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 …

Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …

Although molecular dynamics simulations have become a useful tool in essentially all fields
of chemistry, condensed matter physics, materials science, and biology, there is still a large …

Molecular dynamics (MD) enables the study of physical systems with excellent
spatiotemporal resolution but suffers from severe timescale limitations. To address this …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Progress in the atomic-scale modeling of matter over the past decade has been tremendous.
This progress has been brought about by improvements in methods for evaluating …

Enhancing sampling and analyzing simulations are central issues in molecular simulation.
Recently, we introduced PLUMED, an open-source plug-in that provides some of the most …

Alzheimer's disease (AD) challenges our society with an annual estimated cost of $1.08
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …

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 …