We critically examine how well the evolution of large-scale density perturbations is followed in cosmological $N$-body simulations. We first run a large volume simulation and perform a mode-by-mode analysis in three-dimensional Fourier space. We show that the growth of large-scale fluctuations significantly deviates from linear theory predictions. The deviations are caused by {it nonlinear} coupling with a small number of modes at largest scales owing to finiteness of the simulation volume. We then develop an analytic model based on second-order perturbation theory to quantify the effect. Our model accurately reproduces the simulation results. For a single realization, the second-order effect appears typically as ``zig-zag patterns around the linear-theory prediction, which imprints artificial ``oscillations that lie on the real baryon-acoustic oscillations. Although an ensemble average of a number of realizations approaches the linear theory prediction, the dispersions of the realizations remain large even for a large simulation volume of several hundred megaparsecs on a side. For the standard $Lambda$CDM model, the deviations from linear growth rate are as large as 10 percent for a simulation volume with $L = 500h^{-1}$Mpc and for a bin width in wavenumber of $Delta k = 0.005h$Mpc$^{-1}$, which are comparable to the intrinsic variance of Gaussian random realizations. We find that the dispersions scales as $propto L^{-3/2} Delta k^{-1/2}$ and that the mean dispersion amplitude can be made smaller than a percent only if we use a very large volume of $L > 2h^{-1}$Gpc. The finite box size effect needs to be appropriately taken into account when interpreting results from large-scale structure simulations for future dark energy surveys using baryon acoustic oscillations.
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