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 …

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 …

Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

The introduction of accelerator devices such as graphics processing units (GPUs) has had
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …

Fluorogenic probes for bioimaging have become essential tools for life science and
medicine, and the key to their development is a precise understanding of the mechanisms …

Anton 3 is the newest member in a family of supercomputers specially designed for atomic-
level simulation of molecules relevant to biology (eg, DNA, proteins, and drug molecules) …

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 …

As part of our ongoing efforts to support diverse force fields and simulation programs in
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber …

The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular
dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) …