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

All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

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 …

Here we present a program aimed at free-energy calculations in molecular systems. It
consists of a series of routines that can be interfaced with the most popular classical …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Metadynamics is a widely used and successful method for reconstructing the free‐energy
surface of complex systems as a function of a small number of suitably chosen collective …

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 …

The widely used nonsteroidal anti-inflammatory drugs block the cyclooxygenase enzymes
(COXs) and are clinically used for the treatment of inflammation, pain, and cancers. A …

Metadynamics is an algorithm for accelerating rare events and reconstructing the associated
free energy surface. It works by biasing the evolution of the system by a history‐dependent …

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular
simulation method to generate conformational transition pathway under the condition that a …