Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

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

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

We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …

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 …

The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …

A simple and general implementation of Hamiltonian replica exchange for the popular
molecular dynamics software GROMACS is presented. In this implementation, arbitrarily …

This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …

Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a
powerful strategy to improve the convergence of free energy computations. In particular, it …