Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.

Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm. Research Abstract Details 

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Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm. Abstract Text:

Satoru G Itoh,Yuko Okamoto,Satoru G Itoh,Yuko Okamoto,

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.

Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm. Publishing Authors By Initials

SG Itoh,Y Okamoto,SG Itoh,Y Okamoto,

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Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Physical review. E, Statistical, nonlinear, and so

VOLUME: 76

Page Numbers: 026705

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ISSN: 1539-3755

DAY: 22

MONTH: 08

YEAR: 2007

Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm. Information

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LANGUAGE: eng

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Grant and Affiliation Information for Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.

AFFILIATION: Department of Physics, School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan. itoh@tb.phys.nagoya-u.ac.jp

Country: United States

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MEDLINETA: Phys Rev E Stat Nonlin Soft Ma

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