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Lattice dynamical calculations based on atomic potentials are used in the study of energetic materials for vibrational spectra. Features in the potential energy surface, however, can lead to negative eigenvalues of the dynamical matrix which can signify artifactual underlying dynamic or configurational instabilities or underconvergence. In this paper, using crystalline cellulose Iβ as a representative material, we show that a reactive force field (ReaxFF) necessarily yields structures associated with negative eigenvalues. We then propose a modification through a tapering function to eliminate barriers to potential energy minimization and thereby yield structures with no associated negative eigenvalues. Three particular ReaxFF parameterizations are evaluated with the tapering modification by comparing available electronic structure and experimental results from the literature. The newly minimized structures were evaluated using lattice properties, elastic constants, phonon dispersion, temperature‐dependent entropy, and heat capacity. Though the modification allows the models to produce only non‐imaginary vibrational spectra, the variations in computed properties can be large between the parameterizations, especially for those being used outside of the context for which the parameters were developed. Our calculations provide important information for the study of the phonon properties of molecular crystals such as cellulose and energetic materials.