Sat 19 Jan 2013
More info can be found in the
(for a quick overview) and the
In this chapter we assume the reader is familiar with Molecular
Dynamics and familiar with Unix, including the use of a text editor
such as jot, emacs or vi. We furthermore assume the
GROMACS software is installed properly on your system. When you see a line
you are supposed to type the contents of that line on your computer.
In order to check whether you have access to the GROMACS software, please
start by entering the command:
This command should return a cool quote like:
"Whatever Happened to Pong ?" (F. Black)
If this, in contrast, returns the phrase
luck: command not found.
then you have to verify where your version of GROMACS is installed.
In the default case, the binaries are located in
'/usr/local/gromacs/bin', however, you can ask your local system
administrator for more information. If we assume that GROMACS is
installed in directory XXX you would find the executables (programs) in
XXX/bin. To be able to access the programs without
problems, you will have to edit the login file for your shell. If you
use the C shell, this file is called .cshrc or
.tcshrc, and it is located in your home directory. Add a line
Issue this command at the prompt too, or log off and on again to
automatically get the environment.
You should have an environment variable set now that is called
GMXDATA that we will use further on. Let us check whether this was
If it prints a directory name you are ready to rock, otherwise go back two steps.
Before starting the examples, you have to copy all the neccesary
files, to your own directory, let us call it work.
Mkdir and chdir to the directory you want to put
the examples directory. This directory (named tutor)
about 20 MB of disk space, when it is completely filled.
then copy the examples:
cp -r $GMXDATA/gromacs/tutor .
(NOTE: include the ".")
If that directory doesn't exist you could look for the files
in /usr/local/share/gromacs/tutor, or ask your local GROMACS expert.
You now have a subdirectory
tutor. Move there
and view the contents of this directory
If all is well you will have seven subdirectories with examples
with names like gmxdemo, methanol,
mixed, nmr1, nmr2,
speptide and water.
You are encouraged to look up the different programs and
file formats in
the online manual while you are browsing through the examples.
While going through the tutorial you will find questions
(in a red font). Try to answer them, to increase
your understanding of molecular simulation.
Go to the first step
Here is an overview of the most important GROMACS file types that you will
encounter during the tutorial.
The molecular topology file is generated by the program
pdb2gmx. pdb2gmx translates a pdb structure file of any peptide
to a molecular topology file. This topology file contains a complete
description of all the interactions in your peptide or protein.
When the pdb2gmx program is executed to generate a molecular
topology, it also translates the structure file (.pdb file)
to a gromos
structure file (.gro file). The main difference between a
pdb file and a gromos file is their format and that
a .gro file can also hold velocities. However, if you do not need the
velocities, you can also use a pdb file in all programs.
To generate a box of solvent molecules
around the peptide, the program
genbox is used. First the program
editconf should be used to
define a box of appropriate size around the molecule.
dissolves a solute molecule (the peptide) into any solvent (in this
case water). The output of genbox is a gromos structure file of
the peptide dissolved in water. The genbox program also changes the
molecular topology file (generated by pdb2gmx) to add solvent
to the topology.
The Molecular Dynamics Parameter (.mdp) file contains all
information about the Molecular Dynamics simulation itself
e.g. time-step, number of steps, temperature, pressure etc. The
easiest way of handling such a file is by adapting a sample .mdp
file. A sample mdp file
can be found online.
Sometimes you may need an index file to specify actions on groups of atoms
(e.g. Temperature coupling, accelerations, freezing). Usually the default index
groups will be sufficient, so for this demo we will
not consider the use of index files.
The next step is to combine the molecular structure (.gro file),
topology (.top file) MD-parameters (.mdp file) and
index file (ndx) to generate a run input file (.tpr extension or
.tpb if you don't have XDR).
This file contains all information needed to start a simulation with GROMACS.
grompp program processes all input files and generates the run input
Once the run input file is available, we can start the
simulation. The program which starts the simulation is called
mdrun. The only input file
of mdrun you usually need to start a run
is the run input file (.tpr file).
The output files of
mdrun are the
trajectory file (.trr file
or .trj if you don't have XDR) and a logfile (
- Berendsen, H.J.C., Postma, J.P.M., van
Gunsteren, W.F., Hermans, J. (1981)
Forces, chapter Interaction models for water in relation to
protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company
- Kabsch, W., Sander, C. (1983).
of protein secondary structure: Pattern recognition of hydrogen-bonded
and geometrical features. Biopolymers 22,
- Mierke, D.F., Kessler, H. (1991).
dynamics with dimethyl sulfoxide as a solvent. Conformation of a
cyclic hexapeptide. J. Am. Chem. Soc. 113, 9446.
- Stryer, L. (1988).
vol. 1, p. 211. New York: Freeman, 3 edition.