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The SPIDER experiment's main goal is to test the extraction of negative ions from an ITER-size ion source. It is designed to extract 1 280 negative ion beamlets and accelerate them up to a 100 kV potential. The negative ion beam at exit and the operating parameters will be carefully measured and optimized in order to match the ITER requirements for the Neutral Beam Injector (NBI) ion sources. Inside a negative ion accelerator, there are generally two main factors that can cause the deflection of the ion beamlets: the repulsion among beamlets and the electron suppression magnetic field. These two effects are both to be considered highly detrimental for the ITER NBI since they are expected to cause higher heat loads on the ITER NBI neutralizer and decrease the overall beam quality (in terms of aiming and divergence). Hence, they should also be considered and minimized for the SPIDER device, where it will be possible to precisely investigate the beamlet footprint using an instrumented calorimeter relatively close to the accelerator exit. This paper presents a design optimization process aiming at compensating the two described effects. To make this, a mechanical offset of the grounded grid apertures is considered. The OPERA-3-D code (Vector Fields Co. Ltd.) is used as the main tool for this optimization process because it can take into account beamlet repulsion and the interaction among the beamlets and grids. This is made by solving the electrostatic Poisson's equation with a finite element approach to calculate the particle trajectories of the negative ions under the influence of electrostatic fields, magnetic fields, and space charge.