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

[Tsjerk Wassenaar]

Hi Chitrita,

You'll have to make sure that whatever t-coupling groups you've
specified (referring to groups in pr.ndx) together capture all atoms.
This stands apart from the topology and coordinates. If you're not
sure, paste the temperature related mdp options for us to be able to
help you further. Besides, it seems you're using an old (< 4 .mdp
file) with gromacs 4.

Cheers,

Tsjerk

On Tue, Mar 10, 2009 at 8:45 PM, Chitrita Dutta Roy
<chitrita.md at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623