Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble

Keywords

Statistical physics, Monte Carlo method, Canonical ensemble, Langevin dynamics, Hybrid Monte Carlo

References

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• Optimization by Simulated AnnealingScott Kirkpatrick, C. D. Gelatt, M.P. Vecchi — 1983
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• Hybrid Monte CarloA.D. Kennedy — 1988
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• Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problemUlrich H. E. Hansmann, Yuko Okamoto — 1993
• Multicanonical ensemble: A new approach to simulate first-order phase transitions.Bernd A. Berg, Thomas Neuhaus — 1992
• Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding ProblemUlrich H. E. Hansmann, Yuko Okamoto — 1994
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Cited by

• Computer Simulations of Alzheimers Amyloid β-Protein Folding and Assembly宏志 松原, 博文 青木, 由香 松本 — 2006
• Structural properties and thermodynamics of water clusters: a Wang-Landau study.Junqi Yin, D. P. Landau — 2011
• A Kirkwood-Buff Force Field for polyoxoanions in waterJin Zou — 2010
• Protein folding simulations by generalized-ensemble algorithms.Takao Yoda, Yuji Sugita, Yuko Okamoto — 2014
• Phase Transitions in Long-range Spin Models: The Power of Generalized EnsemblesSylvain Reynal — 2005
• Protein Conformational DynamicsKeli Han, Xin Zhang, Mingjun Yang — 2014
• Analyse thermomécanique multiéchelle de la transformation de phase dans les alliages à mémoire de formeSilvère Vigneron — 2009
• Novel sampling techniques for reservoir history matching optimisation and uncertainty quantification in flow predictionLina Mahgoub Yahya Mohamed — 2011
• Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.Satoru Itoh, Yuko Okamoto — 2006
• Enhanced sampling algorithms.Ayori Mitsutake, Y. Mori, Yuko Okamoto — 2010
• Statistical approaches to the study of protein folding and energeticsNikolas S. Burkoff — 2014
• Mechanisms of cooperativity underlying sequence-independent β-sheet formationChin‐Lin Guo, Margaret S. Cheung, Herbert Levine — 2001
• Algorithms for computational description of large scale conformational transitions of proteinsPeter Májek — 2010
• Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular dockingJunichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo — 2015
• Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.Junichi Higo, Koji Umezawa — 2014
• Conformational ensembles and sampled energy landscapes: Analysis and comparisonFrédéric Cazals, Tom Dreyfus, Dorian Mazauric — 2015
• Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature SetsThomas Vogel, Danny Pérez — 2015
• Length Dependence of Polyglycine Conformations in VacuumSatoru Itoh, Hisashi Okumura — 2011
• Theoretical studies of transition states by the multioverlap molecular dynamics methods.Satoru Itoh, Yuko Okamoto — 2006
• Parallelization of Markov Chain Generation and its Application to the Multicanonical MethodTakanori Sugihara, Junichi Higo, Haruki Nakamura — 2008

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• Comparison of Langevin and Monte Carlo dynamicsRammile Ettelaie, M A Moore — 1984
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