After applying Eq. 7, the Cartesian coordinates of each supercell (r) are guaranteed to exist on a 3(N -1) dimensional hyper-plane specified by the fixed center of mass. In other words, Eq. 7 always creates three singular DOFs in r. These three redundant dimensions were reliably removed from the flow using a PCA whitening layer, initialized on Cartesian coordinates of the oxygen atoms from the entire MD dataset (after applying Eq. 7).