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| VERSION 3.1
Wed 27 Feb 2002 |
Contents
More info can be found in the
flowchart
(for a quick overview) and the
GMX FAQ.
Introduction
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 emacs or vi. We furthermore assume the
software is installed properly on your system. When you see a line
like
you are supposed to type the contents of that line on your computer.
We will also assume that you know where your version of GROMACS is
installed. The default location is '/usr/local/gromacs', but for
local users in the Groningen MD group it is simply
'~gmx'. In the default case, the binaries are located in
'/usr/local/gromacs//bin', where
is the architecture of your computer. For other users that
is probably not the case, contact your local system administrator for
more information. For instance, the GROMACS RPM packages for Linux
install binaries in '/usr/local/bin', and shared data in
'/usr/local/share/gromacs' (according to the Linux standard).
The first step is to make sure the GROMACS binaries are in your path.
On some systems they will simply be linked to /usr/local/bin and found
automatically. If this is not the case on your machine 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 located in
your home directory. Add a line like:
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setenv PATH "/usr/local/gromacs/bin/:${PATH}".
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Issue this command at the prompt too, or
log off and on again to automatically get the environment.
Before starting the examples, you have to copy all the neccesary
files, to your own directory. Chdir to the directory you want to put
the examples directory. This directory (named tutor)
will need
about 20 MB of disk space, when it is completely filled.
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cd ``your own directory''
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then copy the examples:
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cp -r /usr/local/gromacs/share/tutor .
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(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 five subdirectories with examples
with names like gmxdemo, 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.
The demo is designed to demonstrate the user-friendlyness
of the GROMACS software package. The only non-friendly part is
that it requires the C shell to run the script. If your shell
is e.g. bash (common on Linux), first start the C shell with the
command 'tcsh'. To run the demo, first move
to your tutor/gmxdemo directory:
And then start the demo script:
This demo handles a complete Molecular Dynamics simulation of a
peptide in water, starting from a
pdb structure. When you run a
Molecular Dynamics simulation with GROMACS you will encounter the
following file formats:
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The molecular topology file is generated by the program
pdb2gmx. pdb2gmx translates a pdb structure file of any peptide
or protein
to a molecular topology file. This topology file contains a complete
description of all the interactions in your peptide or protein.
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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
