[gmx-developers] Re: [gmx-revision] pair types for free-energy decoupling
hessb at mpip-mainz.mpg.de
Wed Mar 1 09:30:25 CET 2006
Michael Shirts wrote:
>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.
A typo indeed.
It should be:
except that it only USES the ....
>>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
The idea is that for the solute to be decoupled one would replace
the in its [ pairs ] section type 1 by type 2
and exclude all intramolecular non-bonded interactions and replace
add them again explicitly in a [ pairs ] section as type 3.
The standard 3.3 mdrun already subtracts the PME mesh contribution
to the force, energy and dH/dl for exclusions, so there is no double
BTW I tested it and it works.
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