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Several modelling approaches to simulate blood flow patterns in the left atria (LA) have recently been proposed, especially to better understand the relation between left atrial appendage morphology and the risk of thrombus formation in atrial fibrillation patients. Most studies are based on Computational Fluid Dynamics (CFD) but there is not a consensus on the boundary conditions (BC) which provide more realistic simulations due to the lack of shared ground-truth data. In this work, we study the influence of adding localized deformation in the LA wall using dynamic meshes comparing to assuming rigid walls, as well as different BC configurations using a real case.