[gmx-users] Diffusion coefficient depenting on time interval

[Erik Marklund]

Hi users,

I have simulated a box of NVT-water, more specifically the flexible 
urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). 
What I notice is that the diffusion coefficient increases when I 
calculate it from a longer snippet from my trajectory. If I use only 100 
ps; starting at 100, 200 or 300 ps; the caculated coefficient is lower 
than if I use 400 ps (100-500 ps). Is this a known issue, inherent in 
the Einstein relation somehow?

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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys