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

Many biologically important processes such as enzyme catalysis, signal transduction, ligand
binding and allosteric regulation occur on the micro-to millisecond time-scale. Despite the …

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 …

Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …

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 …

A long-standing problem in molecular biology is the determination of a complete functional
conformational landscape of proteins. This includes not only proteins' native structures, but …

Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced
sampling technique that provides efficient free energy calculations of biomolecules. Like the …

Elucidating the detailed process of ligand binding to a receptor is pharmaceutically
important for identifying druggable binding sites. With the ability to provide atomistic detail …

Abstract A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been
developed for simultaneous unconstrained enhanced sampling and free energy calculation …