fix bond/create command

Dear Lammps Users,

I’m working grafted-CNT and “fix bond/create” command is applied.
By the lammps script, I got grafted structure. In my simulation box, there are two molecules, one is CNT, another is 1-proponal.
I have script:
fix 1 all npt temp 300.0 300.0 100.0 iso 100.0 100.0 1000.0
fix 2 all bond/create 1 1 2 1.2 2 prob 1.0 85784
thermo_style custom step temp pe etotal press vol density f_2[1] f_2[2]

to compute the grafting system. However, in this system, the carbon at CNT is not only bonded to type 2 carbon at 1-proponal, but also bonded to the hydrogen which is related to type 2 carbon at 1-proponal.

I’m trying to understand what happened in the grafting system. I think the restriction of bonded is applied by “fix 2 all bond/create 1 1 2 1.2 2”, only type 1 and type 2 would be boned, and there should be nothing happened to hydrogen atom at 1-proponal (the atom type of hydrogen is 5, and not mentioned in whole script). And the thermal style also count the new bond which is 1 in the whole simulation. Can any bond help me out of this problem? Thanks!



Hi Kerwin,

If you attach the example, including the data file, I can help troubleshoot.