Modeling large scale conformational dynamics of biomolecules has been grand challenge due to the wide separation of the spatial and time scales in the system and in a stable discrete computational model. Here we propose to extract the elastic properties of amino acid polymer chains from discrete modeling and apply them to the continuum simulations of the conformational dynamics. The molecular structure is maintained during the continuum deformation by considering the energy steps due to the local structure re-organizations. Numerical simulations demonstrated that our computational model is accurate and robust.