Dynamic Indices

From wiki.gromacs.org

For most analyses we use index files containing atom numbers, e.g. the atoms used for the RDF calculation. Since we want to bring this to a new level of abstraction we'd also need something like "dynamic indices", such that one at each step determines, e.g. which are the oxygen atoms in a protein. This is necessary when the number of atoms is dynamic as well.

This project involves merging make_ndx functionality within all analysis tools.