Abstract
A parallel searching algorithm based on eigenvector-following is used to generate databases of minima and transition states for an all-atom model of the peptide Ac(ala)3NHMe and for a simplified bead model of a protein. We analyze the energy landscapes of both systems using disconnectivity graphs based upon both potential energy and free energy. This approach highlights the role of vibrational entropy in determining the relative free energy of local minima. Thermodynamic properties for Ac(ala)3NHMe calculated using the superposition approach are in reasonable agreement with parallel-tempering Monte Carlo simulations.
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