From: DAI, JIAN (jdai2_at_fsu.edu)
Date: Mon Jul 30 2012 - 08:17:45 CDT
Dear fellows:
We are trying to construct a free energy landscape of a protein using two dimensional ABF calculation. The landscape is divided into 9 equal sized windows, each with a dimension of 2 Angstrom by 2 Angstrom, where each dimension describes the center of mass between two groups of atoms.
Please see the figure by the link.
http://s663.photobucket.com/albums/uu358/djpittdj/?action=view¤t=count.png
The figure shows the number of counts with respect to those two order parameters, and they are not evenly distributed in each window, as I would expect. Instead, in four windows on the left bottom corner, the counts are heavily clustered in their respective boundaries, indicated by those red/yellow regions. Does anybody knows why and can possibly offer us a solution?
The fullSamples parameters is set to 500, and the landscape was obtained using abf_integrate after each window is run for 2 ns with a timestep of 1 fs.
Thanks a lot.
Jian
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