<p>Over the past twenty-five years, I have explored the application of molecular dynamics simulations and lattice dynamics calculations for determining phonon properties and thermal conductivity. Motivated by conversations with my group members and colleagues, I share insights about aspects of these methods that can be overlooked or misunderstood. For molecular dynamics, I focus on how to set up the simulations and apply the Green-Kubo method. For lattice dynamics, I outline the calculation workflow and highlight key decisions. I offer thoughts about the benefits of calculations and how they can be compared to experiments. I share highlights, mistakes, and missteps from my group’s work. I conclude with reflections on the past, present, and future of nanoscale thermal transport modeling.</p>