This paper reviews recent progress in molecular dynamics simulation of atomic-scale friction measured by an atomic force microscopy. Each section of the review focuses on an individual condition or parameter that affects atomic friction including materials, surfaces, compliance, contact area, normal load, temperature, and velocity. The role each parameter plays is described in the context of both experimental measurements and simulation predictions. In addition, the discussion includes an overview of the research community's current understanding of observed effects, guidelines for implementation of those effects in an atomistic simulation, and suggestions for future research to address open questions. Taken together, this review conveys the message that friction at the atomic scale is affected by many interrelated parameters and that the use of molecular dynamics simulation as a predictive tool can be accomplished only through careful model design.