Multidimensional replica-exchange method for free-energy calculations

2000/09/08 by Yuji Sugita, Akio Kitao, Yuko Okamoto · 3 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #Advanced Chemical Physics Studies #Enzyme Structure and Function #Protein Structure and Dynamics #cond-mat.stat-mech

paper · pdf · doi:10.1063/1.1308516

13 pages, (ReVTeX), 9 figures. J. Chem. Phys. 113 (2000), in press

arxiv created 2000/09/08 · openalex publication_date 2000/10/15 · arxiv updated 2009/11/30 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/28

Abstract

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.

Citations

• Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
• Equation of State Calculations by Fast Computing Machines
• Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble
• Monte Carlo study of the phase structure of compact polymer chains
• THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
• Multicanonical ensemble: A new approach to simulate first-order phase transitions

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