[gmx-users] diffusion coefficient of oxygen

Sunil Thapa mephysik at yahoo.com
Wed Mar 10 13:21:31 CET 2010

Respected Experts

I need your help

In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm.

To equilibrate the system to the experimental water density of 997 I used Berendsen thermostat and the same barostat. The density of the system was 980(+-) 10 kg/m3 which is not the experimental value. After equilibration, I subjected the system to NVT ensemble md of 100 ns. I got the msd for oxygen molecule and analyzing first 4 ns (which was a st line part) of the plot, I got the diffusion coefficient of about 2.45 unit which is close to the experimental value. The question is how can the diffusion coefficient be so close when density is not produced. Is this a mere coincidence?

Thinking that I used TIP4P water model with the same number but different force field ffG3a
. I equilibrated the system to the same pressure and temperature with the same algorithms. After equilibration, the correspondng density was 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. Now what I see is that the MSD curve is a hill, initially increasing, reaching maximum and again returning to the base. The diffusion coefficient is 0.7 unit for 100 ns of trajectory.

What would have happened? Is this due to the increased density? Your precious knowledge on the subject matter would give me a sigh of relief.

Looking forward to hearing from you

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