To study the dynamics and mechanisms of the proton wire of wild type green fluorescence protein (wt-GFP) and its S205V mutant, we applied molecular dynamics (MD) simulations and compared the results with the X-ray structures of both proteins and with the proton transfer kinetics of these proteins studied by the time-resolved emission technique. The MD simulations for the wt-GFP show that, in the proton wire, the Ser205 exists in two conformations with similar probabilities. One conformation supports the proton transfer, and the other does not. The fluctuation between the two conformers is relatively slow. This result may explain the time-resolved emission spectrum's long-time fluorescence tail of the wt-GFP chromophore's protonated form. The MD simulations of the S205V mutant show that the water molecule in the proton wire is replaced by other bulk water molecules along the simulations of 60 ns. Furthermore, as in the wt-GFP, the Thr203 also exists in two conformations in which only one conformation supports the proton transfer. These two findings give an insight into the relatively slow proton transfer rate in the S205V mutant in comparison to the wt-GFP.