AMBER Archive (2009)

Subject: [AMBER] What is the unit of RMSF?

From: Catein Catherine (
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 B-factor.


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 B-factor 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 X-ray structure. They are different significantly, Is it normal to see different fluctuation profile (RMSF from MD vs thermal displacements from X-ray)?


For the same residue, I found the thermal displacement for the same residue is 5A in the X-ray structure. How to convert them into similar unit for qualitative analysis?


Best regards,


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