We have tested molecular dynamics as a predictive tool for stability of protein structure. We first used the X-ray crystallographic coordinates of bovine prothrombin fragment 1 to model the structure of the cia domain of human factor IX, an essential coagulation protein. In addition, a mutant protein that differs in only a single amino acid (G[12]A) but is associated with one form of Hemophilia B was also modeled. Simulations performed in an identical fashion for both proteins, with considerable care to accommodate long-range forces in these highly ionic systems, indicated that substantial distortions occur in the mutant structure relative to the wild type factor IX. Surprisingly, the Gla domain (residues 1-34) of the wild type and mutant remain similar. Instead, it is the interaction of the added Ala at position 12 in the mutant that repels the post-Gla region (residues >33, the C-terminal helix) region.