Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm
抄録
We propose a generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multidimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap molecular dynamics methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap molecular dynamics method realizes effective sampling in the configurational space including specific configurations more than the other two methods. Furthermore, from the results of the multicanonical-multioverlap molecular dynamics simulation, we obtain a local-minimum state of the Met-enkephalin system.
収録刊行物
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- Physical Review E
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Physical Review E 76 (2), 026705-, 2007-08
American Physical Society
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詳細情報 詳細情報について
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- CRID
- 1050845763743928704
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- NII論文ID
- 120006545922
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- ISSN
- 24700053
- 24700045
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- HANDLE
- 2237/00029147
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- 本文言語コード
- en
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- 資料種別
- journal article
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- データソース種別
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- IRDB
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