Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations 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 …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …

In this work, we critically assess the ability of the all-atom enhanced sampling method
accelerated molecular dynamics (aMD) to investigate conformational changes in proteins …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

Enhanced sampling has been extensively used to capture the conformational transitions in
protein folding, but it attracts much less attention in the studies of protein–protein …

Free energy calculations are central to understanding the structure, dynamics and function
of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded …

Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years
of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here …

Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW
domain, was simulated via accelerated molecular dynamics (aMD). In comparison with …