# Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Aug 14 2021 - 12:17:53 CDT

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
>
>

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST