The nematode Caenorhabditis elegans has been established as a modeling organism in biomedical research for several decades. Its hermaphrodite germ line encompasses key developmental concepts like stem cell differentiation and apoptosis; therefore it provides a good model system for these basic concepts. Here, we have extended and refined our previous computational model, which encompasses developmental landmarks and the resulting movement of germ cells along the gonadal tube. We have used the molecular dynamics (MD) framework to model the physical movement of cells due to the force arising from cell divisions. The model simulation was calibrated with experimental time and it is in accordance with experimental observations. In addition, the model provides means for testing hypotheses regarding the behaviour of mutated germ lines and the potential mechanisms causing physiological apoptosis, which are difficult to assess experimentally.