Linear ethers such as polyethylene glycol have extensive industrial and medical applications. Additionally, phospholipids containing an ether linkage between the glycerol backbone and hydrophobic tails are prevalent in human red blood cells and nerve tissue. This study uses ab initio results to revise the CHARMM additive (C36) partial-charge and dihedral parameters for linear ethers and develop parameters for the ether-linked phospholipid 1,2-di-O-hexadecyl-sn-glycero-3-phosphocholine (DHPC). The new force field, called C36e, more accurately represents the dihedral potential energy landscape and improves the densities and free energies of hydration of linear ethers. C36e allows more water to penetrate into a DHPC bilayer, increasing the surface area per lipid compared to simulations earned out with the original C36 ether parameters and improving the overall structural properties obtained from X-ray and neutron scattering. Comparison with an ester-linked DPPC bilayer (l,2-dipalmitoyl-sn-phosphatidylcholine) reveals that the ether linkage increases water organization in the headgroup region. This effect is a likely explanation for the experimentally lower water permeability of bilayers composed of ether-linked lipids.