lammps-users Digest, Vol 107, Issue 99

Salam Siavash,
An option that you could do would be run the simulation without minimization, but with a

fix 1 all nve/limit 0.00001

and then gradually increase it, this way your simulation won’t blow up and you will end up with realistic distances. Let me know if that works for you.
Cheers, Vasiliy