To demonstrate the utility of these tools for exploring the structural and thermodynamic properties of oligomers that exhibit secondary structure, we use an illustrative example of a helix-forming Lennard-Jones homo-oligomer containing 1 backbone bead and 1 sidechain bead per residue throughout this work. Using initial estimates of nonbonded (Lennard Jones 12-6) and bonded (bond stretching, bond-bending, and periodic torsion) parameters derived analyze their effects on helix stability, geometry, and cooperativity of folding. Additionally, we investigate the effect of chain length on these properties.