  Bottom-up coarse-grained (CG) models proved to be essential to complement and
sometimes even replace all-atom representations of soft matter systems and
biological macromolecules. The development of low-resolution models takes the
moves from the reduction of the degrees of freedom employed, that is, the
definition of a mapping between a system's high-resolution description and its
simplified counterpart. Even in the absence of an explicit parametrisation and
simulation of a CG model, the observation of the atomistic system in simpler
terms can be informative: this idea is leveraged by the mapping entropy, a
measure of the information loss inherent to the process of coarsening. Mapping
entropy lies at the heart of the extensible coarse-graining toolbox, or
EXCOGITO, developed to perform a number of operations and analyses on molecular
systems pivoting around the properties of mappings. EXCOGITO can process an
all-atom trajectory to compute the mapping entropy, identify the mapping that
minimizes it, and establish quantitative relations between a low-resolution
representation and the geometrical, structural, and energetic features of the
system. Here, the software, which is available free of charge under an
open-source licence, is presented and showcased to introduce potential users to
its capabilities and usage.
  Published on the J. Chem. Inf. Model. on June 11, 2024. DOI:
https://doi.org/10.1021/acs.jcim.4c00490
