Re: ABF Question

From: Haohao Fu (fhh2626_at_gmail.com)
Date: Fri Jun 29 2018 - 01:29:23 CDT

Hi,

Setups 1 and 2 are acceptable. I personally prefer setup 1, since it may be
tricky for the czar estimator to evaluate the PMF of the overlapped area
when using eABF. For plain ABF, both 1 and 2 should be correct.

Haohao

2018-06-29 12:59 GMT+08:00 McGuire, Kelly <mcg05004_at_byui.edu>:

> Should the windows be overlapping or, at least, have no gaps between them?
> For example, say there are two windows. Which is the best window boundary
> setup?
>
>
> Setup #1 (exactly adjacent):
>
>
> Window 1
>
> lowerboundary -2
>
> upperboundary 2
>
>
> Window2
>
> lowerboundary 2
>
> upperboundary 5
>
>
>
>
>
> Setup #2 (some overlap):
>
>
> lowerboundary -2
>
> upperboundary 2
>
>
> Window 2
>
> lowerboundary 1.7
>
> upperboundary 5
>
>
>
>
> Setup #3 (no overlap, some gap):
>
>
> lowerboundary -2
>
> upperboundary 2
>
>
> Window 2
>
> lowerboundary 3
>
> upperboundary 5
>
>
>
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>

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