Recent advances in atomistic molecular dynamics (MD) simulations of biomolecules allow us to explore their conformational spaces widely, observing large-scale conformational fluctuations or transitions between distinct structures. To reproduce or refine experimental data using MD simulations, structure ensembles, which are characterized by multiple structures and their statistical weights on the rugged free-energy landscapes, are often used. Here, we summarize weight average approaches for various experimental measurements. Weight average approaches are now applied to hybrid quantum mechanics/molecular mechanics MD simulations to predict fast vibrational motions in a protein with a high accuracy for better understanding of molecular functions from atomic structures. •Conformational dynamics of biomolecules involves fast vibrational motions and slow transitions between distinct structures.•The conformational dynamics is theoretically described via multidimensional free-energy landscapes with many basins.•structural ensemble from molecular dynamics simulations is used to reproduce dynamical properties observed experimentally.•Weight average approaches are useful to analyze not only slow conformational changes but also fast vibrational motions.