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. Author manuscript; available in PMC: 2019 Sep 17.
Published in final edited form as: J Chem Theory Comput. 2018 Mar 12;14(4):1853–1864. doi: 10.1021/acs.jctc.7b01226

Figure 6:

Figure 6:

The 2D PMF plot of flap RMSD and distance of HIV protease. The trajectories at σ0P = 1.0 kcal/mol of three 100-ns rex-GaMD simulations were collected to calculate the PMF using cumulant expansion to the second order. (A) and (B) indicate the results from σ0P and threshold energy rex-GaMD simulations, respectively. The letter ‘O’ and ‘S’ indicate the flaps at open and semi-open state. The two intermediate states are labeled as ‘I1’ and ‘I2’.