Molecular Dynamics Simulations for Biomolecules with Gromacs 3.-5.2.2004

Introduction

This EMBnet-funded course focused on molecular dynamics (MD) simulation methods in studying large biomolecules. Lectures covered both overall methods and more detailed theoretical background of MD simulations of biomolecules. The lectures were given by Prof. H.J.C. Berendsen (University of Groningen, Netherlands) and Dr André Juffer (University of Oulu). Exercises focused on advanced MD simulations using the program package Gromacs 3.2. The instructor for the exercises was Dr David van der Spoel (Uppsala University, Sweden), one of the main developers of Gromacs.

Program

All the lectures of the course, including the explanations for the exercises, were video recorded. To view the video files you will need a suitable media player in your browser (download Real-player here ).

Tuesday 3.2.2004

09:00-09:05 Welcoming words 
09:05-10:20 "Introduction to Modelling. From quantum to classical mechanics", 
            Video
	    Prof. H.J.C. Berendsen   
	    (Introduction of the prof. Berendsen's book)      
10:20-10:45 Coffee break
10:45-12:00 "Molecular Dynamics simulations. Methods and applications", 
            Video
            Prof. H.J.C. Berendsen
12:00-12:15 Discussion
12:15-13:15 Lunch break
13:15-15:00 Exercises (Dr D. van der Spoel)   
	    All exercises of the course are here and here. 
	    Answers for the exercises are here (html) and here (video).      
15:00-15:20 Coffee break
15:20-17:30 Exercises (continued)
17:30->     Evening program. The evening program is a social event for 
            all participants. It takes place in the premises of CSC, where 
            supper and a possibility for sauna is offered. The evening 
            program is free of charge for all participants.

Wednesday 4.2.2004

09:00-10:15 "Free energy calculations. Analysis of simulation results", 
            Video
	    Prof. H.J.C. Berendsen 
10:15-10:45 Coffee break
10:45-11:15 "Electrostatic interactions; continuum methods", 
            Video
	    Dr A. Juffer 
11:15-12:00 "pKa calculations - methods and applications", (pdf version),
            Video
	    Dr A. Juffer 
12:00-12:15 Discussion
12:15-13:15 Lunch break
13:15-15:00 Exercises (Dr D. van der Spoel)
15:00-15:20 Coffee break
15:20-17:30 Exercises (continued)

Thursday 5.2.2004

09:00-10:15 "Beyond MD: Stochastic methods. Mesoscopic approaches", 
            Video
	    Prof. H.J.C. Berendsen
10:15-10:45 Coffee break
10:45-11:15 "Protein-membrane association. Theoretical model, Lekner summation", 
            Video
            Dr A. Juffer
11:15-12:00 "GROMACS inside", 
            Video
	    Dr D. van der Spoel
12:00-12:15 Discussion
12:15-13:15 Lunch break
13:15-15:00 Exercises (Dr D. van der Spoel) 
15:00-15:20 Coffee break
15:20-17:00 Exercises (continued)

Back to CSC-Chemistry page.