Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS v2

This paper presents a protocol for the development of coarse-grained (CG) structures for macromolecular simulation using the GROMACS software. CG models are widely used in molecular simulations due to their computational efficiency, which allows for the study of large and complex systems. The protocol described here outlines the steps necessary for the creation of CG structures, including the selection of appropriate beads, mapping of the CG beads onto the atomistic structure, and the parameterization of the CG model. The protocol also includes guidelines for validating the accuracy of the CG model, as well as recommendations for future improvements in CG model development. The described protocol will be useful for researchers interested in the development of CG models for macromolecular simulations using GROMACS. The last step contains a supplemental video with extra context and tips, as part of the protocols.io Spotlight series, featuring conversations with protocol authors.