Error in Gromacs run?

User discussions
1

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

2

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

3

@alevilla Thank you for your reply. It is very helpful.

5

tc and tc-grps are not commands. They are settings in the .mdp file. See Molecular dynamics parameters (.mdp options) - GROMACS 2024.1 documentation for the documentation of the options.

7

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):

"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/ and GROMACS Tutorials.