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. 2013 Aug 2;14(8):16058–16075. doi: 10.3390/ijms140816058

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© 2013 by the authors; licensee MDPI, Basel, Switzerland

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).

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Free-energy profile obtained from REMD simulation based on the 34 “states” (or reference conformations) as described in text are shown. We take the reference energy of the free energy in such a way that its observed minimum is set to zero. Five reference conformations are also shown. The ground state (reference conformation 34) is favored thermodynamically and separated from the other low energy states by free-energy barriers. Reference conformation 1 is the fully extended conformation and marginally stable with a small free energy barrier of about 1 kcal/mol. Three reference conformations 10, 19 and 25 are metastable structures. For the free energy profile convergence test, we have carried out additional 50% of simulation time. The resulting two free energy profiles agree to each other within 1 kcal/mol.