I am constructing a crystal structure, with periodic boundary conditions in each direction using LAMMPS. One of the potentials requires the use of angle_style and thus I have defined angles in the data file. (I have not defined any bonds though, since these are not required by the potential. But I don’t know whether I should do so in terms whether it would be better for LAMMPS)
Then I minimise the structure and obtain a lammps trajectory, when I view it with VMD I notice that some of the atoms go out from the top of the cell and re-appear at the bottom, as expected in a periodic boundary condition simulation.
The question is will LAMMPS account for this and adjust the angles accordingly? (as in VMD at least the atom seems to remain bonded with the previous atoms, resulting in bonds formed within the cell itself).
It is most probably a matter of visualization in VMD and has nothing to do with LAMMPS but I would appreciate a confirmation.