I am running a reaxff simulation, I generate the data in vmd. First, I build the model in Material Studio ,then i transform the model in vmd. My bonds are all defined in Material Studio.
that may well be, but they must not be defined when you are doing a
simulation with a manybody potential like reaxff, where bonds are
implicit and dynamically computed by the force field itself. didn't
you see the corresponding warning that LAMMPS printed out?
Also, there is no point running dynamics when you are failing to converge fix qeq/reax on timestep zero:
WARNING: Fix qeq/reax CG convergence failed after 200 iterations at 0 step (…/fix_qeq_reax.cpp:713)
Just use ‘run 0’ to debug your initial set up.