[gmx-users] Mean square displacement on Log-Log plot?

[David van der Spoel]

Den 2018-12-10 kl. 21:57, skrev Kevin Boyd:
> Hi,
> 
> If you're reporting a diffusion coefficient, they're probably looking for
> you to justify that you're out of the short-time subdiffusive regime. My
> experience is in bilayer simulations, where the MSD hits that regime
> typically in the time lag range of ~10-20 ns.
> 
> For a qualitative estimate of whether you've reached the long timescale
> limit, you don't need a log-log plot, you can just eyeball when the MSD
> goes linear, and (again in my experience) that's generally sufficient. A
> log-log plot may make it easier to see, or catch some subtler trends.
> 
> Maybe take a look at "Non-brownian diffusion in lipid membranes:
> experiments and simulations", by Metzler, Jeon, and Cherstvy, particularly
> some of the later figures look at the extent of subdiffusion with log-log
> plots.
> https://www.sciencedirect.com/science/article/pii/S0005273616300219
> 
Thanks!

> Kevin
> 
> On Mon, Dec 10, 2018 at 3:34 PM David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> 
>> Hi,
>>
>> unusual request, but here goes. I am dealing with a referee to one of my
>> papers who is asking for a mean square displacement plots:
>>
>> "a log-log plot of the MSD vs. time, from which one could judge whether
>> the long-time limit subject to multiple collisions and obstructions is
>> actually reached."
>>
>> Any clue what the referee is looking for? References?
>>
>> Cheers,
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se