[gmx-users] ffgmx:diffusion of oxygen

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 28 10:13:59 CEST 2009

Sunil Thapa wrote:
> 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 ?
The problem is that you have only one molecule. If you have a liquid you 
can average over all the molecules.

> 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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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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