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How to get movie from MD

Started by sara abbasi, June 07, 2022, 08:15:40 PM

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sara abbasi

Dear Prof. Dubbeldum

Is there any method to get movies from MD results to show that the molecules with higher diffusion coefficient have higher speed in the framework than molecules with lower diffusion coefficient?

David Dubbeldam

In general no, because diffusion coefficients are by definition the long-time behavior of molecules.
In any short MD-path you might even see opposite behavior. Of course for illustrative purposes you could just select an MD path that shows what you want to show.

sara abbasi

Thanks a lot for your great reply. Do you mean by the fluctuations of MSD, I can comprise diffusion coefficient? I don't understand the meaning of MD path.

David Dubbeldam

An "MD path" is the path or trajectory that a particle follows in MD. if you ran too short, then the molecules have not moved enough.  Diffusion is defined as the limiting behavior of the Mean-Squared Displacement (MSD) at long-times. For diffusional processes, the slope must become linear at long times. If you did not reach that regime yet, then you have ran too short.
Slow diffusion might be outside the reach of MD, e.g. very slow diffusion can not be measured using MD. The maximum is probability up to 10^-14 m^2/s.