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.
[email protected] [email protected] http://folding.bmc.uu.se
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