Understanding the synthesis of periodic mesoporous silica (PMS) is crucial for a more efficient use of these materials and is a necessary first step toward a rational design strategy for the templated synthesis of porous solids. In this paper, the early stages of the synthesis process of PMS materials are simulated directly by molecular dynamics, using realistic atomistic models. It is the first time that such computationally demanding calculations have been attempted. By comparing the self-assembly of cationic surfactants in the presence and absence of silicates, we are able to show that silica promotes the formation of larger aggregates than in a simple surfactant/water solution. The formation of these larger micelles is explained by a strong interaction of the silicate molecules with the surfactant head groups. This strong interaction increases the local concentration of silica at the surface of the micelles, which induces the formation of more condensed silicate species. The surfactant/silica structures observed here are potentially important intermediates in PMS synthesis.