ensure tutorial runs with Gromacs 2018

[orbeckst]

As noted on the gmx-users list, the tutorial does not work with Gromacs 2018:

Missing index groups

On 7/3/18 8:32 AM, Mahmood wrote:
The tutorial contents look a bit outdated
Well the main page says that the release date is Jul 3 and it is compatible with 2018.I changed tau-p to just one value (tau-p = 2.5)

Well, the home page says the tutorials "should be compatible" with the listed versions, but there are several things that I note that won't work with 2018, including a few commands. I encourage you to provide feedback to the author(s) to note the problems with 2018, as surely you have had to change a few commands, e.g. to include -r (which is now mandatory for running grompp with restraints).

Now, I get
Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2682)

Fatal error:
Group PROT referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

Again it seems there are inconsistencies in the input files. I only took a quick look through the tutorial, but I see no mention of making any of the index groups used in comm_grps in md.mdp.

MDP options

On 7/3/18 7:48 AM, Mahmood wrote:
Hi,Following adkgromacstutorial, at the energy minimization step [1], I hit an error. All previous steps are fine.

Command line:
gmx grompp -f md.mdp -p ../top/4ake.top -c ../posres/posres.pdb -o md.tpr -maxwarn 3

Yikes! -maxwarn 3? Very dangerous... :)

ERROR 1 [file md.mdp, line 94]:
Right hand side '2.5 2.5' for parameter 'tau-p' in parameter file is
not a real value

Although it says line 94, I see that parameter is in line 76
$ grep -n tau-p md.mdp
76:tau-p = 2.5 2.5 ; Barostat coupling constant (ps) – Piggot (5.0)

Any idea about that?

[1] https://adkgromacstutorial.readthedocs.io/en/latest/simulation.html

The tutorial contents look a bit outdated (Oliver did just warn about this in another message). tau_p only takes one value. In older versions, additional values were silently ignored, but not in recent GROMACS versions.

If you're trying to use version 2018, may I suggest http://www.mdtutorials.com/gmx/index.html

-Justin

[mahmoodn]

Thanks for the support. I am here.

[orbeckst]

@mahmoodn please feel free to raise more issues. I can't promise that things will get fixed immediately because at the moment only @sseyler and I are – very occasionally – working on the tutorial, and we have many other things to do that are all more urgent and important. However, if you want to fix things and submit a pull request we're happy to look at it and, if we merge it, will include you as an author.