Re: ABF Asymmetry

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Jul 10 2018 - 07:26:07 CDT

I'm not sure I'm clear about this "bicelle" setup. Were the boundary
conditions aperiodic? The origin of z would be tricky in that case, no?

On Tue, Jul 10, 2018 at 1:11 AM, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Thanks for the reply Brian. I will consider what you said. I should
> note, the ABF with asymmetry was done without an infinite bilayer
> setup...more like a bicelle if you will. However, after re-doing the setup
> with an infinite bilayer PBC environment, the asymmetry disappeared, and
> the free energy in bulk water on both sides of the channel/bilayer match.
> Any idea why this would make a big difference? Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* Brian Radak <brian.radak_at_gmail.com>
> *Sent:* Monday, July 9, 2018 7:17:02 PM
> *To:* namd-l; McGuire, Kelly
> *Subject:* Re: namd-l: ABF Asymmetry
>
> 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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