From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Dec 28 2021 - 07:46:56 CST
I'd invite you to try an experiment. Simulate a bilayer for a long time
without applied forces. It'll diffuse along the z dimension over long
periods of time. The applied force probably isn't helping, but for a
well-defined reaction coordinate, where you only care about the
*relative* position between the small molecule and the membrane,
diffusion along the membrane normal axis will not impact the PMF.
On 12/28/21 5:58 AM, Yogesh Sharma wrote:
> Hi all,
> I am studying ligand transport through membrane protein but during
> longer simulation runs. I can see shift in membrane and protein system
> in z direction. Most probably due to forces applied on ligand. Can
> someone guide me through how can i avoid this ? Is it okay, if i
> restrain lipid head groups to avoid this movement and how likely is it
> that this shift in z will effect my pmf with respect to protein z
> coordinates ( since protein and membrane is getting displaced along z
> by the ligand).
> looking forward for your suggestions.
-- Josh Vermaas vermaasj_at_msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!ogEOfBmpNczC8nA5fttgYqbr9UrrPVit71e48xdVVwSenxyEjkWqozmJ3L19KOV7QA$
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