Biomolecular Simulations

Course manual 2017/2018

Course content

Molecular dynamics is a powerful tool to investigate the structure and dynamics of biologically relevant molecules such as proteins, DNA and lipids in atomistic detail. The insight from MD simulation yields quantitative predictions and a 'molecular movie' of important processes that helps experimentalists interpret their results. Such simulations can also be used to predict effects of e.g. point mutations. This course provides an introduction to biomolecular simulation using molecular dynamics, and enhanced sampling methodology to study biomolecular processes.

This course consists of lectures which will cover the following topics: 1) the basics of molecular dynamics, 2) the structural analysis of biomolecules, e.g. through NMR and crystallography, 3) multiscale modeling of biomolecular systems 4) the problem of rare events in conformational changes.

In addition to the lectures there will be a practical tutorial consisting of theoretical exercises as well as computer problems. The course ends with doing a small project including a real simulation on a biomolecular system.

Study materials

Syllabus

Software

Other

• Online tutorials

Objectives

At the end of the course the student is able to

• characterize the structure of proteins, assess the quality of structures contained within the Protein DataBank;
• describe the relevant aspects of statistical mechanics, thermodynamics and transition state theory;
• describe the basic principles of molecular dynamics;
• perform a molecular dynamics simulation on a protein system;
• explain what a rare event is;
• list methods to overcome the rare event problem;
• describe the principles of coarse graining, replica exchange molecular dynamics, biased sampling, in particular metadynamics, and transition path sampling;
• perform a metadynamics simulation and perform a transition path sampling simulation. 

Teaching methods

• Lecture
• Computer lab session/practical training
• Working independently on e.g. a project or thesis

Lectures and werkcolleges/computer practicum.

Learning activities

Attendance

The programme does not have requirements concerning attendance (OER-B).

Assessment

Examination consists of a written report, based on a molecular simulation study of a biomolecule performed during the course, and an oral discussion of the report. 

Inspection of assessed work

The date, time and location of the inspection moment are in the DataNose timetable.

The students will receive an appointment to discuss their report. This discussion will be evaluated and count for 50% of the final grade. 

Assignments

Final report

• The students will do a project during the course, on which they have to write a report. 

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Timetable

The schedule for this course is published on DataNose.

Additional information

Recommended prior knowledge: thermodynamics, statistical mechanics, biochemistry.

Contact information

Coordinator

• dr. Jocelyne Vreede

Contact the course coordinator for questions.