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A perpendicular magnetic recording system has been modeled for the purpose of analyzing transition noise, particularly “jitter.” Conventional perpendicular media and “soft” exchange coupled composite (ECC) media with a conventional soft underlayer (SUL) and an antiferromagnetic soft underlayer (AF-SUL) have been investigated using micromagnetic simulation. The fast Fourier transform (FFT) technique and graphics processing unit (GPU)-based computing have been used to reduce the intensive computation time for magnetostatic interactions between the head, SUL, and recording layer. Interestingly, the jitter is always less dependent on reader offset from track center with the AF-SUL. Jitter for ECC media is also shown to depend less strongly on reader offset than for conventional media. The transition center deviation at the optimal anisotropy for both recording layers is lower with the AF-SUL at both linear densities considered. We further find that the track center moves alternately with direction of fringing field as expected from magnetostatic considerations.