  We applied our previously developed library-based Monte Carlo (LBMC) to
equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can
perform equilibrium sampling of molecules using the pre-calculated statistical
libraries of molecular-fragment configurations and energies. For this study, we
employed residue-based fragments distributed according to the Boltzmann factor
of the OPLS-AA forcefield describing the individual fragments. Two solvent
models were employed: a simple uniform dielectric and the Generalized
Born/Surface Area (GBSA) model. The efficiency of LBMC was compared to standard
Langevin dynamics (LD) using three different statistical tools. The statistical
analyses indicate that LBMC is more than 100 times faster than LD not only for
the simple solvent model but also for GBSA.
