2001/02/16 by Y. Sugita, Y. Okamoto, Sugita, Y. +1
Biochemistry, Genetics and Molecular Biology · Chemistry · Materials Science · Physics and Astronomy · #Advanced Proteomics Techniques and Applications #Enzyme Structure and Function #FOS: Biological sciences #FOS: Physical sciences #Protein Structure and Dynamics #Quantitative Biology (q-bio) #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.stat-mech #q-bio
paper · pdf · doi:10.48550/arxiv.cond-mat/0102296
29 pages, (LaTeX2e), 14 figures, Lecture Notes in Computational Science and Engineering, submitted
arxiv created 2001/02/16 · openalex publication_date 2001/02/16 · arxiv updated 2009/11/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.