[gmx-users] pairlist and nonbonded parameters; a bug?

[David Mobley]

Dear All,

As best I can tell from the manual, the [ pairs ] section allows
manual specification of interaction parameters between pairs of atoms
and is normally used to modify 1-4 interactions.  However, it seems to
not be functioning as advertised.

Particularly, I've been trying to figure out how to turn off only
intermolecular interactions while leaving intramolecular interactions
on using the pairlist, as I mentioned previously. I still haven't been
able to figure out how to do this, but instead, I tried a simple test:

- Put two LJ spheres in vacuum.
- Use the pairlist to specify that there are no interactions between
the two (setting interaction vdW parameters to zero).
- Perturb the vdW parameters of one of the atoms to zero

The free energy of doing this should be identically zero if the two LJ
spheres are noninteracting, as should the potential energy (the
charges are turned off).

Instead, I get nonzero potential energies and dv/dlambdas (thus free
energies) for any calculation which involves perturbing the vdW
parameters, and even if I don't perturb the vdW parameters, I get
nonzero potential energies. So clearly the pairlist isn't working to
set the interaction parameters.

Can anyone help? Is there something else I need to set? Or is this
some sort of a bug? Should I attach my topology?

Thanks,
David