Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations

Donald Hamelberg; Tongye Shen; J. Andrew McCammon

doi:10.1063/1.1942487

Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.1942487 ◽

2005 ◽

Vol 122 (24) ◽

pp. 241103 ◽

Cited By ~ 59

Author(s):

Donald Hamelberg ◽

Tongye Shen ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Kinetic Rates ◽

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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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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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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FPGA-Accelerated Molecular Dynamics Simulations System

2009 International Conference on Scalable Computing and Communications; Eighth International Conference on Embedded Computing ◽

10.1109/embeddedcom-scalcom.2009.71 ◽

2009 ◽

Cited By ~ 1

Author(s):

He Guo ◽

Lili Su ◽

Yuxin Wang ◽

Zhu Long

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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A Comment on the Reweighting Method for Accelerated Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00236 ◽

2015 ◽

Vol 11 (6) ◽

pp. 2395-2397 ◽

Cited By ~ 14

Author(s):

Zhifeng Jing ◽

Huai Sun

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

Computer Physics Communications ◽

10.1016/j.cpc.2012.09.022 ◽

2013 ◽

Vol 184 (2) ◽

pp. 374-380 ◽

Cited By ~ 477

Author(s):

Scott Le Grand ◽

Andreas W. Götz ◽

Ross C. Walker

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Mixed Precision ◽

Dynamics Simulations

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