Viscosities and self-diffusion coefficients of methanol-water mixtures were calculated via molecular dynamics simulation from 298.2 to 476.2 K and at pressures up to 40 MPa. The periodic perturbation method (non-equilibrium molecular dynamics) and the Green-Kubo method with three-site flexible potential models were adopted for evaluating the viscosities and the diffusion coefficients, respectively. The calculated viscosities and diffusion coefficients of methanol-water mixtures agreed qualitatively with literature experimental values. The three-site flexible potential models used in this study provided similar performance to the previous studies that used rigid models. Results correlated with the Stokes- Einstein relation show the possibility that the effective hydrodynamic radii were approximately constant for the studied condition and might be little affected by the clathrate-type structure at lower methanol compositions. (C) 2015 Elsevier B.V. All rights reserved.