Re: ABF Asymmetry

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Jul 10 2018 - 00:11:43 CDT

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

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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<mailto: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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