From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Fri May 23 2008 - 16:55:53 CDT
I am confused. After the calculation has converged, the sampling (n_samples in the last column of the outFile) will ideally be uniform. So what does - kT * ln(sampling) tell you?
---- Original message ----
>Date: Fri, 23 May 2008 13:15:11 -0400
>From: "Jerome Henin" <jhenin_at_cmm.chem.upenn.edu>
>Subject: Re: namd-l: ABF:reversibility and number of samples
>To: "Luca Bellucci" <bellucci14_at_unisi.it>
>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).
>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 ?
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