The use of nanopores is fast becoming a major tool in molecular analysis and detection due to their ability to detect polynucleotides, proteins and small molecules. Biomimetic modelling of pores allows for a specific functional motif to be designed into the molecular structure of the nanopore, based on amino acid motifs found in existing membrane protein structures. An initial beta barrel model was built computationally, based on the transmembrane domain of the 14 stranded beta-barrel pore of alpha-hemolysin. Hydrophobic and hydrophilic residues were designed in a specific arrangement within the structure to replicate an overall hourglass shaped cavity with a central constriction. Molecular dynamics simulations of the model pore embedded in a lipid bilayer membrane were used to explore permeability to water and ions. Selected models were modified to yield hybrid pores in which the location and size of hydrophobic residues were varied to yield constriction regions by hydrophilic pore lining residues. Using umbrella sampling to estimate free energy landscapes for water and ion permeation, a hydrophobic gating mechanism has been established, providing insights into possible biomimetic motifs which could be inserted into native protein nanopores.