Multidimensional replica-exchange method for free-energy calculations
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- 2 October 2000
- journal article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 113 (15) , 6042-6051
- https://doi.org/10.1063/1.1308516
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.Keywords
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This publication has 65 references indexed in Scilit:
- Replica-exchange molecular dynamics method for protein foldingChemical Physics Letters, 1999
- Characterization of flexible molecules in solution: the RGDW peptideJournal of Molecular Biology, 1998
- Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation modelJournal of Molecular Biology, 1998
- Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulationJournal of Molecular Biology, 1998
- Molecular mechanisms for cooperative folding of proteinsJournal of Molecular Biology, 1998
- Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteinsThe Journal of Chemical Physics, 1998
- Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated temperingPhysical Review E, 1996
- First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle ProteinScience, 1995
- Monte Carlo Simulation of a First-Order Transition for Protein FoldingThe Journal of Physical Chemistry, 1994
- Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problemJournal of Computational Chemistry, 1993