scholarly journals Communication: κ-dynamics—An exact method for accelerating rare event classical molecular dynamics

2010 ◽  
Vol 133 (20) ◽  
pp. 201101 ◽  
Author(s):  
Chun-Yaung Lu ◽  
Dmitrii E. Makarov ◽  
Graeme Henkelman
Keyword(s):  
Molecular Dynamics ◽  
Rare Event ◽  
Exact Method ◽  
Classical Molecular Dynamics

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and 13C NMR Spectroscopy

2014 ◽  
Vol 5 (24) ◽  
pp. 4232-4237 ◽  
Author(s):  
David A. Bonhommeau ◽  
Alexandre Perret ◽  
Jean-Marc Nuzillard ◽  
Clara Cilindre ◽  
Thibaud Cours ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
13C Nmr ◽  
13C Nmr Spectroscopy ◽  
Classical Molecular Dynamics
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