Re: combining abf reaction path

From: Chris Chipot (
Date: Sat Jan 31 2009 - 13:03:29 CST


please, see message "namd-l: Stratification schemes" from the NAMD
list (01/24/2009).

Unlike umbrella sampling, which is a histogram-based approach, ABF
is a TI-based one. What is being measured is the force acting along
the reaction coordinate. The average force being continuous across
the reaction path, it obviates the need for overlapping windows.
The only thing you have to do is paste the average-force profiles
together and integrate the resulting curve, remembering that, by
definition, dA(ξ)/dξ = -<Fξ>.


Arturas Ziemys a écrit :
> Hi,
> I do have a surface and heavy big molecule, and I want to calculate free
> energy from file with reaction coordinate being z-coordinate (normal to
> the surface). For a small light molecule with relatively large
> diffusivity it works fine. However I anticipate smaller diffusivity for
> a big one. So I plan split the reaction coordinate into several segments
> for efficiency of calculation.
> How exactly I can combine those segments ? Reaction coordinate segments
> should overlap, or those can be independent and continues ?
> I also expect that each segment will have different offsets. Right ?
> Best
> Arturas


Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078


       To sin by silence when we should protest makes cowards out of men
                                                     Ella Wheeler Wilcox

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