Thanks for your reply.
You and Steve told me that one needs to explicitely define all the bonds.
Ray replied that it depends on the potential, whether it is able to
determine bonds by itself or not, that is whether it is of reactive type or
So i am still confused !!
I am still wondering if, using the REBO potential, because it is of reactive
type, I do need to define all bonds !
What do you think about that. ?
I think you are right. You don't need to define a list of BONDS (or
angles or dihedrals, etc..) for your system if you use AIREBO/REBO.
The AIREBO/REBO potentials for hydrocarbons that Ray recommended
are one of the many potential styles available in LAMMPS. It sounds
like AIREBO might be useful for the simulation you want to run, and
it's certainly cheaper than running a quantum mechanical simulation.
However there are probably many other ways of doing this. (You may
want to try running a quantum chemical simulation?) (I confess I
don't know the best way to run a simulation containing radicals.)
Hopefully you can discuss the simulation with someone who can advise
you what type of simulation you need to run.
The approach Steve and I were proposing is more common. If you
want to link a atoms together in a strong way which prevents the bond
from breaking, then you would create a DATA file containing a "Bonds"
section which has list of pairs of atoms which are bonded. These atom
pairs can not be separated later (unless you use the fixbond/break
This is useful because the forces acting on atoms which have been
bonded together this way can be highly customised (finely tuned) using
many different 3-body angle and 4-body dihedral/improper forces,
including tabular (spline) forces.
It sounds like perhaps REBO/AIREBO approach might be better for you.
Incidentally. LAMMPS you can also use multiple force field styles
together (using pair_style "hybrid",
http://lammps.sandia.gov/doc/pair_hybrid.html), using REBO/AIREBO for
the atoms which need it, and using unbreakable bonds for the atoms
which don't. (This kind of simulation is a little more difficult to