NAMD 2.7b1 ABF + free energy windows

From: Reichert, David (
Date: Tue Sep 29 2009 - 15:33:48 CDT

Hopefully someone can point what I'm missing or the mistake I'm making. I'm using ABF to calculate the free energy of a steroid moving from the center of a lipid bilayer into bulk water over a range of 28 angstroms. I've broken the simulation down into three windows of approximately 10 angstroms over 2 ns, and they've all successfully completed. The sampling could definitely be improved but it's enough for some comparison's I'm looking at. Here's the problem when I plot A(xi) vs Xi for each of these windows, they don't match up. In the overlaps between windows the plots look the same but they're offset on the y-axis in one case by 3 kcal/mol, and in the other by 15 kcal/mol. Am I missing something here, shouldn't the plots match up ?
Thanks in advance,
David E. Reichert, PhD.
Asst. Professor of Radiology
Washington University School of Medicine

voice: 314-362-8461
fax: 314-362-9940

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