Fmoc protected D-Ala-D-Ala dipeptides were known to self-assemble into supramolecular hydrogel with interesting properties. However their molecular mechanisms were not well understood. In this study, a series of coarse grained molecular dynamics simulation were conducted to investigate the formation of this hydrogel at different concentrations. The three dimensional network of hydrogel and the stacking of the Fmoc planes were observed intuitively from the snapshots of the trajectory....