I have noticed that younger generations tend to be shocked to learn the original plot of Andersen’s “The Little Mermaid” (spoiler: she kills herself), hence the scores of articles revealing the real stories behind Disney fairy tales.
Disney made his versions cannon; the originals were reduced to curiosities.
In this article, we review development of the NBFIX (Non-Bonded FIX) corrections to the AMBER and CHARMM force fields and discuss their implications for MD simulations of electrolyte solutions, dense DNA systems, Holliday junctions, protein folding, and lipid bilayer membranes.
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The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity.
However, advances in parallel computing technology have outpaced the development of the underlying theoretical models—the molecular force fields, pushing the MD method into an untested territory.
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The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions.Recent tests of the MD method have found the most commonly used molecular force fields to be out of balance, overestimating attractive interactions between charged and hydrophobic groups, which can promote artificial aggregation in MD simulations of multi-component protein, nucleic acid, and lipid systems.One route towards improving the force fields is through the NBFIX corrections method, in which the intermolecular forces are calibrated against experimentally measured quantities such as osmotic pressure by making atom pair-specific adjustments to the non-bonded interactions.Perrault and the Grimm brothers collected the folk stories peasant women had told their daughters since prehistory.They repackaged them for the landed (and literate) gentry.