Fig 3. Protein energy and dynamics.

(A) The energy of alanine dipeptide in the learned potential for different φ and ψ torsion angles. Conformations are generated with PeptideBuilder at intervals of 2° and scored. (B) Free energy for different φ and ψ torsion angles for all-atom alanine dipeptide. The energy is obtained from direct histogram estimation from all-atom simulations. The data is taken from Wang et al. 2019 [15] and provided by the authors. (C) Cα atom RMSF values for simulations of 6m steps using the learned potential starting from the native structure. An initial burn-in period of 6m steps was discarded. The Cα atom RMSF values from the NMR ensembles are also shown, or the Cα atom crystal temperature factors in the case of villin HP36.