[gmx-users] Grompp error
feenstra at few.vu.nl
Wed May 11 13:35:32 CEST 2005
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.
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