A fundamental appreciation for how biological macromolecules work requires knowledge of
structure and its dynamics. Molecular dynamics simulation provides links between structure and
dynamics by enabling the exploration of the conformational energy landscape accessible to
protein molecules. In this perspective we illustrate the application of molecular dynamics
simulations to biology by describing the conformational changes of Human Telomere Repeat
Binding factor 2 (hTRF2). hTRF2 is a sequence specific 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 huge amount of fluctuation in the region of
N-terminal end of the hTRF2 that give us some new information about the structural changes of
the global protein.