Suppose I define an orthogonal simulation box with random distribution of
atoms inside. Can i apply pbc on one side of the simulation box? It seems
to me that to apply pbc, we need exactly the same configuration of atoms
on both sides.
Can i apply pbc on one side of the simulation box?
No you can’t and that don’t make sense. Let say your box is defined from 0 to 20 along the X direction. If you apply PBC along the X axis they are applied at both positions 0 and 20, i.e. two sides.
It seems to me that to apply pbc, we need exactly the same configuration of atoms on both sides.