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

Tue Sep 13 16:24:29 CEST 2005

Thanks Andrè for your comment.

I performed MD on a fragment of the polymer network in SPC water some time 
ago. In that case the g(r) became 1 in 0.9 nm but the solution behaviour of 
oligomers is different from that of  long chains, I think.

----- Original Message ----- 
From: "Andre Farias de Moura" <andre at qt.dq.ufscar.br>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Tuesday, September 13, 2005 1:10 PM
Subject: Re: [gmx-users] rdf doesn't tend to unity

>
> Hi Ester,
>
> if your polymer chains are not water-soluble, i.e., they
> aggregate in solution, then the water molecules do not
> have too much room arond the polymer. in other words,
> there is an excluded volume where water is not likely to
> be found because the system is micro-heterogeneous. if it
> happens to be so, g(r) would converge to unity only at
> "VERY" large distances, several tens or even hundreds
> of nanometers.
>
> I hope it helps,
>
> Andre'
>
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>
>    Dr. Andre' Farias de Moura
>
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> On Tue, 13 Sep 2005, 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 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
>> >>
>> >>
>> >>
>> >> 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.
>> > 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.
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>> > ________________________________________________________________________
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>> > 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
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