Molecular Dynamics

Faculteit Science and Engineering
Jaar 2019/20
Vakcode MLBB005
Vaknaam Molecular Dynamics
Niveau(s) master
Voertaal Engels
Periode semester I a (14-10-2019 till 02-11-2019)

Uitgebreide vaknaam Molecular dynamics and modeling of membranes and proteins
Leerdoelen At 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 40
Onderwijsvorm Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC)
(Presence during practicals and final project are mandatory)
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
Co├Ârdinator prof. dr. S.J. Marrink
Docent(en) dr. A.H. de Vries ,prof. dr. S.J. Marrink
Verplichte literatuur
Titel Auteur ISBN Prijs
A reader will be made available
Entreevoorwaarden Students in Biomolecular Sciences and Erasmus Mundus Chemistry need to pre subscribe via in June
Opmerkingen 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.
Study load:
Lecture 1 16 hours
Assignment 1 40 hours
Practical 1 24 hours
Self-study 60 hours
Total 140 hours

Location: Research Molecular Dynamics (GBB), Nijenborgh 7, Groningen.

Capacity: 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 verplicht