GROMACS version: 2020.3
GROMACS modification: No
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.