We use molecular dynamics to simulate fluid flows between two parallel plates with constant wall temperature. Unlike the usual approach in molecular dynamics, instead of applying an external force on the molecules, the periodic boundary conditions are modified to create a pressure difference between the inlet and the outlet sections of the computational domain. The simulation results include velocity, pressure, density, and temperature profiles obtained by the new method. These results are compared with approximate solutions for nonisothermal Poiseuille flows. The method is also applied to simulate a flow in a rib-roughened channel.