

AMBER Archive (2009)Subject: [AMBER] What is the unit of RMSF? From: Catein Catherine (askamber23_at_hotmail.com)Date: Sat Sep 12 2009  03:13:02 CDT
Dear Sir/Madam,
I did a MD simulation, then I did the RMSF analysis. I could like to ask the unit of the results should be when i did the ptraj analysis with or without Bfactor.
I also plotted the RMSF as a function of residue, the domain with the highest flucation in the literature is agree with our calculations. However, I found the absolute values of the RMSF values different significantly. Let's say the RMSF of a residue is as high as 1000 (I don't know the unit), but the RMSF values calculated with Bfactor is another values.
In the manual, I found B factor=(fluctation*fluctuation)*8/3*pi**2. What does it means by **2, square or time 2?
I also compare the RMSF profile with thermal displacement of Xray structure. They are different significantly, Is it normal to see different fluctuation profile (RMSF from MD vs thermal displacements from Xray)?
For the same residue, I found the thermal displacement for the same residue is 5A in the Xray structure. How to convert them into similar unit for qualitative analysis?
Best regards,
Cat
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