检索结果-内蒙古大学图书馆

Generalized-ensemble simulations of spin systems and protein systems

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

Tackling the multiple-minima problem in protein folding by Monte Carlo simulated annealing and generalized-ensemble algorithms

引用

INTERNATIONAL JOURNAL OF MODERN PHYSICS C 1999年第8期10卷 1571-1582页

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

Monte Carlo simulations based on simulated annealing and multicanonical algorithm have been performed to predict the secondary and tertiary structures of oligopeptide systems. Two oligopeptides, C-peptide of ribonuclease A and the fragment BPTI(16-36) of bovine pancreatic trypsin inhibitor, were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformations obtained have alpha-helix structure and beta-sheet structure for C-peptide and BPTI(16-36), respectively, in remarkable agreement with experimental results.

关键词： simulated annealing generalized-ensemble algorithms multicanonical algorithm replica-exchange method parallel tempering simulated tempering

来源：评论

学校读者我要写书评

暂无评论

A generalized Wang-Landau algorithm for Monte Carlo computation

引用

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 2005年第472期100卷 1311-1327页

作者： Liang, FM Texas A&M Univ Dept Stat College Stn TX 77843 USA

Inference for a complex system with a rough energy landscape is a central topic in Monte Carlo computation. Motivated by the successes of the Wang-Landau algorithm in discrete systems, we generalize the algorithm to continuous systems. The generalized algorithm has some features that conventional Monte Carlo algorithms do not have. First, it provides a new method for Monte Carlo integration based on stochastic approximation;second, it is an excellent tool for Monte Carlo optimization. In an appropriate setting, the algorithm can lead to a random walk in the energy space, and thus it can sample relevant parts of the sample space, even in the presence of many local energy minima. The generalized algorithm can be conveniently used in many problems of Monte Carlo integration and optimization, for example, normalizing constant estimation, model selection, highest posterior density interval construction, and function optimization. Our numerical results show that the algorithm outperforms simulated annealing and parallel tempering in optimization for the system with a rough energy landscape. Some theoretical results on the convergence of the algorithm are provided.

关键词： 1/k-ensemble sampling importance sampling Markov chain Monte Carlo Monte Carlo integration Monte Carlo optimization multicanonical algorithm Wang-Landau algorithm

来源：评论

学校读者我要写书评

暂无评论

Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations

引用

JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2007年第1期3卷 26-41页

作者： Chodera, John D. Swope, William C. Pitera, Jed W. Seok, Chaok Dill, Ken A. Univ Calif San Francisco Grad Grp Biophys San Francisco CA 94143 USA Univ Calif San Francisco Dept Pharmaceut Chem San Francisco CA 94143 USA IBM Corp Almaden Res Ctr San Jose CA 95120 USA Seoul Natl Univ Coll Nat Sci Dept Chem Seoul 151747 South Korea

The growing adoption of generalized-ensemble algorithms for biomolecular simulation has resulted in a resurgence in the use of the weighted histogram analysis method (WHAM) to make use of all data generated by these simulations. Unfortunately, the original presentation of WHAM by Kumar et al. is not directly applicable to data generated by these methods. WHAM was originally formulated to combine data from independent samplings of the canonical ensemble, whereas many generalized-ensemble algorithms sample from mixtures of canonical ensembles at different temperatures. Sorting configurations generated from a parallel tempering simulation by temperature obscures the temporal correlation in the data and results in an improper treatment of the statistical uncertainties used in constructing the estimate of the density of states. Here we present variants of WHAM, STWHAM and PTWHAM, derived with the same set of assumptions, that can be directly applied to several generalized ensemble algorithms, including simulated tempering, parallel tempering (better known as replica-exchange among temperatures), and replica-exchange simulated tempering. We present methods that explicitly capture the considerable temporal correlation in sequentially generated configurations using autocorrelation analysis. This allows estimation of the statistical uncertainty in WHAM estimates of expectations for the canonical ensemble. We test the method with a one-dimensional model system and then apply it to the estimation of potentials of mean force from parallel tempering simulations of the alanine dipeptide in both implicit and explicit solvent.

