Molecular dynamics simulations is a widely used computer simulations technique to study the conformational dynamics of biological macromolecules such as proteins. Newton's classical equations of motion are solved iteratively to simulate the motion of a system of particles as a function of time. Due to the remarkable resolution in space (single atom), time (femtosecond), and energy, MD represents a powerful complement to experimental techniques, providing mechanistic insight into experimentally observed processes. Consequently, MD simulations can be treated as a virtual experimental method that provides an interface between the theory and a real laboratory experiment. MDS can be used to address specific questions about the properties of a model system, often more straightforwardly than the experiments on real systems. This book gives an overview on the application of MD simulations and Electron paramagnetic resonance (EPR)spectroscopy to study the protein structure and dynamics. A sophisticated approach to compare the data obtained from laboratory EPR experiments with that of the information obtained from in silico computation is introduced.