The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter . Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a -turn motif and restraining to a region of the conformational space that extends from the -helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact helix. Sampling of this conformation is, however, marginal when the range of values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized.
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Research Article| December 29 2005
Exploring the free-energy landscape of a short peptide using an average force
Christophe Chipot, Jérôme Hénin; Exploring the free-energy landscape of a short peptide using an average force. J. Chem. Phys. 22 December 2005; 123 (24): 244906. https://doi.org/10.1063/1.2138694
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