关键词： MOLECULAR-DYNAMICS SIMULATIONS MONTE-CARLO REPLICA-EXCHANGE PHASE-TRANSITIONS multicanonical algorithm FREE-ENERGY ENSEMBLE SYSTEMS ERROR TEMPERATURE

来源：评论

学校读者我要写书评

暂无评论

Dynamical behavior of the multibondic and multicanonic algorithm in the 3D q-state Potts model

引用

JOURNAL OF STATISTICAL PHYSICS 1998年第5-6期90卷 1277-1293页

作者： Carroll, MS Janke, W Kappler, S Johannes Gutenberg Univ Mainz Inst Phys D-55099 Mainz Germany

We investigate the dynamical behavior of the recently proposed multibondic cluster Monte Carlo algorithm in applications to the three-dimensional q-state Potts models with q = 3, 4, and 5 in the vicinity of their first-order phase transition points. For comparison we also report simulations with the standard multicanonical algorithm. Similar to the findings in two dimensions, we how that for the multibondic cluster algorithm the dependence of the autocorrelation time tau on the system size Vis well described by the power law tau proportional to V-alpha, and that the dynamical exponent a is consistent with the optimal random walk estimate alpha = 1. For the multicanonical simulations we obtain, as expected, a larger value of alpha approximate to 1.2.

关键词： first-order phase transitions Potts model cluster representation Monte Carlo simulations multicanonical algorithm multibondic algorithm autocorrelations

来源：评论

学校读者我要写书评

暂无评论

Protein folding simulations and structure predictions

引用

COMPUTER PHYSICS COMMUNICATIONS 2001年第1-3期142卷 55-63页

作者： 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 such as spin glasses and proteins, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the simulated annealing method and generalized-ensemble algorithms in order to overcome this multiple-minima problem. Besides simulated annealing, 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. (C) 2001 Elsevier Science B.V. All rights reserved.

关键词： protein folding simulated annealing 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

Molecular simulations in generalised ensemble

引用

MOLECULAR SIMULATION 2012年第14-15期38卷 1282-1296页

作者： Okamoto, Yuko Nagoya Univ Grad Sch Sci Dept Phys 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

In this article, we review the generalised-ensemble algorithms. 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 presented. We then present further extensions of the above three methods. Finally, we discuss the relations among multicanonical algorithm, Wang-Landau method and metadynamics.

关键词： multicanonical algorithm simulated tempering replica-exchange method Wang-Landau method metadynamics

来源：评论

学校读者我要写书评

暂无评论

Generalized-ensemble algorithms for molecular dynamics simulations

Generalized-ensemble algorithms for molecular dynamics simul...

引用

Symposium on Progress and Future Prospects in Molecular Dynamics Simulation

作者： Itoh, Satoru G. Okumura, Hisashi Okamoto, Yuko Nagoya Univ Sch Sci Dept Phys Nagoya Aichi 4648602 Japan

In complex systems with many degrees of freedom such as biomolecular systems, conventional Monte Carlo and molecular dynamics simulations in canonical ensemble or isobaric-isothermal ensemble suffer from the multiple-minima problem, resulting in entrapment in states of energy local minima. A simulation in generalized ensemble performs a random walk in specified variables and overcomes this difficulty. In this article we review the generalized-ensemble algorithms. multicanonical algorithm is described first. In this method, a random walk in potential energy space is realized and the simulation can avoid the multiple-minima problem. We then present two new generalized-ensemble algorithms, namely multioverlap algorithm and multibaric-multithermal algorithm, which are multi-variable/multi-dimensional extensions of the multicanonical algorithm. In the former method, a random walk in overlap space is realized, and in the latter that in both potential energy space and volume space is obtained. Emphasis is laid in the description of the molecular dynamics versions of these algorithms.

关键词： molecular dynamics simulation generalized-ensemble algorithms multicanonical algorithm multioverlap algorithm multibaric-multithermal algorithm

来源：评论

学校读者我要写书评

暂无评论

Protein folding simulations and structure predictions

Protein folding simulations and structure predictions

引用

Conference on Computational Physics 2000: New Challenges for the New Millenium

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