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

Tetsuro Nagai; George A. Pantelopulos; Takuya Takahashi; John E. Straub

doi:10.1002/jcc.24430

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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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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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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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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Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm

The Journal of Chemical Physics ◽

10.1063/1.4895510 ◽

2014 ◽

Vol 141 (11) ◽

pp. 114111 ◽

Cited By ~ 7

Author(s):

Tetsuro Nagai ◽

Takuya Takahashi

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Mass Scaling ◽

Simpler Algorithm ◽

Computational Resources

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1P321 Mass-scaling replica-exchange molecular dynamics method(30. Miscellaneous topics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s194_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S194

Author(s):

Tetsuro Nagai ◽

Takuya Takahashi

Keyword(s):

Molecular Dynamics ◽

Annual Meeting ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Mass Scaling ◽

Biophysical Society ◽

Dynamics Method

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General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

Journal of the Physical Society of Japan ◽

10.7566/jpsj.86.014003 ◽

2017 ◽

Vol 86 (1) ◽

pp. 014003 ◽

Cited By ~ 2

Author(s):

Tetsuro Nagai

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Mass Scaling

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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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Increasing the time step with mass scaling in Born-Oppenheimerab initioQM/MM molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.21296 ◽

2009 ◽

Vol 30 (16) ◽

pp. 2706-2711 ◽

Cited By ~ 20

Author(s):

Han Zheng ◽

Shenglong Wang ◽

Yingkai Zhang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Time Step ◽

Mass Scaling ◽

Dynamics Simulations

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