The archetypal Viola odorata cyclotide cycloviolacin-O1 and its seven analogs, created by partial or total reduction of the three native S–S linkages belonging to the “cyclic cystine knot” (CCK) motif are studied for their structural and dynamical diversities using molecular dynamics simulations. The results indicate interesting interplay between the constraints imposed by the S–S bonds on the dynamical modes and the corresponding structure of the model peptide. Principal component analysis brings out the variation in the extent of dynamical freedom along the peptide backbone for each model. The motions are characterized by low amplitude diffusive modes in the peptides retaining most of the native S–S linkages in contrast to the large amplitude discrete jumps where at least two or all of the three S–S linkages are reduced. Simulation results further indicate that the disulfide bond between Cys1–18 is formed at a much faster pace compared with its two other peers Cys5–20 and Cys10–25 as found in the native peptide. This gives insight as to why the S–S linkages appear in the native peptide in a particular combination. Model therapeutics and drug delivery engines can potentially utilize this information to customize the engineered S–S bonds and gauge its impact on the dynamic flexibility of a model macrocyclic peptide.