graphtheroytrejctoryAnalysis write comment for "how to use" cite https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b02285 https://www.sciencedirect.com/science/article/pii/S0016236116308602 https://www.sciencedirect.com/science/article/pii/S0301010418302519