Re: DOF during alchemical simulations

From: Brian Radak (
Date: Tue Dec 01 2015 - 10:08:08 CST

On 12/01/2015 08:19 AM, Hannes Loeffler wrote:
>> 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
> thread).
> 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.
This is correct. You effectively have two systems in the same box. I
believe this can involve as many as 5 PME grids, although some of these
are very inexpensive, for example a small ligand interacting with its

> 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.
> couple-intramol:
> no
> 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.
> yes
> 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.
Thanks for brining this up. It would make good sense to see how the rest
of the community handles this also.
> Many thanks,
> Hannes.
> --
> Brian Radak
> Theta Early Science Program Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue
> Building 240, 1.D.16
> Lemont, IL 60439-4871
> Tel: 630/252-8643
> email:

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