We present various computational tools that can aid research of nanoscale systems, by providing concrete examples of multiscale modeling workflows, in which mesoscale models are contructed from atomistic data, and mesoscale simulation methods are used to generate input for finite-element calculations. The link between the micro- and mesoscale is discussed into more detail, in particular the coarse-graining route via the Flory-Huggins theory of mixtures. We investigate a simple method to estimate the Flory-Huggins interaction parameters from force field calculations, based on sampling the density-of-states of molecular clusters in the space spanned by coarse-grained coordinates. We show how we use the density-of-states to calculate the excess free energy of mixing, and how this leads to mesoscale interaction parameters. The role of entropy introduced by the process of coarse-graining and ways to calculate this contribution are discussed.