In the mysim.yaml file you created you should see an analysis section. To learn more about the available options, please see Configuration Options page. The analyses can be ran using the command

webng analysis --opts mysim.yaml

and webng will run the analyses using the configuration options given by the file.

Probability distribution analyses

Average analysis

average will create a N by N set of plots where N is the number of observables you have in the BNG model after running the appropriate WESTPA tools. The results will be saved in the folder written under analyses/average/output (by default it is set to average.png). The plot will look like a matrix of plots where the diagonal contains 1D probability distributions of each observable and every off-diagonal will be a 2D probability heatmap of each pair of observables. For various options available, see Average page.

Evolution analysis

The analysis evolution will make a probability distribution evolution plot for each observable so you can track the progress of your simulation. For various options available, see Evolution page.

Clustering and network analyses

Clustering analysis

cluster analysis will allow you to use the transition matrix estimated from your simulation and do PCCA+ clustering. This type of clustering is useful to maximize transition within stable states and minimize transitions between unstable states and in this way it takes kinetics of the system into account. For various options available, see Cluster page.

Network generation

network analysis will use the results of your clustering and give you gml files that can be used to visualize the clusters. This analysis will give you two files, one for the full transition matrix and one for the clustered result. For various options available, see Network page.