[gmx-users] default groups

[Valentin Gogonea]

Dear Gromacs users:

I am trying tu use the freezegrp option. I defined an .ndx file that 
contains one amino acid from a small peptide which I want to freeze 
during MD. Grompp complained that the Protein group is missing in the 
.ndx file. My questions are:
1) Where are the default groups defined?
2) Do I have to add the default groups to may index file?
3) How do I do that? Using make_ndx?

This is the command that I used:

grompp -f md -c ${MOL}_b4md  -p ${MOL} -o ${MOL}_md -n ${MOL} >& ! 
output.grompp_md

Here is the error that I got from grompp:

initialising group options...
processing index file...
Fatal error: Group protein not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the 
'-n' option of grompp.
In that case use the '-n' option.

I would appreciate any comment or suggestion.

Thank you.

Valentin