The Mars Exploration Rover (MER) mission has returned tremendous scientific information on a daily basis, owing to the efficient sequencing capability of the ground system tools. For planning the mobility and instrument deployment device (IDD) sequences, physical-based simulation is applied to achieve fast and effective sequencing of complex rover and IDD maneuvers. The sequence rehearsal tool of the Rover Sequencing and Visualization Program (RSVP) is based on modeling and simulation of the multi-body mechanical systems. Using configuration kinematics (CK) and 3D terrain models, a methodology was developed to support a real-time, interactive graphics mode for the visualization tool. The sequence simulation is carried out using the on-board flight software modules for realistic rover behavior. This enables the scientists and rover planners to effectively develop the command sequences to maximize the science return of the MER mission while maintaining rover safety. This paper describes the innovative numerical algorithms and the command sequence simulation used by the MER mission for planning surface operations.