[gmx-users] adkgromacstutorial error
jalemkul at vt.edu
Tue Jul 3 14:38:07 CEST 2018
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 The tutorial contents look a bit outdated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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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