Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant-Reference-Cited by-同舟云学术

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant

Published:2018 Issue:0 Volume:15 Page:165-172
ISSN:2189-4779
Container-title:Biophysics and Physicobiology
language:en
Short-container-title:BIOPHYSICS

Author:

Iwai Ryosuke¹,Kasahara Kota²,Takahashi Takuya²

Affiliation:

1. Graduate School of Life Sciences, Ritsumeikan University

2. College of Life Sciences, Ritsumeikan University

Publisher

Biophysical Society of Japan

Subject

General Medicine

Link

https://www.jstage.jst.go.jp/article/biophysico/15/0/15_165/_pdf

Reference21 articles.

1. [2] De Vivo, M., Masetti, M., Bottegoni, G. & Cavalli, A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J. Med. Chem. 59, 4035–4061 (2016).

2. [8] Higo, J., Ikebe, J., Kamiya, N. & Nakamura, H. Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophys. Rev. 4, 27–44 (2012).

3. [9] Kasahara, K., Ma, B., Goto, K., Dasgupta, B., Higo, J., Fukuda, I., et al. myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme. Biophys. Physicobiol. 13, 209–216 (2016).

4. [10] Sugita, Y. & Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141–151 (1999).

5. [11] Souaille, M. & Roux, B. Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput. Phys. Commun. 135, 40–57 (2001).

Cited by 7 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Affinity of Drug Candidates Binding to SARS CoV-2 PLpro Assessed Using a Generalized-ensemble Method;2024-09-05

2. Extended Conformational Selection in the Antigen–Antibody Interaction of the PfAMA1 Protein;The Journal of Physical Chemistry B;2024-08-22

3. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration;Journal of Chemical Theory and Computation;2023-12-01

4. myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling;Biophysics and Physicobiology;2020

5. Correlation effects in parallel tempering and the role of the swapping frequency;Physical Chemistry Chemical Physics;2020