Molecular dynamics simulation: from theoretical concept to application

Abstract

Molecular dynamics is a computer simulation method that calculates the time dependent behavior of a molecular system. It predicts how the atoms of a given system are moving with respect to time by numerically solving the Newtons equation of motion. In this thesis, description of the foundations of molecular dynamics was presented and a MATLAB code built to implement molecular dynamics. Simulations were run from the implementation and the results including some dynamical properties of molecular dynamics were reported and discussed. A comparative study between two numerical integration techniques, Velocity Verlet and Euler's algorithms, of the equations of motion in terms of the computational time was investigated. It was observed that the Velocity Verlet algorithm is faster and more stable than Eulers algorithm. Finally, a real life applica- tion of molecular dynamics techniques for protein structure prediction was presented using the AMBER package; a well-known package for molecular dynamics simulation.