Hybrid Hamiltonian replica exchange molecular dynamics simulation method employing the Poisson–Boltzmann model

Yuguang Mu; Ye Yang; Weixin Xu

doi:10.1063/1.2772264

Hybrid Hamiltonian replica exchange molecular dynamics simulation method employing the Poisson–Boltzmann model

The Journal of Chemical Physics ◽

10.1063/1.2772264 ◽

2007 ◽

Vol 127 (8) ◽

pp. 084119 ◽

Cited By ~ 19

Author(s):

Yuguang Mu ◽

Ye Yang ◽

Weixin Xu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Method ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Poisson Boltzmann ◽

Boltzmann Model

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On the Structural Stability of a Short Three Stranded β-sheet Peptide (Betanova): Replica Exchange Molecular Dynamics Simulation Study

Bulletin of the Korean Chemical Society ◽

10.5012/bkcs.2010.31.8.2386 ◽

2010 ◽

Vol 31 (8) ◽

pp. 2386-2388

Author(s):

Soon-Min Jang ◽

Eun-Ae Kim ◽

Young-Shang Pak

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structural Stability ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Β Sheet

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Phase Behavior of a Lipid Bilayer System Studied by a Replica-Exchange Molecular Dynamics Simulation

Journal of the Physical Society of Japan ◽

10.1143/jpsj.81.024002 ◽

2012 ◽

Vol 81 (2) ◽

pp. 024002 ◽

Cited By ~ 15

Author(s):

Tetsuro Nagai ◽

Ryuichi Ueoka ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Phase Behavior ◽

Lipid Bilayer ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Bilayer System

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In silico study of osmolytic effects of choline-O-sulfate on urea induced unfolding of Trp-cage mini-protein: An atomistic view from replica exchange molecular dynamics simulation

Archives of Biochemistry and Biophysics ◽

10.1016/j.abb.2020.108484 ◽

2020 ◽

Vol 695 ◽

pp. 108484

Author(s):

Srijita Paul ◽

Sandip Paul

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

In Silico ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

In Silico Study

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Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

Molecular Simulation ◽

10.1080/08927020601067581 ◽

2007 ◽

Vol 33 (1-2) ◽

pp. 97-102 ◽

Cited By ~ 7

Author(s):

Y. Kawashima ◽

Y. C. Sasaki ◽

Y. Sugita ◽

T. Yoda ◽

Y. Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

X Ray

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Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation

Physical Chemistry Chemical Physics ◽

10.1039/c3cp44443k ◽

2013 ◽

Vol 15 (33) ◽

pp. 13852 ◽

Cited By ~ 15

Author(s):

Hisashi Okumura ◽

Satoru G. Itoh

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hairpin Structures ◽

Α Helix

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Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation

Biophysical Journal ◽

10.1016/j.bpj.2011.10.019 ◽

2011 ◽

Vol 101 (10) ◽

pp. L44-L46 ◽

Cited By ~ 30

Author(s):

Suyong Re ◽

Naoyuki Miyashita ◽

Yoshiki Yamaguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structural Diversity ◽

Dynamics Simulation ◽

Replica Exchange ◽

Complex Type ◽

Replica Exchange Molecular Dynamics ◽

Conformational Equilibria

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Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation

International Journal of Molecular Sciences ◽

10.3390/ijms160714291 ◽

2015 ◽

Vol 16 (12) ◽

pp. 14291-14304 ◽

Cited By ~ 1

Author(s):

Zanxia Cao ◽

Xiumei Zhang ◽

Lei Liu ◽

Liling Zhao ◽

Haiyan Li ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Effect Of Ph ◽

Replica Exchange Molecular Dynamics ◽

Explicit Water

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Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study

Physical Review Letters ◽

10.1103/physrevlett.93.238105 ◽

2004 ◽

Vol 93 (23) ◽

Cited By ~ 113

Author(s):

Dietmar Paschek ◽

Angel E. García

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Protein Fragment ◽

Replica Exchange Molecular Dynamics ◽

Temperature And Pressure

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Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol

Chemical Physics Letters ◽

10.1016/j.cplett.2005.06.114 ◽

2005 ◽

Vol 412 (4-6) ◽

pp. 280-284 ◽

Cited By ~ 8

Author(s):

Koji Yoshida ◽

Toshio Yamaguchi ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Small Peptide ◽

Replica Exchange Molecular Dynamics

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Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21264 ◽

2006 ◽

Vol 66 (4) ◽

pp. 846-859 ◽

Cited By ~ 45

Author(s):

Takao Yoda ◽

Yuji Sugita ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Folding Mechanism

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