Some recent techniques for free energy calculations.
A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature-accelerated molecular dynamics, which is a method to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi-based free energy method for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones.
Vanden-Eijnden
Eric
E
Courant Institute, New York University, 251 Mercer Street, New York 10012, USA. eve2@cims.nyu.edu