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From: Bimo Ario Tejo <bimo7.gmx.de>

Date: Wed, 10 Mar 2004 12:02:46 +0100 (MET)

Dear Fabian,

I think (8/3)pi**2 is right if we consider fluctuation as displacements of

atom in any particular direction, i.e. all orthogonal axes x, y, and z.

<r**2> = <x**2> + <y**2> + <z**2> = 3<x**2>

Single direction of B-factor is:

B = 8pi**2<x**2>

So, B-factor of atom in terms of radial displacements is:

B = (8/3)pi**2<r**2)

Cheers,

bimo

*> 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
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*> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
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*>
*

Date: Wed, 10 Mar 2004 12:02:46 +0100 (MET)

Dear Fabian,

I think (8/3)pi**2 is right if we consider fluctuation as displacements of

atom in any particular direction, i.e. all orthogonal axes x, y, and z.

<r**2> = <x**2> + <y**2> + <z**2> = 3<x**2>

Single direction of B-factor is:

B = 8pi**2<x**2>

So, B-factor of atom in terms of radial displacements is:

B = (8/3)pi**2<r**2)

Cheers,

bimo

-- +++ NEU bei GMX und erstmalig in Deutschland: TÜV-geprüfter Virenschutz +++ 100% Virenerkennung nach Wildlist. Infos: http://www.gmx.net/virenschutz ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Wed Mar 10 2004 - 11:53:00 PST

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