Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

Rao Huang; Li-Ta Lo; Yuhua Wen; Arthur F. Voter; Danny Perez

doi:10.1063/1.4996922

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

The Journal of Chemical Physics ◽

10.1063/1.4996922 ◽

2017 ◽

Vol 147 (15) ◽

pp. 152717 ◽

Cited By ~ 7

Author(s):

Rao Huang ◽

Li-Ta Lo ◽

Yuhua Wen ◽

Arthur F. Voter ◽

Danny Perez

Keyword(s):

Molecular Dynamics ◽

Cluster Analysis ◽

Molecular Dynamics Simulations ◽

Pt Nanoparticles ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study

The Journal of Chemical Physics ◽

10.1063/1.2794763 ◽

2007 ◽

Vol 127 (17) ◽

pp. 175105 ◽

Cited By ~ 46

Author(s):

César Augusto F. de Oliveira ◽

Donald Hamelberg ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Explicit Solvent ◽

Kinetic Rates ◽

Dynamics Simulations ◽

Alanine Dipeptide

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Enhanced Disrupting Effect of Benzophenone-1 Chlorination Byproducts to the Androgen Receptor: Cell-Based Assays and Gaussian Accelerated Molecular Dynamics Simulations

Chemical Research in Toxicology ◽

10.1021/acs.chemrestox.1c00023 ◽

2021 ◽

Author(s):

Tingjie Zhan ◽

Shixuan Cui ◽

Xujun Liu ◽

Chunlong Zhang ◽

Yu-ming M. Huang ◽

...

Keyword(s):

Molecular Dynamics ◽

Androgen Receptor ◽

Molecular Dynamics Simulations ◽

Receptor Cell ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy: A case study of Sr2+ in methanol solution

The Journal of Chemical Physics ◽

10.1063/1.476398 ◽

1998 ◽

Vol 108 (22) ◽

pp. 9487-9497 ◽

Cited By ~ 28

Author(s):

D. Roccatano ◽

H. J. C. Berendsen ◽

P. D’Angelo

Keyword(s):

Molecular Dynamics ◽

Fine Structure ◽

Molecular Dynamics Simulations ◽

Methanol Solution ◽

Intermolecular Potential ◽

Potential Models ◽

X Ray ◽

Dynamics Simulations ◽

X Ray Absorption

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Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200615k ◽

2011 ◽

Vol 8 (1) ◽

pp. 17-23 ◽

Cited By ~ 25

Author(s):

William Sinko ◽

César Augusto F. de Oliveira ◽

Levi C. T. Pierce ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

High Energy ◽

Energy Barriers ◽

Accelerated Molecular Dynamics ◽

New Equation ◽

Dynamics Simulations

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Bayesian Refinement of Accelerated Molecular Dynamics Simulations for Interpreting SAXS Experiments

Biophysical Journal ◽

10.1016/j.bpj.2016.11.3122 ◽

2017 ◽

Vol 112 (3) ◽

pp. 580a

Author(s):

Samuel Bowerman ◽

Amy Rice ◽

Jeff Wereszczynski

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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Accelerated molecular dynamics simulations of interstitial clusters in pure and Al-doped MgO

Nuclear Instruments and Methods in Physics Research Section B Beam Interactions with Materials and Atoms ◽

10.1016/j.nimb.2006.04.078 ◽

2006 ◽

Vol 250 (1-2) ◽

pp. 12-16 ◽

Cited By ~ 6

Author(s):

B.P. Uberuaga ◽

R. Smith ◽

A.R. Cleave ◽

R.W. Grimes ◽

A.F. Voter ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

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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An investigation of the effects of error correcting code on GPU-accelerated molecular dynamics simulations

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13 ◽

10.1145/2484762.2484774 ◽

2013 ◽

Cited By ~ 1

Author(s):

Ross C. Walker ◽

Robin M. Betz

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Error Correcting Code ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Journal of Chemical Theory and Computation ◽

10.1021/ct500090q ◽

2014 ◽

Vol 10 (7) ◽

pp. 2677-2689 ◽

Cited By ~ 172

Author(s):

Yinglong Miao ◽

William Sinko ◽

Levi Pierce ◽

Denis Bucher ◽

Ross C. Walker ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Free Energy Calculation ◽

Energy Calculation ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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Multi-scale theoretical investigation of molecular hydrogen adsorption over graphene: coronene as a case study

RSC Advances ◽

10.1039/c4ra08487j ◽

2014 ◽

Vol 4 (97) ◽

pp. 54447-54453 ◽

Cited By ~ 26

Author(s):

Md Bin Yeamin ◽

N. Faginas-Lago ◽

M. Albertí ◽

I. G. Cuesta ◽

J. Sánchez-Marín ◽

...

Keyword(s):

Molecular Dynamics ◽

Dft Calculations ◽

Modeling And Simulation ◽

Molecular Dynamics Simulations ◽

Multiscale Modeling ◽

Molecular Hydrogen ◽

Hydrogen Adsorption ◽

Multi Scale ◽

Dynamics Simulations

Multiscale modeling and simulation (MMS) combining B97-D/TZV2P DFT calculations and molecular dynamics simulations are performed to investigate the adsorption of hydrogen over coronene as a model of graphene.

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