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I am trying to run a molecular dynamics simulation with AMBER forcefield. However, it's the first time I use is, and while I know the form of the various intra- and intermolecular energy terms, some details are not clear to me. So, for the AMBER forcefield:

  • What pairs are excluded in the summation of intramolecular Lennard-Jones interactions? Typical choices are “excluding bonded atoms”, “excluding 1-2 and 1-3 pairs”, “excluding 1-2 and 1-3, applying a factor 1/2 to 1-4 pairs”, and “excluding 1-2, 1-3 and 1-4 pairs”.

  • For torsion potentials, is the potential scaled by the number of such torsions? (as is done in the DREIDING forcefield, to ensure a constant torsional barrier for the central bond)

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As for your first question, this site states that 1-4-interactions are scaled by a factor of 0.5, which I suppose implies 1-2 and 1-3 interactions being excluded.

The answer to your second question is yes, as can be seen here (section TORSIONS). The potential is divided (and thus scaled) by Ntors.

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