Simulation trajectories have very large dimensionality not only in terms of number of frames but also for the intrinsic dimensionality of each frame made by all three-dimensional coordinates. It is therefore necessary to reduce this space by projecting these coordinates into a simpler space. HTMD provides many projection types, e.g. MetricCoordinate to only keep the coordinate of few atoms, or MetricDistance to keep the matrix distance between two sets of atoms.