title: Serial Generalized Ensemble Simulations of Biomolecules with Self-Consistent Determination of Weights.
abstract: Serial generalized ensemble simulations, such as simulated tempering, enhance phase space sampling through non-Boltzmann weighting protocols. The most critical aspect of these methods with respect to the popular replica exchange schemes is the difficulty in determining the weight factors which enter the criterion for accepting replica transitions between different ensembles. Recently, a method, called BAR-SGE, was proposed for estimating optimal weight factors by resorting to a self-consistent procedure applied during the simulation (J. Chem. Theory Comput.2010, 6, 1935-1950). Calculations on model systems have shown that BAR-SGE outperforms other approaches proposed for determining optimal weights in serial generalized ensemble simulations. However, extensive tests on real systems and on convergence features with respect to the replica exchange method are lacking. Here, we report on a thorough analysis of BAR-SGE by performing molecular dynamics simulations of a solvated alanine dipeptide, a system often used as a benchmark to test new computational methodologies, and comparing results to the replica exchange method. To this aim, we have supplemented the ORAC program, a FORTRAN suite for molecular dynamics simulations (J. Comput. Chem.2010, 31, 1106-1116), with several variants of the BAR-SGE technique. An illustration of the specific BAR-SGE algorithms implemented in the ORAC program is also provided.
authors.affiliation: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.|European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Chelli
authors.affiliation: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.
authors.forename: Giorgio F
authors.initials: GF
authors.lastname: Signorini