Re: DOF during alchemical simulations

From: Jérôme Hénin (
Date: Thu Nov 26 2015 - 12:00:01 CST


I might be missing something, but I'd say the degrees of freedom of
non-interacting particles should be counted for the purpose of kinetic
pressure calculation.


On 25 November 2015 at 17:31, Brian Radak <> wrote:

> After some griping about this, I've finally implemented a (preliminary)
> correction to the Lennard-Jones tail correction that accounts for
> alchemical modifications. Once this is integrated with other improvements
> to the alchemical code, I hope this will become part of the 2.11 release.
> However, I recently noticed that a similar problem crops up in the degrees
> of freedom calculation. That is, alchemical atoms get counted at the
> endpoints even when they are only ideal gas particles. This was obvious
> when I started double checking single coordinate endpoint energies and
> pressures with dual coordinate alchemical energies and pressures; that is,
> the energies match but the pressures do not quite match.
> The error is admittedly much less than 0.1%, as multiplying a "more
> different" large number by a small number is still just another "kind of
> large" number. Nonetheless, one could view this as an error in the
> specified target pressure for an alchemical simulation (i.e. the pressure
> you input is not the pressure you simulate). Then again, this behavior
> might be exactly what one is expecting, depending on how one draws the
> thermodynamic cycle.
> I guess my question for the community is, does this matter? How do people
> expect degrees of freedom to be determined? Do people usually draw their
> cycles such that non-interacting particles should not contribute? This
> might not be the case, for example, in ligand binding calculations where
> the ligand continues to interact with its own images (although in that
> case, one essentially has two simulations going at the same time when the
> ligand is decoupled).
> Brian
> --
> 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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