Molecular dynamics simulations have been used to study friction in Langmuir-Blodgett monolayers of perfluorocarboxylic acid and hydrocarboxylic acid on SiO2. The frictional force of perfluorocarboxylic acid is found to be about three times as large as that of hydrocarboxylic acid. The qualitative aspects of this simulation results are consistent with known experimental results. In order to interpret the difference in the frictional force, a series of simulations have been carried out by changing molecular potential parameters. The simulation results suggest that the 1-4 van der Waals interaction is the main cause of the larger frictional force for perfluorocarboxylic acid than that for hydrocarboxylic acid. The results also show that frictional force is roughly proportional to the excess root mean square fluctuation of the potential energy under shear from the equilibrium. The relation between the frictional force and the energy needed for molecular deformation under shear condition is also discussed.