[gmx-users] ffgmx:diffusion of oxygen

Sunil Thapa mephysik at yahoo.com
Tue Apr 28 09:40:14 CEST 2009

Respectable Experts
Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostly not more than 10 ns. I also got to see your paper on dynamic property of water/alcohol mixture where you have used time less than 10 ns. Which msd curve is to take ?
Another query : I want to simulate the system in a bit higher temperature 310 K . What are the parameters I should change in the mdp file. I saw the previous mails about it. Eric says that only time step should be small in order to constrain the bonds. Are there any other things?

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