Re: ABF Asymmetry

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 10 2018 - 07:59:54 CDT

I see how the origin could be sorted out - the orientation seems more
complicated still.

On Tue, 10 Jul 2018 at 14:29, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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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