A novel approach for modeling of quantum dynamics and spectroscopy in large polyatomic systems is presented. The recently developed Classical Separable Potential (CSP) method propagates a multidimensional separable quantum wavepacket using effective time-dependent single mode potentials guided by classical trajectories. In this way, couplings between individual degrees of freedom are taken into account in a mean-field approximation. Comparison with 'numerically exact' calculations for small systems and with experiments on large systems show that the CSP scheme is accurate and suitable for the description of short timescale processes in the context of dynamical and spectroscopic applications. Moreover, calculations for systems having up to 1000 coupled modes on scalar and up to 10 000 degrees of freedom on parallel computers are not computationally extremely demanding. This paper presents the program package QDYN which implements the CSP method.