The MD simulations presented here have demonstrated that the QUBE force field, and the parameterization methods used to create it, are sufficiently accurate to recreate conformational propensities of short, flexible peptides. The errors in the simulated dynamics of these molecules are comparable to OPLS-AA/M, and the φ/ψ distributions demonstrate that the major conformations observed in protein structures are populated. Issues with the transferability of torsional parameters have already been identified from the longer peptide simulations, and are solved by applying regularization. In the following subsection, the performance of QUBE for entire proteins is evaluated to demonstrate the feasibility of applying the methodology to macromolecules and to further understand the intricacies of fitting torsional parameters to a system-specific force field.