Type II reverse turn conformation has been shown to play a role in protein folding. In this study, reversible folding of a linear pentamer peptide YPGDV, which was determined by NMR experiments to have a significant population (50%) of a type II turn conformation in aqueous solution, was simulated in water with atomic detailed representation for both the peptide and solvent molecules at 300 K using the self-guided molecular dynamics (SGMD) simulation. During a 2 nanosecond (ns) SGMD simulation starting from a fully extended conformation, the peptide folds into a type II turn-like conformation and then undergoes unfolding and refolding several times, A cluster analysis method was developed based on conformational population and used to analyze the trajectories of the 2 ns SGMD simulation and of other simulations in this study. Five major conformational clusters were obtained from the 2 ns SGMD simulation and the most populated conformational cluster is a type II reverse turn-like conformation. The structure of the most populated conformational cluster identified through the SGMD simulation, or the "folded" states, is entirely consistent with the NMR data and the estimated relative NMR NOE strengths of proton pairs based upon the SGMD trajectory are in good agreement with the experimental data. Structural analysis of these major conformations indicated that the strong charged-charged interactions of the N-terminal positively charged group with the C-terminal and the side chain of Asp4 negatively charged groups and the hydrogen bonding between the amide group of Asp4 and the carboxyl group of Tyr1 are important for the stability of the "folded" states. In comparison, ns conventional MD simulations starting from either a fully extended or a "folded" conformation failed to achieve folding or unfolding of this peptide, suggesting that longer simulations are needed for adequate conformational sampling using the conventional MD method. Based upon our estimated conformational free energy (calculated as the sum of conformational energy and solvation free-energy), the major conformational cluster obtained through the 2 ns SGMD simulation has the lowest estimated conformational energy and has a conformational free energy approximately 5 kcal/mol lower than any conformational cluster obtained through the 2 ns MD simulation started with the fully extended conformation. Folding studies of other short peptides and small proteins with defined secondary and/or tertiary structures using the SGMD simulation method are currently under way and will be reported in due course.