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. Author manuscript; available in PMC: 2017 Oct 20.
Published in final edited form as: J Chem Theory Comput. 2016 Nov 7;12(12):5946–5959. doi: 10.1021/acs.jctc.6b00712

Figure 9.

Figure 9

Backbone RMS deviation from the experimental reference structure for 50 ns MD simulation based on GB-HCPO (red dashed line) compared to the reference explicit-solvent method (TIP3P), reference GB (without approximation), and GB-HCP. The test structures are, from left to right: immunoglobulin binding domain (1BDD, residues 10–55), thioredoxin (2TRX, all residues), and Ubiquitin (1UBQ, all residues). Two independent trajectories were produced for each of GB-HCPO and GB-HCP approximations. Each trajectory is sampled every 1 ns. Connecting lines are shown to guide the eye.