For the record, in case if you refer to this issue with index group names:
that issue specifically was due to having used spaces inside a group’s name.
The GROMACS index group format (as produced by e.g. make_ndx) does not allow for spaces. The main difference between GROMACS and Colvars when a space is there is that GROMACS will just read everything up to the first space to use as the group’s name and discard the rest, whereas Colvars will raise a parsing error.
Giacomo