Lastly, in assessing the states visited during the simulation, it is important not to "cherrypick" snapshots to simply show preferred states. In many respects, these manually identified states may not be truly representative of the behaviors observed over the course of the trajectory. MD simulations should be rigorously analyzed to determine the most representative sub-states that have been visited, using methods like root-mean-squared deviation (RMSD) clustering, t-distributed stochastic neighbor embedding, dimensionality reduction techniques, or Bayesian methods, for example.