Despite the large body of literature published about the Diósi-Penrose model (the seminal paper by Diósi has been cited nearly 600 times, and the one by Penrose 8 received over 1600 citations), the modeling of realistic atomistic and molecular systems is underdeveloped. This paper profits from our experience developing nonadiabatic molecular dynamics methods to derive general atomistic equations to compute the Diósi-Penrose collapse time. We employ these equations for systems ranging from small molecules to macrostructures, propose an experiment, and critically discuss the Diósi-Penrose model from the molecular perspective. (Note: During the revision of our work, Figurato et al. deposited a preprint with an atomistic approach close to ours, although less general.)