From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Nov 27 2012 - 09:12:48 CST
In principle, they do not need to be overlapped. However, I find it useful
to do so in order to judge convergence, as the gradients should also
overlap.
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of DAI, JIAN
Sent: Tuesday, November 27, 2012 8:38 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Should the windows for ABF calculations be overlapped or
not?
Dear all:
In the ABF tutorial, the windows are divided so that they are not
overlapped. But in a paper by Wereszczynski and McCammon 2011 PNAS, they
divide the 2-D conformation space into dozens of overlapping windows. Does
the overlapping windows enhance sampling?
Thanks.
Jian
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