ABF vs Umbrella Sampling entrance barrier heights discrepancy

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Aug 02 2017 - 13:39:16 CDT

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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