[gmx-users] Diffusion coefficient depenting on time interval

Erik Marklund erikm at xray.bmc.uu.se
Thu Oct 22 17:52:12 CEST 2009

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?

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

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