PCC-32806 Molecular Modelling with Applications in Biological Systems


Credits 6.00

Teaching methodContact hours
Course coordinator(s)dr. RJ de Vries
Lecturer(s)dr. RJ de Vries
prof. dr. JT Zuilhof
prof. dr. ir. FAM Leermakers
AH Westphal
Examiner(s)dr. RJ de Vries

Language of instruction:


Assumed knowledge on:

Elementary mathematics; PCC-21802 Introductory Thermodynamics; PCC-22306 Driving Forces in Chemistry, Physics and Biology.

Continuation courses:

Thesis PCC, ORC, BIC, and more.


Computer modelling of (bio)molecules has become an indispensable tool in biomolecular science and technology, next to experiments and theory. For example, it plays a key role in the discovery of new drugs, in structure elucidation of proteins and protein complexes, and in many more fields. Building on a basic background in physical chemistry (see assumed knowledge above), this course introduces the basic theory behind biomolecular simulation techniques such as molecular mechanics (MM), molecular dynamics (MD) and Monte Carlo simulations (MC). A last part of the course deals with Quantum Modelling and introduces a selection of quantum modelling tools that are commonly used in current (bio)chemical research. Tutorial's with exercises are used as an aid to obtain a working understanding of the theory, and computer practicals are used to learn to work with the various simulation techniques on simple example projects.

Learning outcomes:

At the end of the course students are expected to be able to:
- judge relevant basic concepts: molecular forces, energy minimization, statistical thermodynamics, Schrödinger equation;
- analyse the formulas presented in the course text, lectures, and tutorials in a mathematically correct ways, and apply them in simple computations (with due attention to dimensions and units);
- explain the essentials of molecular modelling techniques: molecular mechanics, molecular dynamics, Monte Carlo, Quantum Computations;
- properly interpret the results of computer simulations on relevant systems.


- lectures;
- tutorials;
- computer practicals.


Written exam with open questions.


Alan Hinchliffe. (2008). Molecular Modelling for Beginners. Wiley. 428p. ISBN: 978-0-470-51314-9

Restricted Optional for: MMLMolecular Life SciencesMScD: Physical Chemistry6MO
MMLMolecular Life SciencesMScC: Physical Biology6MO