Figure 4.

Reweighted stochastic embeddings calculated for chignolin in the TIP3P solvent at 340 K simulated using the CHARMM27 force field. Low-dimensional manifolds are colored according to their free energy. (a) Representative conformations from the metastable states estimated by the reweighted embedding methods are shown around the mrse embedding. (b) Embedding obtained using stke. Well-tempered metadynamics is used to generate the training set consisting of sines and cosines of all Φ and Ψ dihedral angles, amounting to 32 variables in total. The training set is generated by performing a 1 μs simulation with a bias factor γ = 20, enhancing the fluctuations of the distance d between the Cα atoms of residues Y1 and Y10 and the radius of gyration r_g. (c) Free-energy surface calculated along for d and r_g. The axes and units for the embeddings are arbitrary and thus not shown. See Supporting Information (Section S1C) for computational details.