The difference between the ion thermal and effective temperatures is investigated through simulations of the Ne gas puff z-pinch reported by Kroupp et al. [Phys. Rev. Lett. 107, 105001 (2011)]. Calculations are performed using a 2D, radiation-magnetohydrodynamic code with Tabular Collisional-Radiative Equilibrium, namely Mach2-TCRE [Thornhill et al., Phys. Plasmas 8, 3480 (2001)]. The extensive data set of imaging and K-shell spectroscopy from the experiments provides a challenging validation test for z-pinch simulations. Synthetic visible images of the implosion phase match the observed large scale structure if the breakdown occurs at the density corresponding to the Paschen minimum. At the beginning of stagnation (−4 ns), computed plasma conditions change rapidly showing a rising electron density and a peak in the ion thermal temperature of ∼1.8 keV. This is larger than the ion thermal temperature (<400 eV) inferred from the experiment. By the time of peak K-shell power (0 ns), the calculated electron density is similar to the data and the electron and ion thermal temperatures are equilibrated, as is observed. Effective ion temperatures are obtained from calculated emission line widths accounting for thermal broadening and Doppler velocity shifts. The observed, large effective ion temperatures (∼4 keV) early in the stagnation of this Ne pinch can be explained solely as a combination of compressional ion heating and steep radial velocity gradients near the axis. Approximations in the modeling are discussed in regard to the higher ion thermal temperature and lower electron density early in the stagnation compared to the experimental results.