Metal-Organic Frameworks (MOFs) have a broad range of applications (e.g., gas storage and catalysis). While a great number of MOF compounds are reported in the literature, there have been few studies probing the self-assembly process. The problem is suitable for computational studies, but they fall short due to the limited timescales of all-atom simulations. To allow simulations to reach much longer timescales, we are optimizing effective potentials that would accelerate the simulations by up to three orders of magnitude. Given a reference all-atom simulation, the uniqueness of the optimized solution can be guaranteed in theory. However, transferring these potentials to slightly different systems remains a difficult problem in practice. We employ a bottom-up approach, where the potentials are optimized for systems in increasing order of complexity, beginning with single-component systems. Once validated, the effective potentials will be used to run large scale coarse-grained simulations that enable us to identify the local structural units appearing as part of the self-assembly process.