[gmx-developers] Re: [gmx-revision] pair types for free-energy decoupling

[Michael Shirts]

Hi, all-

I've been thinking about the free energy coupling changes.  First, I
had a question that Berk posted to the gmx-revision list

On 2/3/06, Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
> Added new pair type 2, which is identical to the standard type 1,
> except that it only the A-state charges and LJ parameters.

Could you restate this?  There appears to be a typo here, and I'm not
sure what the differences are with pair 3.

> Added new pair type 3, which use the non-scaled charges
> and the normal non-bonded parameters, also only from the A-state.

So, as I know understand it, if one were doing free energy decoupling,
which would be done with pair type 3, the atoms of the ligand would
always have the unperturbed interactions.  But if PME or Ewald is
being computed, won't the ligand intramolecular interactions also be
calculated using the scaled charges, leading to double-counding? 
Won't this need to be subtracted off with a separate Ewald
calculation?

Thanks,
Michael