overlapping windows in ABF

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon Jul 23 2018 - 09:52:39 CDT

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

Thanks in advance!


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