[gmx-users] convergence of bilayer simulation

[Justin Lemkul]

On 7/12/19 1:54 PM, Prasanth G, Research Scholar wrote:
> Dear Justin,
>
> Thank you for your inputs.
> After using GridmatMD. I obtained the following results -
> Area per lipid is 62.696275 ±  0.545 Angstrom (square)
> Average thickness of the upper and lower membranes is 3.66 ± 0.28 Angstrom
> (square)

The unit is nm. Distances are not squared.

> I am also attaching the graphs for lateral displacement of lipids and
> density of the lipid along with this mail.
> I hope this is sufficient to say that the membrane is equilibrated.

Your diffusion profile only goes to 15 ns. That's at least an order of 
magnitude shorter than any lipid simulation that one could claim is 
converged. Like any simulation, to claim convergence, you need to prove 
that relevant quantities are invariant (statistically) over time.

-Justin

> Thank you.
>
>   lateral_diffusion.png
> <https://drive.google.com/a/sssihl.edu.in/file/d/1ksjv_VSiS4AtEMF8yyRKJl1lPDDjrPBP/view?usp=drive_web>
>
>   density_lipid.png
> <https://drive.google.com/a/sssihl.edu.in/file/d/1tUvQ5O6o-qqjd5pu5U5pEOv-jfYcbjWJ/view?usp=drive_web>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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