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 …

Large-scale conformational changes are essential to link protein structures with their
function at the cell and organism scale, but have been elusive both experimentally and …

GROMACS is a widely used package for biomolecular simulation, and over the last two
decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration …

High-throughput molecular dynamics (MD) simulations are a computational method
consisting of using multiple short trajectories, instead of few long ones, to cover slow …

Free energy calculation has long been an important goal for molecular dynamics simulation
and force field development, but historically it has been challenged by limited performance …

Alchemical free energy calculations are an increasingly important modern simulation
technique to calculate free energy changes on binding or solvation. Contemporary …

The use of molecular dynamics simulations to provide atomic-level descriptions of biological
processes tends to be computationally demanding, and a number of approximations are …

Molecular dynamics simulations are capable of resolving molecular recognition processes
with chemical accuracy, but their practical application is popularly considered limited to the …

Transition path sampling techniques allow molecular dynamics simulations of complex
systems to focus on rare dynamical events, providing insight into mechanisms and the ability …

Molecular dynamics (MD) simulations that capture the spontaneous binding of drugs and
other ligands to their target proteins can reveal a great deal of useful information, but most …