Figure 3.

Derivation of COFFDROP bonded potential functions using the IBI method. (A) Plot showing the error in the angle probability distributions obtained from BD simulations as a function of IBI iteration number for the amino acids arginine, alanine and tryptophan. (B) Same as A but showing results for dihedral probability distributions. (C) Comparison of the angle probability distributions obtained from MD (lines) with those obtained from BD (circles) for tryptophan. Each color represents a different angle. (D) Same as C but showing results for dihedral probability distributions. (E) Comparison of an example angle potential function (Ace–Cα–Nme for tryptophan) obtained from using IBI (blue) with that obtained from noniterative Boltzmann inversion of the MD probability distribution (red). (F) Same as E but showing an example dihedral potential function (Cγ–Cβ–Cα–Nme for tryptophan).