Fig. 2.

RECCES thermodynamic framework and reweighting. (A) Example systems simulated for this study. Degrees of freedom sampled are colored in white. The relative orientation of first base pair in each helix was fixed (Right, yellow dashes). (Upper and Lower) Folding reactions of two-base-pair and three-base-pair systems, respectively. (B) Density of state estimation by simulated tempering and WHAM. (C) Reweighting demonstration. (Left) State population at room temperature before (blue) and after (green) reweighting. (Right) Two-dimensional population histograms of fa_atr (Lennard–Jones attraction) vs. hbond_sc (hydrogen bonds) energy components, before and after reweighting.