[gmx-users] rdf doesn't tend to unity

[Ester Chiessi]

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, September 12, 2005 2:06 PM
Subject: Re: [gmx-users] rdf doesn't tend to unity



Thanks for your answer.

> On Mon, 2005-09-12 at 13:31 +0200, Ester Chiessi wrote:
>> Hi.
>>
>> I calculated the MD of a polymeric network in SPC water. I was very
>> surprised when I found that the rdf between the oxygen atoms of the 
>> polymer
>> and the water oxygen atoms doesn't reach the value of 1 at high r values.
>> The g(r) remains lower than unity and tends to 0.87.
>> I could expect a value higher than 1, eventually for inhomogeneity, but 
>> not
>> lower.
> Test whether the integral (4 pi r^2 g(r)) goes to #Ow
The number of polymer oxygens is 611.
OW number is 8773.
The box is cubic with size of 6.707 nm.
The integral in the 0-3.3535 nm distance interval results 136.16 nm^3.
> Test whether the RDF goes to distances longer than half the shortest box
> length
g(r) is given from 0 to 3.3535 nm
>>
>> Can this result have a physical meaning or is it an artifact?
>>
>> If there is a lower density at long distances, respect to the average
>> density in the system, it should be some r interval where g(r) becomes
>> higher than unity. Is it correct?
>>
>> I used pbc=full for the trajectory calculation, as polymer chains are
>> covalenty linked to their periodic images.
>>
>> Thanks in advance for any suggestion or comment.
>>
>> Ester
>>
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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