  We adapted existing polymer growth strategies for equilibrium sampling of
peptides described by modern atomistic forcefields with implicit solvent. The
main novel feature of our approach is the use of pre-calculated statistical
libraries of molecular fragments. A molecule is sampled by combining fragment
configurations -- of single residues in this study -- which are stored in the
libraries. Ensembles generated from the independent libraries are reweighted to
conform with the Boltzmann factor distribution of the forcefield describing the
full molecule. In this way, high-quality equilibrium sampling of small peptides
(4-8 residues) typically requires less than one hour of single-processor
wallclock time and can be significantly faster than Langevin simulations.
Furthermore, approximate but clash-free ensembles can be generated for larger
peptides (e.g., 16 residues) in less than a minute of single-processor
computing. We also describe an application to free energy calculation, a
"multi-resolution" implementation of the growth procedure and application to
fragment assembly protein-structure prediction protocols.
