Charge-charge interactions have a significant impact on the free energy landscape of proteins. The role addition or subtraction of charged groups can play in the stabilization or destabilization of meta-stable non-native states of proteins remains relatively unstudied in detail. Problematically, current experimental methods can only indirectly characterize the non-native states of a protein. All-atom molecular dynamics simulations provide a useful tool for studying the non-native states of a protein but are limited in scale to the smallest proteins. Therefore, in order to study effects of charges while ensuring adequate sampling, we choose to simulate a small, fast-folding model protein, the Trp-cage, with replica-exchange molecular dynamics. As most simulations use a neutral end, capped sequence while experiments tend to use a charged end, zwitterionic variant, we chose to simulate and compare the folding of the Trp-cage both with neutral, capped ends and in zwitterionic form with a positively charged N terminus and a negatively charged C terminus. We find that while the native state of the protein remains relatively unchanged, the equilibration time for the charged end simulation is much longer, suggesting a rougher folding landscape. Analysis suggests the formation of meta-stable states characterized by the possession of non-native charge pairs. Furthermore, we also report an increase in beta-sheet content that cannot be directly explained by the formation of a specific non-native charge pair, indicating the addition of charges plays a much more complex role than the direct creation of non-native charge pairs. We finally use string methods to determine the most probable transition path between non-native meta-stable states and the native state in order to better explain the factors resulting in the increase in equilibration time for the simulation.