We lay out the framework to numerically study nonlinear structure formation in the context of scalar-field-coupled cold dark matter models (phivCDM models) where the scalar field phiv serves as dynamical dark energy. Adopting parameters for the scalar field that leave negligible effects on the cosmic microwave background (CMB) spectrum, we generate the initial conditions for our N-body simulations. The simulations follow the spatial distributions of dark matter and the scalar field, solving their equations of motion using a multilevel adaptive grid technique. We show that the spatial configuration of the scalar field depends sensitively on the local density field. The phivCDM model differs from standard ΛCDM at small scales with observable ...