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

Tamas Horvath hotafin at gmail.com
Tue Feb 14 20:16:54 CET 2006

Check out what groups you have. The values at tau_t and ref_t refer to those
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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060214/233fb07a/attachment.html>

More information about the gromacs.org_gmx-users mailing list