The first step in the construction of a regression model or a data-driven analysis, aiming to
predict or elucidate the relationship between the atomic-scale structure of matter and its …

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 …

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 …

Machine learning encompasses tools and algorithms that are now becoming popular in
almost all scientific and technological fields. This is true for molecular dynamics as well …

Highlights•Liquid-liquid phase separation underlies the formation of membraneless
organelles within cells.•Theory and molecular simulations help to relate interactions at the …

Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …

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 …

Automated analyses of the outcome of a simulation have been an important part of atomistic
modeling since the early days, addressing the need of linking the behavior of individual …

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

Intrinsically disordered proteins (IDPs), which in isolation do not adopt a well-defined tertiary
structure but instead populate a structurally heterogeneous ensemble of interconverting …