lammps-users Digest, Vol 94, Issue 7


I would say that this looks like maybe a vmd question on the LAMMPS
forum. What you see in the visualization are the "bonds across the
boundary" problem. You can use the "pbc unwrap ..." or "pbc join ..."
commands in VMD to fix this if your initial model was correct. If your
initial model was not correct, you'll have to eliminate the "bonds
across the boundary" in your original LAMMPS model or *.psf structure to
correct this problem.