From: Reza Namakian (
Date: Mon May 01 2023 - 09:04:06 CDT


I have generated a fully periodic 2D perovskite material with a PDB
extension, and I intend to utilize topotools to produce topological
features for conducting MD on LAMMPS. For additional information, I have
included the PDB file.

However, when I inspect the periodicity of the box along the Y-axis using
VMD, I notice some bonds are absent in that direction. Upon using
topotools, I encounter the same problem after examining the LAMMPS data
file that has already been created in OVITO. Interestingly, when I view the
same PDB file in OVITO, the periodicity appears to be preserved by
duplicating the cell along the Y-axis, and no bonds are missing.

Could someone kindly assist me in resolving this issue?

Best regards,


  • application/octet-stream attachment: n2.pdb