Granularity - Molecular Dynamics

Molecular Dynamics

In molecular dynamics, coarse graining consists of replacing an atomistic description of a biological molecule with a lower-resolution coarse-grained model that averages or smooths away fine details. Coarse-grained models have been developed for investigating the longer time- and length-scale dynamics that are critical to many biological processes, such as lipid membranes and proteins. These concepts not only apply to biological molecules but also inorganic molecules. Coarse graining may simply remove certain degrees of freedom (e.g. vibrational modes between two atoms) or it may in fact simplify the two atoms completely via a single particle representation. The ends to which systems may be coarse grained is simply bound by the accuracy in the dynamics and structural properties one wishes to replicate. This modern area of research is in its infancy, and although it is commonly used in biological modeling, the analytic theory behind it is poorly understood.

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