Thank you, Steve.
Physically, what I am dealing with is reversible bonding like hydrogen
bonding, but with larger association energy, hence longer lifetime (0.1
second or so). Althrough the associcating energy ( much lower than
covalent bonding energy) is the same during the simulation, the atom may
escape when the temperature is high, that's, the "bond" is broken. At
the same time, new bonds come into being when such kind of atoms
encounter each other.
In the frame of LAMMPS, I choose Morse potentials for this reversible
bonding, is this a good choice? My concerning is, is it feasible to
contol the direction of such reversible bonding by adding restraint to
the angle or dihedral where it is involved. As you can see, those
"bonds" are not fixed.
Hope it is clear, thanks again.