Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field

Combination of RISM and Cheminformatics for Efficient Predictions of Hydration Free Energy of Polyfragment Molecules: Application to a Set of Organic Pollutants

(2011) Ekaterina L. Ratkova et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration

(2010) Miguel Jorge et al.   Journal of Chemical Theory and Computation

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

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

(2010) Traian Sulea 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

The SAMPL2 blind prediction challenge: introduction and overview

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

Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge

(2010) Enrico O. Purisima et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

(2010) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

(2009) J. Peter Guthrie   JOURNAL OF PHYSICAL CHEMISTRY B

Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations†

(2009) David L. Mobley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation