检索结果-内蒙古大学图书馆

A new generalized-ensemble algorithm: multicanonical-multioverlap algorithm

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

来源：评论

学校读者我要写书评

暂无评论

A new generalized-ensemble algorithm: multicanonical-multioverlap algorithm

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

generalized-ensemble algorithms for molecular simulations of biopolymers

引用

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

来源：评论

学校读者我要写书评

暂无评论

Molecular simulations by generalized-ensemble algorithms in isothermal–isobaric ensemble

引用

Biophysical Reviews 2019年第3期11卷 457-469页

作者： Yamauchi, Masataka Mori, Yoshiharu Okumura, Hisashi Department of Structural Molecular Science SOKENDAI (The Graduate University for Advanced Studies) Okazaki 444-8585 Aichi Japan Exploratory Research Center on Life and Living Systems (ExCELLS) National Institutes of Natural Sciences Okazaki 444-8787 Aichi Japan Institute for Molecular Science (IMS) National Institutes of Natural Sciences Okazaki 444-8585 Aichi Japan School of Pharmacy Kitasato University Shirokane Minato-ku 108-8641 Tokyo Japan

generalized-ensemble algorithms are powerful techniques for investigating biomolecules such as protein, DNA, lipid membrane, and glycan. The generalized-ensemble algorithms were originally developed in the canonical ensemble. On the other hand, not only temperature but also pressure is controlled in experiments. Additionally, pressure is used as perturbation to study relationship between function and structure of biomolecules. For this reason, it is important to perform efficient conformation sampling based on the isothermal–isobaric ensemble. In this article, we review a series of the generalized-ensemble algorithms in the isothermal–isobaric ensemble: multibaric–multithermal, pressure- and temperature-simulated tempering, replica-exchange, and replica-permutation methods. These methods achieve more efficient simulation than the conventional isothermal–isobaric simulation. Furthermore, the isothermal–isobaric generalized-ensemble simulation samples conformations of biomolecules from wider range of temperature and pressure. Thus, we can estimate physical quantities more accurately at any temperature and pressure values. The applications to the biomolecular system are also presented. © 2019, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： generalized-ensemble algorithm High pressure Molecular simulation Protein folding

来源：评论

学校读者我要写书评

暂无评论

generalized-ensemble simulations of spin systems and protein systems

引用

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

来源：评论

学校读者我要写书评

暂无评论

generalized-ensemble simulations of spin systems and protein systems

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

引用

International Conference on Statistical Physics

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

来源：评论

学校读者我要写书评

暂无评论

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study

引用

JOURNAL OF COMPUTATIONAL CHEMISTRY 2017年第15期38卷 1167-1173页

作者： Mori, Yoshiharu Okamoto, Yuko Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan JST CREST Nagoya Aichi 4648602 Japan Nagoya Univ Grad Sch Sci Struct Biol Res Ctr Nagoya Aichi 4648602 Japan Nagoya Univ Grad Sch Engn Ctr Computat Sci Nagoya Aichi 4648603 Japan Nagoya Univ Ctr Informat Technol Nagoya Aichi 4648601 Japan

Molecular dynamics simulations for the system of ubiquitin were performed with pressure simulated tempering to study pressure-induced conformational changes of ubiquitin. The pressure dependence of ubiquitin was analyzed in a wide range of pressure from atmospheric pressure (0.1 MPa) to 1.0 GPa. The fluctuation of the distance between amino-acid residues and the distribution of a largely fluctuating distance were calculated. The large fluctuation of the L8-E34 distance induced by pressure means that the conformation of ubiquitin changes under high pressure conditions. There were more water molecules near the largely fluctuating region at high pressure than at low pressure. The pressure dependence of interaction energies among ubiquitin and water was also calculated to investigate the role of water for the pressure-induced conformational changes of ubiquitin. The protein-water interaction is important when the conformation of ubiquitin changes at high pressure. (c) 2017 Wiley Periodicals, Inc.

关键词： molecular simulation generalized-ensemble algorithm pressure dependence pressure-induced denaturation

来源：评论

学校读者我要写书评

暂无评论

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

引用

JOURNAL OF COMPUTATIONAL CHEMISTRY 2016年第21期37卷 2017-2028页

作者： Nagai, Tetsuro Pantelopulos, George A. Takahashi, Takuya Straub, John E. Ritsumeikan Univ Dept Bioinformat Coll Life Sci Kusatsu Shiga 5258577 Japan Boston Univ Dept Chem Boston MA 02215 USA Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan

Simulated tempering (ST) is a generalized-ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass-scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. (c) 2016 Wiley Periodicals, Inc.

关键词： generalized-ensemble algorithm simulated tempering mass scaling Nose-Hoover thermostat molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

Multibaric-multithermal ensemble molecular dynamics simulations

引用

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

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：