[gmx-users] adkgromacstutorial error

Oliver Beckstein obeckste at asu.edu
Tue Jul 3 16:53:32 CEST 2018

Thanks for reporting the errors with the tutorial and possible fixes.

On Jul 3, 2018, at 5:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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 The tutorial contents look a bit outdated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 agree that the header with Gromacs versions and current date is misleading – I added a big red warning box and a link to Justin’s tutorials.

Sorry for the issues – it’s hard work keeping content up-to-date, and the amount of work Justin must have put in his tutorials is almost certainly under-appreciated. My point in the other thread was mainly to provide a starting point for writing tutorials in sphinx; for instance, one can now directly link to the Gromacs docs using “intersphinx mappings” (:ref:`gmx grompp` will link to the appropriate page in the current docs).

The best place to report problems with the tutorial is the issue tracker https://github.com/Becksteinlab/AdKGromacsTutorial/issues <https://github.com/Becksteinlab/AdKGromacsTutorial/issues> – I already raised one for the problems reported in this thread. 

Pull requests for fixing the issues are even more welcome :-).


> 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.
> -Justin
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Oliver Beckstein, DPhil * oliver.beckstein at asu.edu

Associate Professor of Physics
Arizona State University
Center for Biological Physics and Department of Physics
Tempe, AZ 85287-1504
Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669

Department of Physics: https://physics.asu.edu/content/oliver-beckstein
Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein

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