From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Aug 14 2021 - 12:28:46 CDT
Hi Giacomo,
yes I can confirm from the writings in the logfile stating:
"Enabling the extended Lagrangian term for colvar .. " for every
colvar.
I make use of the CZAR estimator.
By the way: I am using NAMD 2.14.
René
On 8/14/2021 7:17 PM, Giacomo Fiorin wrote:
> 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 <mailto: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
>
-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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