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Free energy guided sampling

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T. Zhou; A. Caflisch

Journal: J. Chem. Theory Comput.
Year: 2012
Volume: 8
Issue: 6
Pages: 2134-2140
DOI: 10.1021/ct300147t
Type of Publication: Journal Article

Advanced sampling methods; clustering; complex network; cut-based free energy profile; molecular dynamics; phase space exploration; reaction coordinate-free


A free energy-guided sampling (FEGS) method is proposed for accelerating exploration of conformational space in unbiased molecular dynamics. Using the cut-based free energy profile and Markov state models, FEGS speeds up sampling of the canonical ensemble by iteratively restarting multiple short simulations in parallel from regions of the free energy surface visited rarely. This exploration stage is followed by a refinement stage in which multiple independent runs are initiated from Boltzmann distributed conformations. Notably, FEGS does not require either collective variables or reaction coordinates and can control the kinetic distance from the starting conformation. We applied FEGS to the alanine dipeptide, which has a human-comprehensible two-dimensional free energy landscape, and a three-stranded antiparallel β-sheet peptide of 20 residues whose folding/unfolding process is governed by a delicate interplay of enthalpy and entropy. For these two systems, FEGS speeds up the exploration of conformational space by 1 to 2 orders of magnitude with respect to conventional sampling and preserves the basins and barriers on the free energy profile.