[gmx-users] Self Diffusion contant

[Javier Cerezo]

This is the normal behaviour for a MSD vs. time plot. Actually, as set 
by default in g_msd, neither the first seconds nor the last ones are 
taking into consideration to calculate the difussion constant.

The explanation for the non-liear curves might be the following. On one 
hand, at the begining, the behavior is not brownian -- in some places it 
is refered as "free-flight" or  just as difussion at short times 
(JCP,125,204703 is a good ref) -- On the other hand, as the average is 
obtained by taking different starting times along the trajectory, there 
would be much more points to average corresponding to the first seconds 
of MSD, but for large times, just the few reference times corresponding 
to the begining of the trajectory will contribute to the average and the 
these final values turn to be not reliable.

So, the slope at the last 2 ns is not related to any physical event. You 
should take the linear part corresponding to the middle of the time 
range. Anyway, check if that region is large enough, if not you might 
enlarge you simulation time (maybe 40-50ns).

Javier


El 07/10/10 18:36, teklebrh at ualberta.ca escribió:
> Dear Gromacs,
>
> I have been calculating the self Diffusion constant of my system. 
> Surfactants in a different solvents of the same volume. After 
> simulation for 20ns I found the following data for the trajectory of 
> the mean square displacement.
>
> # D[       TPA] = 0.2039 (+/- 0.0503) (1e-5 cm^2/s)
>          0           0
>          2   0.0105286
>          4   0.0162435
>          6   0.0212711
>          8    0.026031
>         10   0.0307584
>         12    0.035134
>         14   0.0393323
>         16   0.0434628
>         18   0.0475354
>         20   0.0516609
>          -
>          -
>          -
>          -
>          -
>          -
>        920     1.16467
>        922     1.16756
>        924      1.1703
>        926     1.17267
>        928     1.17383
>        930     1.17483
>        932     1.17581
>        934     1.17754
>        936     1.17957
>        938     1.18199
>        940      1.1829
>        942     1.18596
>        944     1.18871
>        946     1.19099
>        948     1.19219
>        950     1.19321
>        952     1.19445
>        954     1.19613
>        956     1.19838
>
>          -
>          -
>          -
>          -
>          -
>          -
>      10576     11.7747
>      10578      11.785
>      10580     11.7817
>      10582     11.7833
>      10584     11.7847
>      10586      11.784
>      10588     11.7855
>      10590     11.7904
>      10592     11.7926
>      10594     11.7943
>      10596     11.8036
>      10598     11.8141
>      10600     11.8112
>
>          -
>          -
>          -
>          -
>          -
>          -
>      19960     36.4106
>      19962     36.2607
>      19964     39.9243
>      19966     39.7493
>      19968     39.6744
>      19970     39.5838
>      19972     39.6723
>      19974     39.6374
>      19976      39.518
>      19978     39.4935
>      19980     39.3834
>      19982     39.1136
>      19984     42.3888
>      19986      42.168
>      19988     42.1337
>      19990     41.9395
>      19992     42.0065
>      19994     42.0993
>      19996     41.8652
>      19998     41.8419
>      20000     41.9419
>      20002     41.6049
>
>
> From my data, the graph shows a linear trend until 18ns but as soon as 
> it reaches around 19, 20ns it dramatically increases the MSD value. 
> Since the surfactants form aggregation I was expecting the MSD curve 
> to go down. Is any explanation for that. Why? suddenly increases the 
> MSD curve. Which is then the correct slop then!
>
>
> Thank you
>
> Rob
>
>
>

-- 
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434