Teaching by: Doros N. Theodorou or Theodorou N. Doros, Giannis Samios and Alice Vegiri

Outline:

Molecular Dynamics (MD) Simulations: Constructing a molecular model: force fields, periodic boundary conditions. Generalised coordinates. Extracting the equations of motion from the Lagrangian. Integration algorithms (Verlet, Gear).

MD in Cartesian coordinates in the presence of holonomic constraints: SHAKE, RATTLE, Edberg-Evans-Morriss algorithm. Free energy perturbation methods. Extended ensemble methods: NPH, NVT, NPT, Parrinello-Rahman. Car-Parrinello ab initio MD.

Monte Carlo (MC) Simulations MC integration. Importance sampling of prescribed probability distributions. The Metropolis algorithm. Canonical, isothermal-isobaric and grand canonical MC. Gibbs Ensemble MC. Designing efficient MC moves: Configurational Bias and End Bridging MC for polymers. Umbrella sampling and histogram reweighting methods.

Analysing the Structure Pair distribution functions. Static structure factor and its measurement through scattering experiments. Orientational correlation functions and their experimental measurement through NMR.