Due to the challenges involved with modeling complex molecular systems, it is essential that computationally intelligent schemes be produced that put the computational effort where and when it is needed to capture important phenomena, and maintain needed accuracy at minimum costs. In this work, we investigate and propose some key issues for the adaptive modeling and simulation of the dynamic behavior of highly complex multiscale processes. This is accomplished through the appropriate use of an adaptive hybridization of existing, newly developed, and proposed advanced multibody dynamics algorithms and modeling strategies for forward dynamic simulation. The adaptive multiscale simulation technique discussed here benefits from the highly parallelizable structure of the divide and conquer (DCA) framework for modeling multibody systems. These algorithms include Flexible Divide and Conquer Algorithm (FDCA), Orthogonal Complement Divide-and-Conquer Algorithm (ODCA) and generalized momentum approaches for modeling discontinuous changes in the system. These algorithms permits a large complex molecule (or systems of molecules) to be seamlessly treated using a hierarchy of reduced order models ranging from atomistic to the continuum scale.