1PT188 Improvement of sampling efficiency through combined use of molecular dynamics simulations with implicit and explicit solvent models(The 50th Annual Meeting of the Biophysical Society of Japan)

Hiroko Kondo; Noriaki Okimoto; Makoto Taiji

doi:10.2142/biophys.52.s101_2

1PT188 Improvement of sampling efficiency through combined use of molecular dynamics simulations with implicit and explicit solvent models(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s101_2 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S101

Author(s):

Hiroko Kondo ◽

Noriaki Okimoto ◽

Makoto Taiji

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Sampling Efficiency ◽

Solvent Models ◽

Explicit Solvent ◽

Combined Use ◽

Biophysical Society ◽

Dynamics Simulations ◽

Implicit And Explicit

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Improvement of Sampling Efficiency through Combined use of Molecular Dynamics Simulations with Implicit and Explicit Solvent Models

Biophysical Journal ◽

10.1016/j.bpj.2012.11.961 ◽

2013 ◽

Vol 104 (2) ◽

pp. 170a-171a ◽

Cited By ~ 1

Author(s):

Hiroko X. Kondo ◽

Noriaki Okimoto ◽

Makoto Taiji

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sampling Efficiency ◽

Solvent Models ◽

Explicit Solvent ◽

Combined Use ◽

Dynamics Simulations ◽

Implicit And Explicit

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Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.23853 ◽

2015 ◽

Vol 36 (10) ◽

pp. 751-762 ◽

Cited By ~ 7

Author(s):

Andrzej Eilmes ◽

Piotr Kubisiak

Keyword(s):

Molecular Dynamics ◽

Ionic Liquid ◽

Molecular Dynamics Simulations ◽

Lithium Salt ◽

Liquid Lithium ◽

Salt Solutions ◽

Solvent Models ◽

Explicit Solvent ◽

Dynamics Simulations ◽

Implicit And Explicit

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1P242 1I1435 Analysis of the effect of water molecules on lipid bilayer dynamics in aqueous salt solutions using molecular dynamics simulations(Biol & Artifi memb.:Dynamics,Oral Presentations,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s62_2 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S62

Author(s):

Rina Kagawa ◽

Yoshinori Hirano ◽

Kenji Yasuoka ◽

Masato Yasui

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Lipid Bilayer ◽

Water Molecules ◽

Salt Solutions ◽

Aqueous Salt Solutions ◽

Biophysical Society ◽

Dynamics Simulations ◽

Oral Presentations

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3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.53.s264_1 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S264

Author(s):

Shigehisa Watanabe ◽

Suyong Re ◽

Eiro Muneyuki ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Conformational Analysis ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Dynamics Simulations

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1P-030 Analysis of Tension Sensing Sites of E-coli Mechanosensitive Channel MscL Using Molecular Dynamics Simulations(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s25_4 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S25

Author(s):

Yasuyuki Sawada ◽

Masaki Murase ◽

Masahiro Sokabe

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Mechanosensitive Channel ◽

E Coli ◽

Biophysical Society ◽

Dynamics Simulations

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3B1010 Molecular dynamics simulations of dynein motor domain in explicit water(Proteins:Structure & Function III:Dynamics and Circadian Rhythm,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s58_4 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S58

Author(s):

Narutoshi Kamiya ◽

Tadaaki Mashimo ◽

Yu Takano ◽

Takahide Kon ◽

Genji Kurisu ◽

...

Keyword(s):

Molecular Dynamics ◽

Circadian Rhythm ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Oral Presentation ◽

Motor Domain ◽

Dynein Motor ◽

Biophysical Society ◽

Dynamics Simulations ◽

Explicit Water

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2P135 Analysis of translocation of tRNA molecules through ribosome using electron microscopy density map and molecular dynamics simulations(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s106_1 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S106

Author(s):

Hisashi Ishida

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Biophysical Society ◽

Density Map ◽

Dynamics Simulations

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2PT166 Theoretical analysis of fully-hydrated structures of human adult hemoglobin exploiting molecular dynamics simulations(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s133_5 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S133

Author(s):

Tetsuhiko Itagaki ◽

Jiyoung Kang ◽

Masaru Tateno

Keyword(s):

Molecular Dynamics ◽

Theoretical Analysis ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Human Adult ◽

Biophysical Society ◽

Adult Hemoglobin ◽

Dynamics Simulations

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3TA1-05 Investigation of Protein Domain Motions by Molecular Dynamics Simulations(The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s52_2 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S52

Author(s):

Hiroko Kondo ◽

Noriaki Okimoto ◽

Gentaro Morimoto ◽

Makoto Taiji

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Protein Domain ◽

Biophysical Society ◽

Dynamics Simulations ◽

Domain Motions

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3TA5-02 Conformational changes of a peptide induced by temperature and pressure : multibaric-multithermal molecular dynamics simulations(The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s58_2 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S58

Author(s):

Hisashi Okumura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Conformational Changes ◽

Biophysical Society ◽

Temperature And Pressure ◽

Dynamics Simulations

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