User:Lmuonl/Coarse graining

Coarse Graining in a physical sense refers to the act of removing degrees of freedom in a physical system. This is most common in computational sciences (specifically Molecular Dynamics) where computation time imposes size and time scale limitations on the studied system. By removing degrees of freedom we may approach length and time scales that are of biological significance (e.g. protein interactions). What is commonly referred to as Molecular Dynamics is in fact a form of coarse graining it's self as it removes the degrees of freedom associated with the electrons and also commonly constrains molecular bond distances which would otherwise exhibit vibrations.

A figure showing meta-particles compositions.

The compositions of a water meta-particle in MARTINI.

The most widely used coarse graining of biological molecules is contained within the Molecular Dynamics package GROMACS and is referred to as the MARTINI force-field. The MARTINI force-fields are a set of coarse grained force-fields for many of the most studied molecules in biological modeling. The most common practice within these force-fields is to replace four non-hydrogen atoms with a single meta-particle. This however is not always the case in some complex molecules such as benzene rings. These force-fields have been a significant factor in some of the most recent pioneering research into lipid bi-layer formation and dynamics as the size and time scales involved were simply unreachable with standard Molecular Dynamics.

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