Re: ABF questions

From: Jérôme Hénin (
Date: Wed Jan 13 2010 - 10:40:49 CST

Dear Austin,
Low free energy regions do not always accumulate more sampling than
others. The ABF bias acts precisely to counter that tendency. In the
present case, most of the sampling time is spent trying to climb a
very steep wall at low values of the coordinate. In such a case, the
second derivative of the PMF also diverges, and the grid-based
description of the PMF used by ABF breaks down. To prevent this from
happening, it is recommended to exclude such high-energy regions from
the sampling interval (i.e. increase the value of lowerBoundary).

2010/1/13 Austin B. Yongye <>:
> Dear Dr. Henin,
> I performed an ABF simulation, and plotted the data from the .pmf and .count output vs reaction coordinate (see .jpg attached file). I was expecting to see more samples/counts in the lowest energy point, but it's not the case. Could you please let me know why this is the case?
> In addition, for low values of the reaction coordinate (1.5 to 2.1) the bins are not occupied and I get some very high positive energies. I have attached the .pmf and .count files. Any explanations?
> Thanks,
> Austin-

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