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Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensionalPESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard micro canonical (NVE) and canonical (NVT) MD simulations.The method is applied to the pyramidal inversion of a NH3molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.