DOF during alchemical simulations

From: Brian Radak (
Date: Wed Nov 25 2015 - 10:31:11 CST

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

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 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

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