Figure 13.

Results for alanine tetrapeptide in vacuum at 300 K. (a) Conditional FESs (eq 21), obtained from the WT-MetaD simulation, shown as a function of Φ₁ and Φ₂ for two minima of Φ₃ labeled as A and B. We denote the ten metastable states as s₁ to s₁₀. (b) Alanine tetrapeptide system with the backbone dihedral angles Φ ≡ (Φ₁, Φ₂, Φ₃) and Ψ ≡ (Ψ₁, Ψ₂, Ψ₃) that we use as the input features for the MRSE embeddings. (c) Free energy profile F(Φ₃), obtained from the WT-MetaD simulation, with the two minima A and B. The gray-shaded area indicates the areas integrated over in eq 21. The FESs are obtained using KDE as described in Section 3.4.