Unsupervised learning is becoming an essential tool to analyze the increasingly large
amounts of data produced by atomistic and molecular simulations, in material science, solid …

▪ Abstract This article reviews the concepts and methods of transition path sampling. These
methods allow computational studies of rare events without requiring prior knowledge of …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

Molecular self-organization driven by concerted many-body interactions produces the
ordered structures that define both inanimate and living matter. Here we present an …

Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …

Metadynamics is a powerful and well-established enhanced sampling method for exploring
and quantifying free energy surfaces of complex systems as a function of appropriately …

We introduce a powerful method for exploring the properties of the multidimensional free
energy surfaces (FESs) of complex many-body systems by means of coarse-grained non …

Metadynamics is a commonly used and successful enhanced sampling method. By the
introduction of a history dependent bias which depends on a restricted number of collective …

The ability to predict the mechanisms and the associated rate constants of protein–ligand
unbinding is of great practical importance in drug design. In this work we demonstrate how a …

The study of chemical reactions in aqueous media is very important for its implications in
several fields of science, from biology to industrial processes. However, modeling these …