SSP 1994 project summary:

Estimating Polar Interaction Energies in the Presence of Water

• molecular dynamics, which allows the thermodynamic equilibrium of a system to be found, useful for example in solving protein structure, and

• interactive visualisation, which allows the chemist to study molecular interactions directly, for example interactions between biomolecules and small organic molecules.

The second of these techniques is of special interest to Pharmacists and Biochemists, but requires simple force fields which can potentially be solved on single graphics workstations. One of the greatest sources of inaccuracy in these models is the fact that most biological systems use water as their solvent, and water has a large dipole which masks long range polar interactions. Molecular dynamics simulations can include water molecules explicitly, but for real-time calculations this is currently impossible. It would be useful to have a way of accounting for the masking effect of water without having to account for each water molecule, and this is a problem which could potentially be solved using a set of high performance parallel algorithms.

David Grierson worked on this project.

Compressed PostScript of Dave's final report is available here (184289 bytes) .

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