Creating index for diferent timestep

GROMACS version: 2020.3
GROMACS modification: No

Dear community,

I intend to do hydrogen bond analysis and other analyzes only to a specific region of the simulation box. As a subbox of the main box. Hence I only need to use the tools within that subbox.

Is it possible to do that through make_ndx ?, Obviously the problem is that the indices would change over time because different molecules enter and leave that subbox. Therefore also my question is whether gmx hbond and other tools can read indices that change over time.

kind regards

You would have to create per-frame index groups using gmx select, which is the only tool that can generate such groups based on geometric criteria. The subsequent analysis in gmx hbond would have to be done on individual frames, one at a time, using the corresponding index file for each frame.