Combined ab Initio Quantum Mechanics and Classical Molecular Dynamics Studies of Polyphosphazene Polymer Electrolytes:  Competitive Solvation of Li+and LiCF3SO3

2004 ◽  
Vol 108 (40) ◽  
pp. 15694-15702 ◽  
Author(s):  
Yixuan Wang ◽  
Perla B. Balbuena
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
Polymer Electrolytes ◽  
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 Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

2008 ◽  
Vol 121 (5-6) ◽  
pp. 321-326 ◽  
Author(s):  
Hassan K. Khartabil ◽  
Marilia T. C. Martins-Costa ◽  
Philippe C. Gros ◽  
Yves Fort ◽  
Manuel F. Ruiz-López
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

Structure of layered C60 on Si(100) surface studied by ab initio and classical molecular dynamics simulations

1993 ◽  
Vol 19 (1-2) ◽  
pp. 165-171 ◽  
Author(s):  
Yoshiyuki Kawazoe ◽  
Yutaka Maruyama ◽  
Hashem Rafii-Tabar ◽  
Makoto Ikeda ◽  
Hiroshi Kamiyama ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Molecular dynamics and charge transport in organic semiconductors: a classical approach to modeling electron transfer

2017 ◽  
Vol 8 (4) ◽  
pp. 2597-2609 ◽  
Author(s):  
Kenley M. Pelzer ◽  
Álvaro Vázquez-Mayagoitia ◽  
Laura E. Ratcliff ◽  
Sergei Tretiak ◽  
Raymond A. Bair ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electron Transfer ◽  
Charge Transfer ◽  
Charge Transport ◽  
Ab Initio ◽  
Organic Semiconductors ◽  
Multiscale Approach ◽  
Classical Approach ◽  
Classical Molecular Dynamics

Using ab initio calculations of charges in PCBM fullerenes, a multiscale approach applies classical molecular dynamics to model charge transfer.

Classical versus ab initio structural relaxation: electronic excitations and optical properties of Ge nanocrystals embedded in a SiC matrix

2004 ◽  
Vol 832 ◽  
Author(s):  
Giancarlo Cappellini ◽  
H.-Ch. Weissker ◽  
D. De Salvator ◽  
J. Furthmüller ◽  
F. Bechstedt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Properties ◽  
Ab Initio ◽  
First Principles ◽  
Electronic Excitation ◽  
First Principle ◽  
Electronic Excitations ◽  
Combined Method ◽  
Classical Molecular Dynamics ◽  
Ge Nanocrystals

ABSTRACTWe discuss and test a combined method to efficiently perform ground- and excited-state calculations for relaxed structures using both a quantum first-principles approach and a classical molecular-dynamics scheme. We apply this method to calculate the ground state, the optical properties, and the electronic excitations of Ge nanoparticles embedded in a cubic SiC matrix. Classical molecular dynamics is used to relax the large-supercell system. First-principles quantum techniques are then used to calculate the electronic structure and, in turn, the electronic excitation and optical properties. The proposed procedure is tested with data resulting from a full first-principles scheme. The agreement is quantitatively discussed between the results after the two computational paths with respect to the structure, the optical properties, and the electronic excitations. The combined method is shown to be applicable to embedded nanocrystals in large simulation cells for which the first-principle treatment of the ionic relaxation is presently out of reach, whereas the electronic, optical and excitation properties can already be obtained ab initio. The errors incurred from the relaxed structure are found to be non-negligible but controllable.

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