I have polymer chains and nanoparticles in my system and all the bonds are FENE. When I run the simulations, it gives me an error saying that the FENE bond is too long. MY monomers are separated by a distance of around 1 (0.966474 LJ units) and I want it to be that distance apart. Can someone suggest me what could be done to rectify this.
It seems to me that there are overlapping atoms in your system. Run a short simulation (around 20 in units of LJ time, or maybe more depending on the overlap) using soft pair style (see lammps doc) while keeping the FENE bonds. Swith on the full LJ potential once this is done and all should be ok.