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
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