I want to delete the overlap between two water boxes.
I have uesd the command "delete atom seli ( .byres. ( segi sol .and. type o1 .and. ( ( .not. segi sol .and. hydrogen ) .around. 2.6 ) ) ) end"
where sol is the new water box which is translated anong bilayer normal & make an overlap of 6A with the previous water box.But after deletion a gap is generated at the interface of two boxes,smaller but a significant gap persist even if the deletion distance is reduced to 2.4. Can I further reduce the distance to 2.2 or 2 or use another command? Any suggestion will be highly appreciated.