Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms
Abstract
Description
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel tempering. We present a new generalized-ensemble algorithm that combines the merits of the two methods; it is referred to as the replica-exchange multicanonical algorithm. We also give a multidimensional extension of the replica-exchange method. Its realization as an umbrella sampling method, which we refer to as the replica-exchange umbrella sampling, is a powerful algorithm that can give free energy in wide reaction coordinate space.
29 pages, (LaTeX2e), 14 figures, Lecture Notes in Computational Science and Engineering, submitted
29 pages, (LaTeX2e), 14 figures, Lecture Notes in Computational Science and Engineering, submitted