This work endeavours to explain molecular dynamic causes of resistance in Human Immunodeficiency Virus (HIV) Integrase through simulation of Prototype Foamy Virus (PFV) Intergrase interaction with DNA in the presence of Raltegravir (RLT) for the purpose of efficient and automatic drug ranking of Integrase inhibitors. Chapter One introduces the problem of Acquired Immunodeficiency Syndrome (AIDS) through both historical perspective and current situation by some crude analysis of geographical and social distribution. Similarly HIV is introduced both as a biological species and biochemical system with particular focus on Integrase, one of its essential protein enzymes. Chapter Two contains methods of Molecular Dynamics which are used extensively throughout this thesis (Chapters Four to Six), as well as some scientific background to those methods. Chapter Three describes efforts towards generating viable structure of HIV Integrase intasome for the purpose of Molecular Dynamic analyses. Methods of homology modelling are employed using known homologues of HIV Integrase as input data. The remaining parts of this thesis are made up of three experimental chapters describing Molecular Dynamic simulations of several biochemical systems and their analyses.