[gmx-users] gmx msd unusual unit

[Justin Lemkul]

On 3/16/20 10:07 AM, Joe Paul-Taylor wrote:
> Hello
>
> With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated.

The unit is correct. GROMACS does all distance calculations in terms of 
nm. You get an interpreted output of the MSD in traditional units for 
the diffusion constant.

-Justin

> # Created by:
> #                       :-) GROMACS - gmx msd, 2019.2 (-:
> # Command line:
> #   gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg
> # gmx msd is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @    title "Mean Square Displacement"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "MSD (nm\S2\N)"
> @TYPE xy
> # MSD gathered over 10000 ps with 1001 restarts
> # Diffusion constants fitted from time 1000 to 9000 ps
> # D[       UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s)
>
> Thank you
>
> Joe
>
>

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Justin A. Lemkul, Ph.D.
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