The simplest approach is to define the atoms as separate groups in gromacs and write out their coordinates. You can then even use excel to analyze distances and angles, etc.

1. Measure the relevant distances and angles.

2. Set distance and angle cut-offs.

3. Calculate the occupancies (% of the trajectory).

First you have to make index file of atoms or groups of interest using gmx make_ndx. Then use basic commands like gmx distance, gmx analyze etc. to calculate distance and probabilities of salt bridges.

For hydrogen bonds gmx hbond will serve the purpose. For specific time, use -b and -e flag. For example:

gmx make_ndx -f *.gro -o index.ndx

gmx distance -f *.xtc......etc -b 0 -e 100000

gmx analyze -f *.xvg (generated in gmx distance) -dist distribution.xvg