Re: ABF Asymmetry

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Jul 10 2018 - 12:20:05 CDT

So, my first system didn't have the membrane going all the way to the edges of the water box, so it was more like a lipid raft. I created a new system where the membrane did go to the edges of the water box and was more like an infinite bilayer. My free energy profile went from asymmetric to symmetric with that change...

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: Tuesday, July 10, 2018 6:26:07 AM
To: McGuire, Kelly
Cc: namd-l
Subject: Re: namd-l: ABF Asymmetry

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<mailto: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<mailto: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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