Molecular dynamics were carried out to simulate binding interactions between S' subsites of thrombin and hirudin-based thrombin inhibitors. These inhibitors include three segments: an active-site segment, N alpha-acetyl-(D-Phe)-Pro-Arg-Pro-; a fibrinogen-recognition exo-site segment, hirudin 55-65; and a 13-atom-long linker. These linkers have been reported (Szewczuk et al. (1993) Biochemistry 32, 3396) to influence the binding potency while keeping the same active and exo-site segments. The study found that, by combining different omega-amino acids, the potency could be increased 8-fold or decreased 4-fold compared to the native hirudin linker, -Gln-Ser-His-Asn-Asp-Gly-. Five typical linkers were simulated and compared. Analyzing the trajectory files led to the classification of three different dynamic behaviours for the linkers. The flexible linkers had no influence on the antithrombin activity. Other linkers formed hydrogen bonds with the thrombin S' subsite residues Glu39, leu40, and Gln 151. Formations of some hydrogen bonds enhanced the potency of the inhibitor. In other cases, the hydrogen bonds caused the distortion of the inhibitor conformation while affected the binding potency. Based on these observations, a general binding mode in the S' subsites of thrombin is proposed and potential applications are discussed.