Introduction and Outline

The aim of this tutorial is to investigate similarities and differences in the conformation and dynamics of related proteins. At the end of the tutorial the student should be able to:

• Set up and run Molecular Dynamics Simulations of proteins using Gromacs
• Perform quality assurance checks and analysis on simulation results
• Compare simulation results obtained from different simulations

For this tutorial, students may team up in groups. Then each group will perform simulations on a number of proteins, and each member chooses one protein as the subject of the tutorial. At the end of the tutorial, the results from the simulations will be combined.

Each student should write a report, reflecting on the purpose of the work and the results obtained. Specific questions are given in the tutorial, which have to be answered in the report. A description of the report, what it should contain and which questions are to be answered, is given on the report page. In the text, questions and assigments are indicated by grey boxes, like the following:

Write down your name and those of the members of your group

Commands are given in white on a blue background. These have to be typed carefully, since the shell (the program parsing the commands) is case-sensitive. A common error that may occur is replacing a 0 (digit zero) for an O (capital letter O), an l (lower case letter l) for a 1 (digit one), or vice-versa. You might want to copy-paste the commands, which is as simple as selecting them with the mouse and pressing the middle mouse button on the spot where the command should be entered. Now first try the following commands:

whoami

This lists your current user name. Make sure you're not logged in as "root".

ls -l

This gives a listing of the things that are in the directory where you are. Use this if you encounter errors like "file not found".

pwd

This command shows you the full path of the directory where you are.

Mind that copy-pasting does not relief you from reading the text! You can't run this tutorial without the instructions around the commands. It is naively assumed that the intention of the one following the tutorial is to learn something. In some cases you might be reminded to read carefully, by a comment like the following:

Read carefully!

Molecular Dynamics

Classical molecular dynamics simulations use Newton's equations of motion to calculate trajectories of particles, starting from a defined configuration. For each particle in the system, the total force acting on it is calculated from the interactions with other particles, as described by the force field. The force divided by the mass of the particle gives the acceleration, which, together with the prior position and velocity, determines what the new position will be after a small time step. The high spatial and temporal resolution make molecular dynamics simulations useful for testing models based on experimental data, for understanding principles underlying the function and to formulate new hypotheses. Unfortunately, system sizes are limited, as are time scales.

Gromacs

This tutorial uses Gromacs (http://www.gromacs.org/) for performing and analysing molecular dynamics simulations. Gromacs is a suite of programs which is freely available under the GNU GPL (General Public License). The programs have a command-line interface, which means that each step involves typing the name of the program and a number of arguments. Note that the commands are case sensitive and each command has to be typed exactly as in the tutorial. More information about Gromacs as well as the manual can be found on the web site.

Linux

Since the programs have a command-line interface, there is no escape from using a terminal. Although it is possible to run Gromacs under Windows in a DOS terminal, there are several benefits attached to using Linux, which is the choice for this tutorial. For some students the transfer to Linux from Windows will form an obstacle as they are much used to the interface Windows offers. It is important to note that Linux is not intended to be a free clone of Windows. It is a powerful, highly costumizable operating system, which allows one to get much more performance from a computer. The transfer from Windows to Linux is sometimes described as switching from a motor cycle to a car. To start using the Linux terminal, it is necessary to know the most basic commands (ls,cd,mkdir,cp,mv,rm,more). Some more information about linux/unix can be found here and here. A reference card (cheat sheet) can be found here

Preparation

To get started, make a directory where you will perform your simulation. As results may be combined in the end, use a self-explanatory and unique directory name. It is good practice to keep your directories organized, starting with a directory for the project, which in this case could be 'md-tutorial', or 'prion' if the subject is prion proteins. In that directory, there should be directories for each simulation or for sets of simulations that reflect part of the project. Combine the four-letter PDB id with a personal identifier (e.g. group number or student name). Copy the structure file into the directory and change the directory. The name of the protein is changed to 'protein.pdb' to match the commands that are given in the tutorial. Student Pietje Puk, performing simulations on the human form of the prion protein (1qlz) could, for example, type:

mkdir md-tutorial

cd md-tutorial

mkdir 1qlz_pietje_puk

cp 1qlz.pdb 1qlz_pietje_puk/protein.pdb

cd 1qlz_pietje_puk

Renaming your protein "protein.pdb" allows simply copy-pasting all commands. Be sure to read carefully and to check at each step whether it was successful. Read the output! In case a program gives an error message, it is usually self-explanatory. Check file formats and program output to understand the processes at each step. Most of the files are readable, except for files ending in .tpr, .xtc, .trr and .edr.

If you feel ready, click here to proceed.

Quick Links

• Introduction
• Starting structures
• Simulation
• Analysis
• Report