We present results of nonlinear, two-dimensional, numerical simulations of magneto-acoustic wave propagation in the photosphere and chromosphere of small-scale flux tubes with internal structure. Waves with realistic periods of three to five minutes are studied, after horizontal and vertical oscillatory perturbations are applied to the equilibrium model. Spurious reflections of shock waves from the upper boundary are minimized by a special boundary condition. This has allowed us to increase the duration of the simulations and to make it long enough to perform a statistical analysis of oscillations. The simulations show that deep horizontal motions of the flux tube generate a slow (magnetic) mode and a surface mode. These modes are efficiently transformed into a slow (acoustic) mode in the v A< c S atmosphere. The slow (acoustic) mode propagates vertically along the field lines, forms shocks, and remains always within the flux tube. It might effectively deposit the energy of the driver into the chromosphere. When the driver oscillates with a high frequency, above the cutoff, nonlinear wave propagation occurs with the same dominant driver period at all heights. At low frequencies, below the cutoff, the dominant period of oscillations changes with height from that of the driver in the photosphere to its first harmonic (half period) in the chromosphere. Depending on the period and on the type of the driver, different shock patterns are observed.