Computational Fluid Dynamics (CFD) and the Finite Element Method (FEM) are common and validated tools in research and industry for solving fluid flow or performing structural analysis respectively. Despite being rather challenging, also the numerical simulation of screw compressors benefits from development and enhancement of numerical models, tools and methodologies. Differences between the real machine and the numerical model are inevitable, yet increasing accuracy and prognosis quality are desired by refining existing models and accounting for specific phenomena. Clearances within the working chamber (mainly intermesh clearance between rotors and axial and radial gaps between rotors and housing) strongly affect the flow characteristics, efficiency and thus the overall compressor performance. These clearances change under operating conditions because of thermal expansion or due to forces acting on the structure, whereas the clearance size is often only known for the reference state out of operation. The extent of deformation and the quantification of the resulting clearances is therefore of high interest in order to get the numerical model closer to real operating conditions. In this paper numerical simulation was used to determine the change in radial gap size between rotors and housing when the compressor is running and exposed to thermal and pressure loads. For a specific operating point, a 3D-CFD simulation for a 4-6 twin screw compressor with SRM profiles was conducted for the undeformed reference compressor geometry to calculate the flow field within the machine. Also, the temperature field within the housing and rotor solids was computed using the Conjugated Heat Transfer (CHT) method. The temperature and pressure fields were then submitted to the FEM solver to compute the deformation of rotors and housing. The results of this structural analysis served as input for a modification of geometry and numerical grids to account for the change in radial gap size. A re-run of the flow simulation in the deformed state enabled to quantify the impact on the machine performance and specific flow quantities. It could be shown that taking deformation into account, the volumetric efficiency is clearly affected. Commercial solvers from Ansys were utilized for solving fluid and structure. The spatial discretization of the fluid volume around the rotors was realized by employing pre-generated grids using the mesh generator TwinMesh. Here, the rotor deformation can be defined in dependence of the axial position. The mesh of the housing maintained unchanged for all CFD simulations as a resulting gap size was determined by considering housing and rotor deformation relative to each other.