AMBER Archive (2004)

Subject: AMBER: factor used in b-factor calculation

From: Fabian Boes (fabian.boes_at_itb.uni-stuttgart.de)
Date: Tue Mar 09 2004 - 02:12:11 CST

Hi,

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
(8/3)*pi*pi.

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
fluctuations!!!
   */

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.

Bye,

Fabian 

-- 

Fabian Bös

Institute of Technical Biochemistry
University of Stuttgart / Germany

Phone:   +49-711-6857481
Fax:     +49-711-6853196
Email:   fabian.boes_at_itb.uni-stuttgart.de

http://www.itb.uni-stuttgart.de

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