From: DAI, JIAN (jdai2_at_fsu.edu)
Date: Mon Jul 30 2012 - 08:17:45 CDT
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.
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.
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