Aims

To provide a basic knowledge of modern molecular

mechanics and simulation methods and their

statistical mechanical foundations. To familiarise

the student with computer modelling and graphics

tools for analysing the structure, function and

dynamics of biomolecules.

Content

Maxwell-Boltzmann distributions, ensembles, partition functions, kinetic gas theory, transition

state theory, configurational distribution functions, non-ideal gases, simple liquids, analytical

force fields for interacting systems, energy optimisation, Monte Carlo methods, molecular

dynamics (MD) simulation methods and algorithms, termodynamic perturbation techniques.

Laboratory work: Force fields and molecular mechanics of small molecules, potential energy

surfaces, energy minimisation, conformational analysis and computer graphics. MD simulations

of liquid water and short peptides. Pair distribution functions. MD of proteins, free energy

simulations, drug design.

Instruction

Lectures and laboratory work.

Assessment

Written exam at the end of the course. Passed laboratory work.