title: Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble.
abstract: 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.
authors.affiliation: University of Washington Department of Chemical Engineering, Seattle, Washington, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Deighan
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and §California Institute of Quantitative Biosciences, University of California, San Francisco, California, United States.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Bonomi
authors.affiliation: University of Washington Department of Chemical Engineering, Seattle, Washington, United States.
authors.forename: Jim
authors.initials: J
authors.lastname: Pfaendtner