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Author Bochicchio, Davide ♦ Panizon, Emanuele ♦ Ferrando, Riccardo ♦ Rossi, Giulia ♦ Monticelli, Luca
Source United States Department of Energy Office of Scientific and Technical Information
Content type Text
Language English
Subject Keyword INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY ♦ ALGORITHMS ♦ COMPARATIVE EVALUATIONS ♦ ERRORS ♦ FREE ENERGY ♦ LECITHINS ♦ MEMBRANES ♦ POLYETHYLENES ♦ POLYPROPYLENE ♦ SIMULATION ♦ SOLUTES ♦ WATER
Abstract We compare the performance of two well-established computational algorithms for the calculation of free-energy landscapes of biomolecular systems, umbrella sampling and metadynamics. We look at benchmark systems composed of polyethylene and polypropylene oligomers interacting with lipid (phosphatidylcholine) membranes, aiming at the calculation of the oligomer water-membrane free energy of transfer. We model our test systems at two different levels of description, united-atom and coarse-grained. We provide optimized parameters for the two methods at both resolutions. We devote special attention to the analysis of statistical errors in the two different methods and propose a general procedure for the error estimation in metadynamics simulations. Metadynamics and umbrella sampling yield the same estimates for the water-membrane free energy profile, but metadynamics can be more efficient, providing lower statistical uncertainties within the same simulation time.
ISSN 00219606
Educational Use Research
Learning Resource Type Article
Publisher Date 2015-10-14
Publisher Place United States
Journal Journal of Chemical Physics
Volume Number 143
Issue Number 14


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