[gmx-users] diffusion coefficient of oxygen molecule
erikm at xray.bmc.uu.se
Fri Mar 5 10:36:38 CET 2010
Sunil Thapa skrev:
> Respected experts
> I want to calculate the self diffusion cofficient of an oxygen
> molecule in water. The experimental value in the literature is found
> to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have
> considered cut-off Lennard Jones interaction between water and oxygen.
> I want to reproduce this value. In your experience, which model of
> water would give the closer value. I have seen that the self diffusion
> of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual
> value is 2.4 unit. For oxygen the bonding potential has been taken to
> be harmonic. Any knowledge of related literature would be helpful
> because I could not find by googling.
> Your idea will really help me.
I do know that there are finite size effects that affects the diffusion
coefficient, so you should make sure you use a big enough box.
Furthermore, for water polarizability has an impact on the diffusion
coefficient, so if you want to reproduce experimental values, consider
using a polarizable model.
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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