Issue 48: fix residue coordinates by aligning index group

[BerndDoser]

If the residue numbering is not continuously the assignment to the atomic coordinates can be challenging. Therefore, it is strongly recommended to use the renumbering feature during the FDA run (https://github.com/HITS-MBM/gromacs-fda#residue-renumbering). If this is not possible, what ever the reason may be, a workaround could be to align the index group.

In the example src/gromacs/gmxana/fda/tests/data/alagly/conf.gro alanine has the residue number 2 and glycine 3. It is possible to add an index group (e.g. C-alpha), which is in alignment to the desired atomic coordinate. Here: Residue 2 is using the coordinate of atom 5 and residue 3 of atom 15, which are the alpha-carbon atoms.

[ C-alpha ]
   1    1    5   15