Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space

Physical Review E ◽

10.1103/physreve.91.052708 ◽

2015 ◽

Vol 91 (5) ◽

Author(s):

Changjun Chen ◽

Yi Xiao ◽

Yanzhao Huang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Efficient Sampling ◽

Dynamics Method

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3PT157 Surface tension replica exchange molecular dynamics method for an efficient sampling of lipid bilayer structures(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s168_1 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S168

Author(s):

Takaharu Mori ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Annual Meeting ◽

Lipid Bilayer ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Efficient Sampling ◽

Biophysical Society ◽

Dynamics Method

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Surface-Tension Replica-Exchange Molecular Dynamics Method for Efficient Conformational Sampling of Biological Membrane Systems

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3894 ◽

2014 ◽

Vol 106 (2) ◽

pp. 704a ◽

Author(s):

Takaharu Mori ◽

Jaewoon Jung ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Biological Membrane ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Conformational Sampling ◽

Membrane Systems ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method

Parallel Computing for Bioinformatics and Computational Biology ◽

10.1002/0471756504.ch17 ◽

2005 ◽

pp. 395-425

Author(s):

Ruhong Zhou

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b03277 ◽

2018 ◽

Vol 122 (41) ◽

pp. 9435-9442 ◽

Author(s):

Wei Jiang ◽

Jonathan Thirman ◽

Sunhwan Jo ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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A Refined Free Energy Perturbation Hamiltonian Replica Exchange Molecular Dynamics Method for Absolute Binding Affinity Predictions

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3639 ◽

2018 ◽

Vol 114 (3) ◽

pp. 675a

Author(s):

Wei Jiang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Affinity ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method

Journal of Computational Chemistry ◽

10.1002/jcc.24371 ◽

2016 ◽

Vol 37 (17) ◽

pp. 1565-1575 ◽

Author(s):

Changjun Chen ◽

Yanzhao Huang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Replica-exchange molecular dynamics method for protein folding

Chemical Physics Letters ◽

10.1016/s0009-2614(99)01123-9 ◽

1999 ◽

Vol 314 (1-2) ◽

pp. 141-151 ◽

Cited By ~ 2913

Author(s):

Yuji Sugita ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Implementation of the replica-exchange molecular dynamics method for rigid bodies

International Journal of Quantum Chemistry ◽

10.1002/qua.20940 ◽

2006 ◽

Vol 106 (10) ◽

pp. 2208-2213 ◽

Author(s):

A. A. Moskovsky ◽

V. V. Vanovschi ◽

S. S. Konyukhov ◽

A. V. Nemukhin

Keyword(s):

Molecular Dynamics ◽

Rigid Bodies ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation

Biophysical Journal ◽

10.1016/s0006-3495(03)74897-8 ◽

2003 ◽

Vol 84 (2) ◽

pp. 775-786 ◽

Author(s):

Young Min Rhee ◽

Vijay S. Pande

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Folding Simulation ◽

Dynamics Method

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A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints

Methods ◽

10.1016/j.ymeth.2019.05.001 ◽

2019 ◽

Vol 162-163 ◽

pp. 96-107 ◽

Author(s):

Parisa Ebrahimi ◽

Simi Kaur ◽

Lorenzo Baronti ◽

Katja Petzold ◽

Alan A. Chen

Keyword(s):

Molecular Dynamics ◽

Rna Folding ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Two Dimensional ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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