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Two-dimensional simulated tempering for the isobaric-isothermal ensemble with fast on-the-fly weight determination

MOLECULAR PHYSICS 2021年第19-20期119卷 e1904156-e1904156页

作者： Wada, Hiromune Okamoto, Yuko Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan Nagoya Univ Grad Sch Engn Ctr Computat Sci Nagoya Aichi 4648603 Japan Nagoya Univ Informat Technol Ctr Nagoya Aichi 4648601 Japan

We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters for temperature-update and pressure-update are self-updated independently according to the trapezoidal rule. In order to test the effectiveness of the algorithm, we applied our proposed method to a peptide, chignolin, in explicit water. After setting all weight parameters to zero, the weight parameters were quickly determined during the simulation. The simulation realised a uniform random walk in the entire temperature-pressure space.

关键词： generalised-ensemble algorithm simulated tempering molecular dynamics isobaric-isothermal ensemble high-pressure denaturation

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Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide

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MOLECULAR SIMULATION 2015年第10-12期41卷 1035-1040页

作者： Mori, Yoshiharu Okumura, Hisashi Natl Inst Nat Sci Inst Mol Sci Dept Theoret & Computat Mol Sci Okazaki Aichi 4448585 Japan Natl Inst Nat Sci Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Struct Mol Sci Okazaki Aichi 4448585 Japan

While most proteins unfold under high-pressure conditions, some high-pressure experiments suggest that an AK16 peptide forms more helical structures. In order to understand this abnormality, molecular dynamics simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 0.1MPa to 1.4GPa. It was found that the fraction of the folded state decreases once and increases after that with increasing pressure. The partial molar volume change from the folded state to unfolded state increases monotonically from a negative value to a positive value with pressure. The behaviour under high-pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure. Moreover, interatomic distances of AK16 become shorter at high pressure than at low pressure. These behaviours indicate that the helical structures are squeezed by high pressure.

关键词： generalised-ensemble algorithm pressure dependence helical peptide partial molar volume simulated tempering

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Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide

Molecular dynamics simulation study on the high-pressure beh...

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3rd International Conference on Molecular Simulation (ICMS)

关键词： generalised-ensemble algorithm pressure dependence helical peptide partial molar volume simulated tempering

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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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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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