scholarly journals Isomorphic classical molecular dynamics model for an excess electron in a supercritical fluid

2008 ◽  
Vol 129 (19) ◽  
pp. 194502 ◽  
Author(s):  
Thomas F. Miller
Keyword(s):  
Molecular Dynamics ◽  
Supercritical Fluid ◽  
Excess Electron ◽  
Dynamics Model ◽  
Classical Molecular Dynamics

scholarly journals Reactivity of an Excess Electron with Monovalent Cations in Bulk Water by Mixed Quantum Classical Molecular Dynamics Simulations

2004 ◽  
Vol 30 (11-12) ◽  
pp. 749-754 ◽  
Author(s):  
Riccardo Spezia ◽  
Cédric Nicolas ◽  
François-Xavier Coudert ◽  
Pierre Archirel ◽  
Rodolphe Vuilleumier ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bulk Water ◽  
Excess Electron ◽  
Monovalent Cations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

Classical molecular dynamics model for coupled two component plasmas

2007 ◽  
Vol 3 (1-2) ◽  
pp. 52-56 ◽  
Author(s):  
A. Calisti ◽  
T. del Río Gaztelurrutia ◽  
B. Talin
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Model ◽  
Classical Molecular Dynamics ◽  
Two Component

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.

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