MOLECULAR DYNAMICS AND SIMULATION OF COLLAGEN USING THE AVOGADRO SOFTWARE.

ABSTRACT

Molecular dynamics (MD) simulation is a computational technique used to study the physical movements of atoms and molecules. It involves using computer algorithms to integrate the equations of motion for a system of particles, to predict the behaviors of the particles over time. MD simulation can be used to study a wide range of phenomena, including chemical reactions, phase transitions, and the physical properties of materials. It is a powerful tool for understanding the dynamics of complex systems at the atomic and molecular scale. In an MD simulation, the positions and velocities of the particles in the system are typically updated at discrete time steps In the context of collagen, MD simulation can be used to study the structural and functional properties of this important biomolecule at the atomic level. Collagen is the most abundant protein in mammals and is a key component of various tissues including skin, bone, and connective tissue. This study indicates the importance of molecular dynamics simulation in the study of complex molecules like collagen. In this study, we are to carry out molecular dynamics simulation of the collagen molecule using the Avogadro software, by importing the molecule, visualising, optimising its geometry, and carrying out MD simulation to obtain results. The results show that the minimised energy is the same of any steps per update used for geometry optimisation.