[gmx-users] Grompp error

[Anton Feenstra]

Andrea Carotti wrote:

>> 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)

Please note, that in general it is not necessary to couple water (SOL) 
and solvated ions (NA+) separately. Depending on how many ions there 
are, and their distribution over the box, it may even lead to artefacts.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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