The all-atom and the Ising-based models have both played their own roles to help our understanding of helix-coil transition. In this study, we address to what degree these two theoretical models can be consistent with each other in the nonstationary regime, complementing the preceding equilibrium study. We conducted molecular dynamics simulations of an all-atom model polyalanine chain and Monte Carlo simulations of a corresponding kinetic Ising chain. Nonstationary properties of each model were characterized through power spectrum, Allan variance, and autocorrelation analyses regarding the time course of a system order parameter. A clear difference was indicated between the two models: the Ising-based model showed a Lorentzian spectrum in the frequency domain and a single exponential form in the time domain, whereas the all-atom model showed a 1/f spectrum and a stretched exponential form. The observed stretched exponential form is in agreement with a very recent T-jump experiment. The effect of viscous damping on helix-coil dynamics was also studied. A possible source of the observed difference between the two models is discussed by considering the potential energy landscape, and the idea of dynamical disorder was introduced into the original Glauber model in the hope of bridging the gap between the two models. Other possible sources, e. g., the limitations of the Ising framework and the validity of the Markovian dynamics assumption, are also discussed. (C) 2003 American Institute of Physics.