The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

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 …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

For a number of years, we have been exploring the underpinnings of algorithms for
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was
introduced in 1976, while the extensive acceptance of this methodology started in the 1990s …

QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …

The quantitative assessment of uncertainty and sampling quality is essential in molecular
simulation. Many systems of interest are highly complex, often at the edge of current …