Dear gromacs users,
I am preparing topology for a small molecule. I have prepared the itp file using acpype for generalized amber forcefield. In moleculetype definition it is used: nrexcl = 3, i.e. excluding non-bonded interactions for atoms separated by less than three bonds. Then again we are using another directive [pairs] where possible pairs are defined explicitly. My question is in this case where we have nrexcl = 3 as well as [pairs] defined, are the non-bonded interactions double counted?
One more question is that: sometimes we parametrize the protein and ligands separately. For example: for the protein I am using amber99 forcefield and there in the forcefield.itp we have: gen-pairs = yes
When we include the ligand itp file where the pairs are explicitly defined, does the gen-pairs = yes reassign the pairs or double count them?