We quantify the protein fold integrity using native contacts. The atomistic starting structure is used to define a set of native contact residue pairs. We defined a residue pair as a native contact if any of their closest heavy atoms are within 0.45 nm of each other (note that the native contact network is not identical to the OLIVES network). We used the atomistic native contacts as a reference for both the atomistic and coarse-grained simulations to make the comparison consistent. To quantify how native contacts change over the simulation trajectories, we defined the smooth function Q commonly used to track protein folding and conformational changes: