Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo

Ying Ding; Artem B. Mamonov; Daniel M. Zuckerman

doi:10.1016/j.bpj.2009.12.3102

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arXiv · 0910.2509

Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo

Ying Ding·Artem B. Mamonov·Daniel M. Zuckerman

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Abstract

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.

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Ying Ding, Artem B. Mamonov, Daniel M. Zuckerman. 2010-01-26. Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo. https://doi.org/10.1016/j.bpj.2009.12.3102

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