**From:** René Hafner TUK (*hamburge_at_physik.uni-kl.de*)

**Date:** Fri Aug 27 2021 - 08:47:26 CDT

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Hi Jérôme,

alright, I'll try it like that!

Best

René

On 8/27/2021 2:05 PM, Jérôme Hénin wrote:

*> Hi René,
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*>
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*> ----- On Aug 26, 2021, at 8:52 PM, René Hafner TUK
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*> <hamburge_at_physik.uni-kl.de> wrote:
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*>
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*> Hi Jérôme!
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*>
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*> The way I extract it was to run second abf instance with only
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*> the distanceFromMembrane colvar that is **not** applied.
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*>
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*> Which turned out to be the same as when just weighting the
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*> zgrad(x,y,z) by the respective counts and average over X,Y.
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*>
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*> But we were wondering whether this is the correct way.
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*>
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*> I don't think that is correct, because the simulation is biased in the
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*> directions X and Y, so you are not computing an unbiased average at
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*> each z value.
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*>
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*>
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*> I even tried an easier setup with an almost flat membrane
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*> surface where I can compare results to a simple distanceZ
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*> variable.
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*>
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*> Here the distanceMin 1D case returns 4.6 (+. 0.1) kcal/mol
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*> (same as distanceZ)
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*>
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*> the 3D case returns dG = 4.3 (+- 0.1)
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*> kcal/mol (with the above assumption)
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*>
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*>
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*> Though what you suggest is to calculate the marginal
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*> distribution via the following?
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*>
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*> Just an integral instead of an average:
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*>
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*> What I additionally needed to do in order to gain a smooth
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*> curve here was to weight every grid point by its counts (such
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*> that "bad" guesses with low counts get suppressed). But I am
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*> not yet the sure the scale is correct.
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*>
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*> With the expression above you won't need to worry about that.
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*>
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*> Jérôme
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-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany

**Next message:**Gumbart, JC: "Re: Error: psfgen) unknown atom type H"**Previous message:**Jérôme Hénin: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**In reply to:**Jérôme Hénin: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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