You will be using one system throughout: deca-alanine. Deca-alanine is a peptide composed of ten alanine residues. You will simulate it in vacuum. In vacuum deca-alanine forms an alpha-helix. That is, the alpha-helix is the stable conformation of the molecule in vacuum, as opposed to the beta-strand or the random coil. The helix is shown in the top figure. It is stabilized by six hydrogen bonds (shown in green).
Using IMD and SMD, you will stretch the molecule by applying an external force. As the molecule is stretched, it will undergo a gradual conformational change from the alpha-helix to the random coil (bottom figure). Using SMD trajectories and employing Jarzynski's equality, we will calculate the PMF involved in the helix-coil transition.