Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

(2016) Xiaodong Pang et al.   Communications in Computational Physics

The influence of water interfacial potentials on ion hydration in bulk water and near interfaces

(2013) Thomas L. Beck   CHEMICAL PHYSICS LETTERS

Length scales and interfacial potentials in ion hydration

(2013) Yu Shi et al.   JOURNAL OF CHEMICAL PHYSICS

The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation

(2013) Lorand Horváth et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol–Water Partition Coefficients

(2013) Niels Hansen et al.   Journal of Chemical Theory and Computation

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

A Proposal for the Revision of Molecular Boundary Typology

(2012) Deok-Soo Kim et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

How intermolecular charge transfer influences the air-water interface

(2012) Collin D. Wick et al.   JOURNAL OF CHEMICAL PHYSICS

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations

(2012) Björn Dahlgren et al.   Journal of Chemical Theory and Computation

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations

(2012) Jun Wang et al.   Journal of Chemical Theory and Computation

Protein–Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations

(2012) Anita de Ruiter et al.   Journal of Chemical Theory and Computation

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns

(2011) Rio Yokota et al.   COMPUTER PHYSICS COMMUNICATIONS

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions

(2011) Maria M. Reif et al.   JOURNAL OF CHEMICAL PHYSICS

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

(2011) Maria M. Reif et al.   JOURNAL OF CHEMICAL PHYSICS

DynamO: a free ${\cal O}$(N) general event-driven molecular dynamics simulator

(2011) M. N. Bannerman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding the Surface Potential of Water

(2011) Shawn M. Kathmann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The hidden energetics of ligand binding and activation in a glutamate receptor

(2011) Albert Y Lau et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Response to “Comment on ‘Ab initio molecular dynamics calculation of ion hydration free energies’  [J. Chem. Phys. 133, 047103 (2010)]”

(2010) Susan B. Rempe et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate Estimates of Free Energy Changes in Charge Mutations

(2010) Brittany R. Morgan et al.   Journal of Chemical Theory and Computation

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

(2010) Halvor S. Hansen et al.   Journal of Chemical Theory and Computation

Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries

(2010) Halvor S. Hansen et al.   Journal of Chemical Theory and Computation

Tofu: A 6D Mesh/Torus Interconnect for Exascale Computers

(2009) Yuichiro Ajima et al.   COMPUTER

Ab initio molecular dynamics calculations of ion hydration free energies

(2009) Kevin Leung et al.   JOURNAL OF CHEMICAL PHYSICS

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions

(2009) Maria M. Reif et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Surface Potential at the Air−Water Interface Computed Using Density Functional Theory

(2009) Kevin Leung   Journal of Physical Chemistry Letters

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

On the origin of the electrostatic potential difference at a liquid-vacuum interface

(2008) Edward Harder 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

On the Dielectric Boundary in Poisson−Boltzmann Calculations

(2008) Harianto Tjong et al.   Journal of Chemical Theory and Computation

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

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

Single Mutation Induced H3N2 Hemagglutinin Antibody Neutralization: A Free Energy Perturbation Study

(2008) Ruhong Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electronic Effects on the Surface Potential at the Vapor−Liquid Interface of Water

(2008) Shawn M. Kathmann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multilevel summation of electrostatic potentials using graphics processing units

(2008) David J. Hardy et al.   PARALLEL COMPUTING