Re: ABF:reversibility and number of samples

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri May 23 2008 - 12:15:11 CDT

Luca,
I am not sure how non-uniform your sampling is. Even in the
best-behaved systems, you never get a strictly flat histogram. What I
usually plot is the "free energy transform", - kT * ln(sampling), and
I compare it to the measured PMF.
Now to add to what Chris wrote, even though the coordinate you are
watching seems to evolves reversibly, there might be other degrees of
freedom in its environment (maybe neighboring residues) that are
either drifting or getting trapped. At this point the problem is
mostly qualitatively deciding if the system is actually undergoing the
transformation you wanted to observe (I mean in a global sense,
besides the particular dihedral used as a RC).
Best,
Jerome

On Fri, May 23, 2008 at 8:33 AM, Luca Bellucci <bellucci14_at_unisi.it> wrote:
> 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 ?
> Luca
>
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