We explore the stability of matching boundary conditions in one space dimension, which were proposed recently for atomic simulations (Wang and Tang, Int. J. Numer. Mech. Eng., 93 (2013), pp. 1255-1285). For a finite segment of the linear harmonic chain, we construct explicit energy functionals that decay along with time. For a nonlinear atomic chain with its nonlinearity vanished around the boundaries, an energy functional is constructed for the first order matching boundary condition. Numerical verifications are also presented.