Abstract
The free energy landscape of a peptide molecule was observed from the enhanced conformational sampling method, the multicanonical molecular dynamics simulation, which was developed by our group. In addition, an algorithm for revealing the free energy barrier among stable states was also developed by combining the multicanonical ensemble with the Weighted Histogram Analysis Method (WHAM). The method, called multicanonical WHAM, was applied to the cis-trans imide isomerization of a peptide dimer, -Ala-Pro-. The landscape of the potential of mean force covering the transition states and the two stable isomer states was observed with the structural transition paths.
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