[gmx-users] adkgromacstutorial error

[Justin Lemkul]

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 The tutorial contents look a bit outdated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.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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