Closed classical equations of motion are obtained for a molecular complex in a polar medium. It is found that the classical part of the polarization of the medium creates an effective potential for the particles of the molecular complex which is nonlocal in time and involves memory effects. Using the effective Hamiltonian method it is shown that the form of the effective potential depends on the complex dielectric function of the medium. The effect of the medium is not reduced in general by the introduction of a dielectric constant into the Coulomb interaction potentials. The equations derived can serve as a basis for molecular dynamics simulations of various systems in polar media.