Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

Theoretical Chemistry Accounts ◽

10.1007/s002140050424 ◽

1999 ◽

Vol 101 (1-3) ◽

pp. 163-169

Author(s):

Gerald Löffler

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Potential ◽

Poisson Boltzmann ◽

Dynamics Simulations

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Redox potentials in the decaheme cytochrome MtrF: Poisson–Boltzmann vs. molecular dynamics simulations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1716813114 ◽

2017 ◽

Vol 114 (47) ◽

pp. E10028-E10028 ◽

Cited By ~ 2

Author(s):

Marian Breuer ◽

Kevin M. Rosso ◽

Jochen Blumberger

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Redox Potentials ◽

Poisson Boltzmann ◽

Dynamics Simulations

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Evaluation of Protein Electrostatic Potential from Molecular Dynamics Simulations in the Presence of Exogenous Electric Fields: The Case Study of Myoglobin

Computational Electrostatics for Biological Applications ◽

10.1007/978-3-319-12211-3_13 ◽

2014 ◽

pp. 255-270

Author(s):

P. Marracino ◽

M. Casciola ◽

M. Liberti ◽

F. Apollonio

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electric Fields ◽

Electrostatic Potential ◽

Dynamics Simulations

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The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2011.12.055 ◽

2012 ◽

Vol 102 (4) ◽

pp. 829-838 ◽

Cited By ~ 49

Author(s):

Serdal Kirmizialtin ◽

Alexander R.J. Silalahi ◽

Ron Elber ◽

Marcia O. Fenley

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Ionic Atmosphere ◽

Poisson Boltzmann ◽

Dynamics Simulations

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Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

The Journal of Chemical Physics ◽

10.1063/1.3702195 ◽

2012 ◽

Vol 136 (14) ◽

pp. 145101 ◽

Cited By ~ 20

Author(s):

Fu-Feng Liu ◽

Zhen Liu ◽

Shu Bai ◽

Xiao-Yan Dong ◽

Yan Sun

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Molecular Mechanics ◽

Surface Area ◽

Molecular Interactions ◽

Amyloid Β ◽

Free Energy Calculations ◽

Poisson Boltzmann ◽

Dynamics Simulations

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A polarizable high-rank quantum topological electrostatic potential developed using neural networks: Molecular dynamics simulations on the hydrogen fluoride dimer

International Journal of Quantum Chemistry ◽

10.1002/qua.21507 ◽

2007 ◽

Vol 107 (14) ◽

pp. 2817-2827 ◽

Cited By ~ 36

Author(s):

S. Houlding ◽

S. Y. Liem ◽

P. L. A. Popelier

Keyword(s):

Neural Networks ◽

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Hydrogen Fluoride ◽

Electrostatic Potential ◽

High Rank ◽

Dynamics Simulations

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Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-011-9464-7 ◽

2011 ◽

Vol 25 (9) ◽

pp. 795-811 ◽

Cited By ~ 14

Author(s):

Matthias Negri ◽

Maurizio Recanatini ◽

Rolf W. Hartmann

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Electrostatic Potential ◽

Molecular Electrostatic Potential ◽

Binding Mode ◽

Free Energy Calculations ◽

Computational Investigation ◽

Dynamics Simulations ◽

Molecular Electrostatic Potential Maps

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Molecular dynamics simulations of rubredoxin fromClostridium pasteurianum: Changes in structure and electrostatic potential duringredox reactions

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340220208 ◽

1995 ◽

Vol 22 (2) ◽

pp. 154-167 ◽

Cited By ~ 36

Author(s):

Robert B. Yelle ◽

Noh-Sum Park ◽

Toshiko Ichiye

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Potential ◽

Dynamics Simulations

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Direct Observation of Salt Effects on Molecular Interactions through Explicit-Solvent Molecular Dynamics Simulations: Differential Effects on Electrostatic and Hydrophobic Interactions and Comparisons to Poisson−Boltzmann Theory

Journal of the American Chemical Society ◽

10.1021/ja058637b ◽

2006 ◽

Vol 128 (24) ◽

pp. 7796-7806 ◽

Cited By ~ 31

Author(s):

Andrew S. Thomas ◽

Adrian H. Elcock

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Direct Observation ◽

Molecular Interactions ◽

Hydrophobic Interactions ◽

Salt Effects ◽

Explicit Solvent ◽

Electrostatic And Hydrophobic Interactions ◽

Poisson Boltzmann ◽

Dynamics Simulations

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Molecular dynamics simulations of charged plates and electrolyte in a bilayer-like geometry: molecular ordering and electrostatic potential

Proceedings of the Second Joint 24th Annual Conference and the Annual Fall Meeting of the Biomedical Engineering Society] [Engineering in Medicine and Biology ◽

10.1109/iembs.2002.1136841 ◽

2003 ◽

Author(s):

J.N. Sachs ◽

T.B. Woolf

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Potential ◽

Molecular Ordering ◽

Dynamics Simulations

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Poisson–Boltzmann modeling and molecular dynamics simulations of polyelectrolyte gel diodes in the static regime

Soft Matter ◽

10.1039/c9sm02232e ◽

2020 ◽

Vol 16 (4) ◽

pp. 1091-1101

Author(s):

Vasilii Triandafilidi ◽

Savvas G. Hatzikiriakos ◽

Jörg Rottler

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Md Simulations ◽

Polyelectrolyte Gel ◽

Static Regime ◽

Poisson Boltzmann ◽

Coupling Strengths ◽

Dynamics Simulations ◽

Electrostatic Coupling

We compare MD simulations of a model polyelectrolyte gel diode (PGD) to a Poisson–Boltzmann (PB) model. We study the rectifying behaviour at different electrostatic coupling strengths and suggest an updated PB model for improved modelling of PGDs.

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