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

Molecular dynamics simulations hold the promise of providing an atomic-level description of
protein folding that cannot easily be obtained from experiments. Here, we examine the …

Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …

The high arithmetic performance and intrinsic parallelism of recent graphical processing
units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is …

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

Equilibrium molecular dynamics simulations, in which proteins spontaneously and
repeatedly fold and unfold, have recently been used to help elucidate the mechanistic …

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several
features with larger globular proteins. Although the system has been intensively investigated …

We introduce a new class of collective variables which allow forming efficiently beta-sheet
structures in all-atom explicit-solvent simulations of proteins. By this approach we are able to …

Metadynamics calculations allow investigating structure, plasticity, and energetics in a
variety of biological processes spanning from molecular docking to protein folding. Recent …