Re: DOF during alchemical simulations

From: Aron Broom (
Date: Thu Nov 26 2015 - 12:28:27 CST

This is really interesting. My knowledge of alchemical transformations in
limited, but given their successes I'd like to understand more (and will
happily be corrected on my errors in thinking).

If you leave those degrees of freedom in, then the end-point simulations
are actually different than a similar simulation of that system where you
aren't doing an alchemical transformation. That raises for me a kind of
intuitive red-flag, which I think is the same point you are making? But on
the other hand, if at the end-points you suddenly eliminate those degrees
of freedom completely, doesn't that create a discontinuity in the
transformation, which is a bad thing and source of much misery?

Probably an idiotic question from someone with limited physics
understanding, but I suppose non-integer degrees of freedom are disallowed
(assuming similar fractional counting of mass and velocity)?

On Thu, Nov 26, 2015 at 1:00 PM, Jérôme Hénin <> wrote:

> Brian,
> 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.
> Jerome
> 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--047d7b3a9c76ae521d052575bd84--

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