Fix bugs in gmx dos

- Velocity autocorrelations were not normalized
  by default, so they did not agree with gmx velacc.
- The normalize option had no effect on the VACs.
- The index group option was available, but no
  index groups were processed.
- Since the DoS is calculated from the mass-weighted
  VAC and by default only from the real part, it was
  not clear why these results would differ from data
  obtained with gmx velacc. There is at least a note
  about this now, and more docs will be added in the
  future.
- The hidden option to dump some plots has been
  removed since it was not documented what these
  contained (beyond a paper reference), and the
  contents was not based on any data from the
  trajectory, but rather plotting a custom function.

Fixes #1608.

Change-Id: Icfca060f94efb34bd7871bd90245ab0ddbbe91c1