I know about the ‘[ exclusions ]’ section you can introduce to a topology file, but my impression is that it turns off all interactions between the specified atom pairs. Is it possible to selectively turn off only the coulomb interaction between selected sets of atoms, and leave the LJ alone?
I suspect this might be possible with input similar to FEP, using A,B columns in input PDB files, but I was trying to achieve this in the ITP/topology if possible.
I think see a way to do this - there is a user-define potential function where it looks like I could just keep only the standard LJ contribution (this is described in the section on tabulated functions). Moreover I can use energy groups to apply the modified potential only to selected subsets of atoms.
Do you see any obvious problem with that? I am going to try to work it out.