Re: DOF during alchemical simulations

From: Brian Radak (bradak_at_anl.gov)
Date: Mon Nov 30 2015 - 09:36:55 CST

I'm glad this is intriguing rather than a non-issue. I agree that
whatever systematic errors are present are likely quite negligible.
Nonetheless, they can still be discerned from simple tests and I dislike
being incorrect when the right answer can be easily achieved.

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). Does it make sense for ideal gas
degrees of freedom to impact the pressure? My first thought would be
that they should not impact sampling at all; I believe manipulations
with ideal gas partition functions ought to confirm this is true.

Would it make sense to have different behavior when alchDecouple is on
or off? This would only meaningfully differ at alchLambda = 0,1, as the
intervening values are totally arbitrary, so long as sampling is not
grossly impacted.

Brian

On 11/27/2015 03:31 AM, Jérôme Hénin wrote:
> On 26 November 2015 at 19:28, Aron Broom <broomsday_at_gmail.com
> <mailto:broomsday_at_gmail.com>> wrote:
>
> 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?
>
>
> I agree with you on this. This is among the terms that we neglect when
> doing alchemical calculations in an isobaric simulations. If you
> decouple n particles among N and have a barostat set at pressure P0,
> you will generate an ensemble for the (N-n) particles at pressure P =
> P0 - Pn, where Pn is the kinetic pressure from just n particles at the
> given volume and temperature. If I get my orders of magnitude right:
> decoupling one particle in a thousand from a condensed phase will
> underestimate the pressure by (on the order of) 1 bar. That's
> something I can live with: I can say worse things about my simulations.
>
> 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?
>
>
> Unless you do TI, it's not a problem in and of itself: other
> estimators explicitly give FE differences between discrete states. The
> tricky part may be to account for that explicitly in the free energy
> estimator.
>
> 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)?
>
>
> Nothing prevents us from using a fractional number when calculating
> kinetic pressure, although it doesn't have much physical meaning.
> That's pretty much the spirit of alchemical transformations. Again,
> I'd be totally happy with it if the estimators were rewritten with
> that in mind.
>
> Jerome
>
> On Thu, Nov 26, 2015 at 1:00 PM, Jérôme Hénin
> <jerome.henin_at_ibpc.fr <mailto:jerome.henin_at_ibpc.fr>> 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 <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> 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 <tel:630%2F252-8643>
> email: bradak_at_anl.gov <mailto:bradak_at_anl.gov>
>
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>
> --
> 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: bradak_at_anl.gov

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