special_bonds with multiple atom types in one molecule

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1

I am having problems getting special_bonds to work when I have two or three types of beads in one molecule. I want to use “special_bonds lj 0.0 1 1”

The simulation doesn’t crash but hangs on the first step and there are no error messages. The Van der Waals energy, total energy and potential energy on this first step are all extremely high but but the bond energy seems normal. Some times it does crash with “bond atoms missing”. When I run the system without special bonds everything works fine. I am using class 2 bonds, fix langevin and fix nve.

Thanks,

A LAMMPS user

2

The special_bonds command doesn't really have anything to do
with the types of atoms. It only has to do with whether
they are bonded or not, and by how many bonds two atoms
are separated. If you are getting huge forces/energies then
you are likely computing a pairwise interaction bewteen two
overlapping atoms. Special_bonds can turn this off, but
only if your bond topology is correct.

Steve