A method simulating the formation of densely cross-linked polymeric networks was developed that incorporates both intramolecular as well as intermolecular interactions and the subsequent effects they have on the end network structure. The all-atom nature of the model allows for the simulation of network formation in a variety of conditions including differing solvent qualities, presence of inert species, as well as nonlocal effects such as polymerization in the presence of a template molecule. We employed an all-atom kinetic gelation technique that utilized an off-lattice approach that tracked the position and interaction of all atoms throughout the simulation. This model was then used to study the formation of polymeric networks capable of recognizing and binding a specific molecule out of a host of competing species. Simulation of the imprinted network formation was done using the all-atom kinetic gelation framework, which helped identify the interactions central to recognition. These results were verified by comparison with previous experimental results.