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.
