The reliability of a full-scale flow simulation is an important topic in terms of predictability of the energy efficiency in ships. Using full-scale resistance simulations, it is possible to avoid a scaling effects, which limit accuracy of model-scale predictions. An advanced ship hydrodynamic simulation requires a two-phase flow solution where the free surface is taken into account. In the computational domain, the free surface causes a discontinuity to several physical quantities, which requires advanced numerical methods. The finite volume method (FVM) is commonly used in fluid mechanics to discretize the governing equations. However, the standard FVM causes a numerical error at the discontinuity location. The first research topic in this thesis is the application of the ghost fluid method (GFM) for the free surface discretization. Another key research topic in this work is the utilization of resolved turbulence in the ship simulations. The third research topic of this thesis is related to the ship hull surface roughness modeling methods.