The recent development of in-silico methods has opened a new avenue for the study of biomolecules. Biochemical features that in the past were not amenable to study by typical methods can now be explored on a virtual molecular level. Collagen II is a structural protein found in cartilage and skeletal growth plates. Point mutation are known to result in a spectrum of skeletal disorders from achondrogenesis, a neonatally fatal condition where the skeleton fails to mineralize, to spondyloepiphyseal dysplasia congenital (SEDC); a disorder characterized by short stature and bone abnormalities. Hydrochondrogenesis is an intermediate disorder where bones are short, malformed and poorly mineralized. Hydrochondrogenesis often results in stillbirth. Most collagen point mutations in the triple helical region, where the amino acid motif is GXY, are G to Z mutations. It is known that the introduction of point mutations into model collagen homotrimer peptides results in a reduction of the trimer dissociation temperature; often called the melting temperature. It is speculated that the loss of stability is due to structural disruptions introduced into the superhelical structure by non-glycine sidechains. A novel method of determining the effect of point mutations on the structure of collagen II like peptide was used to analyze the Amber8 molecular dynamic trajectories of (GPO)10, (GPP)10, and (GPO)5APO(GPO)4 homotrimers. G900S and G705S, two known collagen II human mutations were also examined in their native sequence. The G900S containing peptide trimer is as follows: (GPO)2GPSGAEZPOGPQGLA(GPO)2, where Z is G in the wild type and S in the mutation. G900S is associated with achondrogenesis. G705S is associated with hydrochondrogenesis and its sequence is (GPO)2GEDGEKZPEGAOGKD(GPO)2.