Quantum chemistry: Single- and multiple electron systems. Ab initio-methods, Hartree-Fock equations, gaussian basis sets. Orbitals, calculation of partial charges, practical program usage.
Molecular force fields: Bonds, angles, torsions. Electrostatics and van der Waal forces, parameterisation from experiments or quantum chemistry. Effective pair potentials, hydrogen bonds. Computation of molecular properties and limitations, examples of commonly used force fields.
Energy landscapes: Minimizations, algorithms, normal modes, transition states and reaction pathways.
Simulation methods: Molecular dynamics, equilibration, thermodynamical properties from simulations, stochastic dynamics, energy conservation. Monte Carlo methods and conformational analysis.
Bioinformatics: Sequence analysis, protein structure, homology modeling, 3D structure prediction from sequence, chemoinformatics, combinatorial databases.
Advanced applications: Free energy calculations from simulations, free energy of solvation, chemical reactions, molecular docking, modern drug design with simulations and quantum chemistry.