The results for MTD simulations of the proton transfer in malonaldehyde and cycle breaking in cyclohexene are given in the insets (b), (c), and (d) of Figs. and, respectively. In insets (b), we can see the representations of the MTD trajectories as the atomic density distributions computed with the CubeTheMD script using an algorithm similar to that used in the Trajectory Analyzer and Visualizer (TRAVIS) software. From there, we can see that during the MTD simulation, the only major change in the malonaldehyde was the proton transfer, whether, in the case of cyclohexene, it was the dissociation of the C 2 H 4 to form a complex. The same can be inferred from the trajectories of the CVs, mapping out the bias potential, which is given in the insets (c) of Figs. and.