Hi Geo, this is a bit confusing because you are giving bits of information, but asking to validate a whole input. It is you and your direct collaborators who know the purpose of the computation, and it’s your job to divide them up into specific questions: for most of these you’ll find the answer in the doc. For a few of these specifically, a question on the forum may help.
The distanceXY function computes the distance from the axis that passes through the center of mass of the ref group. The direction of that axis is by default parallel to the Z axis. For cylindrical symmetry, the lowest possible value of distanceXY is zero, when main and ref both lie along the axis. If you want to confine main to be within a cylinder of given radius, use that radius as upperWalls for a walls restraint.
Most importantly, there are two things you need to be careful about with GROMACS:
- Please use either Å or nm consistently, be explicit about your choice when you are asking for help and please only use nm in GROMACS, as that’s the unit that it uses.
- I already mentioned that the unit cell for GROMACS has a corner on the origin, but its center is (Lx/2, Ly/2, Lz/2). I don’t know what’s in your unit cell but you may have to adjust that setting.
Giacomo