[gmx-users] Not enough ref_t and tau_t values!

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 7 15:04:44 CET 2006

Hi Miguel,

and then tried to make the index file again from the latter file. It
> didn't work either. But I thought the problem might be in the 'pdb'
> structure file produced by mdrun.
> Could this happen?


Is it possible that the three groups you give don't cover all the atoms in
your system? Besides, don't couple a handful of sodium atoms to a private
heat bath. Check the mailing lists... This has passed so many times. In your
case, go for two groups: Protein and Non-Protein, for which you don't need
an index file in the first place.

> Miguel




Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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