Figure 4. Potential of mean force for alanine dipeptide.

Alanine dipeptide was simulated in boxes of 4 different sizes (A). (B) The molecule undergoes a well defined transition characterized by rotation around its Ψ dihedral backbone angle. (C) Free energy profiles along the reaction coordinate: the Ψ dihedral angle. The sub-panels going from top to bottom depict profiles constructed from an increasing amount of simulation data: 0.1%, 1%, 10% and 100% of the whole available data. Uncertainties are depicted by shaded areas and represent standard errors obtained from 10 independent repeats.