MOLECULAR DYNAMICS AND SIMULATION OF DEOXYRIBONUCLEIC ACID (DNA)

ABSTRACT

Molecular dynamics simulation has become a widely used tool for investigating the structural and dynamic behavior of biomolecules. In this study, we performed molecular dynamics simulations of deoxyribonucleic acid (DNA) using AVOGADRO software package. Our simulation focused on the visualization of 1BNA: structure of a B-DNA dodecamer, in various display form provided by the Avogadro software package. We also carries out geometry optimization which gave the minimization energy for different time step. This study has helped identify the number of atoms in 1BNA molecule, the molecular properties, the bond properties, the atomic properties and the torsion properties of the molecule using the AVOGADRO software package.