In this paper, we propose a running gait generation method for a biped robot using the dynamics model with two foot masses, an inverted pendulum and a flywheel. The inverted pendulum and flywheel represent the horizontal motion and the bending motion of the upper body respectively. Initially the acceleration of the inverted pendulum is determined to satisfy the desired ZMP. If the horizontal ground reaction force exceeds its limit, the acceleration of the inverted pendulum is modified and the flywheel is accelerated to compensate this modification. To guarantee the continuity of gait generation, we extend previously proposed concept ``the divergent component of the motion'' to be applicable for the inverted pendulum under time-varying ground reaction force. Using this concept as the boundary condition, the current gait converges to the next cyclic gait. Compared with the boundary condition using position and velocity, proposed boundary condition requires smaller amount of modification of the desired ZMP trajectory.