63 atoms are not part of any of the T-Coupling groups

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1

GROMACS version: version 2020
GROMACS modification: Yes/No
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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 ?

2

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.

3

This code didn’t work for me

4

It worked when I set tc-grps to system.

5

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