Re: ABF Question

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Sep 27 2018 - 04:35:25 CDT

To get the same unit as ABF's output (kcal/mol), use the factor -0.6, and
of course natural logarithm (which I write ln rather than log, but I know
notations vary). Then you can plot the ABF PMF together with the effective,
flattened PMF, to see how flattened it is. In practice it is impossible to
reach uniform sampling i real systems - it is also not necessary or even
desirable.

Jerome

On Thu, 27 Sep 2018 at 04:37, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I have a question about ABF convergence. I have used
> -1.99*300*log(counts) to determine if convergence has been reached. I am
> not experienced with this part of ABF. I read that the line of the
> log(counts) should be flat if the ABF has converged. Mine is getting
> flatter, but in your experience, when is the line sufficiently flat to call
> the ABF converged? I would show the graph here, but I don't think we can
> attach files to our emails. So far, I have 9 windows that have run for 160
> nanoseconds each. I'm wondering if someone experienced can give me some
> advice on how far to go with convergence. I can send you a graph of the
> log(counts) if you need more information to give advice.
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>

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