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. Author manuscript; available in PMC: 2019 Jan 31.
Published in final edited form as: Phys Chem Chem Phys. 2018 Jan 31;20(5):3523–3530. doi: 10.1039/c7cp08296g

Fig. 2. BBL samples the native and denatured basins as well as an intermediate states in a pH-dependent manner.

Fig. 2

a) Potential of mean force as a function of the fraction of native contacts q at different pH in units of kT, where k is the Boltzmann constant. Following Brooks and coworkers 50, two residues were considered in contact, if the distance between the center of geometry of the sidechain heavy atoms is within 6.5 Å. A contact was considered native, if it occurs with a probability above 0.5 in the control simulation. b) Average fraction of native contacts at different pH.