From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri May 23 2008 - 17:21:35 CDT
You stated the answer in your question: it's just a way to look at
exactly how non-ideal a non-ideal situation is.
On Fri, May 23, 2008 at 5:55 PM, Subramanian Vaitheeswaran
> 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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