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).

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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

Introduction to UNIX, introduction to Python programming, data representation and processing, computational errors, algorithms and scaling, sorting and searching, numerical algorithms, algorithmic strategies, computer simulation, computer architecture, operating systems, programming languages, computer networks, databases, representation of chemical structures, molecular simulation.

Seminar series covering current developments in Physical Chemistry

The laws of thermodynamics: empirical temperature, energy, entropy. Models and standard states: ideal gases, ideal solutions and mixtures, activity, standard thermodynamic values. Reaction thermodynamics: chemical potential, thermodynamic parameters of reactions, equilibrium conditions and their temperature and pressure dependence, biochemical reactions, surface effects, colligative properties.

Thermodynamic foundations of phase equilibria, intermolecular interactions, and molecular self-assembly; kinetics of chemical reactions and transport processes

Principles and applications of statistical mechanics and equilibrium molecular dynamics, Monte Carlo simulation, stochastic dynamics and free energy calculation.Exercises using a MD simulation program to generate ensembles and subsequently calculate ensemble averages.

The student will carry out a literature study on a topic of his or her liking or suggested by the supervisor in the area of computer simulation in chemistry, the results of which are to be presented both orally and in written form.

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