We report a study of the frictional properties of alkanethiol self-assembled monolayers (SAMs) on Au(111) at room temperature using hybrid molecular simulations at the atomic force/frictional force microscopy (AFM/FFM) experimental time scale. Various parameters influencing frictional properties were investigated, including chain length, terminal group, scan direction, and scan velocity. Simulation results show that frictional force decreases with an increase of chain length and that hydrophilic -OH-terminated SAMs have higher frictional force than hydrophobic -CH3-terminated SAMs. Frictional force as a function of normal load exhibits different behaviors for -CH3- and -OH-terminated SAMs. Simulation results further show friction anisotropy on SAMs at low and high temperatures. Frictional force is the smallest when scanned along the tilt direction, the largest when scanned against the tilt direction, and between when scanned perpendicular to the tilt direction. Finally, simulation results also show the dependence of friction on scan velocity. Friction exhibits a maximum for hydrophobic -CH3-terminated SAMs and decreases for hydrophilic -OH-terminated SAMs as scan velocity increases. It approaches a constant value at high scan velocities for both surfaces.