Fig. 2.

Atomic pairwise KB PMF. For each of the 167 atom types used here, a pairwise PMF was derived to describe its energy of interaction with every other atom type. Shown here are three such energy profiles: AN is the alanine backbone nitrogen, AO is the alanine backbone carbonyl oxygen, and ACA is the alanine α carbon. This set of curves was initially discretized into 0.1-Å bins. A repulsive part is added in the region of low distance to account for steric overlap, and the curves are fit to a quintic spline function to give a continuous, smoothly differentiable energy term for use in ENCAD. The symbols shown are the energies from the PMF derivation, and the fit shown is a simple smooth curve fit in Excel, not the quintic spline as generated in ENCAD.