2 hr lecture + 2 hr exercise session in our computer room; the students can choose between two alternative exercise sessions, either on Tuesdays 7:30-9:30 a.m. or on Thursdays 7:45-9:45 a.m.; the course was previously named CSCBP (the content remains the same, but the new title is more adequate)
Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS).
Learning objective
Introduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations.
Content
Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS).
Lecture notes
Script booklet (copies of powerpoint slides) distributed at the first or second lecture.
Since the exercises on the computer do convey and test essentially different skills than 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).
Performance assessment as a semester course