Fig. 6.

Paths and work done via SMD for a nanomer in vacuo. (A) Free energy profiles for the LFEP paths shown in Fig. 2 A as function of normalized path length (s) in (H, R _g) space, (solid line passes through the global minimum and dotted line avoids it). (B) Work done via SMD for the paths shown in A. (C) A trajectory associated with a zipper-like mechanism in the (Ω,Λ) space. (D) Work done via SMD for the path shown in C (dashed line) and for another trajectory associated with an “en masse” flipping of the cis-trans bonds (solid line). (E and F) Time evolution of the cosines for each individual prolyl bond. Here, (E) is associated with the zipper-like transition and (F) with the “en masse” flipping mechanism (except for one bond).