Trp-cage is an artificial 20-residue protein and forms a hydrophobic core at its central cage upon folding. In the present study, the folding of Trp-cage was addressed by parallel cascade selection molecular dynamics (PaCS-MD). Our results of PaCSMD indicate that flip of the side chain of tryptophan (W6) was correlated with the overall folding. In conclusion, flip of stochastic side chain of W6 regulates the folding into the native or mis-folded states of Trp-cage.