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A hybrid multiscale method is developed for simulating micro- and nano-scale fluid flows. The continuum Navier–Stokes equation is used in one flow region and atomistic molecular dynamics in another. The spatial coupling between continuum equations and molecular dynamics is achieved through constrained dynamics in an overlap region. The proposed multiscale method is used to simulate sudden-start Couette flow and channel flow with nano-scale rough walls, showing quantitative agreement with results from analytical solutions and full molecular dynamics simulations for different parameter regimes. Potential applications of the proposed multiscale method are discussed.