# Error in Gromacs run? **URL:** \ **Category:** User discussions\ **Created:** [August 24, 2021, 11:43am UTC](https://gromacs.bioexcel.eu/t/error-in-gromacs-run/2726 "2021-08-24T11:43:22Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Pallavi](https://avatars.discourse-cdn.com/v4/letter/p/3be4f8/32.png) [@Pallavi](https://gromacs.bioexcel.eu/u/Pallavi)\ **Post date:** [August 24, 2021, 11:43am UTC](https://gromacs.bioexcel.eu/t/error-in-gromacs-run/2726/1 "2021-08-24T11:43:22Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I have done md simulation of DNA ( G quadruplex) having potassium ion in centre with ligand. given command- gmx grompp -f nvt.mdp -c em.gro -r em.gro -p Complex.top -n index.ndx -o nvt.tpr i have get Fatal error: Atom 489 in multiple T-Coupling groups (2 and 3) nvt.mdp file includes tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = DNA\_UNK Water\_and\_ions K ; three coupling groups - more accurate tau\_t = 0.1 0.1 0.1 ; time constant, in ps ref\_t = 300 300 300 ; reference temperature, one for each group, in K ; Pressure coupling index file- 0 System : 16581 atoms 1 DNA : 488 atoms 2 K : 1 atoms 3 UNK : 59 atoms 4 NA : 28 atoms 5 CL : 15 atoms 6 Ion : 44 atoms 7 K : 1 atoms 8 UNK : 59 atoms 9 NA : 28 atoms 10 CL : 15 atoms 11 Other : 59 atoms 12 K : 1 atoms 13 UNK : 59 atoms 14 NA : 28 atoms 15 CL : 15 atoms 16 Water : 15990 atoms 17 SOL : 15990 atoms 18 non-Water : 591 atoms 19 Water\_and\_ions : 16034 atoms nr : group ‘!’: not ‘name’ nr name ‘splitch’ nr Enter: list groups ‘a’: atom ‘&’: and ‘del’ nr ‘splitres’ nr ‘l’: list residues ‘t’: atom type ‘|’: or ‘keep’ nr ‘splitat’ nr ‘h’: help ‘r’: residue ‘res’ nr ‘chain’ char “name”: group ‘case’: case sensitive ‘q’: save and quit ‘ri’: residue index > 1|3 Copied index group 1 ‘DNA’ Copied index group 3 ‘UNK’ Merged two groups with OR: 488 59 → 547 20 DNA\_UNK : 547 atoms > q Please reply Thanks in advance ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [August 26, 2021, 10:02am UTC](https://gromacs.bioexcel.eu/t/error-in-gromacs-run/2726/2 "2021-08-26T10:02:49Z")
Hi, the groups used for temperature coupling (defined in mdp file as tc-grps) can not have common atoms. In your case groups Water\_and\_ions and K have an atom in common (atom number 489). That is what the error says. Currently you can couple directly to system. Or in alternative if you want to have different coupling groups, I will suggest to have 2 coupling group (one with DNA UNK and the bound potassium and one with the rest). It does not make sense to have a group with one atom in this context. Kind regards Alessandra ---
**Author:** ![Pallavi](https://avatars.discourse-cdn.com/v4/letter/p/3be4f8/32.png) [@Pallavi](https://gromacs.bioexcel.eu/u/Pallavi)\ **Post date:** [September 23, 2021, 4:18pm UTC](https://gromacs.bioexcel.eu/t/error-in-gromacs-run/2726/3 "2021-09-23T16:18:30Z")
@alevilla Thank you for your reply. It is very helpful. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [April 25, 2024, 6:53am UTC](https://gromacs.bioexcel.eu/t/error-in-gromacs-run/2726/5 "2024-04-25T06:53:24Z")
`tc` and `tc-grps` are not commands. They are settings in the .mdp file. See [Molecular dynamics parameters (.mdp options) - GROMACS 2024.1 documentation](https://manual.gromacs.org/current/user-guide/mdp-options.html) for the documentation of the options. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [April 25, 2024, 6:32pm UTC](https://gromacs.bioexcel.eu/t/error-in-gromacs-run/2726/7 "2024-04-25T18:32:22Z")
You said you are trying to run “the tc command” and “tc-grps: command not found”. The discussion above said nothing about any “tc command”, but discussed settings in the .mdp file (simulation settings file): ```auto "nvt.mdp file includes tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = DNA_UNK Water_and_ions K ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 ; reference temperature, one for each group, in K ; Pressure coupling" ``` You have not written anything about what you are attempting to do, so it is difficult to help you. I would suggest that you have a look at some of the tutorials at [https://tutorials.gromacs.org/](https://tutorials.gromacs.org/) and [GROMACS Tutorials](http://www.mdtutorials.com/gmx/index.html).