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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 .

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    $\begingroup$ Please describe the system you are trying to simulate. What exactly does 'blow up' refer to? If it is uncontrollably high energies, then you probably will not benefit at all from having a low value for the cut-off, since the energy from LJ-potential grows only when the intermolecular distances are small. $\endgroup$ – Bdrs Feb 19 '17 at 11:19
  • $\begingroup$ Still need more info: Which forcefield are you using? If you are not using any general FF, then please point to the source where you are getting the parameter values. Which simulator are you using, or are you doing the calculations yourself? Which molecules are you trying to simulate? Are you simulating them in a solvent, or in vacuum? Do all of the particles have LJ-sites? Also, please elaborate on the 'blowing up'. If you are using any standard MD software (GROMACS, DL_POLY etc.) you should be able to see which energy term(s) grow unphysically high. $\endgroup$ – Bdrs Feb 19 '17 at 11:51
  • $\begingroup$ I am building my own simple force field in python, using parameters from : github.com/labello/amberff/blob/master/gaffparams.py . I am doing all the calculations myself .I hope to simulate simple molecules in vacuum like hydrocarbons . I am programming everything from scratch including the optimization method , the Lennard-Jones term keeps getting very large $\endgroup$ – Mac Sat Feb 19 '17 at 13:10
  • $\begingroup$ LJ potentials should get really large only if distances are small. Maybe that's what you got? $\endgroup$ – Felipe S. S. Schneider Feb 20 '17 at 12:16
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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.
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