[gmx-users] g_rdf

[Kay Gottschalk]

Thanks, I'll try that!
Cheers,
K.
On Friday, August 8, 2003, at 10:26 AM, David wrote:

> On Thu, 2003-08-07 at 17:39, Anton Feenstra wrote:
>> Kay Gottschalk wrote:
>>> Hi Christoph,
>>>
>>> danke fuer das Angebot! I'd like to try it. But perhaps I should  
>>> restate
>>> my problem to make it (even more:)) clear: The relative probability  
>>> of
>>> finding a water water molecule at a given distance r is  
>>> (approximately
>>> as stated in the manual)
>>>
>>> g(r) = <N(r)>/(4*pi*r^2*dr*rho), where N(r) is the number of water  
>>> in a
>>> sperical shell (4*pi*r^2*dr), normalized by the water density rho.
>>> However, this is only true for symmetrical systems. The problem in my
>>> case is that the protein excludes water from certain regions, thus I
>>> have a assymetrical system. Therefore, the spherical shell is not the
>>> correct volume over which to normalize the function.
>>
>> Hmm, I'm not sure actually how it is implemented. It could be either  
>> as a
>> distribution function, which is normalized to an integral of 1, or it  
>> is
>> normalized to a bulk density (i.e. at 'infinite' or 'large'  
>> distances) of 1,
>> which is taken from your actual distribution, not an 'external'  
>> reference
>> value. In any case, there is no normalization to a 'reference'  
>> average water
>> density (which would also be pressure & temperature dependent, and  
>> water
>> model dependent as well).
>>
>> In either case, I believe three columns are written in the output  
>> (.xvg)
>> file, first the distance, then the normalized rdf and finally the  
>> 'raw'
>> numbers (if not, it would be straightforward to add to the source  
>> code).
>> If you type 'xmgrace -nxy rdf.xvg', you will see all available plots  
>> in
>> the file.
>
> I don't think there is any reason to renormalize, the normalization is
> done based on the number of water molecules (oxygens) in the
> computational box, and since your site of interest is partially  
> occluded
> by protein the number of bound water molecules will not be the same as
> for a particle in solution.
>
> Try to take the integral of the RDF (using Int 4 pi r^2 g(r) from 0 to
> the first minimum), that will give you the average number of hydrogen
> bonded water molecules.
>
>
>
> --  
> Groeten, David.
> _______________________________________________________________________ 
> _
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel