# How to overcome gromacs make_ndx automatic ranking of atomic indexes?

When working with gmx make_ndx I found very annoying the fact that atomic indexes are automatically ranked in the outputted index .ndx file. No matter how the selection is provided, the list of indexes in a group is always ranked.

This is particularly problematic when building indexes for things such dihedral angles, where the ranking is obviously critical.

Is anyone aware of a way to avoid this automatic and un-necessary ranking in the indexes?

• It strictly requires a tpr file as input, while make ndx also accept gro files to build indexes. Jan 28 at 9:48