Molecular dynamics simulations for a binary system are carried out using a
temperature scaling procedure under isothermal conditions to keep the tempe
rature constant. However, the temperatures of each atomic species are diver
se in the casts of component atoms with significantly different masses. The
causes of the deviation of atomic temperatures in the ordinary scaling met
hod with one thermostat are examined. The deviations appear when the mass r
atio of light atoms to heavy is below 0.4. We apply the two-temperature con
trol method using different heat baths for individual species to render the
temperatures of the two different species the same, although this generall
y breaks the momentum conservation law as reported by Nose [Mol. Phys. 57 (
1986) 187 and Frog. Theor. Phys. Suppl. (1991) No. 103, 1]. It is found tha
t the deviation from the conservation law of the system is not very large a
nd the method is useful except under extraordinary conditions.