Density functional theory (DFT) methods for calculating the quantum mechanical ground states of condensed matter systems are now a common and significant component of materials research. The growing importance of DFT reflects the development of sufficiently accurate functionals, efficient algorithms and continuing improvements in computing capabilities. As the materials problems to which DFT is applied have become large and complex, so have the sets of calculations necessary for investigating a given problem. Highly versatile, powerful codes exist to serve the practitioner, but designing useful simulations is a complicated task, involving intricate manipulation of many variables, with many pitfalls for the unwary and the inexperienced. We discuss several of the most important issues that go into designing a meaningful DFT calculation. We emphasize the necessity of investigating these issues and reporting the critical details.