Problem with bonds that cross periodic boundaries

LAMMPS doesn’t find the bond partner and so the bond effectively doesn’t exist.

How do you know this ?

Are you measuring the bond energies ?


I haven’t printed out the bond energy of the “missing bonds”, but I think I see your point.

When I wrote that the bond doesn’t effectively exist, what I meant is that the two atoms in the missing bond pair behave as though there is no bond present between them. Specifically the distance separation between them is no where near that of the mean bond length for that bond type- after unwrapping the coordinates. This is in contrast to what happens when I run the same input deck in which the simulation box size has been increased. In this case, the bonds that previously crossed a periodic boundary no longer do so and the formerly problematic bonds quickly form as the atoms are dragged to interatomic distance that is consistent with that bond type. So, my I think my question is really about how to pin point to origin of this behavior. I’ll try see if I can print out the bond energies of the missing bonds and see if something interesting appears in the output. Thanks- Vanessa