Quantum Mechanics: Validity of Classical Molecular Dynamics

2016 ◽  
Author(s):  
T. Prevenslik
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
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 The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

2021 ◽  
Vol 23 (10) ◽  
pp. 6252-6265
Author(s):  
Alexander Gheorghiu ◽  
Peter V. Coveney ◽  
Alya A. Arabi
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Proton Transfer ◽  
Molecular Mechanics ◽  
Electric Fields ◽  
Base Pair ◽  
Realistic Model ◽  
External Electric Fields ◽  
Classical Molecular Dynamics

A detailed investigation is reported of mutagenic guanine–cytosine tautomerization in a realistic model of DNA bathed in intense electric fields using a combination of classical molecular dynamics and quantum mechanics/molecular mechanics methods.

Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal–organic frameworks

2021 ◽  
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
Farnaz A. Shakib
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Catalytic Activity ◽  
Metal Organic Frameworks ◽  
Structural Flexibility ◽  
Classical Molecular Dynamics ◽  
Structural Deformations ◽  
Metal Organic

A combined quantum mechanics and classical molecular dynamics approach is used to unravel the effects of structural deformations and heterogeneity on catalytic activity of 2D π-stacked layered metal–organic frameworks.

Absorption and Fluorescence of PRODAN in Phospholipid Bilayers: A Combined Quantum Mechanics and Classical Molecular Dynamics Study

2011 ◽  
Vol 115 (41) ◽  
pp. 11428-11437 ◽  
Author(s):  
Lukasz Cwiklik ◽  
Adelia J. A. Aquino ◽  
Mario Vazdar ◽  
Piotr Jurkiewicz ◽  
Jiří Pittner ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Phospholipid Bilayers ◽  
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.

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