  Understanding the mechanisms underlying ion channel function from the
atomic-scale requires accurate ab initio modelling as well as careful
experiments. Here, we present a density functional theory (DFT) study of the
ion channel gramicidin A, whose inner pore conducts only monovalent cations and
whose conductance has been shown to depend on the side chains of the amino
acids in the channel. We investigate the ground-state geometry and electronic
properties of the channel in vacuum, focusing on their dependence on the side
chains of the amino acids. We find that the side chains affect the ground state
geometry, while the electrostatic potential of the pore is independent of the
side chains. This study is also in preparation for a full, linear scaling DFT
study of gramicidin A in a lipid bilayer with surrounding water. We demonstrate
that linear scaling DFT methods can accurately model the system with reasonable
computational cost. Linear scaling DFT allows ab initio calculations with
10,000 to 100,000 atoms and beyond, and will be an important new tool for
biomolecular simulations.
