We revisit the numerical construction of the initial condition for the dipole amplitude from the McLerran-Venugopalan model in the context of the JIMWLK evolution equation. We observe large finite volume effects induced by the Poisson equation formulated on a torus. We show that the situation can be partially cured by introducing an infrared regularization. We propose a procedure that has negligible finite volume corrections. The control of the finite volume and finite lattice spacings effects is crucial when considering the numerical solutions of the JIMWLK evolution equation with the collinear improvement.