From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Aug 10 2017 - 12:45:48 CDT
thank you for replying to my question. By "wall" you mean the boundary
potential or the physical walls of the pore? Would there be a similar
effect inside the pore, if the pore is wide?
On Sun, Aug 6, 2017 at 11:17 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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.
> 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
>> I will appreciate any input.
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