I am using a Lennard-Jones potential in a computer simulation and I was wondering if i should place a cut-off for low distances since the potential blows up quickly making the calculations quite difficult. I am trying to simulate basic molecules ( few atoms ) , calculating bonds stretching , bond angle bending and lennard-jones interactions and trying to minimize the total energy to get an optimal structure prediction .
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.