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multibaric-multithermal molecular dynamics simulation: generalized Nose-Poincare-Andersen method

MOLECULAR SIMULATION 2007年第1-2期33卷 91-96页

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

The multibaric-multithermal (MUBATH) algorithm is a generalized-ensemble algorithm with which a random walk both in potential-energy space and in volume space is realized. The MUBATH simulation thus can escape from any local-minimum free-energy states and one can obtain thermodynamic quantities as functions of any temperature and pressure from a single simulation run. We applied the MUBATH molecular dynamics (MD) algorithm to an alanine dipeptide in explicit water. The MUBATH algorithm sampled a wide range of the dihedral-angle space and enabled the simulation to investigate peptide structures including those which cannot be sampled by the conventional isobaric-isothermal simulation.

关键词： molecular dynamics simulation multibaric-multithermal algorithm symplectic integrator alanine dipeptide

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multibaric-multithermal molecular dynamics simulation: generalized Nose-Poincare-Andersen method

Multibaric-multithermal molecular dynamics simulation: gener...

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Symposium on Progress and Future Prospects in Molecular Dynamics Simulation

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

关键词： molecular dynamics simulation multibaric-multithermal algorithm symplectic integrator alanine dipeptide

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Generalised-ensemble algorithms for studying temperature and pressure dependence of complex systems

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MOLECULAR SIMULATION 2012年第5期38卷 452-457页

作者： Mori, Yoshiharu Okamoto, Yuko Nagoya Univ Dept Phys Nagoya Aichi 4648602 Japan Nagoya Univ Struct Biol Res Ctr Nagoya Aichi 4648602 Japan Nagoya Univ Ctr Computat Sci Nagoya Aichi 4648603 Japan

Generalised-ensemble algorithms for isobaric-isothermal molecular simulations are described in this article. In addition to the multibaric-multithermal algorithm and replica-exchange method for the isobaric-isothermal ensemble, which have already been proposed, the simulated tempering method for this ensemble is explained in detail. Molecular dynamics simulations were performed with these algorithms for an alanine dipeptide system in explicit water molecules to test the effectiveness of the algorithms. It was found that these generalised-ensemble algorithms are all useful for conformational sampling of complex systems such as biomolecular systems in the isobaric-isothermal ensemble.

关键词： generalised-ensemble algorithm multibaric-multithermal algorithm simulated tempering replica-exchange method isobaric isothermal ensemble

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Generalized-ensemble algorithms for molecular dynamics simulations

Generalized-ensemble algorithms for molecular dynamics simul...

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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

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Generalised-ensemble algorithms for studying temperature and pressure dependence of complex systems

Generalised-ensemble algorithms for studying temperature and...

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21st IUPAC International Conference on Chemical Thermodynamics (ICCT)

关键词： generalised-ensemble algorithm multibaric-multithermal algorithm simulated tempering replica-exchange method isobaric isothermal ensemble

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Generalized-ensemble algorithms for molecular dynamics simulations

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MOLECULAR SIMULATION 2007年第1-2期33卷 47-56页

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

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

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