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This paper describes the configuration of a topography-following (sigma) coordinate, numerical ocean model for studying the circulation in the South Atlantic. An analysis is performed (i) to ensure that the model configuration does not introduce a numerical bias in the model solution and (ii) to give estimates of numerical errors. The model is the Semi-spectral Primitive Equation Model (SPEM) from Rutgers University (Haidvogel et al., 1991). Two important issues relating to the sigma-coordinate are investigated: the pressure gradient calculation and the diffusion of tracers. Errors in the pressure gradient calculation are investigated by simulating an ocean at rest, and the choice is made to reduce errors by smoothing the bathymetry. A smoothing criterion is derived that permits a limitation of the errors in the pressure gradient calculation to an acceptable level (i.e. maximum errors on velocities below a millimeter per …