Table 4.

Analysis methods and required simulation outputs.

Analysis	Simulation requirements
Measure similarities between two structures: RMSD, Paired RMSD and Local RMSD	Position of each elementary molecule for two simulations
A dendrogram for discovering structural diversity within one parameter set	Particle position for multiple simulations of one parameter set
A dendrogram for discovering structural diversity between two parameter sets	Particle position for multiple simulations of multiple parameter sets
Discover irrelevant reactions	Frequency of realized bounds averaged over several simulations

All these analysis methods can be extended to the dimension of time.