BBA5 is a 23-residue protein that folds at microsecond timescale. The native structure (or fold) of BBA5 shows a β-hairpin involving residues 1–10 and centering about residues 4–5. It also includes an α-helix involving the remaining residues 11–23. By convention, residues are numbered increasingly from the N-terminal to C-terminal of a protein. Figure 1(a) illustrates the native conformation of BBA5. The two folding trajectories, referred to as T23 and T24 respectively, are of different length. T23 consists of a series of 192 conformations (or frames), while T24 has 150 frames. Each conformation is described at atomistic level in PDB format adopted by the Protein Data Bank programs. GSGS (or Beta3s) is a 20-residue peptide with an average folding rate of microseconds. Its NMR conformation shows a three-stranded anti-parallel β-sheet with turns at residues 6 – 7 and 14 – 15. Figure 2(a) depicts this native conformation. There are a total of 5 GSGS folding trajectories: T1, T2, T3, T4, and T5. The number of conformations in each trajectory is listed in Table 1. Similar to BBA5, each conformation corresponds to one PDB file. Pande et al. explained in detail on the simulation model and methods employed to produce such trajectories [8,9].