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Author Fidiani, Elok
Source United States Department of Energy Office of Scientific and Technical Information
Content type Text
Language English
Subject Keyword CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS ♦ ALGORITHMS ♦ ATOMS ♦ CHEMICAL BONDS ♦ COMPUTERIZED SIMULATION ♦ EQUATIONS OF MOTION ♦ G CODES ♦ HYDROCHLORIC ACID ♦ HYDROGEN ♦ J CODES ♦ M CODES ♦ MOLECULAR DYNAMICS METHOD ♦ MOLECULES ♦ MORSE POTENTIAL ♦ N CODES ♦ NUMERICAL ANALYSIS ♦ TIME DEPENDENCE
Abstract Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.
ISSN 0094243X
Educational Use Research
Learning Resource Type Article
Publisher Date 2016-03-11
Publisher Place United States
Volume Number 1719
Issue Number 1


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