Structure and Electronic Properties of Liquids and Complex Molecular Systems in Solution: Coupling Many-Body Energy Decomposition Schemes to Born-Oppenheimer Molecular Dynamics

2015 ◽  
pp. 197-217
Author(s):  
Benedito J. C. Cabral ◽  
K. Coutinho ◽  
S. Canuto
Keyword(s):  
Molecular Dynamics ◽  
Electronic Properties ◽  
Energy Decomposition ◽  
Many Body ◽  
Molecular Systems ◽  
Body Energy ◽  
Decomposition Schemes

scholarly journals Many-body energy decomposition of hydrogen-bonded glycine clusters in gas-phase

2010 ◽  
Vol 491 (1-3) ◽  
pp. 86-90 ◽  
Author(s):  
Puspitapallab Chaudhuri ◽  
Sylvio Canuto
Keyword(s):  
Gas Phase ◽  
Energy Decomposition ◽  
Many Body ◽  
Body Energy ◽  
Hydrogen Bonded

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

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.

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