Molecular dynamics (MD) simulations are ideally suited to investigate protein and peptide
plasticity and flexibility simultaneously at high spatial (atomic) and high time resolution …

Observations of microstructural coarsening at cryogenic temperatures, as well as numerous
simulations of grain boundary motion that show faster migration at low temperature than at …

Simulating the conformational dynamics of biomolecules is extremely difficult due to the
rugged nature of their free energy landscapes and multiple long-lived, or metastable, states …

Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable
tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft …

We derive simple analytical expressions for the error and computational efficiency of replica
exchange molecular dynamics (REMD) simulations (and by analogy replica exchange …

Replica exchange molecular dynamics is a multicanonical simulation technique commonly
used to enhance the sampling of solvated biomolecules on rugged free energy landscapes …

The Binding energy distribution analysis method (BEDAM) is employed to compute the
standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) …

We present an efficient density‐based adaptive‐resolution clustering method APLoD for
analyzing large‐scale molecular dynamics (MD) trajectories. APLoD performs the k‐nearest …

Parallel replica exchange sampling is an extended ensemble technique often used to
accelerate the exploration of the conformational ensemble of atomistic molecular …

BEDAM calculations are described to predict the free energies of binding of a series of
anaesthetic drugs to a recently characterized acyclic cucurbituril host. The modeling …