ABF:reversibility and number of samples

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Fri May 23 2008 - 07:33:27 CDT

Dear all,
I used ABF to understand some aspects of
lingand binding mode.
A this moment I have a "good" energy profile but
I do not have an uniform number of samples:I explore along a
dihedral angle in the range 0-180 and I get to peaks at 20 and about 160 degrees.
There is a reversibility but sampling is not uniform.
In particular I have
a minimun energy that coincide with a minimun sampling.(at 60 degrees)
I ran my simulation (enzyme+ligand) for about 30ns and
I can not hope/think that things can change even if increasing
the simulation length of some tens of ns.

At this point I think about two possibilities:
1-Interpretation of these results. Do you guess they can be reliable? How can I use them?
2-Split the coordinate to try to reach sampling uniformity within each smaller range.
  For instance: 0-60, 60-120, 120-180.
  Do you have any suggestions ?


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