Dipeptide Structure and Dynamics

by Adam, Ahmad Y.

Classical mechanical calculations have been performed to minimize the structure of alanine dipeptide using different Amber force fields. The minimization process leads to the second lowest conformer, the C5 conformer, compared to ab initio methods and experiment which identify the C7eq conformer as the lowest energy conformer. Then, a classical molecular dynamics calculation was done to search for the structure of the C7eq conformer. Starting from the C5 conformer, the structure of the C7eq conformer was identified after 28 ps of the simulation process. Possible reasons for this behavior are discussed.