Paper Citing NAMD - Abstract
Mamonov, Artem B.; Bhatt, Divesh; Cashman, Derek J.; Ding, Ying; Zuckerman, Daniel M.
General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models
JOURNAL OF PHYSICAL CHEMISTRY B, 113:10891-10904, AUG 6 2009
We introduce "library-based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on precalculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained model,, as we demonstrate in this "proof-of-principle" report. We first verify the approach in a toy model and in implicitly solvated all-atom polyalanine systems. We next study five proteins, up to 309 residues in size. On the basis of atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified G (o) over bar -like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while ail arbitrary subset of interactions is "turned on".
