Re: ABF questions (Concatenate output files/force constant)

From: Jérôme Hénin (
Date: Thu Dec 09 2010 - 04:51:14 CST

Hi Parisa,

> I am wondering how the program does this. I mean for the total.dat file the
> values of A(xi) in all of the bins are the same as window1. For the other
> windows, it adds a value to all A(xi)s  in each window which is different
> for different windows but the same for all bins in each window. I did not
> find any discussion about the method for concatenating on the website. I
> would really appreciate if any one could address me how I can learn about
> this.

Imagine that the program did not have that functionality, and you had
to merge the data yourself. How would you do it? Start from the
equations in the 2004 ABF paper, then it's just a small amount of
simple maths.

> 2) I am also using "abf forceConst 10.0 " to confine the ion movement
> "channel ion" inside the channel. I know the force is supposed to act at
> just the boundaries (Xmin and Xmax). But, my boundaries in the windows
> above (I have 11 windows) are part of RC. So, my assumption is that this
> force is going to affect the PMF profile at least at the boundaries of my
> windows. Right? Does the program finally correct this? Or am I missing
> something here?

In each window, the boundary potentials act outside the range where
ABF data is collected. Taking your windowing scheme: the window from
-16.5 to -13.5 will apply the upper boundary force for xi > -13.5, but
only collect data for xi <= -13.5. The PMF above that value will only
use data from the next window - in that window, the lower boundary
potential is only applied for xi < -13.5.


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