Fourier analysis, using the atomic trajectory calculated by molecular dynamics simulation at 300 K, is applied to the study of low-frequency phonons of guanine dihydrate. The vibrational modes of guanine bases are analyzed, and the optically active modes associated with the guanine moieties are extracted. There are a few significant peaks in the low-frequency region. A possible assignment of the, Raman active mode near 27 cm(-1), whose origin would be common to the S-mode of DNA double helices, is discussed.