From: Chris Chipot (chipot_at_illinois.edu)
Date: Thu May 06 2021 - 08:18:32 CDT
Hi, Ethan,
I am afraid we do not have a comprehensive, self-contained tool to do
error analyses of ABF calculations. The ingredients that you need is an
estimation of the correlation length of the force time series in a given
bin, and the standard deviation of the force. Once you have these
ingredients, you can propagate the error across the PMF, as spelled out
in dx.doi.org/10.1021/jp506633n.
Chris Chipot
On 5/5/21 7:57 PM, Ethan Croitoru wrote:
> Hello,
>
> I am trying to quantify my error for free energy calculations. I used
> the geometrical transformation from this tutorial
> (https://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf
> <https://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf>)
> which utilizes ABF calculations. I have seen papers talking about the
> methodology to calculate the errors, but I was wondering if there are
> resources that illustrate an implementation?
>
> Thank you,
> Ethan Croitoru
--
Chris Chipot, Ph.D.
CNRS research director, University of Lorraine
Adjunct professor of physics, University of Illinois, Urbana-Champaign
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3161 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801 Phone: (217) 244-4361
E-mail: chipot_at_illinois.edu
Christophe.Chipot_at_Univ-Lorraine.fr
Web: https://physics.illinois.edu
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_______________________________________________________________________
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