BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations

(2015) Gerhard König et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes

(2015) Phillip S. Hudson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions

(2015) Levi N. Naden et al.   Journal of Chemical Theory and Computation

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

(2015) Phillip S. Hudson et al.   Journal of Physical Chemistry Letters

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

(2014) Gerhard König et al.   Journal of Chemical Theory and Computation

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites

(2014) Levi N. Naden et al.   Journal of Chemical Theory and Computation

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

(2014) Samuel Genheden 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

Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability

(2013) Gerhard König et al.   BIOPHYSICAL JOURNAL

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

(2013) Joseph W. Kaus et al.   Journal of Chemical Theory and Computation

Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space

(2012) Ilsoo Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

(2012) Jimmy Heimdal et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

(2011) Tri T. Pham et al.   JOURNAL OF CHEMICAL PHYSICS

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

(2011) Yilin Meng et al.   Journal of Chemical Theory and Computation

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

(2011) Himanshu Paliwal et al.   Journal of Chemical Theory and Computation

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

(2010) Thomas Steinbrecher et al.   CURRENT MEDICINAL CHEMISTRY

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

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration

(2010) Stefan Bruckner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unorthodox uses of Bennett's acceptance ratio method

(2009) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using bijective maps to improve free-energy estimates

(2009) A. M. Hahn et al.   PHYSICAL REVIEW E

Statistically optimal analysis of samples from multiple equilibrium states

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

Variance Minimization of Free Energy Estimates from Optimized Expanded Ensembles

(2008) Francisco J. Martínez-Veracoechea et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA