AMBER Archive (2004)Subject: AMBER: factor used in bfactor calculation
From: Fabian Boes (fabian.boes_at_itb.unistuttgart.de)
Date: Tue Mar 09 2004  02:12:11 CST
Hi,
i have a question about the bfactor calculation with ptraj. As far as i
have understood, the bfactor 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:
/*
* Bfactors 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: +497116857481
Fax: +497116853196
Email: fabian.boes_at_itb.unistuttgart.de
http://www.itb.unistuttgart.de

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