A software package for modeling segmented High-Purity Segmented Germanium detectors, AGATAGeFEM, is presented. The choices made for geometry implementation and the calculations of the electric and weighting fields are discussed. Models used for charge-carrier velocities are described. Numerical integration of the charge-carrier transport equation is explained. Impact of noise and crosstalk on the achieved position resolution in AGATA detectors are investigated. The results suggest that crosstalk as seen in the AGATA detectors is of minor importance for the position resolution. The sensitivity of the pulse shapes to the parameters in the pulse-shape calculations is determined, this as a function of position in the detectors. Finally, AGATAGeFEM has been used to produce pulse-shape data bases for pulse-shape analyses of experimental data. The results with the new data base indicate improvement with respect to those with the standard AGATA data base.