Molecular models, Force fields, Boundary conditions, Electrostatic interactions, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation.
Objective
Introduction to computer simulation of (bio)molecular systems, development of skills to carry out and interpret computer simulations of biomolecular systems.
Content
Molecular models, Force fields, Spatial boundary conditions, Calculation of Coulomb forces, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation.
Lecture notes
Available (copies of powerpoint slides distributed before each lecture)
Since the exercises on the computer do convey and test essentially different skills as those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam (learning component, possible bonus of up to 0.25 points on the exam mark).