We have applied a new nonequilibrium molecular dynamics (NEMD) method [F. Muller-Plathe, J. Chem. Phys. 106, 6082 (1997)] previously applied to monatomic Lennard-Jones fluids in the determination of the thermal conductivity of molecular fluids. The method was modified in order to be applicable to systems with holonomic constraints. Because the method involves imposing a known heat flux it is particularly attractive for systems involving long-range and many-body interactions where calculation of the microscopic heat flux is difficult. The predicted thermal conductivities of liquid n-butane and water using the imposed-flux NEMD method were found to be in a good agreement with previous simulations and experiment.