[gmx-users] gmxdemo: peptide to real protein and boom

[Tamas Horvath]

Check out what groups you have. The values at tau_t and ref_t refer to those
groups.
In the default case, in the demo, those refer to "protein" and "SOL" groups.

On 2/14/06, David Mathog <mathog at caltech.edu> wrote:
>
> I'm still struggling with gromacs.  The gmxdemo script runs.
> So I tried to scale up a bit and chose more or less at random a
> protein with some CYS-CYS bonds (H2MCM.PDB) and tried to plug it
> into the gmxdemo script instead of "cpeptide".
>
> No Joy.
>
> It eventually comes completely off the rails at the grompp pr section
> where it comes up with this gem:
>
> Fatal error:
> Not enough ref_t and tau_t values!
>
> pr.mdp has these lines:
>
> tau_t         =   0.1    0.1
> ref_t         =   300    300
>
> which are straight from the gmxdemo script.
>
> The 3.2 manual has no matches on "tau_t" or "ref_t".
>
> It looks like the programs wants more columns on these lines, but
> how many, and why that many???
>
> Thanks,
>
>
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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