In this contribution an analysis of influence of model parameters on the results of simulations of material properties under free-electron laser irradiation is presented. It is based on the in-house hybrid code XTANT (X-ray-induced Thermal And Nonthermal Transition; N. Medvedev et. al, Phys. Rev. B 91 (2015) 054113), which combines tight binding molecular dynamics for atoms with Monte Carlo treatment of high-energy electrons and core-holes, and Boltzmann collision integrals for nonadiabatic (electron-phonon) coupling. Different parameterizations of transferable tight binding method for silicon are analyzed, namely basis sets sp 3 and sp 3 s*. The sp 3 parameterization seems to provide a better agreement of the silicon damage threshold with experimental data. Further, the influence of different schemes of molecular dynamics periodic boundaries simulation is compared: constant volume vs Parrinello-Rahman constant pressure. Constant-volume scheme gives a better agreement with experimental transient properties, as could be expected. Parameters entering the calculations of optical properties are analyzed, showing virtually no effect on the outcome beyond trivial broadening of the peaks of the optical coefficients.