python ∼/seekr2/seekr2/analyze.py \ SEEKR_simulation/model.xml The analyze.py script takes the model.xml file as an argument. It constructs the milestoning model, populates it with transition probabilities and simulation times within each milestone, and computes error margins. For a detailed understanding of the MMVT error margins, please refer to the SEEKR2 manuscript . Figure shows the free energy profile per milestone for the trypsin-benzamidine complex, obtained by executing the analyze.py script.