Coarse-grained modeling


Coarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water. In these models, molecules are represented not by individual atoms, but by "pseudo-atoms" approximating groups of atoms, such as whole amino acid residue. By decreasing the degrees of freedom much longer simulation times can be studied at the expense of molecular detail. Coarse-grained models have found practical applications in molecular dynamics simulations.
The coarse-grained modeling originates from work by Michael Levitt and Ariel Warshel in 1970s. Coarse-grained models are presently often used as components of multiscale modeling protocols in combination with reconstruction tools and atomistic resolution models. Atomistic resolution models alone are presently not efficient enough to handle large system sizes and simulation timescales.

Software packages