Modeling of diatomic molecule using the Morse potential and the Verlet algorithm
- Department of Physics, Parahyangan Catholic University, Bandung-Jawa Barat (Indonesia)
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.
- OSTI ID:
- 22590862
- Journal Information:
- AIP Conference Proceedings, Vol. 1719, Issue 1; Conference: 4. international conference on theoretical and applied physics (ICTAP) 2014, Bali (Indonesia), 16-17 Oct 2014; Other Information: (c) 2016 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); ISSN 0094-243X
- Country of Publication:
- United States
- Language:
- English
Similar Records
ENERGY TRANSFER ATTENDING COLLISIONS OF ATOMS WITH DIATOMIC MOLECULES
Nonadiabatic Molecular Dynamics Simulations Based on Time-Dependent Density Functional Tight-Binding Method