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

Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator

(2010) Tang-Qing Yu et al.   CHEMICAL PHYSICS

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

(2010) Tyler Luchko et al.   Journal of Chemical Theory and Computation

SAMPL2 challenge: prediction of solvation energies and tautomer ratios

(2010) A. Geoffrey Skillman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS)

(2009) Clara D. Christ et al.   Journal of Chemical Theory and Computation

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

Basic ingredients of free energy calculations: A review

(2009) Clara D. Christ et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations

(2009) Daniel K. Shenfeld et al.   PHYSICAL REVIEW E

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

(2008) Yuqing Deng et al.   JOURNAL OF CHEMICAL PHYSICS

Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions

(2008) Clara D. Christ et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

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

Hit Identification and Binding Mode Predictions by Rigorous Free Energy Simulations

(2008) Julien Michel et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

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

Variance Minimization of Free Energy Estimates from Optimized Expanded Ensembles

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