  Due to the time-scale limitations of all-atom simulation of proteins, there
has been substantial interest in coarse-grained approaches. Some methods, like
"Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)]
can accelerate canonical all-atom sampling, but require properly distributed
coarse ensembles. We therefore demonstrate that full sampling can indeed be
achieved in a sufficiently simplified protein model, as verified by a recently
developed convergence analysis. The model accounts for protein backbone
geometry in that rigid peptide planes rotate according to atomistically defined
dihedral angles, but there are only two degrees of freedom (phi and psi
dihedrals) per residue. Our convergence analysis indicates that small proteins
(up to 89 residues in our tests) can be simulated for more than 50 "structural
decorrelation times" in less than a week on a single processor. We show that
the fluctuation behavior is reasonable, as well as discussing applications,
limitations, and extensions of the model.
