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Students perform Molecular Dynamics Simulation without understanding why they are setting such parameter and why does those parameters even exist in the first place. We have designed the course to provide a brief introduction of Molecular Dynamics Simulation and why different parameter exists in its simulation. An introduction to the software is provided with an explanation as to why we have selected this software in particular. Furthermore, how to install, operate and understand the different parameters of software is also involved. In this course we will be subtly answering those unasked questions about why this? By the end of this course, you will have a good grasp and understanding of Molecular Dynamics Simulation instead of a general idea. For the study of biomolecules molecular dynamics simulations have become a common technique. Simulations of ever larger systems are carried out, with more realistic boundary conditions and better sampling owing to longer sample durations. Realistic simulations of complicated systems like transmembrane channels have just become possibles.Simulations help us comprehend biological processes and give structural data a dynamic dimension; for example, the transition of the disease-causing prion protein into a harmless protein has been modelled.Molecular dynamics the science of simulating the motions of a system of particles applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in aprotein or in DNA as a function of time.