Methods to compute free energy differences between different states of a molecular system
are reviewed with the aim of identifying their basic ingredients and their utility when applied …

Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …

In the host of numerical schemes devised to calculate free energy differences by way of
geometric transformations, the adaptive biasing force algorithm has emerged as a promising …

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 …

As access to computational resources continues to increase, free-energy calculations have
emerged as a powerful tool that can play a predictive role in a wide range of research areas …

In free energy calculations based on thermodynamic integration, it is necessary to compute
the derivatives of the free energy as a function of one (scalar case) or several (vector case) …

Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to
drug design, toxicology, and signaling. These rates can be estimated using molecular …

Metadynamics is a powerful technique that has been successfully exploited to explore the
multidimensional free energy surface of complex polyatomic systems and predict transition …

Association of unconstrained molecular dynamics (MD) and the formalisms of
thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115 …

Membrane ion channels are the fundamental electrical components in the nervous system.
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …