Re: membrane system displacing in z during ABF or metadynamics

From: Josh Vermaas (
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
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!ogEOfBmpNczC8nA5fttgYqbr9UrrPVit71e48xdVVwSenxyEjkWqozmJ3L19KOV7QA$ 

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