The key to nanoscale control of physical, chemical, and biological processes lies in well-founded models of noncovalent binding. Atomistic simulations probe the free-energy surface underlying molecular assembly processes in solution. Two examples of noncovalent binding studied by molecular dynamics simulations are discussed, the dimerization of a water-soluble perylene bisimide derivative in aqueous solution with a focus on the influence of solvent composition on the aggregation strength and the binding of 1-butanol to -cyclodextrin at infinite dilution with the focus on the determination of method-independent binding free energies.