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
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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