[gmx-users] Grompp error

[Andrea Carotti]

> I've been trying to find correlation between the
> ligand and some residues of the protein.
> Then, I did the indexfile with them.
> But when I try to run grompp with the md.mdp,
> gromacs give me the follow error:  Fatal error:
> Not enough ref_t and tau_t values!
Dear Monique, probaly there is a problem in your md.mdp file.
in the section where you define the weak coupling, must be present all the 
groups of your system.
Look at this example
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = yes
; Groups to couple separately
tc_grps                  = Protein SOL NA+
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1 0.1 0.1
ref_t                    = 300 300 300

As you can see, this a system made of a protein, water and an Na+ ion.
Now you must define it to match you system, (a look at the groups in your 
index file will help you)
I'll hope this help you
Andrea