The density functional theory code, ONETEP, uniquely combines near-complete basis set accuracy with a computational cost that scales linearly with the number of atoms. Recent methodological advances include robust geometry optimization, an implicit solvent model and an interface with the natural bond orbital analysis code, NBO 5. We demonstrate two applications in molecular biology: 1) By simulating large (>1000 atoms) models of ligand binding to the heme protein myoglobin, we show how the protein is able to discriminate between carbon monoxide and oxygen and determine how the charge transfer to the ligand converges with system size; 2) Natural bond orbital analysis extracts chemical insight from first principles calculations by outputting orbitals corresponding to the classical notion of localized Lewis-type bond and lone pairs. We use this picture to track intra-molecular interactions during conformational changes in potassium ion channels.

Biomolecular simulation with the linear-scaling DFT code ONETEP

243rd National Meeting (2012)

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