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

Ester Chiessi ester.chiessi at uniroma2.it
Tue Sep 13 15:30:49 CEST 2005

```----- 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 7:22 PM
Subject: Re: [gmx-users] rdf doesn't tend to unity

> On Mon, 2005-09-12 at 17:30 +0200, Ester Chiessi wrote:
>> ----- 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
>>
>>
>>
>>
>> > 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.
> It should go to 8773, did you include the terms above in the integral?

I calculated the integral of    (4 pi r^2 g(r))  with r from 0 to 3.3535 nm
and the result was 136.16 nm^3.

If you multiply this value for #OW and divide for the box volume, you obtain
a number of oxygens (3959)  lower than that you can estimate (4593) by
considering a sphere of water with radius 3.3535 and density equal to the
water average density in the box.

The ratio 3959/4593 is 0.86, the limiting value of g(r). If it is not a
chance, what could it mean?

>
>
>> > 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.
>> > 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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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> 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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