From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Wed Jan 13 2010 - 11:45:51 CST
Thanks Dr. Henin.
When the simulation started, that reaction coordinate was ~ 4.5 Angs. With the ABF force, the RC was mostly trapped at 2.1 Angs. Given that the barrier is so high, why did the ABF move the RC to this distance? Probably an obvious question, but not sure.
My aim for this simulation is to get the approach trajectories for a nucleophilic addition at various sites on a molecule, and then determine which pathways are preferred.
--- On Wed, 1/13/10, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> From: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> Subject: Re: ABF questions
> To: "Austin B. Yongye" <ybausty_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Date: Wednesday, January 13, 2010, 8:40 AM
> 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
> 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
> 2010/1/13 Austin B. Yongye <ybausty_at_yahoo.com>:
> > 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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