[gmx-users] about T-Coupling groups

[Mark Abraham]

Rui Li wrote:
> Dear all,
> I want run a Position-restrained dynamics simulation for my system
> and I write a pr.mdp file.
> 
> below is part of the mdp file:
> 
> Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.1       0.1     0.1
> tc-grps             =  Protein   SOL     Cl
> ref_t               =  300       300     300

We discussed why this was a bad idea just last week.

> When I use grompp, it warns:
> 
> Fatal error:
> 149 atoms are not part of any of the T-Coupling groups
> 
> what's wrong with it?

You have 149 atoms that are not in Protein, SOL or Cl. All atoms must be 
T-coupled if any atoms are T-coupled.

Mark