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Higher diffusivity in united atom model for protein
- Rajat Desikan
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11 years 8 months ago - 11 years 8 months ago #1051
by Rajat Desikan
Higher diffusivity in united atom model for protein was created by Rajat Desikan
Hi
In the Martini world, shouldn't I get a higher value of diffusivities from the MSD plots? Here, I carried out simulations of a protein in water, one in Martini and the other using Gromos53a6. The gromos diffusivity (~ 8*e-11 m2/s) is higher than the Martini diffusivity (~ 5*e-11 m2/s). I wish to attach the MSD plots. Can you please take a look? I have checked and the water doesn't seem to be frozen. The temperature is 300 K, and the temperature plot looks stable. The MSD trends are good.
Thanks
In the Martini world, shouldn't I get a higher value of diffusivities from the MSD plots? Here, I carried out simulations of a protein in water, one in Martini and the other using Gromos53a6. The gromos diffusivity (~ 8*e-11 m2/s) is higher than the Martini diffusivity (~ 5*e-11 m2/s). I wish to attach the MSD plots. Can you please take a look? I have checked and the water doesn't seem to be frozen. The temperature is 300 K, and the temperature plot looks stable. The MSD trends are good.
Thanks
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- djurre
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11 years 8 months ago #1054
by djurre
Replied by djurre on topic Higher diffusivity in united atom model for protein
Looking at the plots I agree with you that both diffuse about as fast (the values you calculated are also very close).
Very interesting behavior. It is often hard to understand and predict if something will diffuse faster. The factor 4 was originally calculated for lipids, but also there it might not be general. People have looked in to the problem (Depa, Chen, Maranas, Journal of Chemical Physics 134, (2011)), but that might not be the final answer.
Very interesting behavior. It is often hard to understand and predict if something will diffuse faster. The factor 4 was originally calculated for lipids, but also there it might not be general. People have looked in to the problem (Depa, Chen, Maranas, Journal of Chemical Physics 134, (2011)), but that might not be the final answer.
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