# 63 atoms are not part of any of the T-Coupling groups **URL:** \ **Category:** User discussions\ **Created:** [May 20, 2022, 10:08am UTC](https://gromacs.bioexcel.eu/t/63-atoms-are-not-part-of-any-of-the-t-coupling-groups/4189 "2022-05-20T10:08:17Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [May 20, 2022, 10:08am UTC](https://gromacs.bioexcel.eu/t/63-atoms-are-not-part-of-any-of-the-t-coupling-groups/4189/1 "2022-05-20T10:08:17Z")
GROMACS version: version 2020 GROMACS modification: Yes/No Here post your question I want to apply md simulation my dna structure using amber force field in gromacs.Until the equilibration system,there was no error.for nvt step,gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr I got 63 atoms are not part of any of the T-Coupling groups this error. my nvt.mpd file: title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 \* 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = DNA SOL ; two coupling groups - more accurate tau\_t = 0.1 0.1 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp = 300 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed After this error,I created index file : 0 System : 1362371 atoms 1 DNA : 2015 atoms 2 NA : 63 atoms 3 Water : 1360293 atoms 4 SOL : 1360293 atoms 5 non-Water : 2078 atoms 6 Ion : 63 atoms 7 NA : 63 atoms 8 Water\_and\_ions : 1360356 atoms But I am still dont understand how to fix this error could anybody gives me any suggestion please ? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [May 20, 2022, 10:20am UTC](https://gromacs.bioexcel.eu/t/63-atoms-are-not-part-of-any-of-the-t-coupling-groups/4189/2 "2022-05-20T10:20:25Z")
> [@imrbay](#): > > 63 atoms are not part of any of the T-Coupling groups this error > [@imrbay](#): > > tc-grps = DNA SOL > [@imrbay](#): > > 6 Ion : 63 atoms There you have it. You have 63 ions, none of which are listed among `tc-grps`. You shouldn’t be using `SOL` in `tc-grps`, you should be using `Water_and_ions`. ---
**Author:** ![mirjr](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mirjr/32/2067_2.png) [@mirjr](https://gromacs.bioexcel.eu/u/mirjr)\ **Post date:** [April 12, 2023, 3:53pm UTC](https://gromacs.bioexcel.eu/t/63-atoms-are-not-part-of-any-of-the-t-coupling-groups/4189/3 "2023-04-12T15:53:57Z")
> [@jalemkul](#): > > There you have it. You have 63 ions, none of which are listed among `tc-grps`. You shouldn’t be using `SOL` in `tc-grps`, you should be using `Water_and_ions`. This code didn’t work for me ---
**Author:** ![mirjr](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mirjr/32/2067_2.png) [@mirjr](https://gromacs.bioexcel.eu/u/mirjr)\ **Post date:** [April 12, 2023, 4:02pm UTC](https://gromacs.bioexcel.eu/t/63-atoms-are-not-part-of-any-of-the-t-coupling-groups/4189/4 "2023-04-12T16:02:33Z")
It worked when I set `tc-grps` to `system`. ---
**Author:** ![Sadia](https://avatars.discourse-cdn.com/v4/letter/s/ea666f/32.png) [@Sadia](https://gromacs.bioexcel.eu/u/Sadia)\ **Post date:** [July 14, 2023, 6:17am UTC](https://gromacs.bioexcel.eu/t/63-atoms-are-not-part-of-any-of-the-t-coupling-groups/4189/5 "2023-07-14T06:17:25Z")
Hello mirjir I am also facing similar error as you were facing I am unable to solve this issue while running equilibration steps of MD simulation the error appeared which says 59196 atoms are not part of any of the coupling group . I will be grateful to you if you help me in fixing this error. I am beginner in MD simulation and don’t know much about this Thank you in advance