Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

Using MD Simulations To Calculate How Solvents Modulate Solubility

(2016) Shuai Liu et al.   Journal of Chemical Theory and Computation

Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field

(2016) Richard T. Bradshaw et al.   Journal of Chemical Theory and Computation

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5

(2016) Samuel Genheden et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

(2015) Jin Zhang et al.   Journal of Chemical Information and Modeling

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model

(2015) Samuel Genheden   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

(2014) Daniel J. Cole et al.   Journal of Chemical Theory and Computation

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field

(2014) Silvia A. Martins et al.   Journal of Chemical Theory and Computation

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field

(2014) Francesco Manzoni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of solvation free energies from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration

(2014) Christopher J. Fennell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration

(2014) Joakim P. M. Jämbeck et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations

(2014) Magnus Lundborg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

(2014) Daniel R. Roe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

(2014) Xiaojiao Mu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins

(2013) Maria M. Reif et al.   Journal of Chemical Theory and Computation

Calculations of the Electric Fields in Liquid Solutions

(2013) Stephen D. Fried et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

(2012) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Generalized Born Solvation Model SM12

(2012) Aleksandr V. Marenich et al.   Journal of Chemical Theory and Computation

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

(2012) Lee-Ping Wang et al.   Journal of Chemical Theory and Computation

Automation of AMOEBA polarizable force field parameterization for small molecules

(2012) Johnny C. Wu et al.   THEORETICAL CHEMISTRY ACCOUNTS

Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation

(2011) Fabien Cailliez et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

(2011) Carl Caleman et al.   Journal of Chemical Theory and Computation

Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation

(2011) Andrew S. Paluch et al.   Journal of Chemical Theory and Computation

Development of the CHARMM Force Field for Lipids

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

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

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Multipole electrostatics in hydration free energy calculations

(2010) Yue Shi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The SAMPL2 blind prediction challenge: introduction and overview

(2010) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

(2010) François-Yves Dupradeau et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

(2008) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY