Molecular imprinted polymers (MIP) allows the preparation of tailored and high specific materials able to recognize a specific template. In this work, we simulated the affinity of a new high selective MIP able to specifically bind the isobutylphenylpropanoic acid (ibuprofen, template molecule). We have performed a series of molecular dynamics (MD) simulations of different mixtures in order to undercover the mechanisms occurring during the process of molecular imprinted polymers. The simulations were performed using the GROMACS 5.0 and the the OPLS-AA force field were used to parameterize and verifiy the studied molecules. A single system were simulated representing the pregelification state of the system. The radial distribution function (RDF) analysis and cluster analysis were used to evaluate the affinity of the template molecule, ibuprofen, for the gel backbone. Results confirm that the new material is high-selective and MD simulations are essential to study the molecular imprinting process because can give a deeper knowledge of the mechanism occurring during the imprinting process.