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Abstract
A simulation in generalized ensemble is based on a non-Boltzmann weight factor and performs a random walk in potential energy space, which allows the simulation to avoid getting trapped in states of local-minimum energy states. In this article, we review uses of the generalized-ensemble algorithms. Three well-known methods, namely, multicanonical algorithm (MUCA), simulated tempering (ST) and replica-exchange method (REM), are described first. Both Monte Carlo (MC) and molecular dynamics (MD) versions of the algorithms are given. We then present the results of the application of replica-exchange MC method to the predictions of membrane protein structures.
Acknowledgements
The computations were performed on the computers at the Research Center for Computational Science, Institute for Molecular Science, Japan Atomic Energy Research Institute. This work was supported, in part, by the Grants-in-Aid for the Next Generation Super Computing Project, Nanoscience Program and for Scientific Research in Priority Areas, “Water and Biomolecules”, from the Ministry of Education, Culture, Sports, Science and Technology, Japan.