Upper and lower leaflets switch positioning

[MishterBluesky]

Dear TS2CG team,

I have loved ts2cg, it works in general however there seems to be one flaw,

What happens when you have two layers of bilayer and the upper and Lower leaflets switch?

I have provided a good .tsi file, (which is oriented in the x plane rather than z if this may make a difference) and looking at the resulting .gro files, the lipid insertion works, however the inner and upper leaflets cross at two places, resulting in artifacts when later taken to sim.

How might I be able to fix this issue? or alternatively manually get around this issue with deletion of points at the pointilism step if possible.

[MishterBluesky]

In reality its more an Inner and outer leaflet set, inner for all phosphates between the two planes, and outer for any that are on the outer edge and accessible by these waters, however its crossed over without good reasoning in an attempt to make a bilayer

[MishterBluesky]

This configuration makes sense as a vesicle, however how can we let two bilayers interact in pores such as this?