Quantum simulation uses a well-known quantum system to predict the behavior of another quantum system. Certain limitations in this technique arise, however, when applied to specific problems, as we demonstrate with a theoretical and experimental study of an algorithm to find the low-lying spectrum of a Hamiltonian. While the number of elementary quantum gates does scale polynomially with the size of the system, it increases inversely to the desired error bound $\epsilon$. Making such simulations robust to decoherence using fault-tolerance constructs requires an additional factor of $1/ \epsilon$ gates. These constraints are illustrated by using a three qubit nuclear magnetic resonance system to simulate a pairing Hamiltonian, following the algorithm proposed by Wu, Byrd, and Lidar.