Andrew Pohorille

TL;DR: In this article, a general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived, defined as the forces acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero.

TL;DR: The approach based on time derivatives can be combined with the adaptive biasing force method, an enhanced sampling technique that rapidly yields uniform sampling of the order parameters, and by doing so greatly improves the efficiency of free energy calculations.

TL;DR: This model is shown to account quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes and the simplicity and flexibility of the approach suggest that it should permit applications to conformational equilibria of nonpolar solute andhydrophobic residues in biopolymers.

TL;DR: The current best practices for carrying out free- energy calculations using free energy perturbation and nonequilibrium work methods are discussed, demonstrating that at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates.

TL;DR: In this contribution, the adaptive biasing force algorithm is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability, and inherent limitations, as well as introducing novel extensions.