The MD/OPX code is designed for the simulation of nanoscale systems with all-atom resolution over milliseconds or longer. The methodology makes use of the extrapolation of slowly evolving order parameters to accelerate MD. The order parameters are generated automatically from orthogonal polynomials of atomic coordinates and capture the slow behaviors of the nanostructure and the host medium in which it resides. The method has rigorous justification in the all-atom multiscale analysis of the Liouville equation for dynamical nanosystems and includes the following features: (a) averaging replica short MD runs with different atomic velocity initializations to accurately incorporate a more representative set of configurations as needed to extrapolate order parameters over long time periods; (b) reconstructing the atomic-scale configuration after OPX by energy-minimizing the high energy configurations, heat, anneal and equilibrate the system to target temperature through short-time MD runs; (c) automatically choosing of the critical number of order parameters needed for accurate modeling; (d) achieving the simulation of bionanosystems in host media under biological conditions with periodic boundary conditions applied; and (e) performing accurate all-atom dynamics simulations by tracking their output energies, temperature, pressure, etc.