AMBER Archive (2004)

Subject: AMBER: factor used in b-factor calculation

From: Fabian Boes (
Date: Tue Mar 09 2004 - 02:12:11 CST


i have a question about the b-factor calculation with ptraj. As far as i
have understood, the b-factor is the atomic fluctuation multiplied by

Now, to my confusion, i found on the ptraj homepage the following statement:

... multiplied by 8pi**2 ...

and in the sourcecode of actions.c:

   * B-factors are 8*PI*PI * <r>**2 hence we do not sqrt the

But some lines above:

bfactor = (8.0/3.0)*PI*PI;

So, i seems that actually the value is calculated with 8/3 and not with
8 as stated on the homepage and in the sourcecode. Can someone please
confirm this?

And second, it would be nice if someone could give me some literature
references where it is explained, how the 8/3*pi*pi factor was derived.




Fabian Bös

Institute of Technical Biochemistry University of Stuttgart / Germany

Phone: +49-711-6857481 Fax: +49-711-6853196 Email:

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