I am not sure what could be wrong. But many things could be wrong. It may be a problem with your input.
- Check whether all the force parameters are right.
- When you say you are relaxing the system, do you have abnormally large bonds ?. Try visualizing your data file.
- What is your initial potential energy of the system ?. Do you have overlaps ?. Are you using periodic boundary conditions ?. Are you minimizing the system prior to equilibration ?
- When you say simulation runs fine for how long ?. what is the time step ?. How fast is the simulation box shrinking ? How are you assigning velocities to the atom ?
If the problem persists after checking the above, please post the output from lammps.
Thanks
Arun