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From: Fabian Boes <fabian.boes.itb.uni-stuttgart.de>

Date: Tue, 09 Mar 2004 09:12:11 +0100

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

Date: Tue, 09 Mar 2004 09:12:11 +0100

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.itb.uni-stuttgart.de http://www.itb.uni-stuttgart.de ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Tue Mar 09 2004 - 08:53:00 PST

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