Re: overlapping windows in ABF

From: Jérôme Hénin (
Date: Mon Jul 23 2018 - 16:16:55 CDT

Hi Olga,

for a quick diagnosis, you could plot the free energy gradients from all
windows on the same graph. Overlapping regions should have similar values
of the gradient (keeping in mind that the gradient is always "noisier" than
the free energy itself, so there can be some variation). Any inconsistency
indicates that the two windows haven't sampled the same values of other
important degrees of freedom. See the literature on ABF for more info on
this, eg. this:


On Mon, 23 Jul 2018 at 16:55, Olya Kravchenko <> wrote:

> Dear all,
> In my current ABF simulations two out of eight windows overlap slightly
> with neighboring windows, i.e. instead of 52-56, 56-60 etc. they are
> defined as 52-56.5, 56-60.5 (by accident).
> I tried both merging files as is as well as merging them after removing
> the overlapping portion of the data (i.e. cutting off data for 56.-56.5 and
> 60.-60.5) and resulting pmf plot looks different after modification.
> My question is, how does namd treat such overlaps? Should I concatenate
> overlapping windows manually without cutting off the data for overlapping
> 0.5A?
> Thanks in advance!
> Olga

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