Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

We describe our efforts to prepare common starting structures and models for the SAMPL5
blind prediction challenge. We generated the starting input files and single configuration …

We discuss the description of water and hydration effects that employs an approximate
density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to …

Molecular modeling is widely utilized in subjects including but not limited to physics,
chemistry, biology, materials science and engineering. Impressive progress has been made …

Umbrella sampling efficiently yields equilibrium averages that depend on exploring rare
states of a model by biasing simulations to windows of coordinate values and then …

Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the
electrostatic potential is modeled by fixed point charges. Among other consequences, the …

We introduce Gaussian Process Regression (GPR) as an enhanced method of
thermodynamic extrapolation and interpolation. The heteroscedastic GPR models that we …

We show how thermodynamic properties of molecular models can be computed over a
large, multidimensional parameter space by combining multistate reweighting analysis with …

Existing united‐atom models for non‐polar hydrocarbons lead to systematic deviations in
predicted solvation free energies in hydrophobic solvents. In this article, an improved set of …