ABSTRACT
Most biomolecular processes involve macromolecular aggregates (on the size scale of 10-100 nm or more, including the cell membranes) and occur on a time scale of microseconds to milliseconds (or even hours to days, including folding and amyloid aggregation, for instance). Computer simulations based on atomic force elds are not yet able to reach these scales, since they are currently restricted in most cases to systems comprising fewer than a million atoms for times of less than 1 μs. In consideration of these facts, the idea of simplifying the description of a macromolecular system by including groups of atoms in a single interaction center (coarse-graining, CG) in order to reduce the number of internal degrees of freedom and, with them, the computational cost, is quite simple and somewhat natural, even considering the hierarchical structural organization of the proteins and nucleic acids.
