A fundamental appreciation for how biological macro molecules work requires knowledge of structure and its dynamics. Molecular dynamics simu lation provides links between structure and dynamics by enabling the exploration of the conform ational energy landscape accessible to protein molecules. In this perspective we illustrat e the application of molecular dynamics simulations to biology by describing the conformati onal changes of Human Telomere Repeat Binding factor 2 (hTRF2). hTRF2 is a sequence speci fic DNA-binding protein. The progress of the simulation was monitored by calculating several structural parameters over time in both the vacuum and water condition. The result shows some h uge amount of fluctuation in the region of N-terminal end of the hTRF2 that give us some new i nformation about the structural changes of the global protein.