**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Sat Aug 14 2021 - 12:17:53 CDT

**Next message:**René Hafner TUK: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Previous message:**René Hafner TUK: "eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**In reply to:**René Hafner TUK: "eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Next in thread:**René Hafner TUK: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Reply:**René Hafner TUK: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello René, can you confirm that you are using extended ABF, and more

specifically what estimator you used? (CZAR or Zheng/Yang).

Orthogonality between variables is only required for straight ABF, where

the force on the variable is obtained by projecting the atomic total forces

directly, rather than using the extended-mass trick.

Giacomo

On Sat, Aug 14, 2021 at 11:24 AM René Hafner TUK <hamburge_at_physik.uni-kl.de>

wrote:

*> Hi,
*

*>
*

*> I am trying to use a distance like colvar to sample a surface with a
*

*> ligand using extended ABF.
*

*>
*

*> In order to speed up the surface sampling process I turned the abf line
*

*> into a 3D one where I also sample the X and Y direction.
*

*>
*

*>
*

*> My colvar file roughly looks like:
*

*>
*

*> colvar { name X; distanceZ ... } # Ligand distance from Membrane Center
*

*> in X direction
*

*>
*

*> colvar { name Y; distanceZ ... } # Ligand distance from Membrane Center
*

*> in Y direction
*

*>
*

*> colvar { name distanceFromMembrane} # Ligand local distance from Membrane
*

*> Surface (selfdefined)
*

*>
*

*> abf { colvars X Y distanceFromMembrane; ... }
*

*>
*

*>
*

*> This means the third variable is not independent from/orthogonal to X and
*

*> Y but that shouldn't be and issue when using eABF.
*

*>
*

*>
*

*> Comparing 1D run and 3D run (averaged the 3D PMF over X,Y to get
*

*> PMF(distMembrane) )
*

*>
*

*>
*

*> * When I did 1D sampling ( only distanceFromMembrane) I obtained rougly
*

*> 5.5kcal/mol as dG (difference from Minimum to a point far away from
*

*> Membrane)
*

*>
*

*> * When I do *3D sampling* using "subtractAppliedForce *on*" *in all 3
*

*> colvars* I obtained dG ~ 4kcal/mol. (I used the term
*

*> "subtractAppliedForce" because I initially used metadynamics +eABF)
*

*>
*

*> * When I do *3D sampling* using "subtractAppliedForce *off*" *in all 3
*

*> colvars* I obtained dG ~ 1-2kcal/mol.
*

*>
*

*>
*

*> *What is the correct way to sample non-independent variables with proper
*

*> guesses?*
*

*>
*

*> (I expect the 3D to reconstruct the 1D sampling case when done correctly
*

*> and just help improving the sampling of the whole surface)
*

*>
*

*>
*

*> Kind regards
*

*>
*

*> René
*

*>
*

*>
*

*> --
*

*> --
*

*> Dipl.-Phys. René Hafner
*

*> TU Kaiserslautern
*

*> Germany
*

*>
*

*>
*

**Next message:**René Hafner TUK: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Previous message:**René Hafner TUK: "eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**In reply to:**René Hafner TUK: "eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Next in thread:**René Hafner TUK: "Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling"**Reply:**René Hafner TUK: "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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