Lennard-jones cut-off
It's hard/impossible to pinpoint the reason for your problems without seeing the  code and knowing which terms you use. If you feel like sharing it, then you should probably head over to Computational Science and make a post there.

A few general things come to mind:


Check that you have $\sigma$ and $\epsilon$ values inserted in the correct order.
Check the correctness of the combination rules you are using. It seems the force field you linked previously contains noncovalent terms from OPLS/AA. Make sure that the rest of the FF is compatible with OPLS/AA.
Check the units you are using, and make sure they are all the same. Probably won't make your simulation blow up, but it's still worth to take a look, especially if you are using parameters from different FFs.