[gmx-users] Self Diffusion contant

[Igor Leontyev]

It is an interesting question. Is it not worthwhile to have a separate forum 
board for such methodological issues?
Some time ago I raised the similar question regarding the convergence of 
Self Diffusion Coefficient. The reasoning given in the paper mentioned by 
Javier seems to be related to my issue too. Indeed if diffusion have several 
regimes on different timescales then msd plot should have several linear 
regions with different slopes. For lipid membrane "The diffusion 
coefficients measured on short time scales come from fast motions of lipids 
in a local free volume, while diffusion coefficients at long times comes 
from the Brownian motion of lipids in a viscous fluid" I am wondering 
whether the same reasoning is applicable for liquid water where timescales 
are essentially shorter than those for lipid membrane? Can someone comment 
the results at the following link?
http://lists.gromacs.org/pipermail/gmx-users/2010-June/052119.html

Thanks,
Igor

This seems to be pleasable reasoning for
there are several linear comparison with experiment should be

> Javier Cerezo wrote:

> 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