A computer model of sedimentation of magnetic nanoparticles in a magnetic field of a set of moving permanent magnets is developed. It is shown that the magnets' motion leads not only to more uniform distribution of the nanoparticles over sedimentation plane, but sufficiently accelerates the process. It is shown that the orientation of the magnets poles significantly affects the characteristics of sedimentation, and the optimal condition-both for the most uniform distribution of nanoparticles and the acceleration of process-is when opposite magnetic poles are located next to each other. This model is used to calculate the characteristics of the magnetofection device.