We present a new multiscale hierarchical numerical approach combining ab initio, molecular dynamics, and metadynamics to model molecular motions in polymers over widely different time scales. We demonstrate that molecular motions corresponding to gamma and beta secondary (subglassy) relaxations can be described precisely in terms of free enthalpy, activation energy, and time scales and may be identified with relaxations detected experimentally by spectroscopic and other techniques. This method is illustrated in the case of aliphatic and semiaromatic polyamides. The highlight of this innovative approach in polymers is the ability to simulating long time scale motions while retaining an all-atomistic description of the polymer material. A complete description of the free energy landscape, in terms of conformational (intramolecular) and interactional (intermolecular) contributions, is obtained (energy barriers and time scales). This method thus may provide a predictive tool to understand secondary relaxations in amorphous polymers.