A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum.