Hello Everyone, I have MD consist consist of four graphene filled with crosslinked epoxy on both sides. I want to study the half system consist of two graphene with epoxy on one side. For that, I select the atoms half of box. Then, deleted.

Due to periodicity and epoxy have bond with other side of epoxy so I updated the hydrogen. Later, when I changed the Z direction from 118 to 70. some epoxy molecule have come out across graphene. Why is this happening? How can I get half MD system correctly?

Thanks,