Re: DOF during alchemical simulations

From: Hannes Loeffler (
Date: Tue Dec 01 2015 - 08:19:00 CST

> My thought was that the degrees of freedom ought to depend on the
> decoupling scheme (alchdecouple on/of), as this determines whether or
> not the annihilated atoms see their images (exist as a periodic "gas")
> or not (are an ideal gas molecule).

Sorry, if I don't really contribute to this discussion (and answering
to the wrong email because I have deleted all other emails in the

But this got me a bit confused now. Does this mean that when
alchdecouple=on (the decoupling case) the non-bonded interactions with
its environment are scaled, the intra-molecular non-bonded
interactions are not scaled but the decoupled molecule would still see
its images? In the annihilation case (alchdecouple=off), all
non-bonded interactions are scaled and there's nothing to see anymore
at the end point.

I have just read in the Gromacs manual about the analogous (is it
really?) option which seems to me that in the "no" case (see below)
interactions with the images are explicitly switched off.


  All intra-molecular non-bonded interactions for moleculetype
  couple-moltype are replaced by exclusions and explicit pair
  interactions. In this manner the decoupled state of the molecule
  corresponds to the proper vacuum state without periodicity effects.

  The intra-molecular Van der Waals and Coulomb interactions are also
  turned on/off. This can be useful for partitioning free-energies of
  relatively large molecules, where the intra-molecular non-bonded
  interactions might lead to kinetically trapped vacuum conformations.
  The 1-4 pair interactions are not turned off.

Many thanks,

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