for a system with N atoms atoms in which N fix of them are subject to fixed-atom constraints. As a result of this reduction in dimensionality, such a calculation cannot be expected to afford an accurate estimate of the vibrational entropy. In a previous study, we demonstrated that the use of soft harmonic confining potentials for anchor atoms achieves the same objective as immobilizing those atoms but without producing imaginary frequencies in the first place. As such, no "zeroing-out" of the Hessian is required, and unconstrained geometry optimization algorithms can be used. In the present study, we compare the harmonic-confiner method to the aforementioned technique of zeroing out the Hessian matrix elements associated with fixed atoms. We assess the im-pact of either approach on the shape of potential energy surfaces for a variety of peptide and protein model systems.