Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

There is notable discrepancy between experiments and coarse-grained model studies
regarding the thermodynamic driving force in polyelectrolyte complex coacervation …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Gas hydrates have an important role in environmental and astrochemistry, as well as in
energy materials research. Although it is widely accepted that gas accumulation is an …

TCR-signaling strength generally correlates with peptide-MHC binding affinity; however,
exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high …

A software framework is introduced that facilitates the application of biasing algorithms to
collective variables of the type commonly employed to drive massively parallel molecular …