Molecular dynamics (MD) simulation is one of the widely used techniques in structural bioinformatics. This method plays an important role in understanding and investigating biological structures and their dynamic processes. From studying proteins and peptides to large-scale complexes like biological membranes, all are feasible with different types of MD. In addition to traditional and well-known MD simulations, new methods are being developed that can capture free energy, thermodynamic parameters, and chemical reaction processes. The main goal of this field is to simulate a system that is close to natural conditions. In this seminar, the basis, applications, and studies on several techniques like SMD, REMD, aMD, and Metadynamics will be discussed.