Simple Harmonic Oscillator Model of O2 Molecule in Vacuum: A Classical Molecular Dynamics Study

Salmahaminati Salmahaminati(1),
(1) Chemistry Department, Universitas Islam Indonesia

Abstract


The simple harmonic oscillator model allows a basic understanding of all processes and can be used to analyse optical vibrational modes and electronic transitions in atoms, molecules and crystals, in order to derive general properties of harmonic generation to all orders. In particular, we are done to investigate single, ten, and twenty harmonic oscillator of O2 molecule using GROMACS 4.55. Time is the important factor in simulation because the best result of simulation can be obtained by increasing the number of steps and by decreasing the timesteps. Since the properties only depend on time and not on the specific microscopic model, they can also be adopted for the quantum-mechanical description by using in the classical molecular dynamics.

 


Keywords


classical molecular dynamics; harmonic oscillator; GROMACS

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References


Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl., 2008. GROMACS 4: Algorithms For Highly Efficient, Load-balanced, And Scalable Molecular Simulation. J. Chem. Theory Comput. 4 , 435–447. DOI: 10.1021/ct700301q

Charles B. Harris, David E. Smith, and Daniel J. Russell., 1990. Vibrational relaxation of diatomic molecules in liquids. Chem. Rev. 90, 481-488. DOI: 10.1021/cr00101a003

F. Iachello., 1998. Algebraic Approach to Molecular Rotation‐Vibration spectra. I. Diatomic Molecules. J. Chem. Phys. 77, 3046. doi.org/10.1063/1.444228

Guillaume Lamoureux., 2003. A Simple Polarizable Model of Water Based on Classical Drude Oscillators. J. Chem. Phys. 119, 5185. doi.org/10.1063/1.1598191

J. J. Rael and A.A. Abidi, 2000. Physical Processes of Phase Noise in Differential LC Oscillators. Custom Integrated Circuits Conference, 2000. CICC. Proceedings of the IEEE 2000

Keith., 1971. Mechanics. Reading, MA: Addison-Wesley. ISBN 0-201-07392-7.

Kevin Jensen., 2018. Maxwell–Boltzmann distribution; Introduction to the Physics of Electron Emission. Wiley Online Library. DOI: 10.1002/9781119051794.ch5

Simo, J. C. Hughes, T. J. R. 1998. Computational Inelasticity. Springer. ISBN 9780387975207.

O. S. van Roosmalen., 1998. Algebraic Approach to Molecular Rotation‐Vibration Spectra. II. Triatomic Molecules. J. Chem. Phys. 79, 2515. doi.org/10.1063/1.446164

Philip M. Kiefer and James T. Hynes., 2002. Nonlinear Free Energy Relations For Adiabatic Proton Transfer Reactions In A Polar Environment. II. Inclusion of The Hydrogen Bond Vibration. J. Phys. Chem. 106, 1850–1861. DOI: 10.1021/jp013425w

Ugural, A. C. Fenster, S. K., 2003. Advanced Strength and Applied Elasticity (4th ed.). Prentice-Hall. ISBN 978-0-13-047392-9

N. Goga, M.N. Melo, A.J. Rzepiela, A.H. de Vries, A. Hadar, S.J. Marrink, H.J.C. Berendsen., 2015. Benchmark of Schemes For Multiscale Molecular Dynamics Simulations. J. Chem. Theory Comput. 11, 1389-1398. DOI: 10.1021/ct501102b




Indonesian Journal of Chemical Research
ISSN 2354-9610 (print), ISSN 2614-5081 (online)
Published by: 
Chemistry Department
Faculty of Mathematics and Natural Science
Universitas Islam Indonesia, Yogyakarta

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