Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

Jens Kleinjung; Walter R. P. Scott; Jane R. Allison; Wilfred F. van Gunsteren; Franca Fraternali

doi:10.1021/ct200390j

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200390j ◽

2012 ◽

Vol 8 (7) ◽

pp. 2391-2403 ◽

Cited By ~ 15

Author(s):

Jens Kleinjung ◽

Walter R. P. Scott ◽

Jane R. Allison ◽

Wilfred F. van Gunsteren ◽

Franca Fraternali

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Implicit Solvation ◽

Solvation Parameters ◽

Dynamics Simulations ◽

Explicit Water

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Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00380 ◽

2021 ◽

Author(s):

Masatake Sugita ◽

Satoshi Sugiyama ◽

Takuya Fujie ◽

Yasushi Yoshikawa ◽

Keisuke Yanagisawa ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Permeability ◽

Lipid Bilayer ◽

Cyclic Peptides ◽

Large Scale ◽

Enhanced Sampling ◽

Permeability Prediction ◽

Dynamics Simulations

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Mechanistic Insights from Molecular Dynamics Simulations of Large-Scale Conformational Transitions in the INDY Transport Cycle

Biophysical Journal ◽

10.1016/j.bpj.2020.11.153 ◽

2021 ◽

Vol 120 (3) ◽

pp. 3a-4a

Author(s):

Noah Trebesch ◽

David B. Sauer ◽

Da-Neng Wang ◽

Emad Tajkhorshid

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Conformational Transitions ◽

Transport Cycle ◽

Dynamics Simulations

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Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

Journal of Vacuum Science & Technology A Vacuum Surfaces and Films ◽

10.1116/1.4953404 ◽

2016 ◽

Vol 34 (4) ◽

pp. 041509 ◽

Cited By ~ 19

Author(s):

Daniel Edström ◽

Davide G. Sangiovanni ◽

Lars Hultman ◽

Ivan Petrov ◽

J. E. Greene ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Epitaxial Film ◽

Film Growth ◽

Dynamics Simulations ◽

Epitaxial Film Growth

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Nanoscale Transport Phenomena in PEM of PEFC by Large Scale Molecular Dynamics Simulations

ECS Transactions ◽

10.1149/05002.0859ecst ◽

2013 ◽

Vol 50 (2) ◽

pp. 859-868 ◽

Cited By ~ 2

Author(s):

T. Tokumasu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Transport Phenomena ◽

Nanoscale Transport ◽

Dynamics Simulations

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Bimodal Grain-Size Scaling of Thermal Transport in Polycrystalline Graphene from Large-Scale Molecular Dynamics Simulations

Nano Letters ◽

10.1021/acs.nanolett.7b01742 ◽

2017 ◽

Vol 17 (10) ◽

pp. 5919-5924 ◽

Cited By ~ 11

Author(s):

Zheyong Fan ◽

Petri Hirvonen ◽

Luiz Felipe C. Pereira ◽

Mikko M. Ervasti ◽

Ken R. Elder ◽

...

Keyword(s):

Molecular Dynamics ◽

Grain Size ◽

Molecular Dynamics Simulations ◽

Thermal Transport ◽

Large Scale ◽

Size Scaling ◽

Dynamics Simulations ◽

Bimodal Grain Size

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Large-scale molecular-dynamics simulations of martensitic nucleation and shape-memory effects in transition metal alloys

Phase Transitions ◽

10.1080/01411599808209282 ◽

1998 ◽

Vol 65 (1-4) ◽

pp. 79-108 ◽

Cited By ~ 10

Author(s):

P. Entel ◽

K. Kadau ◽

R. Meyer ◽

H. C. Herper ◽

M. Schröter ◽

...

Keyword(s):

Molecular Dynamics ◽

Transition Metal ◽

Shape Memory ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Metal Alloys ◽

Transition Metal Alloys ◽

Shape Memory Effects ◽

Dynamics Simulations ◽

Martensitic Nucleation

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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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Large-scale molecular dynamics simulations of nanomachining

Advanced Machining Processes ◽

10.1201/b21863-6 ◽

2017 ◽

pp. 141-177 ◽

Cited By ~ 3

Author(s):

Stefan J. Eder ◽

Ulrike Cihak-Bayr ◽

Davide Bianchi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Dynamics Simulations

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Large-scale molecular dynamics simulations of charged particle stopping in strongly coupled plasmas: definitive tests of plasma kinetic theories

10.2172/1055321 ◽

2012 ◽

Author(s):

Michael S. Murillo ◽

Paul E. Grabowski ◽

Michael P. Surh

Keyword(s):

Molecular Dynamics ◽

Charged Particle ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Strongly Coupled ◽

Strongly Coupled Plasmas ◽

Plasma Kinetic ◽

Dynamics Simulations ◽

Coupled Plasmas

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Large-Scale Molecular Dynamics Simulations of Energetic Ni Nanocluster Impact onto the Surface

Journal of Cluster Science ◽

10.1007/s10876-008-0185-6 ◽

2008 ◽

Vol 19 (2) ◽

pp. 411-419 ◽

Cited By ~ 3

Author(s):

K. Mirabbaszadeh ◽

E. Zaminpayma ◽

P. Nayebi ◽

S. Saramad

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Large Scale ◽

Dynamics Simulations

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