Molecular Dynamics

Faculteit Science and Engineering
Jaar 2021/22
Vakcode WMBS003-05
Vaknaam Molecular Dynamics
Niveau(s) master
Voertaal Engels
Periode semester I a (18-10-2021 till 07-11-2021)

Uitgebreide vaknaam Molecular Dynamics
Leerdoelen Location: Centre for Life ScienAt the end of the course, the student is able to:

1) assess the advantages/disadvantages of a variety of computational modeling techniques

2) assess the general ideas and key numerical techniques behind Molecular Dynamics (MD) simulation techniques

3) assess the concepts of statistical thermodynamics relevant for interpretation of MD simulations (e.g., phase space, partition function, ensembles)

4) interpret data from MD simulations as reported in primary scientific literature

5) generate and analyze data using the MD software GROMACS

6) apply MD simulations to study a (bio)physical process such as self-assembly of lipids and internal motions of proteins

7) point out the assumptions made in a MD simulation and their limitations in relation to (bio)chemical reality

8) report on MD simulations during a presentation
Omschrijving Together with experiment and theory, computational modeling is one of the three pillars of modern science. In chemistry as well as in life sciences, modeling of the interactions between molecules is essential to understand the emerging behavior of complex systems. In particular the Molecular Dynamics (MD) simulation technique provides a detailed view of the behavior of molecules in space and time, at a resolution that cannot be attained by any single experimental technique.

In a series of lectures, the underlying theory (statistical thermodynamics), the diversity of molecular models (atomistic, coarsegrained), and numerical techniques (integration of Newton's equations of motion) used in MD simulations will be discussed.
Applications of the technique will be shown, with a focus on simulation of biomolecular processes.

An important part of the course is hands-on experience using the GROMACS modeling software in a series of tutorials and practicals covering the basics of the techniques and selected applications, e.g. self-assembly of lipids in water or sampling the conformational space of proteins.
Uren per week
Onderwijsvorm Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC)
(Presence during practicals and final project are mandatory, otherwise the student will fail this part. Attendance of the lectures is highly recommended but the material is also available on Nestor and can be learned through selfstudy.)
Toetsvorm Practisch werk (PR), Presentatie (P), Schriftelijk tentamen (WE)
(Final grade is a weighed average of the written exam and the practical assignment (which includes the oral presentation). Student passes when final grade is 5.5 or higher, provided the grades for both the written exam and the practical assignment are at least 4.5)
Vaksoort master
Coördinator prof. dr. S.J. Marrink
Docent(en) dr. A.H. de Vries ,prof. dr. S.J. Marrink
Entreevoorwaarden The course unit assumes prior knowledge acquired from Calculus, Classical Mechanics, Introduction to Thermodynamics, and Structural Biology, all at Bachelor Life Science and Technology level. This material is offered in various Life Science, Chemistry, and Physics courses.
Opmerkingen Students from the degree programme Biomolecular Sciences have priority, to register please send an email to:

Max. 30 students
Opgenomen in
Opleiding Jaar Periode Type
MSc Biology: Research  (Compulsory master courses) - semester I a keuze
MSc Biology: Science, Business and Policy  (Compulsory master courses) - semester I a keuze
MSc Biomolecular Sciences  ( Compulsory courses general programme (3 out of 9)) - semester I a keuzegroep
MSc Biomolecular Sciences  (Electives/Optional modules) - semester I a keuze
MSc Chemistry: Advanced Materials  (Electives) - semester I a keuze
MSc Chemistry: Catalysis and Green Chemistry  (Electives) - semester I a keuze
MSc Chemistry: Chemical Biology  (Electives) - semester I a keuze
MSc Chemistry: Erasmus Mundus Theoretical Chemistry and Computing Modelling  (Core Programma) 1 semester I a verplicht
MSc Chemistry: Science, Business and Policy  (Electives) - semester I a keuze
MSc Courses for Exchange Students: Biology - semester I a