This archive contains molecular dynamics trajectories for the MM (molecular mechanics) and QM/MM (quantum mechanics/molecular mechanics) simulations described in the article, in extended XYZ format (https://libatoms.github.io/QUIP/io.html#extendedxyz). Then files can be read with e.g. the Atomic Simulation Environment (https://wiki.fysik.dtu.dk/ase/) or the OVITO visualisation program (https://www.ovito.org/). A description of the columns contained within each file is provided in the metadata header on the comment line.