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

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Aug 14 2021 - 10:22:37 CDT


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

* 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

(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


Dipl.-Phys. René Hafner
TU Kaiserslautern

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