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作者： Ayori Mitsutake Yoshiharu Mori Yuko Okamoto

In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced conformational sampling techniques are thus in great demand. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present various extensions of these three generalized-ensemble algorithms. The effectiveness of the methods is tested with short peptide and protein systems. less

关键词： Molecular Dynamics Simulation Monte Carlo generalized-ensemble algorithm Replica-exchange method Simulated tempering Multicanonical algorithm

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A new generalized-ensemble algorithm: multicanonical-multioverlap algorithm

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MOLECULAR SIMULATION 2007年第1-2期33卷 83-89页

作者： Itoh, S. G. Okamoto, Y. Nagoya Univ Sch Sci Dept Phys Nagoya Aichi 4648602 Japan Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 444 Japan

We introduce a new 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 multi-dimensional, 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 (MD) method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap MD methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap MD method realizes effective sampling in the configurational space including specific configurations more than the other two methods.

关键词： molecular dynamics simulation generalized-ensemble algorithm protein folding transition state

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A new generalized-ensemble algorithm: multicanonical-multioverlap algorithm

A new generalized-ensemble algorithm: multicanonical-multiov...

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Symposium on Progress and Future Prospects in Molecular Dynamics Simulation

作者： Itoh, S. G. Okamoto, Y. Nagoya Univ Sch Sci Dept Phys Nagoya Aichi 4648602 Japan Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 444 Japan

关键词： molecular dynamics simulation generalized-ensemble algorithm protein folding transition state

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Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

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MOLECULAR SIMULATION 2007年第1-2期33卷 97-102页

作者： Kawashima, Y. Sasaki, Y. C. Sugita, Y. Yoda, T. Okamoto, Y. Japan Sci & Technol Agcy CREST Sasaki Tokyo 1900012 Japan Nagoya Univ Sch Sci Dept Phys Chikusa Ku Nagoya Aichi 4648602 Japan JASRI SPring8 Mikazuki Hyogo 6795198 Japan Univ Tokyo Inst Mol & Cellular Biosci Bunkyo Ku Tokyo 1130032 Japan Nagahama Inst Biosci & Technol Shiga 5260829 Japan Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 444 Japan

We examine the effects of the nanocrystal covalently bonded to one end, utilizing replica-exchange molecular dynamics simulation of a peptide with the sequence Ac-YGKAAAAKAAAAKAAAAKC-amide, to simulate the diffraction X-ray tracking (DXT) method. We performed three different simulations in this study. A simulation with no constraint, a simulation with one end fixed, and a simulation with one end fixed and also considering the effect of the nanocrystal by changing the mass of the sulfur atom in the C-terminus, which covalently bonded with the An nanocrystal in diffraction DXT method, was performed. The average configuration parameters of the three simulations are compared and discussed. We analyzed our simulation results utilizing principal component analysis. The obtained free-energy landscape indicated that the condition of the DXT technique will not affect the global-minimum state, however, it may affect the folding pathway.

关键词： generalized-ensemble algorithm REMD diffracted X-ray tracking DXT

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Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

Replica-exchange molecular dynamics simulation of diffracted...

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Symposium on Progress and Future Prospects in Molecular Dynamics Simulation

关键词： generalized-ensemble algorithm REMD diffracted X-ray tracking DXT

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Replica-exchange methods and predictions of helix configurations of membrane proteins

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MOLECULAR SIMULATION 2006年第10-11期32卷 791-801页

作者： Kokubo, Hironori Okamoto, Yuko Nagoya Univ Dept Phys Aichi 4648602 Japan Univ Houston Dept Chem Houston TX 77204 USA

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.

关键词： replica-exchange method Monte Carlo generalized-ensemble algorithm membrane proteins

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Multibaric-multithermal ensemble molecular dynamics simulations

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2006年第3期27卷 379-395页

作者： Okumura, H Okamoto, Y Inst Mol Sci Dept Theoret Studies Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Struct Mol Sci Okazaki Aichi 4448585 Japan Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multi baric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nose thermostat and the Andersen barostat, (2) the Nose-Poincare thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system. (c) 2005 Wiley Periodicals, Inc.

关键词： multibaric-multithermal ensemble isobaric-isothermal ensemble generalized-ensemble algorithm symplectic algorithm molecular dynamics simulation Lennard-Jones potential

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generalized-ensemble simulations of spin systems and protein systems

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COMPUTER PHYSICS COMMUNICATIONS 2002年第1期146卷 69-76页

作者： Nagasima, T Sugita, Y Mitsutake, A Okamoto, Y Inst Mol Sci Dept Theoret Studies Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Funct Mol Sci Okazaki Aichi 4448585 Japan Keio Univ Fac Sci & Technol Dept Phys Yokohama Kanagawa 2238522 Japan

In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this multiple-minima problem. Three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. Effectiveness of the new methods are tested with a Potts model and protein systems. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： Potts model protein folding generalized-ensemble algorithm multicanonical algorithm simulated tempering replica-exchange method

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generalized-ensemble simulations of spin systems and protein systems

Generalized-ensemble simulations of spin systems and protein...

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International Conference on Statistical Physics

关键词： Potts model protein folding generalized-ensemble algorithm multicanonical algorithm simulated tempering replica-exchange method

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generalized-ensemble algorithms for molecular simulations of biopolymers

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BIOPOLYMERS 2001年第2期60卷 96-123页

作者： Mitsutake, A Sugita, Y Okamoto, Y Inst Mol Sci Dept Theoret Studies Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Funct Mol Sci Okazaki Aichi 4448585 Japan

In complex systems with many degrees of freedom such cis peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. lit this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The, effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems. (C) 2001 John Wiley & Sons, Inc.

关键词： protein folding generalized-ensemble algorithm multicanonical algorithm simulated tempering replica-exchange method parallel tempering

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