The rapid growth in biotechnology over the last few years has highlighted the importance of understanding the link between molecular structure and function. Despite the huge increase in computational power in recent times, modelling large bio-molecules is still primarily limited by computation size allowing analysis only of short timeframes, which in many cases are not biologically significant. The goal is to provide new insight into experimentally less accessible properties such as evolution, structure dynamics and definition of thermodynamic stability criteria. In this work we use the analysis of Hamiltonian path analysis to enable calculation of the behaviour of a molecular system along large time frames. We look to develop molecular trajectories using a boundary value approach derived from experimentally determine starting and ending conformations. This method will provide information throughout the whole time span of the path.