Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

Herein, we report significant reduction in the cost of combined parallel tempering and metadynamics simulations (PTMetaD). The efficiency boost is achieved using the recently proposed well-tempered ensemble (WTE) algorithm. We studied the convergence of PTMetaD-WTE conformational sampling and free e...

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Veröffentlicht in:Journal of chemical theory and computation 2012-07, Vol.8 (7), p.2189-2192
Hauptverfasser: Deighan, Michael, Bonomi, Massimiliano, Pfaendtner, Jim
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creator Deighan, Michael
Bonomi, Massimiliano
Pfaendtner, Jim
description Herein, we report significant reduction in the cost of combined parallel tempering and metadynamics simulations (PTMetaD). The efficiency boost is achieved using the recently proposed well-tempered ensemble (WTE) algorithm. We studied the convergence of PTMetaD-WTE conformational sampling and free energy reconstruction of an explicitly solvated 20-residue tryptophan-cage protein (trp-cage). A set of PTMetaD-WTE simulations was compared to a corresponding standard PTMetaD simulation. The properties of PTMetaD-WTE and the convergence of the calculations were compared. The roles of the number of replicas, total simulation time, and adjustable WTE parameter γ were studied.
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title Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble
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