Voltage Gating in Potassium Channels

(2012) M. O. Jensen et al.   SCIENCE

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature

(2011) Norbert Kučerka et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Development of the CHARMM Force Field for Lipids

(2011) R. W. Pastor et al.   Journal of Physical Chemistry Letters

Membrane protein sequestering by ionic protein–lipid interactions

(2011) Geert van den Bogaart et al.   NATURE

On the hydration of the phosphocholine headgroup in aqueous solution

(2010) Fabrizia Foglia et al.   JOURNAL OF CHEMICAL PHYSICS

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

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

GROW: A gradient-based optimization workflow for the automated development of molecular models

(2009) Marco Hülsmann et al.   COMPUTER PHYSICS COMMUNICATIONS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers

(2009) See-Wing Chiu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electrostatic Contribution to the Surface Pressure of Charged Monolayers Containing Polyphosphoinositides

(2008) I. Levental et al.   BIOPHYSICAL JOURNAL

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Automated conformational energy fitting for force-field development

(2008) Olgun Guvench et al.   JOURNAL OF MOLECULAR MODELING

Collective and Noncollective Models of NMR Relaxation in Lipid Vesicles and Multilayers†

(2008) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B