Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

Article Abstract:

A study of an important development that speeds up metadynamics calculations by order of magnitude and renders the algorithm much more robust by using multiple interacting simulations, walkers, for exploring and reconstructing the same free energy surface is illustrated. Metadynamics is able to sample rarely occurring transitions and reconstructs the free energy as a function of several variables with a controlled accuracy.

Analysis, Usage, Crystals, Crystal structure, Gibbs' free energy, Histograms

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Influence of outer shell metal ligands on the structural and electronic properties of horse liver alcohol dehydrogenase zinc active site

Article Abstract:

First principles quantum chemical calculations based on both localized (G) and delocalized (PW) basis sets are carried out for models of increasing complexity representing the LADH ternary complex, which features the Zn-His-Asp-water motif. The calculations suggest that second (Asp49) and third- shell (WAT) ligands affect the structure, electronic properties and energetics of the LADH active site.

Spectra, Alcohol dehydrogenase, Alcohol dehydrogenases, Zinc compounds, Structure

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Assessing the accuracy of metadynamics

Article Abstract:

Metadynamics, a powerful technique, explores the multidimensional free energy surface of complex polyatomic systems and predicts transition mechanisms in different fields like chemistry, solid-state physics and biophysics. An explicit expression for the accuracy of the methodology is derived and a way to choose the parameters of the method in order to optimize its performance is provided.

Molecular dynamics, Chemistry, Physical and theoretical, Physical chemistry

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