We extend the hyperdynamics method developed for lowdimensional energy-dominated systems, to simulate slow dynamics in more general atomistic systems. We show that a few functionals of the pair distribution function forms a low-dimensional collective space, which is a good approximation to distinguish stable and transitional conformations. A bias potential that raises the energy in stable regions, where the system is at local equilibrium, is constructed in the pair-correlation space on the fly. Thus a new MD scheme is present to study any time-scale dynamics with atomic details. We examine the slow gas-liquid transition of Lennard-Jones systems and show that this method can generate correct long-time dynamics and focus on the transition conformations without prior knowledge of the systems. We also discuss the application and possible improvement of the method for more complex systems.