I am currently receiving this error while attempting to cross-link a polymer system. I utilize a static method in which I run a program to cross-link atoms within a specified cut-off distance. This distance is only 4 Angstroms, and my box size is much larger than this. I have written the program to recognize periodic boundaries and cross-link atoms accross them if they are within the cut-off. From what I can gather about this error (I am still very unclear how it works and what it prevents), I think that I am creating bonds/angles/dihedrals across periodic boundaries and lammps is not able to recognize this. I run the crosslink program on dump files generated from previous simulations. I do not change the coordinates of any atoms after the crosslinking process. Is LAMMPS able to identify whether or not a bond should be created across a periodic boundary? Any help with this error, or suggestions on how to get around it would be greatly appreciated. I was thinking I might run a minimization with only new bond data after crosslinking and then add the angles and dihedrals after the system is minimized using only bond data…Thoughts?
Thanks a million,