By using molecular dynamics (MD) simulation

the diffusion of 12 amino acids

such as glycine and alanine was simulated at 298. 15 K with constant NVT ensemble trajectory

and the diffusion coefficients were calculated with differentiation-interval variation. The results showed that the diffusion coefficients of the same solution differed greatly when they were calculated with different molecule-number samples

and the one which was calculated with the sample with the maximum number of molecules was closest to the experimental value. Comparing calculated diffusion coefficients of 5 amino-acids in water with the values reported in literature showed an error less than 7%. Furthermore，the diffusion of oxygen in water was simulated with the same method

and satisfactory results in good agreement with the experimental value were obtained. This paper is aimed to show that the diffusion coefficients for industrial use can be calculated with the MD simulation method

which would be helpful to the development of computational mass transfer theory.