The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function

Amadei, Andrea; Apol, M. E. F.; Nola, Alfredo Di; Berendsen, H.J.C.

doi:10.1063/1.470744

Cited by 40 publications

(53 citation statements)

References 8 publications

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“…53,54 A gamma distribution is qualitatively satisfactory here but not as accurate as the Gumbel distribution. As does the present work, those previous studies emphasized realizability in free energy models: free energy evaluations can benefit from restriction to legitimate probability distributions.…”

Section: Resultsmentioning

confidence: 76%

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

Asthagiri

Merchant

Pratt

2008

The Journal of Chemical Physics

136

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On the basis of a Gaussian quasichemical model of hydration, a model of non-van der Waals character, we explore the role of attractive methane-water interactions in the hydration of methane and in the potential of mean force between two methane molecules in water. We find that the hydration of methane is dominated by packing and a mean-field energetic contribution. Contributions beyond the mean-field term are unimportant in the hydration phenomena for a hydrophobic solute such as methane. Attractive solute-water interactions make a net repulsive contribution to these pair potentials of mean force. With no conditioning, the observed distributions of binding energies are super-Gaussian and can be effectively modeled by a Gumbel (extreme value) distribution. This further supports the view that the characteristic form of the unconditioned distribution in the high-epsilon tail is due to energetic interactions with a small number of molecules. Generalized extreme value distributions also effectively model the results with minimal conditioning, but in those cases the distributions are sufficiently narrow that the details of their shape are not significant.

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Section: Resultsmentioning

confidence: 76%

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

Asthagiri

Merchant

Pratt

2008

The Journal of Chemical Physics

136

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“…In the theory section, we briefly outline the statistical mechanical model, based on the Quasi Gaussian Entropy (QGE) theory, [23][24][25][26] we utilize to describe the peptide folding/unfolding thermodynamics. Such a model, specifically designed to treat conformational transitions, has been introduced and described in details in a previous article.…”

Section: Introductionmentioning

confidence: 99%

Structural, thermodynamic, and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics

et al. 2009

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Gramicidin S (GS) analogues belong to an important class of cyclic peptides, characterized by an antiparallel double-stranded beta-sheet structure with Type II' beta-turns. Such compounds can be used as model systems to understand the folding/unfolding process of beta-hairpins and more in general of beta-structures. In the present study, we specifically investigate the folding/unfolding behavior of the hexameric Gramicidin S analogue GS6 by using all-atoms molecular dynamics (MD) simulations at different temperatures, coupled to a statistical mechanical model based on the Quasi Gaussian Entropy theory. Such an approach permits to describe the structural, thermodynamic, and kinetic properties of the peptide and to quantitatively characterize its folding/unfolding transitions.

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“…11,12 It also forms the basis of complete equations of state for the Lennard-Jones fluid 13 and water. 14,15 The potential power of the method is indicated by the fact the same model is applicable to systems that differ so much in polarity.…”

Section: Introductionmentioning

confidence: 99%

Statistical mechanics and thermodynamics of magnetic and dielectric systems based on magnetization and polarization fluctuations: Application of the quasi-Gaussian entropy theory

Apol

Amadei

Nola

2002

The Journal of Chemical Physics

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Theoretical equations of state for temperature and electromagnetic field dependence of fluid systems, based on the quasi-Gaussian entropy theory On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. I. Prediction of temperature dependence of thermodynamic propertiesThe quasi-Gaussian entropy ͑QGE͒ theory employs the fact that a free-energy change can be written as the moment-generating function of the appropriate probability distribution function of macroscopic fluctuations of an extensive property. In this article we derive the relation between the free energy of a system in an external magnetic or electric field and the distribution of the ''instantaneous'' magnetization or polarization at zero field. The physical-mathematical conditions of these distributions are discussed, and for several continuous and discrete model distributions the corresponding thermodynamics, or ''statistical state,'' is derived. Some of these statistical states correspond to well-known descriptions, such as the Langevin and Brillouin models. All statistical states have been tested on several magnetic and dielectric systems: antiferromagnetic MnCl 2 , the two-dimensional Ising spin model, and the simulated extended simple point charge ͑SPC/E͒ water under an electric field. The results indicate that discrete modeling of magnetization and polarization is rather essential for all systems. For the Ising model the ''discrete uniform'' state ͑corresponding to a Brillouin function͒ gives the best description. MnCl 2 is best described by a ''symmetrized binomial state,'' which reflects the two opposing magnetic sublattices. For simulated water it is found that the polarization, as well as the type of distribution of the fluctuations, is strongly affected by the shape of the system.

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The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function

Cited by 40 publications

References 8 publications

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

Structural, thermodynamic, and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics

Statistical mechanics and thermodynamics of magnetic and dielectric systems based on magnetization and polarization fluctuations: Application of the quasi-Gaussian entropy theory

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