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

[Tsjerk Wassenaar]

Hi Chitrita,

> I am not very clear about the parameters used in mdp files. So I am sending the mdp file here.

This is of course vital when performing simulations. Do read up on these things.

This is the part of the .mdp file that determines the how and what of
temperature coupling:

> ; Berendsen temperature coupling is on
> Tcoupl                =  V-rescale
> tau_t                 =  0.1    0.1
> tc_grps               =  Protein    SOL
> ref_t                 =  300        300

It says that you have two groups for temperature coupling: protein and
solvent. It doesn't say ions anywhere (and it shouldn't actually). You
may want to use Protein and Non-Protein. Check the archives and the
wiki on the how and what.

Cheers,

Tsjerk

-- 
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