[gmx-users] MSD and self diffusion

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Wed Apr 12 09:32:41 CEST 2006

Hi Roman.

Let me guess... in theory the MSD should start non-linear and after some 
time become linear until the end of simulation but the g_msd output 
starts linear and after become anything.

I don´t know if I´m correct about your results but this was the results 
I had when trying to calculate MSD for an ion. This happen due to poor 
statistic of "long" times. For example, you have much more statistic 
when you calculate <|r(10)-r(0)|^2> than when you calculate 
<|r(100)-r(0)|^2>, so the results for times in the beggin of simulation 
are supposed to be better than in the end of it.

Like Tsjerk said, attach an image of your output so we can try to help you.


Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil

Roman Holomb wrote:

> Dear all,
> I have strange MSD graphs when I use g_msd for trajectory 
> analysis...... It not look like (<|r(t)-r(0)|^2>)....
> The simulation time was 5ns. Have someone problems with using g_msd?
> Thanks.
> /Roman
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