Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering

Nicolas Lenner; Gerald Mathias

doi:10.1021/acs.jctc.5b00751

Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00751 ◽

2016 ◽

Vol 12 (2) ◽

pp. 486-498 ◽

Cited By ~ 6

Author(s):

Nicolas Lenner ◽

Gerald Mathias

Keyword(s):

Molecular Dynamics ◽

Deterministic Approach ◽

Simulated Tempering

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High Pressure Effect on a Helical Peptide Studied by Simulated Tempering Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3379 ◽

2014 ◽

Vol 106 (2) ◽

pp. 611a ◽

Cited By ~ 1

Author(s):

Yoshiharu Mori ◽

Hisashi Okumura

Keyword(s):

Molecular Dynamics ◽

High Pressure ◽

Molecular Dynamics Simulations ◽

Pressure Effect ◽

Helical Peptide ◽

Simulated Tempering ◽

Dynamics Simulations ◽

High Pressure Effect

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On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Journal of Computational Chemistry ◽

10.1002/jcc.24430 ◽

2016 ◽

Vol 37 (21) ◽

pp. 2017-2028 ◽

Cited By ~ 4

Author(s):

Tetsuro Nagai ◽

George A. Pantelopulos ◽

Takuya Takahashi ◽

John E. Straub

Keyword(s):

Molecular Dynamics ◽

Mass Scaling ◽

Simulated Tempering

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Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations

The Journal of Physical Chemistry Letters ◽

10.1021/jz400769w ◽

2013 ◽

Vol 4 (12) ◽

pp. 2079-2083 ◽

Cited By ~ 16

Author(s):

Yoshiharu Mori ◽

Hisashi Okumura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Helical Structure ◽

Simulated Tempering ◽

Dynamics Simulations

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2P052 Pressure dependence of the secondary structure of a peptide : A simulated tempering molecular dynamics study(01C. Protein: Property,Poster)

Seibutsu Butsuri ◽

10.2142/biophys.53.s167_4 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S167

Author(s):

Yoshiharu Mori ◽

Hisashi Okumura

Keyword(s):

Molecular Dynamics ◽

Secondary Structure ◽

Pressure Dependence ◽

Protein Property ◽

Simulated Tempering

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3P075 Pressure dependence of protein conformations studied by generalized simulated tempering molecular dynamics simulations(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s158_1 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S158

Author(s):

Yoshiharu Mori ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Pressure Dependence ◽

Protein Conformations ◽

Protein Property ◽

Biophysical Society ◽

Simulated Tempering ◽

Dynamics Simulations

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Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations

Physical Review E ◽

10.1103/physreve.87.023301 ◽

2013 ◽

Vol 87 (2) ◽

Cited By ~ 10

Author(s):

Yoshiharu Mori ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Proton Transfer ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Umbrella Sampling ◽

Simulated Tempering ◽

Dynamics Simulations

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Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation

Chemical Physics Letters ◽

10.1016/j.cplett.2004.05.046 ◽

2004 ◽

Vol 392 (1-3) ◽

pp. 34-39 ◽

Cited By ~ 8

Author(s):

Jae Gil Kim ◽

Yoshifumi Fukunishi ◽

Haruki Nakamura

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Average Energy ◽

Folding Simulation ◽

Simulated Tempering

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Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study

Journal of Computational Chemistry ◽

10.1002/jcc.24767 ◽

2017 ◽

Vol 38 (15) ◽

pp. 1167-1173 ◽

Cited By ~ 8

Author(s):

Yoshiharu Mori ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

High Pressure ◽

Conformational Changes ◽

Simulated Tempering

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Nonequilibrium Molecular Dynamics

10.1017/9781139017848 ◽

2017 ◽

Cited By ~ 25

Author(s):

Billy D. Todd ◽

Peter J. Daivis

Keyword(s):

Molecular Dynamics ◽

Nonequilibrium Molecular Dynamics

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Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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