[gmx-users] diffusion coefficient of oxygen molecule

Erik Marklund 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.
> Neal

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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