Payman Pirzadeh wrote:
Yes and no!
Sometimes there is an overlap, but sometimes I could find nothing! In the
simplest case, how can we avoid overlaps in a way that the crystal structure
is maintained under pbc?
Can the option "-dist" help here?
Replicating a box that was not designed for periodicity will always have
this problem. Whether the box is too small or two large, there will
either be steric clashes, or vacuums that will need filling. The general
solution is to equilibrate your box under PBC prior to replication. Now
the box size and the atomic spacings will be plausible, and the
replication will not of necessity introduce artifacts.
Mark
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