We report a theoretical study on the relaxation dynamics of Staphylococcus nuclease following photon excitation. Molecular dynamics simulations were implemented for both ground state and excited state surface of Trp140. Over the course of 40 ns ground state simulation, a structural transition was observed from one isomeric protein configuration to another. No obvious isomerization process was exhibited in the excited state simulations. Using linear response theory and direct nonequilibrium approach, time-dependent Stokes shift, as well as its time-infinity value, was evaluated for both ground state isomers. Comparison between these methods exhibits severe disagreement. The nonequilibrium simulations show the similar relaxation dynamics as the excited state linear response approach, whereas they severely differ from the ground state linear response evaluation. Further examination reveals that the isomerization process breaks the characteristics of the energy gap histogram from Gaussian statistics. We also made the comparison between the experimental and simulation results. The significant inertial decay, in theory, is absent in the experiment. The ground state linear response evaluation provides a better agreement with the experimental results among all three approaches.