From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Aug 26 2021 - 07:01:19 CDT
Hi René,
> What is the correct way to sample non-independent variables with proper guesses?
I'm not sure I can add much to answer this question. What you did seems correct, as far as I can tell.
The one concern I have is how you extract the "marginal" free energy profiles from the 3D profile. That is not very clear to me. A correct way would be to compute the integral of the Boltzmann factor (exp(-A(x,y,z)/RT)) over coordinates x and y.
Best,
Jérôme
----- On Aug 14, 2021, at 7:28 PM, René Hafner TUK <hamburge_at_physik.uni-kl.de> wrote:
> 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 < [
>> mailto:hamburge_at_physik.uni-kl.de | 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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