[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

[Chitrita Dutta Roy]

I am performing grompp for md simulation after position restrained MD.
Before final md simulation by grompp I have made pr.ndx file and did
necessary corrections in it to insert added Na+ to be counted properly. But
after running the following command -

grompp -f md.mdp -c pr.gro -p scr8.top -o md.tpr

the output came:

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA+'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:  2670      OTHER residues
There are:    28    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...

-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: readir.c, line: 1050

Fatal error:
2 atoms are not part of any of the T-Coupling groups
-------------------------------------------------------

Even the .top file was also modified to include extra Na+.


Please help to get a solution.


Chitrita..
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