From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sun Aug 06 2017 - 10:17:44 CDT
Hi Olga,
my best guess is that your ABF simulation is hurt by slow lateral diffusion
around the pore entrance. Essentially, the ion bumps into the wall, giving
the high barrier you are seeing. In umbrella sampling, the ion doesn't do
that - or anything else, for that matter. Therein lies the beauty of that
method.
Jerome
On 2 August 2017 at 20:39, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
> Hi all,
>
> I ran a number of ABF and umbrella simulations to obtain pmf for the ion
> permeation through the pores of a spherical protein and in all of my
> simulations I see discrepancy in the estimate of the barrier heights at the
> entrance of the pore (i.e. where ions enter the protein from the cytosol
> region). For example, umbrella sampling may give me ~20 kcal/mol, while ABF
> is ~100kcal/mol (I have more precise numbers, but the difference is more or
> less in this order). My reaction coordinate is the distance between the ion
> and the center of mass of the protein, i.e. the central axis of the pore)
> and my ABF windows are 2-4 A wide.
>
> I am wondering if anyone else sees this when comparing ABF with US? I have
> not found anything specific in literature yet. Essentially I am trying to
> figure out if there are known problems with ABF method near the entrance of
> the channel that I should have taken into an account while setting up
> simulations?
>
> I will appreciate any input.
>
> Olga
>
>
>
>
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