[gmx-users] Constraining a small molecule in a region

[ehsan shahini]

Dear all,

For the study of adsorption properties of a small molecule on a substrate
(such as graphene), I would like to constrain the spatial mobility of the
small molecule into a small cylindrical (or cubic) region so it can only
move inside the region. A schematic image of my problem is attached. The
entire simulation box is filled with an explicit water model and PBC in XYZ.

How can I define this region in GROMACS?

I was wondering if introducing a condition in the source code of mdrun
could make it possible. That said, if any atom of the small molecule
crosses the defined region then we get back a step and start the
calculation for this step again. Is it possible?

Kind regards,
Ehsan.