Free Fatty Acids (FFAs) are one of the major constituents of biofuel feedstock. Unfortunately they do not play any direct role in fuel synthesis and their presence can slow reaction time. However, FFAs have potential value in other markets; healthcare and beauty. For this reason effective sequestration of FFAs is very desirable and potentially profitable. Current methods are chemical or energy intensive and thus, pricey. The exploration of FFAs interactions with different size pores show us how they will react to filtration. Herein Molecular Dynamics (MD) is used to construct systems of non-functionalized pores of four different sizes (10, 15, 20, 25 Å) and seven different FFAs (Arachidic acid, Cis-11-Eicosenoic acid, Eicosapentaenoic acid, Linoleic acid, Oleic acid, Palmitic acid, and Palmitoleic acid). The parameterization of these 28 systems and any associated calculations leading to functionalization are herein examined. Density functional theory (DFT) has been used to optimize the FFA structures and to calculate the charge distribution. The restrained electrostatic potential (RESP) method was used to assign classical point charges to quantum charge distribution. The general amber force field (GAFF) was modified with the newly created point charges resulting in the creation of a GAFF-FFA force field. The FFAs were then simulated to gather densities, radii of gyration, and radial distribution functions. Densities were found to be within 5% deviation of experimental data.Simulations have also elucidated the structural and energetic properties of pure FFAs, and FFAs in hexane in addition to insights on the sequestering capability of unmodified silicon dioxide pores.