Re: ABF Asymmetry

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Jul 09 2018 - 20:17:02 CDT

The symmetry only holds if all other orthogonal degrees of freedom are
fully converged. Is the x/y position of the ligand equally sampled for all
z? What about the ligand orientation?

You can also impose symmetry when computing the profile by averaging the
force about the mirror plane. Assuming symmetry about z = 0: F_sym(z) =
F_sym(-z) = [F(z) + F(-z)] / 2

On Mon, Jul 9, 2018 at 5:48 PM, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I am getting asymmetry in my free energy results from an ABF simulation
> with a ligand going from bulk water on one end of an ion channel to the the
> bulk water on the other side of the ion channel, which is embedded in a
> DMPC bilayer, and the PBC is set up so that the membrane is infinite. We
> expect the free energy to be essentially the same on one side of the
> channel as the other side. Instead, the free energy on the C-terminus bulk
> water side is quite lower than the free energy on the N-terminus bulk water
> side. Is our assumption correct the the free energies should match on both
> sides of the channel since the ligand is in bulk water on each side?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>

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