Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

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 …

We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …

Several molecular dynamics (MD) simulations were used to sample conformations in the
neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories …

Growing computing capacity and algorithmic advances have facilitated the study of
increasingly large biomolecular systems at longer timescales. However, with these larger …

Computer simulations play an important role in the study of transformation processes of
condensed matter, including phase transitions, chemical reactions, and conformational …

Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years
of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here …

Publisher Summary In an alchemical transformation, a chemical species is transformed into
another via a pathway of nonphysical (alchemical) states. Many physical processes, such as …

The widespread popularity of replica exchange and expanded ensemble algorithms for
simulating complex molecular systems in chemistry and biophysics has generated much …

The traditional structure–function paradigm has provided significant insights for well-folded
proteins in which structures can be easily and rapidly revealed by X-ray crystallography …