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

[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

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.
>
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.se&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&amp;sdata=wxcRUd55ynF4cbEOJVbKHbG%2BCeL6DAU8WlAbaG5wrQs%3D&amp;reserved=0
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&amp;sdata=xs%2BZ9IA%2FzoeJPfpSIhIFZFF0kA624QnSyN1DqmVdaMk%3D&amp;reserved=0
> before posting!
>
> * Can't post? Read
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&amp;sdata=42CTt8iaJj2VC2RBUcz%2BI%2F%2BjU%2BKbX23srdKhAvuNBI4%3D&amp;reserved=0
>
> * For (un)subscribe requests visit
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&amp;sdata=oNjdubSZHzZqp4yN4Rezu4Trjl8cc9FDJMvEkkUmESQ%3D&amp;reserved=0
> or send a mail to gmx-users-request at gromacs.org.
>