Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms
Abstract
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.
Cite
@article{arxiv.cond-mat/0102296,
title = {Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms},
author = {Y. Sugita and Y. Okamoto},
journal= {arXiv preprint arXiv:cond-mat/0102296},
year = {2007}
}
Comments
29 pages, (LaTeX2e), 14 figures, Lecture Notes in Computational Science and Engineering, submitted