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Bennett acceptance ratio
About: Bennett acceptance ratio is a research topic. Over the lifetime, 106 publications have been published within this topic receiving 23651 citations.
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TL;DR: The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.
Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...
13,164 citations
TL;DR: In this paper, an expression for the equilibrium free energy difference between two configurations of a system, in terms of an ensemble of finite-time measurements of the work performed in parametrically switching from one configuration to the other, is derived.
Abstract: An expression is derived for the equilibrium free energy difference between two configurations of a system, in terms of an ensemble of finite-time measurements of the work performed in parametrically switching from one configuration to the other. Two well-known identities emerge as limiting cases of this result.
4,496 citations
TL;DR: The multistate Bennett acceptance ratio estimator (MBAR) as mentioned in this paper is an estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment.
Abstract: We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which we call the multistate Bennett acceptance ratio estimator (MBAR) because it reduces to the Bennett acceptance ratio estimator (BAR) when only two states are considered, has significant advantages over multiple histogram reweighting methods for combining data from multiple states. It does not require the sampled energy range to be discretized to produce histograms, eliminating bias due to energy binning and significantly reducing the time complexity of computing a solution to the estimating equations in many cases. Additionally, an estimate of the statistical uncertainty is provided for all estimated quantities. In the large sample limit, MBAR is unbiased and has the lowest variance of any known estimator for making use of equilibrium data collected from multiple states. We illustrate this method by producing a highly precise estimate of the potential of mean force for a DNA hairpin system, combining data from multiple optical tweezer measurements under constant force bias.
1,265 citations
TL;DR: A new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment is presented, which has significant advantages over multiple histogram reweighting methods for combining data from multiple states.
Abstract: We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which we term the multistate Bennett acceptance ratio (MBAR) estimator because it reduces to the Bennett acceptance ratio when only two states are considered, has significant advantages over multiple histogram reweighting methods for combining data from multiple states. It does not require the sampled energy range to be discretized to produce histograms, eliminating bias due to energy binning and significantly reducing the time complexity of computing a solution to the estimating equations in many cases. Additionally, an estimate of the statistical uncertainty is provided for all estimated quantities. In the large sample limit, MBAR is unbiased and has the lowest variance of any known estimator for making use of equilibrium data collected from multiple states. We illustrate this method by producing a highly precise estimate of the potential of mean force for a DNA hairpin system, combining data from multiple optical tweezer measurements under constant force bias.
1,193 citations
TL;DR: In this paper, the free energy of hydration of methanol and ethane in dilute soluton was calculated using Monte Carlo simulations using double-wide sampling, and it was shown that only two or three Monte-Carlo simulations are necessary to obtain results with high precision.
Abstract: Perturbation theory has been applied to calculate the relative free energies of hydration of methanol and ethane in dilute soluton. It is demonstrated that only two or three Monte Carlo simulations using double‐wide sampling are necessary to obtain results with high precision. The small statistical uncertainty in the computed change in free energy of hydration and the good accord with experimental thermodynamic data are most encouraging for application of the procedure to a wide range of problems. Structural effects accompanying the mutation of methanol to ethane in water are also discussed; hydrogen bonding to the solute is essentialy eliminated by only a 25% reduction in the atomic charges of methanol.
644 citations