These are some GROMACS tutorials for beginners. It’s not
necessary to do the tutorials in order, but the first two
tutorials are essential before going on to the others, as the structure file
methane.pdb) and topology file (
topol.top) for methane from tutorial 2 are
used in all subsequent tutorials. The tutorials are designed for GROMACS version
5.1 and up. If you are using an older version, some of the commands or
parameters may have changed. Note especially that the pull code for umbrella
sampling has changed since 5.0 and older releases.
I assume you have some working knowledge of the command line. Specifically, you
should know how to make directories, change into them, edit text files, and
download files to your system. When you see a
> this is the prompt on
the commandline and indicates you should type the text following it. If the
commandline is new to you, consider going through CodeAcademy’s
I also assume you have GROMACS installed on a machine available to you. Source code and installation instructions can be found on the GROMACS documentation page.
Throughout the tutorials we’ll be using OPLS methane and TIP4PEW water.
If there is an error or mistake in a tutorial, or if something is unclear, please open an issue, and I will be happy to address it. If you have a general question about GROMACS see the GROMACS documentation. You can also direct general questions about GROMACS to their mailing list.