Molecular dynamics (MD) simulations are a powerful computational tool grounded in classical mechanics and quantum principles that enables the detailed study of atomic and molecular interactions. MD simulations have evolved throughout the years to become indispensable for investigating complex macromolecular systems, such as proteins. In addition to insights into protein structure, dynamics, and function, MD simulations very often complement experimental data, providing in-depth analysis for findings that are otherwise challenging to explain. Herein, we describe an MD simulation protocol focusing on D-Dopachrome tautomerase (D-DT or MIF-2), a protein with diverse biological activities. Our protocol provides a step-by-step procedure for structure preparation, minimization, equilibration, and production run. Additionally, we describe how the conformational flexibility and correlated movements of D-DT are examined through the use of root mean square fluctuation (RMSF) and correlation analyses, respectively. With minor modifications, this protocol is applicable to proteins with diverse sizes and biological assemblies.