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

[David Mathog]

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