Problems with tutorials in GROMACS 4.5.4
There is an extra pd-temp parameter in all the grompp.mdp files
The online documentation tells you to use the ngmx trajectory viewer but that one is not default included with GROMACS 4.5.4 (so maybe adding some text about installing ngmx would be helpful)
In the mixed tutorial the topol.top file includes
but methanol.itp is not included in GROMACS 4.5.4 (but is included in the methanol tutorial) so
also in the mixed tutorial
g_density -n index -o dens0 -b 0 -e 50 -d X
command is missing the -ng 2 (so that you can select x2 groups)
The speptide tutorial also has quite a few inconsistencies.
Sadly a new/updated version of the tutorials and online getting started guide might be needed.
#3 Updated by Justin Lemkul over 7 years ago
Helgi Ingolfsson wrote:
They are under “Getting Started” in the online manual http://manual.gromacs.org/
And the tutorial files are provided with gromacs in the folder gromacs/share/gromacs/tutor
Maybe these where meant to be discontinued?
The tutorials are somewhat outdated. Significantly better tutorial material exists on the Tutorials page on gromacs.org. The provided material may be updated, but I've never seen anyone raise the issues you have, indicating that likely very few people use them.
#5 Updated by Justin Lemkul almost 7 years ago
Roland Schulz wrote:
Since it is outdated and better exists, should we simply remove it and replace it with a README containing a link to http://www.gromacs.org/Documentation/Tutorials ?
That could be a good idea. I suppose if anything changed about the organization of www.gromacs.org, then we could make this corresponding change, as well.